added retrain code

.gitea/workflows/ci.yaml

@@ -8,7 +8,6 @@ on:
 
 jobs:
   test:
-    if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
     runs-on: ubuntu-latest
 
     services:
@@ -100,18 +99,6 @@ jobs:
       - name: Setup venv
         run: |
           uv sync --locked --all-extras --dev
-          source .venv/bin/activate
-          playwright install --with-deps
-
-      - name: Run PNPM Commands
-        run: |
-          uv run python scripts/pnpm_wrapper.py install
-          cat << 'EOF' > pnpm-workspace.yaml
-          onlyBuiltDependencies:
-            - '@parcel/watcher'
-            - '@tailwindcss/oxide'
-          EOF
-          uv run python scripts/pnpm_wrapper.py run build
 
       - name: Wait for services
         run: |
@@ -123,12 +110,7 @@ jobs:
           source .venv/bin/activate
           python manage.py migrate --noinput
 
-      - name: Run frontend tests
-        run: |
-          source .venv/bin/activate
-          python manage.py test --tag frontend
-
       - name: Run Django tests
         run: |
           source .venv/bin/activate
-          python manage.py test tests --exclude-tag slow --exclude-tag frontend
+          python manage.py test tests --exclude-tag slow

.gitignore

@@ -6,7 +6,6 @@ static/django_extensions/
 .env
 debug.log
 scratches/
-test-results/
 
 data/
 

envipath/settings.py

@@ -49,23 +49,9 @@ INSTALLED_APPS = [
     "oauth2_provider",
     # Custom
     "epdb",
-    # "migration",
+    "migration",
 ]
 
-TENANT = os.environ.get("TENANT", "public")
-
-if TENANT != "public":
-    INSTALLED_APPS.append(TENANT)
-
-EPDB_PACKAGE_MODEL = os.environ.get("EPDB_PACKAGE_MODEL", "epdb.Package")
-
-
-def GET_PACKAGE_MODEL():
-    from django.apps import apps
-
-    return apps.get_model(EPDB_PACKAGE_MODEL)
-
-
 AUTHENTICATION_BACKENDS = [
     "django.contrib.auth.backends.ModelBackend",
 ]

envipath/urls.py

@@ -23,20 +23,12 @@ from .api import api_v1, api_legacy
 
 urlpatterns = [
     path("", include("epdb.urls")),
+    path("", include("migration.urls")),
     path("admin/", admin.site.urls),
     path("api/v1/", api_v1.urls),
     path("api/legacy/", api_legacy.urls),
     path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
 
-if "migration" in s.INSTALLED_APPS:
-    urlpatterns.append(path("", include("migration.urls")))
-
 if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path("", include("epauth.urls")))
-
-# Custom error handlers
-handler400 = "epdb.views.handler400"
-handler403 = "epdb.views.handler403"
-handler404 = "epdb.views.handler404"
-handler500 = "epdb.views.handler500"

epdb/admin.py

@@ -1,31 +1,29 @@
-from django.conf import settings as s
 from django.contrib import admin
 
 from .models import (
-    Compound,
-    CompoundStructure,
-    Edge,
-    EnviFormer,
-    ExternalDatabase,
-    ExternalIdentifier,
-    Group,
-    GroupPackagePermission,
-    JobLog,
-    License,
-    MLRelativeReasoning,
-    Node,
-    ParallelRule,
-    Pathway,
-    Reaction,
-    Scenario,
-    Setting,
-    SimpleAmbitRule,
     User,
     UserPackagePermission,
+    Group,
+    GroupPackagePermission,
+    Package,
+    MLRelativeReasoning,
+    EnviFormer,
+    Compound,
+    CompoundStructure,
+    SimpleAmbitRule,
+    ParallelRule,
+    Reaction,
+    Pathway,
+    Node,
+    Edge,
+    Scenario,
+    Setting,
+    ExternalDatabase,
+    ExternalIdentifier,
+    JobLog,
+    License,
 )
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 class UserAdmin(admin.ModelAdmin):
     list_display = ["username", "email", "is_active"]

epdb/apps.py

@@ -1,9 +1,4 @@
-import logging
-
 from django.apps import AppConfig
-from django.conf import settings
-
-logger = logging.getLogger(__name__)
 
 
 class EPDBConfig(AppConfig):
@@ -12,6 +7,3 @@ class EPDBConfig(AppConfig):
 
     def ready(self):
         import epdb.signals  # noqa: F401
-
-        model_name = getattr(settings, "EPDB_PACKAGE_MODEL", "epdb.Package")
-        logger.info(f"Using Package model: {model_name}")

epdb/context_processors.py

@@ -5,7 +5,7 @@ Context processors automatically make variables available to all templates.
 """
 
 from .logic import PackageManager
-from django.conf import settings as s
+from .models import Package
 
 
 def package_context(request):
@@ -20,7 +20,7 @@ def package_context(request):
 
     reviewed_package_qs = PackageManager.get_reviewed_packages()
 
-    unreviewed_package_qs = s.GET_PACKAGE_MODEL().objects.none()
+    unreviewed_package_qs = Package.objects.none()
 
     # Only get user-specific packages if user is authenticated
     if current_user.is_authenticated:

epdb/legacy_api.py

@@ -1,35 +1,27 @@
-from typing import Any, Dict, List, Optional
+from typing import List, Dict, Optional, Any
 
-import nh3
-from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse
 from django.shortcuts import redirect
-from ninja import Field, Form, Router, Schema, Query
+from ninja import Router, Schema, Field, Form
-from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
-from utilities.misc import PackageExporter
+from .logic import PackageManager, UserManager, SettingManager
-
-from .logic import GroupManager, PackageManager, SettingManager, UserManager, SearchManager
 from .models import (
     Compound,
     CompoundStructure,
-    Edge,
+    Package,
-    EPModel,
-    Node,
-    Pathway,
-    Reaction,
-    Rule,
-    Scenario,
-    SimpleAmbitRule,
     User,
     UserPackagePermission,
-    ParallelRule,
+    Rule,
+    Reaction,
+    Scenario,
+    Pathway,
+    Node,
+    Edge,
+    SimpleAmbitRule,
 )
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 def _anonymous_or_real(request):
     if request.user.is_authenticated and not request.user.is_anonymous:
@@ -37,7 +29,8 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-router = Router(auth=SessionAuth(csrf=False))
+# router = Router(auth=SessionAuth())
+router = Router()
 
 
 class Error(Schema):
@@ -125,16 +118,13 @@ class SimpleEdge(SimpleObject):
     identifier: str = "edge"
 
 
-class SimpleModel(SimpleObject):
-    identifier: str = "relative-reasoning"
-
-
 ################
 # Login/Logout #
 ################
-@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
+@router.post("/", response={200: SimpleUser, 403: Error})
 def login(request, loginusername: Form[str], loginpassword: Form[str]):
-    from django.contrib.auth import authenticate, login
+    from django.contrib.auth import authenticate
+    from django.contrib.auth import login
 
     email = User.objects.get(username=loginusername).email
     user = authenticate(username=email, password=loginpassword)
@@ -177,13 +167,9 @@ class UserSchema(Schema):
         return SettingManager.get_all_settings(obj)
 
 
-class Me(Schema):
-    whoami: str | None = None
-
-
 @router.get("/user", response={200: UserWrapper, 403: Error})
-def get_users(request, me: Query[Me]):
+def get_users(request, whoami: str = None):
-    if me.whoami:
+    if whoami:
         return {"user": [request.user]}
     else:
         return {"user": User.objects.all()}
@@ -200,61 +186,6 @@ def get_user(request, user_uuid):
         }
 
 
-class Search(Schema):
-    packages: List[str] = Field(alias="packages[]")
-    search: str
-    method: str
-
-
-@router.get("/search", response={200: Any, 403: Error})
-def search(request, search: Query[Search]):
-    try:
-        packs = []
-        for package in search.packages:
-            packs.append(PackageManager.get_package_by_url(request.user, package))
-
-        method = None
-
-        if search.method == "text":
-            method = "text"
-        elif search.method == "inchikey":
-            method = "inchikey"
-        elif search.method == "defaultSmiles":
-            method = "default"
-        elif search.method == "canonicalSmiles":
-            method = "canonical"
-        elif search.method == "exactSmiles":
-            method = "exact"
-
-        if method is None:
-            raise ValueError(f"Search method {search.method} is not supported!")
-
-        search_res = SearchManager.search(packs, search.search, method)
-        res = {}
-        if "Compounds" in search_res:
-            res["compound"] = search_res["Compounds"]
-
-        if "Compound Structures" in search_res:
-            res["structure"] = search_res["Compound Structures"]
-
-        if "Reaction" in search_res:
-            res["reaction"] = search_res["Reaction"]
-
-        if "Pathway" in search_res:
-            res["pathway"] = search_res["Pathway"]
-
-        if "Rules" in search_res:
-            res["rule"] = search_res["Rules"]
-
-        for key in res:
-            for v in res[key]:
-                v["id"] = v["url"].replace("simple-ambit-rule", "simple-rule")
-
-        return res
-    except ValueError as e:
-        return 403, {"message": f"Search failed due to {e}"}
-
-
 ###########
 # Package #
 ###########
@@ -320,110 +251,67 @@ def get_packages(request):
     }
 
 
-class GetPackage(Schema):
+@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema, 403: Error})
-    exportAsJson: str | None = None
+def get_package(request, package_uuid):
-
-
-@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 403: Error})
-def get_package(request, package_uuid, gp: Query[GetPackage]):
     try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if gp.exportAsJson and gp.exportAsJson.strip() == "true":
-            return PackageExporter(p).do_export()
-
-        return p
     except ValueError:
         return 403, {
             "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
         }
 
 
-class CreatePackage(Schema):
-    packageName: str
-    packageDescription: str | None = None
-
-
 @router.post("/package")
 def create_packages(
-    request,
+    request, packageName: Form[str], packageDescription: Optional[str] = Form(None)
-    p: Form[CreatePackage],
 ):
     try:
-        if p.packageName.strip() == "":
+        if packageName.strip() == "":
             raise ValueError("Package name cannot be empty!")
 
-        new_pacakge = PackageManager.create_package(
+        new_pacakge = PackageManager.create_package(request.user, packageName, packageDescription)
-            request.user, p.packageName, p.packageDescription
-        )
         return redirect(new_pacakge.url)
     except ValueError as e:
         return 400, {"message": str(e)}
 
 
-class UpdatePackage(Schema):
-    packageDescription: str | None = None
-    hiddenMethod: str | None = None
-    permissions: str | None = None
-    ppsURI: str | None = None
-    read: str | None = None
-    write: str | None = None
-
-
 @router.post("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 400: Error})
-def update_package(request, package_uuid, pack: Form[UpdatePackage]):
+def update_package(
+    request,
+    package_uuid,
+    packageDescription: Optional[str] = Form(None),
+    hiddenMethod: Optional[str] = Form(None),
+    exportAsJson: Optional[str] = Form(None),
+    permissions: Optional[str] = Form(None),
+    ppsURI: Optional[str] = Form(None),
+    read: Optional[str] = Form(None),
+    write: Optional[str] = Form(None),
+):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        if pack.hiddenMethod:
+        if hiddenMethod:
-            if pack.hiddenMethod == "DELETE":
+            if hiddenMethod == "DELETE":
                 p.delete()
 
-        elif pack.packageDescription is not None:
+        elif packageDescription and packageDescription.strip() != "":
-            description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
+            p.description = packageDescription
-
-            if description:
-                p.description = description
             p.save()
-                return HttpResponse(status=200)
+            return
-            else:
+        elif exportAsJson == "true":
-                raise ValueError("Package description cannot be empty!")
+            pack_json = PackageManager.export_package(
-        elif all([pack.permissions, pack.ppsURI, pack.read]):
+                p, include_models=False, include_external_identifiers=False
-            if "group" in pack.ppsURI:
+            )
-                grantee = GroupManager.get_group_lp(pack.ppsURI)
+            return pack_json
-            else:
+        elif all([permissions, ppsURI, read]):
-                grantee = UserManager.get_user_lp(pack.ppsURI)
+            PackageManager.update_permissions
+        elif all([permissions, ppsURI, write]):
+            pass
 
-            PackageManager.grant_read(request.user, p, grantee)
-            return HttpResponse(status=200)
-        elif all([pack.permissions, pack.ppsURI, pack.write]):
-            if "group" in pack.ppsURI:
-                grantee = GroupManager.get_group_lp(pack.ppsURI)
-            else:
-                grantee = UserManager.get_user_lp(pack.ppsURI)
-
-            PackageManager.grant_write(request.user, p, grantee)
-            return HttpResponse(status=200)
     except ValueError as e:
         return 400, {"message": str(e)}
 
 
-@router.delete("/package/{uuid:package_uuid}")
-def delete_package(request, package_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.administrable(request.user, p):
-            p.delete()
-            return redirect(f"{s.SERVER_URL}/package")
-        else:
-            raise ValueError("You do not have the rights to delete this Package!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Package with id {package_uuid} failed due to insufficient rights!"
-        }
-
-
 ################################
 # Compound / CompoundStructure #
 ################################
@@ -621,83 +509,6 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
         }
 
 
-class CreateCompound(Schema):
-    compoundSmiles: str
-    compoundName: str | None = None
-    compoundDescription: str | None = None
-    inchi: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/compound")
-def create_package_compound(
-    request,
-    package_uuid,
-    c: Form[CreateCompound],
-):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-        # inchi is not used atm
-        c = Compound.create(
-            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
-        )
-        return redirect(c.url)
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
-@router.delete("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}")
-def delete_compound(request, package_uuid, compound_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            c = Compound.objects.get(package=p, uuid=compound_uuid)
-            c.delete()
-            return redirect(f"{p.url}/compound")
-        else:
-            raise ValueError("You do not have the rights to delete this Compound!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Compound with id {compound_uuid} failed due to insufficient rights!"
-        }
-
-
-@router.delete(
-    "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
-)
-def delete_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            c = Compound.objects.get(package=p, uuid=compound_uuid)
-            cs = CompoundStructure.objects.get(compound=c, uuid=structure_uuid)
-
-            # Check if we have to delete the compound as no structure is left
-            if len(cs.compound.structures.all()) == 1:
-                # This will delete the structure as well
-                c.delete()
-                return redirect(p.url + "/compound")
-            else:
-                if cs.normalized_structure:
-                    c.delete()
-                    return redirect(p.url + "/compound")
-                else:
-                    if c.default_structure == cs:
-                        cs.delete()
-                        c.default_structure = c.structures.all().first()
-                        return redirect(c.url + "/structure")
-                    else:
-                        cs.delete()
-                        return redirect(c.url + "/structure")
-        else:
-            raise ValueError("You do not have the rights to delete this CompoundStructure!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting CompoundStructure with id {compound_uuid} failed due to insufficient rights!"
-        }
-
-
 #########
 # Rules #
 #########
@@ -861,73 +672,6 @@ def _get_package_rule(request, package_uuid, rule_uuid):
 
 
 # POST
-class CreateSimpleRule(Schema):
-    smirks: str
-    name: str | None = None
-    description: str | None = None
-    reactantFilterSmarts: str | None = None
-    productFilterSmarts: str | None = None
-    immediate: str | None = None
-    rdkitrule: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/simple-rule")
-def create_package_simple_rule(
-    request,
-    package_uuid,
-    r: Form[CreateSimpleRule],
-):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if r.rdkitrule and r.rdkitrule.strip() == "true":
-            raise ValueError("Not yet implemented!")
-        else:
-            sr = SimpleAmbitRule.create(
-                p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
-            )
-
-        return redirect(sr.url)
-
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
-class CreateParallelRule(Schema):
-    simpleRules: str
-    name: str | None = None
-    description: str | None = None
-    reactantFilterSmarts: str | None = None
-    productFilterSmarts: str | None = None
-    immediate: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/parallel-rule")
-def create_package_parallel_rule(
-    request,
-    package_uuid,
-    r: Form[CreateParallelRule],
-):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        srs = SimpleRule.objects.filter(package=p, url__in=r.simpleRules)
-
-        if srs.count() != len(r.simpleRules):
-            raise ValueError(
-                f"Not all SimpleRules could be found in Package with id {package_uuid}!"
-            )
-
-        sr = ParallelRule.create(
-            p, list(srs), r.name, r.description, r.reactantFilterSmarts, r.productFilterSmarts
-        )
-
-        return redirect(sr.url)
-
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
 @router.post(
     "/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error}
 )
@@ -977,41 +721,6 @@ def _post_package_rule(request, package_uuid, rule_uuid, compound: Form[str]):
         }
 
 
-@router.delete("/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}")
-def delete_rule(request, package_uuid, rule_uuid):
-    return _delete_rule(request, package_uuid, rule_uuid)
-
-
-@router.delete(
-    "/package/{uuid:package_uuid}/simple-rule/{uuid:rule_uuid}",
-)
-def delete_simple_rule(request, package_uuid, rule_uuid):
-    return _delete_rule(request, package_uuid, rule_uuid)
-
-
-@router.delete(
-    "/package/{uuid:package_uuid}/parallel-rule/{uuid:rule_uuid}",
-)
-def delete_parallel_rule(request, package_uuid, rule_uuid):
-    return _delete_rule(request, package_uuid, rule_uuid)
-
-
-def _delete_rule(request, package_uuid, rule_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            r = Rule.objects.get(package=p, uuid=rule_uuid)
-            r.delete()
-            return redirect(f"{p.url}/rule")
-        else:
-            raise ValueError("You do not have the rights to delete this Rule!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Rule with id {rule_uuid} failed due to insufficient rights!"
-        }
-
-
 ############
 # Reaction #
 ############
@@ -1100,82 +809,6 @@ def get_package_reaction(request, package_uuid, reaction_uuid):
         }
 
 
-class CreateReaction(Schema):
-    reactionName: str | None = None
-    reactionDescription: str | None = None
-    smirks: str | None = None
-    educt: str | None = None
-    product: str | None = None
-    rule: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/reaction")
-def create_package_reaction(
-    request,
-    package_uuid,
-    r: Form[CreateReaction],
-):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if r.smirks is None and (r.educt is None or r.product is None):
-            raise ValueError("Either SMIRKS or educt/product must be provided")
-
-        if r.smirks is not None and (r.educt is not None and r.product is not None):
-            raise ValueError("SMIRKS and educt/product provided!")
-
-        rule = None
-        if r.rule:
-            try:
-                rule = Rule.objects.get(package=p, url=r.rule)
-            except Rule.DoesNotExist:
-                raise ValueError(f"Rule with id {r.rule} does not exist!")
-
-        if r.educt is not None:
-            try:
-                educt_cs = CompoundStructure.objects.get(compound__package=p, url=r.educt)
-            except CompoundStructure.DoesNotExist:
-                raise ValueError(f"Compound with id {r.educt} does not exist!")
-
-            try:
-                product_cs = CompoundStructure.objects.get(compound__package=p, url=r.product)
-            except CompoundStructure.DoesNotExist:
-                raise ValueError(f"Compound with id {r.product} does not exist!")
-
-            new_r = Reaction.create(
-                p, r.reactionName, r.reactionDescription, [educt_cs], [product_cs], rule
-            )
-        else:
-            educts = r.smirks.split(">>")[0].split("\\.")
-            products = r.smirks.split(">>")[1].split("\\.")
-
-            new_r = Reaction.create(
-                p, r.reactionName, r.reactionDescription, educts, products, rule
-            )
-
-        return redirect(new_r.url)
-
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
-@router.delete("/package/{uuid:package_uuid}/reaction/{uuid:reaction_uuid}")
-def delete_reaction(request, package_uuid, reaction_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            r = Reaction.objects.get(package=p, uuid=reaction_uuid)
-            r.delete()
-            return redirect(f"{p.url}/reaction")
-        else:
-            raise ValueError("You do not have the rights to delete this Reaction!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Reaction with id {reaction_uuid} failed due to insufficient rights!"
-        }
-
-
 ############
 # Scenario #
 ############
@@ -1190,7 +823,7 @@ class ScenarioSchema(Schema):
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
-    linkedTo: List[Dict[str, str]] = Field([], alias="linked_to")
+    linkedTo: List[Dict[str, str]] = Field({}, alias="linked_to")
     name: str = Field(None, alias="name")
     pathways: List["SimplePathway"] = Field([], alias="related_pathways")
     relatedScenarios: List[Dict[str, str]] = Field([], alias="related_scenarios")
@@ -1241,38 +874,6 @@ def get_package_scenario(request, package_uuid, scenario_uuid):
         }
 
 
-@router.delete("/package/{uuid:package_uuid}/scenario")
-def delete_scenarios(request, package_uuid, scenario_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            scens = Scenario.objects.filter(package=p)
-            scens.delete()
-            return redirect(f"{p.url}/scenario")
-        else:
-            raise ValueError("You do not have the rights to delete Scenarios!")
-    except ValueError:
-        return 403, {"message": "Deleting Scenarios failed due to insufficient rights!"}
-
-
-@router.delete("/package/{uuid:package_uuid}/scenario/{uuid:scenario_uuid}")
-def delete_scenario(request, package_uuid, scenario_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            scen = Scenario.objects.get(package=p, uuid=scenario_uuid)
-            scen.delete()
-            return redirect(f"{p.url}/scenario")
-        else:
-            raise ValueError("You do not have the rights to delete this Scenario!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Scenario with id {scenario_uuid} failed due to insufficient rights!"
-        }
-
-
 ###########
 # Pathway #
 ###########
@@ -1412,67 +1013,46 @@ def get_package_pathway(request, package_uuid, pathway_uuid):
         }
 
 
-class CreatePathway(Schema):
-    smilesinput: str
-    name: str | None = None
-    description: str | None = None
-    rootOnly: str | None = None
-    selectedSetting: str | None = None
-
-
 @router.post("/package/{uuid:package_uuid}/pathway")
 def create_pathway(
     request,
     package_uuid,
-    pw: Form[CreatePathway],
+    smilesinput: Form[str],
+    name: Optional[str] = Form(None),
+    description: Optional[str] = Form(None),
+    rootOnly: Optional[str] = Form(None),
+    selectedSetting: Optional[str] = Form(None),
 ):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        stand_smiles = FormatConverter.standardize(pw.smilesinput.strip())
+        stand_smiles = FormatConverter.standardize(smilesinput.strip())
 
-        new_pw = Pathway.create(p, stand_smiles, name=pw.name, description=pw.description)
+        pw = Pathway.create(p, stand_smiles, name=name, description=description)
 
         pw_mode = "predict"
-        if pw.rootOnly and pw.rootOnly.strip() == "true":
+        if rootOnly and rootOnly == "true":
             pw_mode = "build"
 
-        new_pw.kv.update({"mode": pw_mode})
+        pw.kv.update({"mode": pw_mode})
-        new_pw.save()
+        pw.save()
 
         if pw_mode == "predict":
             setting = request.user.prediction_settings()
 
-            if pw.selectedSetting:
+            if selectedSetting:
-                setting = SettingManager.get_setting_by_url(request.user, pw.selectedSetting)
+                setting = SettingManager.get_setting_by_url(request.user, selectedSetting)
 
-            new_pw.setting = setting
+            pw.setting = setting
-            new_pw.save()
+            pw.save()
 
-            from .tasks import dispatch, predict
+            from .tasks import predict
 
-            dispatch(request.user, predict, new_pw.pk, setting.pk, limit=-1)
+            predict.delay(pw.pk, setting.pk, limit=-1)
 
-        return redirect(new_pw.url)
+        return redirect(pw.url)
     except ValueError as e:
-        return 400, {"message": str(e)}
+        print(e)
-
-
-@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
-def delete_pathway(request, package_uuid, pathway_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            pw.delete()
-            return redirect(f"{p.url}/pathway")
-        else:
-            raise ValueError("You do not have the rights to delete this pathway!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
-        }
 
 
 ########
@@ -1563,52 +1143,6 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         }
 
 
-class CreateNode(Schema):
-    nodeAsSmiles: str
-    nodeName: str | None = None
-    nodeReason: str | None = None
-    nodeDepth: str | None = None
-
-
-@router.post(
-    "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 403: Error},
-)
-def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-        pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-
-        if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(n.nodeDepth)
-        else:
-            node_depth = -1
-
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
-
-        return redirect(n.url)
-    except ValueError:
-        return 403, {"message": "Adding node failed!"}
-
-
-@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node/{uuid:node_uuid}")
-def delete_node(request, package_uuid, pathway_uuid, node_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            n = Node.objects.get(pathway=pw, uuid=node_uuid)
-            n.delete()
-            return redirect(f"{pw.url}/node")
-        else:
-            raise ValueError("You do not have the rights to delete this Node!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Node with id {node_uuid} failed due to insufficient rights!"
-        }
-
-
 ########
 # Edge #
 ########
@@ -1672,200 +1206,6 @@ def get_package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
         }
 
 
-class CreateEdge(Schema):
-    edgeAsSmirks: str | None = None
-    educts: str | None = None  # Node URIs comma sep
-    products: str | None = None  # Node URIs comma sep
-    multistep: str | None = None
-    edgeReason: str | None = None
-
-
-@router.post(
-    "/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
-    response={200: str | Any, 403: Error},
-)
-def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-        pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-
-        if e.edgeAsSmirks is None and (e.educts is None or e.products is None):
-            raise ValueError("Either SMIRKS or educt/product must be provided")
-
-        if e.edgeAsSmirks is not None and (e.educts is not None and e.products is not None):
-            raise ValueError("SMIRKS and educt/product provided!")
-
-        educts = []
-        products = []
-
-        if e.edgeAsSmirks:
-            for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
-                educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
-
-            for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
-                products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
-        else:
-            for ed in e.educts.split(","):
-                educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
-
-            for pr in e.products.split(","):
-                products.append(Node.objects.get(pathway=pw, url=pr.strip()))
-
-        new_e = Edge.create(
-            pathway=pw,
-            start_nodes=educts,
-            end_nodes=products,
-            rule=None,
-            name=e.name,
-            description=e.edgeReason,
-        )
-
-        return redirect(new_e.url)
-    except ValueError:
-        return 403, {"message": "Adding node failed!"}
-
-
-@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
-def delete_edge(request, package_uuid, pathway_uuid, edge_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            e = Edge.objects.get(pathway=pw, uuid=edge_uuid)
-            e.delete()
-            return redirect(f"{pw.url}/edge")
-        else:
-            raise ValueError("You do not have the rights to delete this Edge!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Edge with id {edge_uuid} failed due to insufficient rights!"
-        }
-
-
-#########
-# Model #
-#########
-class ModelWrapper(Schema):
-    relative_reasoning: List["SimpleModel"] = Field(..., alias="relative-reasoning")
-
-
-class ModelSchema(Schema):
-    aliases: List[str] = Field([], alias="aliases")
-    description: str = Field(None, alias="description")
-    evalPackages: List["SimplePackage"] = Field([])
-    id: str = Field(None, alias="url")
-    identifier: str = "relative-reasoning"
-    #   "info" : {
-    #       "Accuracy (Single-Gen)" : "0.5932962678936605" ,
-    #       "Area under PR-Curve (Single-Gen)" : "0.5654653182134282" ,
-    #       "Area under ROC-Curve (Single-Gen)" : "0.8178302405034772" ,
-    #       "Precision (Single-Gen)" : "0.6978730822873083" ,
-    #       "Probability Threshold" : "0.5" ,
-    #       "Recall/Sensitivity (Single-Gen)" : "0.4484149210261006"
-    #     } ,
-    name: str = Field(None, alias="name")
-    pathwayPackages: List["SimplePackage"] = Field([])
-    reviewStatus: str = Field(None, alias="review_status")
-    rulePackages: List["SimplePackage"] = Field([])
-    scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
-    status: str
-    statusMessage: str
-    threshold: str
-    type: str
-
-
-@router.get("/model", response={200: ModelWrapper, 403: Error})
-def get_models(request):
-    pass
-
-
-@router.get("/package/{uuid:package_uuid}/model", response={200: ModelWrapper, 403: Error})
-def get_package_models(request, package_uuid, model_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-        return EPModel.objects.filter(package=p)
-    except ValueError:
-        return 403, {
-            "message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
-        }
-
-
-class Classify(Schema):
-    smiles: str | None = None
-
-
-@router.get(
-    "/package/{uuid:package_uuid}/model/{uuid:model_uuid}",
-    response={200: ModelSchema | Any, 403: Error, 400: Error},
-)
-def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-        mod = EPModel.objects.get(package=p, uuid=model_uuid)
-
-        if c.smiles:
-            if c.smiles == "":
-                return 400, {"message": "Received empty SMILES"}
-
-            try:
-                stand_smiles = FormatConverter.standardize(c.smiles)
-            except ValueError:
-                return 400, {"message": f'"{c.smiles}" is not a valid SMILES'}
-
-            from epdb.tasks import dispatch_eager, predict_simple
-
-            pred_res = dispatch_eager(request.user, predict_simple, mod.pk, stand_smiles)
-
-            result = []
-
-            for pr in pred_res:
-                if len(pr) > 0:
-                    products = []
-                    for prod_set in pr.product_sets:
-                        products.append(tuple([x for x in prod_set]))
-
-                    res = {
-                        "probability": pr.probability,
-                        "products": list(set(products)),
-                    }
-
-                    if pr.rule:
-                        res["id"] = pr.rule.url
-                        res["identifier"] = pr.rule.get_rule_identifier()
-                        res["name"] = pr.rule.name
-                        res["reviewStatus"] = (
-                            "reviewed" if pr.rule.package.reviewed else "unreviewed"
-                        )
-
-                    result.append(res)
-
-            return result
-
-        return mod
-    except ValueError:
-        return 403, {
-            "message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
-        }
-
-
-@router.delete("/package/{uuid:package_uuid}/model/{uuid:model_uuid}")
-def delete_model(request, package_uuid, model_uuid):
-    try:
-        p = PackageManager.get_package_by_id(request.user, package_uuid)
-
-        if PackageManager.writable(request.user, p):
-            m = EPModel.objects.get(package=p, uuid=model_uuid)
-            m.delete()
-            return redirect(f"{p.url}/model")
-        else:
-            raise ValueError("You do not have the rights to delete this Model!")
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Model with id {model_uuid} failed due to insufficient rights!"
-        }
-
-
 ###########
 # Setting #
 ###########

epdb/logic.py

@@ -1,40 +1,39 @@
-import json
-import logging
 import re
-from typing import Any, Dict, List, Optional, Set, Union
+import logging
+import json
+from typing import Union, List, Optional, Set, Dict, Any
 from uuid import UUID
 
 import nh3
-from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
+from django.conf import settings as s
 from pydantic import ValidationError
 
 from epdb.models import (
-    Compound,
-    CompoundStructure,
-    Edge,
-    EnzymeLink,
-    EPModel,
-    Group,
-    GroupPackagePermission,
-    Node,
-    Pathway,
-    Permission,
-    Reaction,
-    Rule,
-    Setting,
     User,
+    Package,
     UserPackagePermission,
+    GroupPackagePermission,
+    Permission,
+    Group,
+    Setting,
+    EPModel,
     UserSettingPermission,
+    Rule,
+    Pathway,
+    Node,
+    Edge,
+    Compound,
+    Reaction,
+    CompoundStructure,
+    EnzymeLink,
 )
 from utilities.chem import FormatConverter
-from utilities.misc import PackageExporter, PackageImporter
+from utilities.misc import PackageImporter, PackageExporter
 
 logger = logging.getLogger(__name__)
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 class EPDBURLParser:
     UUID_PATTERN = r"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
@@ -579,39 +578,30 @@ class PackageManager(object):
         else:
             _ = perm_cls.objects.update_or_create(defaults={"permission": new_perm}, **data)
 
-    @staticmethod
-    def grant_read(caller: User, package: Package, grantee: Union[User, Group]):
-        PackageManager.update_permissions(caller, package, grantee, Permission.READ[0])
-
-    @staticmethod
-    def grant_write(caller: User, package: Package, grantee: Union[User, Group]):
-        PackageManager.update_permissions(caller, package, grantee, Permission.WRITE[0])
-
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
         data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
     ):
-        from collections import defaultdict
-        from datetime import datetime
         from uuid import UUID, uuid4
-
+        from datetime import datetime
-        from envipy_additional_information import AdditionalInformationConverter
+        from collections import defaultdict
-
         from .models import (
+            Package,
             Compound,
             CompoundStructure,
-            Edge,
+            SimpleRule,
-            Node,
+            SimpleAmbitRule,
             ParallelRule,
-            Pathway,
-            Reaction,
-            Scenario,
             SequentialRule,
             SequentialRuleOrdering,
-            SimpleAmbitRule,
+            Reaction,
-            SimpleRule,
+            Pathway,
+            Node,
+            Edge,
+            Scenario,
         )
+        from envipy_additional_information import AdditionalInformationConverter
 
         pack = Package()
         pack.uuid = UUID(data["id"].split("/")[-1]) if keep_ids else uuid4()

epdb/management/commands/create_ml_models.py

@@ -2,9 +2,7 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer, MLRelativeReasoning
+from epdb.models import MLRelativeReasoning, EnviFormer, Package
-
-Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):
@@ -77,13 +75,11 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(
+        print(f"Creating models: {options['model_names']}\n"
-            f"Creating models: {options['model_names']}\n"
               f"Data packages: {options['data_packages']}\n"
               f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
               f"Eval Packages: {options['eval_packages']}\n"
-            f"Threshold: {options['threshold']:.2f}"
+              f"Threshold: {options['threshold']:.2f}")
-        )
         data_packages = decode_packages(options["data_packages"])
         eval_packages = decode_packages(options["eval_packages"])
         rule_packages = decode_packages(options["rule_packages"])
@@ -94,7 +90,7 @@ class Command(BaseCommand):
                     pack,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options["threshold"],
+                    threshold=options['threshold'],
                     name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"EnviFormer transformer trained on {options['data_packages']} "
                                 f"evaluated on {options['eval_packages']}.",
@@ -105,7 +101,7 @@ class Command(BaseCommand):
                     rule_packages=rule_packages,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options["threshold"],
+                    threshold=options['threshold'],
                     name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
                                 f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",

epdb/management/commands/load_enviformer.py

@@ -8,9 +8,7 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer
+from epdb.models import EnviFormer, Package
-
-Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):

epdb/management/commands/localize_urls.py

@@ -1,8 +1,8 @@
 from django.apps import apps
-from django.conf import settings as s
 from django.core.management.base import BaseCommand
-from django.db.models import F, JSONField, TextField, Value
+
-from django.db.models.functions import Cast, Replace
+from django.db.models import F, Value, TextField, JSONField
+from django.db.models.functions import Replace, Cast
 
 from epdb.models import EnviPathModel
 
@@ -23,13 +23,10 @@ class Command(BaseCommand):
         )
 
     def handle(self, *args, **options):
-        Package = s.GET_PACKAGE_MODEL()
-        print("Localizing urls for Package")
-        Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
-
         MODELS = [
             "User",
             "Group",
+            "Package",
             "Compound",
             "CompoundStructure",
             "Pathway",

epdb/models.py

@@ -2,41 +2,40 @@ import abc
 import hashlib
 import json
 import logging
-import math
 import os
 import secrets
 from abc import abstractmethod
 from collections import defaultdict
 from datetime import datetime
-from typing import Any, Dict, List, Optional, Set, Tuple, Union
+from typing import Union, List, Optional, Dict, Tuple, Set, Any
 from uuid import uuid4
-
+import math
 import joblib
 import nh3
 import numpy as np
 from django.conf import settings as s
 from django.contrib.auth.models import AbstractUser
-from django.contrib.contenttypes.fields import GenericForeignKey, GenericRelation
+from django.contrib.contenttypes.fields import GenericRelation, GenericForeignKey
 from django.contrib.contenttypes.models import ContentType
 from django.contrib.postgres.fields import ArrayField
 from django.db import models, transaction
-from django.db.models import Count, JSONField, Q, QuerySet
+from django.db.models import JSONField, Count, Q, QuerySet
 from django.utils import timezone
 from django.utils.functional import cached_property
 from envipy_additional_information import EnviPyModel
 from model_utils.models import TimeStampedModel
 from polymorphic.models import PolymorphicModel
-from sklearn.metrics import jaccard_score, precision_score, recall_score
+from sklearn.metrics import precision_score, recall_score, jaccard_score
 from sklearn.model_selection import ShuffleSplit
 
-from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
+from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
 from utilities.ml import (
-    ApplicabilityDomainPCA,
-    Dataset,
-    EnsembleClassifierChain,
-    EnviFormerDataset,
-    RelativeReasoning,
     RuleBasedDataset,
+    ApplicabilityDomainPCA,
+    EnsembleClassifierChain,
+    RelativeReasoning,
+    EnviFormerDataset,
+    Dataset,
 )
 
 logger = logging.getLogger(__name__)
@@ -45,6 +44,8 @@ logger = logging.getLogger(__name__)
 ##########################
 # User/Groups/Permission #
 ##########################
+
+
 class User(AbstractUser):
     email = models.EmailField(unique=True)
     uuid = models.UUIDField(
@@ -52,10 +53,7 @@ class User(AbstractUser):
     )
     url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
     default_package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL,
+        "epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
-        verbose_name="Default Package",
-        null=True,
-        on_delete=models.SET_NULL,
     )
     default_group = models.ForeignKey(
         "Group",
@@ -245,7 +243,7 @@ class UserPackagePermission(Permission):
     )
     user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
+        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -261,7 +259,7 @@ class GroupPackagePermission(Permission):
     )
     group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
+        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -730,13 +728,10 @@ class Package(EnviPathModel):
         rules = sorted(rules, key=lambda x: x.url)
         return rules
 
-    class Meta:
-        swappable = "EPDB_PACKAGE_MODEL"
-
 
 class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     default_structure = models.ForeignKey(
         "CompoundStructure",
@@ -786,7 +781,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
             raise ValueError("SMILES is required")
@@ -1066,7 +1061,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     # # https://github.com/django-polymorphic/django-polymorphic/issues/229
@@ -1079,10 +1074,6 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     def apply(self, *args, **kwargs):
         pass
 
-    @abc.abstractmethod
-    def get_rule_identifier(self) -> str:
-        pass
-
     @staticmethod
     def cls_for_type(rule_type: str):
         if rule_type == "SimpleAmbitRule":
@@ -1176,7 +1167,7 @@ class SimpleAmbitRule(SimpleRule):
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
+        package: Package,
         name: str = None,
         description: str = None,
         smirks: str = None,
@@ -1237,9 +1228,6 @@ class SimpleAmbitRule(SimpleRule):
     def _url(self):
         return "{}/simple-ambit-rule/{}".format(self.package.url, self.uuid)
 
-    def get_rule_identifier(self) -> str:
-        return "simple-rule"
-
     def apply(self, smiles):
         return FormatConverter.apply(smiles, self.smirks)
 
@@ -1253,7 +1241,7 @@ class SimpleAmbitRule(SimpleRule):
 
     @property
     def related_reactions(self):
-        qs = s.GET_PACKAGE_MODEL().objects.filter(reviewed=True)
+        qs = Package.objects.filter(reviewed=True)
         return self.reaction_rule.filter(package__in=qs).order_by("name")
 
     @property
@@ -1285,9 +1273,6 @@ class ParallelRule(Rule):
     def _url(self):
         return "{}/parallel-rule/{}".format(self.package.url, self.uuid)
 
-    def get_rule_identifier(self) -> str:
-        return "parallel-rule"
-
     @cached_property
     def srs(self) -> QuerySet:
         return self.simple_rules.all()
@@ -1319,57 +1304,6 @@ class ParallelRule(Rule):
 
         return res
 
-    @staticmethod
-    @transaction.atomic
-    def create(
-        package: "Package",
-        simple_rules: List["SimpleRule"],
-        name: str = None,
-        description: str = None,
-        reactant_filter_smarts: str = None,
-        product_filter_smarts: str = None,
-    ):
-        if len(simple_rules) == 0:
-            raise ValueError("At least one simple rule is required!")
-
-        for sr in simple_rules:
-            if sr.package != package:
-                raise ValueError(
-                    f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
-                )
-
-        r = ParallelRule()
-        r.package = package
-
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if name is None or name == "":
-            name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
-
-        r.name = name
-        if description is not None and description.strip() != "":
-            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
-            if not FormatConverter.is_valid_smarts(reactant_filter_smarts.strip()):
-                raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
-            else:
-                r.reactant_filter_smarts = reactant_filter_smarts.strip()
-
-        if product_filter_smarts is not None and product_filter_smarts.strip() != "":
-            if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
-                raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
-            else:
-                r.product_filter_smarts = product_filter_smarts.strip()
-
-        r.save()
-
-        for sr in simple_rules:
-            r.simple_rules.add(sr)
-
-        return r
-
 
 class SequentialRule(Rule):
     simple_rules = models.ManyToManyField(
@@ -1379,9 +1313,6 @@ class SequentialRule(Rule):
     def _url(self):
         return "{}/sequential-rule/{}".format(self.compound.url, self.uuid)
 
-    def get_rule_identifier(self) -> str:
-        return "sequential-rule"
-
     @property
     def srs(self):
         return self.simple_rules.all()
@@ -1402,7 +1333,7 @@ class SequentialRuleOrdering(models.Model):
 
 class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     educts = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@@ -1424,7 +1355,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
+        package: Package,
         name: str = None,
         description: str = None,
         educts: Union[List[str], List[CompoundStructure]] = None,
@@ -1583,7 +1514,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     setting = models.ForeignKey(
         "epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
@@ -2145,7 +2076,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     def _url(self):
@@ -2154,17 +2085,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
 
 class PackageBasedModel(EPModel):
     rule_packages = models.ManyToManyField(
-        s.EPDB_PACKAGE_MODEL,
+        "Package",
         verbose_name="Rule Packages",
         related_name="%(app_label)s_%(class)s_rule_packages",
     )
     data_packages = models.ManyToManyField(
-        s.EPDB_PACKAGE_MODEL,
+        "Package",
         verbose_name="Data Packages",
         related_name="%(app_label)s_%(class)s_data_packages",
     )
     eval_packages = models.ManyToManyField(
-        s.EPDB_PACKAGE_MODEL,
+        "Package",
         verbose_name="Evaluation Packages",
         related_name="%(app_label)s_%(class)s_eval_packages",
     )
@@ -3469,7 +3400,7 @@ class PluginModel(EPModel):
 
 class Scenario(EnviPathModel):
     package = models.ForeignKey(
-        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     scenario_date = models.CharField(max_length=256, null=False, blank=False, default="No date")
     scenario_type = models.CharField(
@@ -3624,7 +3555,7 @@ class Setting(EnviPathModel):
     )
 
     rule_packages = models.ManyToManyField(
-        s.EPDB_PACKAGE_MODEL,
+        "Package",
         verbose_name="Setting Rule Packages",
         related_name="setting_rule_packages",
         blank=True,

epdb/tasks.py

@@ -1,22 +1,19 @@
 import csv
 import io
 import logging
+from datetime import datetime
 from typing import Any, Callable, List, Optional
 from uuid import uuid4
 
 from celery import shared_task
 from celery.utils.functional import LRUCache
-from django.conf import settings as s
-from django.utils import timezone
 
 from epdb.logic import SPathway
-from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
+from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 def get_ml_model(model_pk: int):
     if model_pk not in ML_CACHE:
@@ -32,7 +29,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
         log.task_id = uuid4()
         log.job_name = job.__name__
         log.status = "SUCCESS"
-        log.done_at = timezone.now()
+        log.done_at = datetime.now()
         log.task_result = str(x) if x else None
         log.save()
 

epdb/urls.py

@@ -142,11 +142,6 @@ urlpatterns = [
         v.package_pathway,
         name="package pathway detail",
     ),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/predict$",
-        v.package_predict_pathway,
-        name="package predict pathway",
-    ),
     # Pathway Nodes
     re_path(
         rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",

epdb/views.py

@@ -1,60 +1,58 @@
 import json
 import logging
-from typing import Any, Dict, List
+from typing import List, Dict, Any
 
-import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
+from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
-from django.shortcuts import redirect, render
+from django.shortcuts import render, redirect
 from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
 from oauth2_provider.decorators import protected_resource
+import nh3
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
 from utilities.misc import HTMLGenerator
-
 from .logic import (
-    EPDBURLParser,
     GroupManager,
     PackageManager,
-    SearchManager,
-    SettingManager,
     UserManager,
+    SettingManager,
+    SearchManager,
+    EPDBURLParser,
 )
 from .models import (
-    APIToken,
+    Package,
-    Compound,
-    CompoundStructure,
-    Edge,
-    EnviFormer,
-    EnzymeLink,
-    EPModel,
-    ExternalDatabase,
-    ExternalIdentifier,
-    Group,
     GroupPackagePermission,
-    JobLog,
+    Group,
-    License,
+    CompoundStructure,
-    MLRelativeReasoning,
+    Compound,
-    Node,
-    Pathway,
-    Permission,
     Reaction,
     Rule,
+    Pathway,
+    Node,
+    EPModel,
+    EnviFormer,
+    MLRelativeReasoning,
     RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
-    User,
+    APIToken,
     UserPackagePermission,
+    Permission,
+    License,
+    User,
+    Edge,
+    ExternalDatabase,
+    ExternalIdentifier,
+    EnzymeLink,
+    JobLog,
 )
 
 logger = logging.getLogger(__name__)
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 def log_post_params(request):
     if s.DEBUG:
@@ -62,26 +60,6 @@ def log_post_params(request):
             logger.debug(f"{k}\t{v}")
 
 
-def get_error_handler_context(request, for_user=None) -> Dict[str, Any]:
-    current_user = _anonymous_or_real(request)
-
-    if for_user:
-        current_user = for_user
-
-    ctx = {
-        "title": "enviPath",
-        "meta": {
-            "site_id": s.MATOMO_SITE_ID,
-            "version": "0.0.1",
-            "server_url": s.SERVER_URL,
-            "user": current_user,
-            "enabled_features": s.FLAGS,
-            "debug": s.DEBUG,
-        },
-    }
-    return ctx
-
-
 def error(request, message: str, detail: str, code: int = 400):
     context = get_base_context(request)
     error_context = {
@@ -96,48 +74,6 @@ def error(request, message: str, detail: str, code: int = 400):
     return render(request, "errors/error.html", context, status=code)
 
 
-def handler400(request, exception):
-    """Custom 400 Bad Request error handler"""
-    context = get_error_handler_context(request)
-    context["public_mode"] = True
-    return render(request, "errors/400_bad_request.html", context, status=400)
-
-
-def handler403(request, exception):
-    """Custom 403 Forbidden error handler"""
-    context = get_error_handler_context(request)
-    context["public_mode"] = True
-    return render(request, "errors/403_access_denied.html", context, status=403)
-
-
-def handler404(request, exception):
-    """Custom 404 Not Found error handler"""
-    context = get_error_handler_context(request)
-    context["public_mode"] = True
-    return render(request, "errors/404_not_found.html", context, status=404)
-
-
-def handler500(request):
-    """Custom 500 Internal Server Error handler"""
-    context = get_error_handler_context(request)
-
-    error_context = {}
-    error_context["error_message"] = "Internal Server Error"
-    error_context["error_detail"] = "An unexpected error occurred. Please try again later."
-
-    if request.headers.get("Accept") == "application/json":
-        return JsonResponse(error_context, status=500)
-
-    context["public_mode"] = True
-    context["error_code"] = 500
-    context["error_description"] = (
-        "We encountered an unexpected error while processing your request. Our team has been notified and is working to resolve the issue."
-    )
-    context.update(**error_context)
-
-    return render(request, "errors/error.html", context, status=500)
-
-
 def login(request):
     context = get_base_context(request)
 
@@ -147,7 +83,8 @@ def login(request):
         return render(request, "static/login.html", context)
 
     elif request.method == "POST":
-        from django.contrib.auth import authenticate, login
+        from django.contrib.auth import authenticate
+        from django.contrib.auth import login
 
         username = request.POST.get("username").strip()
         if username != request.POST.get("username"):
@@ -254,8 +191,8 @@ def register(request):
 
 
 def editable(request, user):
-    # if user.is_superuser:
+    if user.is_superuser:
-    #     return True
+        return True
 
     url = request.build_absolute_uri(request.path)
     if PackageManager.is_package_url(url):
@@ -437,22 +374,6 @@ def predict_pathway(request):
     return render(request, "predict_pathway.html", context)
 
 
-@package_permission_required()
-def package_predict_pathway(request, package_uuid):
-    """Package-specific predict pathway view."""
-    if request.method != "GET":
-        return HttpResponseNotAllowed(["GET"])
-
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    context = get_base_context(request)
-    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
-    context["meta"]["current_package"] = current_package
-
-    return render(request, "predict_pathway.html", context)
-
-
 def packages(request):
     current_user = _anonymous_or_real(request)
 
@@ -935,7 +856,7 @@ def package_models(request, package_uuid):
                 request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
             )
 
-        from .tasks import build_model, dispatch
+        from .tasks import dispatch, build_model
 
         dispatch(current_user, build_model, mod.pk)
 
@@ -969,10 +890,9 @@ def package_model(request, package_uuid, model_uuid):
             if classify:
                 from epdb.tasks import dispatch_eager, predict_simple
 
-                pred_res = dispatch_eager(
+                res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
-                    current_user, predict_simple, current_model.pk, stand_smiles
-                )
 
+                pred_res = current_model.predict(stand_smiles)
                 res = []
 
                 for pr in pred_res:
@@ -1132,7 +1052,9 @@ def package(request, package_uuid):
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
-                    PackageManager.grant_read(current_user, current_package, g)
+                    PackageManager.update_permissions(
+                        current_user, current_package, g, Permission.READ[0]
+                    )
                 return redirect(current_package.url)
             elif hidden == "copy":
                 object_to_copy = request.POST.get("object_to_copy")
@@ -2471,9 +2393,9 @@ def package_scenarios(request, package_uuid):
         context["unreviewed_objects"] = unreviewed_scenario_qs
 
         from envipy_additional_information import (
-            SEDIMENT_ADDITIONAL_INFORMATION,
             SLUDGE_ADDITIONAL_INFORMATION,
             SOIL_ADDITIONAL_INFORMATION,
+            SEDIMENT_ADDITIONAL_INFORMATION,
         )
 
         context["scenario_types"] = {

migration/views.py

@@ -1,21 +1,24 @@
+import gzip
 import json
 import logging
 import os.path
+from datetime import datetime
 
 from django.conf import settings as s
 from django.http import HttpResponseNotAllowed
 from django.shortcuts import render
+
+from epdb.logic import PackageManager
+from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
+from epdb.views import get_base_context, _anonymous_or_real
+from utilities.chem import FormatConverter
+
+
 from rdkit import Chem
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
-from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
-from epdb.views import get_base_context
-from utilities.chem import FormatConverter
-
 logger = logging.getLogger(__name__)
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 def normalize_smiles(smiles):
     m1 = Chem.MolFromSmiles(smiles)
@@ -56,7 +59,9 @@ def run_both_engines(SMILES, SMIRKS):
         set(
             [
                 normalize_smiles(str(x))
-                for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
+                for x in FormatConverter.sanitize_smiles(
+                    [str(s) for s in all_rdkit_prods]
+                )[0]
             ]
         )
     )
@@ -80,7 +85,8 @@ def migration(request):
                 url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
             )
             ALL_SMILES = [
-                cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
+                cs.smiles
+                for cs in CompoundStructure.objects.filter(compound__package=BBD)
             ]
             RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
@@ -136,7 +142,9 @@ def migration(request):
             )
 
         for r in migration_status["results"]:
-            r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
+            r["detail_url"] = r["detail_url"].replace(
+                "http://localhost:8000", s.SERVER_URL
+            )
 
         context.update(**migration_status)
 
@@ -144,6 +152,8 @@ def migration(request):
 
 
 def migration_detail(request, package_uuid, rule_uuid):
+    current_user = _anonymous_or_real(request)
+
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -225,7 +235,9 @@ def compare(request):
         context["smirks"] = (
             "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
         )
-        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        context["smiles"] = (
+            "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        )
         return render(request, "compare.html", context)
 
     elif request.method == "POST":

pyproject.toml

@@ -45,8 +45,6 @@ dev = [
     "poethepoet>=0.37.0",
     "pre-commit>=4.3.0",
     "ruff>=0.13.3",
-    "pytest-playwright>=0.7.1",
-    "pytest-django>=4.11.1",
 ]
 
 [tool.ruff]
@@ -68,31 +66,47 @@ docstring-code-format = true
 
 [tool.poe.tasks]
 # Main tasks
-setup = { sequence = [
+setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
-    "db-up",
+dev = { shell = """
-    "migrate",
+# Start pnpm CSS watcher in background
-    "bootstrap",
+pnpm run dev &
-], help = "Complete setup: start database, run migrations, and bootstrap data" }
+PNPM_PID=$!
-dev = { cmd = "uv run python scripts/dev_server.py", help = "Start the development server with CSS watcher", deps = [
+echo "Started CSS watcher (PID: $PNPM_PID)"
-    "db-up",
+
-    "js-deps",
+# Cleanup function
-] }
+cleanup() {
-build = { sequence = [
+    echo "\nShutting down..."
-    "build-frontend",
+    if kill -0 $PNPM_PID 2>/dev/null; then
-    "collectstatic",
+        kill $PNPM_PID
-], help = "Build frontend assets and collect static files" }
+        echo "✓ CSS watcher stopped"
+    fi
+    if [ ! -z "${DJ_PID:-}" ] && kill -0 $DJ_PID 2>/dev/null; then
+        kill $DJ_PID
+        echo "✓ Django server stopped"
+    fi
+}
+
+# Set trap for cleanup
+trap cleanup EXIT INT TERM
+
+# Start Django dev server in background
+uv run python manage.py runserver &
+DJ_PID=$!
+
+# Wait for Django to finish
+wait $DJ_PID
+""", help = "Start the development server with CSS watcher", deps = ["db-up", "js-deps"] }
+build = { sequence = ["build-frontend", "collectstatic"], help = "Build frontend assets and collect static files" }
 
 # Database tasks
 db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
 db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
 
 # Frontend tasks
-js-deps = { cmd = "uv run python scripts/pnpm_wrapper.py install", help = "Install frontend dependencies" }
+js-deps = { cmd = "pnpm install", help = "Install frontend dependencies" }
 
 # Full cleanup tasks
-clean = { sequence = [
+clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
-    "clean-db",
-], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
 clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
 
 # Django tasks
@@ -110,14 +124,6 @@ echo "  Password: SuperSafe"
 """, help = "Bootstrap initial data (anonymous user, packages, models)"  }
 shell = { cmd = "uv run python manage.py shell", help = "Open Django shell" }
 
-
+# Build tasks
-build-frontend = { cmd = "uv run python scripts/pnpm_wrapper.py run build", help = "Build frontend assets using pnpm", deps = [
+build-frontend = { cmd = "pnpm run build", help = "Build frontend assets using pnpm", deps = ["js-deps"] }
-    "js-deps",
+collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = ["build-frontend"] }
-] } # Build tasks
-
-
-collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = [
-    "build-frontend",
-] }
-
-frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" }

scripts/dev_server.py

@@ -1,201 +0,0 @@
-#!/usr/bin/env python3
-"""
-Cross-platform development server script.
-Starts pnpm CSS watcher and Django dev server, handling cleanup on exit.
-Works on both Windows and Unix systems.
-"""
-
-import atexit
-import shutil
-import signal
-import subprocess
-import sys
-import time
-
-
-def find_pnpm():
-    """
-    Find pnpm executable on the system.
-    Returns the path to pnpm or None if not found.
-    """
-    # Try to find pnpm using shutil.which
-    # On Windows, this will find pnpm.cmd if it's in PATH
-    pnpm_path = shutil.which("pnpm")
-
-    if pnpm_path:
-        return pnpm_path
-
-    # On Windows, also try pnpm.cmd explicitly
-    if sys.platform == "win32":
-        pnpm_cmd = shutil.which("pnpm.cmd")
-        if pnpm_cmd:
-            return pnpm_cmd
-
-    return None
-
-
-class DevServerManager:
-    """Manages background processes for development server."""
-
-    def __init__(self):
-        self.processes = []
-        self._cleanup_registered = False
-
-    def start_process(self, command, description, shell=False):
-        """Start a background process and return the process object."""
-        print(f"Starting {description}...")
-        try:
-            if shell:
-                # Use shell=True for commands that need shell interpretation
-                process = subprocess.Popen(
-                    command,
-                    shell=True,
-                    stdout=subprocess.PIPE,
-                    stderr=subprocess.STDOUT,
-                    text=True,
-                    bufsize=1,
-                )
-            else:
-                # Split command into list for subprocess
-                process = subprocess.Popen(
-                    command,
-                    stdout=subprocess.PIPE,
-                    stderr=subprocess.STDOUT,
-                    text=True,
-                    bufsize=1,
-                )
-            self.processes.append((process, description))
-            print(f"✓ Started {description} (PID: {process.pid})")
-            return process
-        except Exception as e:
-            print(f"✗ Failed to start {description}: {e}", file=sys.stderr)
-            self.cleanup()
-            sys.exit(1)
-
-    def cleanup(self):
-        """Terminate all running processes."""
-        if not self.processes:
-            return
-
-        print("\nShutting down...")
-        for process, description in self.processes:
-            if process.poll() is None:  # Process is still running
-                try:
-                    # Try graceful termination first
-                    if sys.platform == "win32":
-                        process.terminate()
-                    else:
-                        process.send_signal(signal.SIGTERM)
-
-                    # Wait up to 5 seconds for graceful shutdown
-                    try:
-                        process.wait(timeout=5)
-                    except subprocess.TimeoutExpired:
-                        # Force kill if graceful shutdown failed
-                        if sys.platform == "win32":
-                            process.kill()
-                        else:
-                            process.send_signal(signal.SIGKILL)
-                        process.wait()
-
-                    print(f"✓ {description} stopped")
-                except Exception as e:
-                    print(f"✗ Error stopping {description}: {e}", file=sys.stderr)
-
-        self.processes.clear()
-
-    def register_cleanup(self):
-        """Register cleanup handlers for various exit scenarios."""
-        if self._cleanup_registered:
-            return
-
-        self._cleanup_registered = True
-
-        # Register atexit handler (works on all platforms)
-        atexit.register(self.cleanup)
-
-        # Register signal handlers (Unix only)
-        if sys.platform != "win32":
-            signal.signal(signal.SIGINT, self._signal_handler)
-            signal.signal(signal.SIGTERM, self._signal_handler)
-
-    def _signal_handler(self, signum, frame):
-        """Handle Unix signals."""
-        self.cleanup()
-        sys.exit(0)
-
-    def wait_for_process(self, process, description):
-        """Wait for a process to finish and handle its output."""
-        try:
-            # Stream output from the process
-            for line in iter(process.stdout.readline, ""):
-                if line:
-                    print(f"[{description}] {line.rstrip()}")
-
-            process.wait()
-            return process.returncode
-        except KeyboardInterrupt:
-            # Handle Ctrl+C
-            self.cleanup()
-            sys.exit(0)
-        except Exception as e:
-            print(f"Error waiting for {description}: {e}", file=sys.stderr)
-            self.cleanup()
-            sys.exit(1)
-
-
-def main():
-    """Main entry point."""
-    manager = DevServerManager()
-    manager.register_cleanup()
-
-    # Find pnpm executable
-    pnpm_path = find_pnpm()
-    if not pnpm_path:
-        print("Error: pnpm not found in PATH.", file=sys.stderr)
-        print("\nPlease install pnpm:", file=sys.stderr)
-        print("  Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
-        print("  Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
-        sys.exit(1)
-
-    # Determine shell usage based on platform
-    use_shell = sys.platform == "win32"
-
-    # Start pnpm CSS watcher
-    # Use the found pnpm path to ensure it works on Windows
-    pnpm_command = f'"{pnpm_path}" run dev' if use_shell else [pnpm_path, "run", "dev"]
-    manager.start_process(
-        pnpm_command,
-        "CSS watcher",
-        shell=use_shell,
-    )
-
-    # Give pnpm a moment to start
-    time.sleep(1)
-
-    # Start Django dev server
-    django_process = manager.start_process(
-        ["uv", "run", "python", "manage.py", "runserver"],
-        "Django server",
-        shell=False,
-    )
-
-    print("\nDevelopment servers are running. Press Ctrl+C to stop.\n")
-
-    try:
-        # Wait for Django server (main process)
-        # If Django exits, we should clean up everything
-        return_code = manager.wait_for_process(django_process, "Django")
-
-        # If Django exited unexpectedly, clean up and exit
-        if return_code != 0:
-            manager.cleanup()
-            sys.exit(return_code)
-    except KeyboardInterrupt:
-        # Ctrl+C was pressed
-        manager.cleanup()
-        sys.exit(0)
-
-
-if __name__ == "__main__":
-    main()

scripts/pnpm_wrapper.py

@@ -1,59 +0,0 @@
-#!/usr/bin/env python3
-"""
-Cross-platform pnpm command wrapper.
-Finds pnpm correctly on Windows (handles pnpm.cmd) and Unix systems.
-"""
-
-import shutil
-import subprocess
-import sys
-
-
-def find_pnpm():
-    """
-    Find pnpm executable on the system.
-    Returns the path to pnpm or None if not found.
-    """
-    # Try to find pnpm using shutil.which
-    # On Windows, this will find pnpm.cmd if it's in PATH
-    pnpm_path = shutil.which("pnpm")
-
-    if pnpm_path:
-        return pnpm_path
-
-    # On Windows, also try pnpm.cmd explicitly
-    if sys.platform == "win32":
-        pnpm_cmd = shutil.which("pnpm.cmd")
-        if pnpm_cmd:
-            return pnpm_cmd
-
-    return None
-
-
-def main():
-    """Main entry point - execute pnpm with provided arguments."""
-    pnpm_path = find_pnpm()
-
-    if not pnpm_path:
-        print("Error: pnpm not found in PATH.", file=sys.stderr)
-        print("\nPlease install pnpm:", file=sys.stderr)
-        print("  Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
-        print("  Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
-        sys.exit(1)
-
-    # Get all arguments passed to this script
-    args = sys.argv[1:]
-
-    # Execute pnpm with the provided arguments
-    try:
-        sys.exit(subprocess.call([pnpm_path] + args))
-    except KeyboardInterrupt:
-        # Handle Ctrl+C gracefully
-        sys.exit(130)
-    except Exception as e:
-        print(f"Error executing pnpm: {e}", file=sys.stderr)
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()

static/css/input.css

@@ -34,30 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-/* Loading Spinner - Benzene Ring */
-.loading-spinner {
-  display: flex;
-  justify-content: center;
-  align-items: center;
-  padding: 2rem;
-}
-
-.loading-spinner svg {
-  width: 48px;
-  height: 48px;
-  animation: spin 2s linear infinite;
-}
-
-.loading-spinner .hexagon,
-.loading-spinner .double-bonds {
-  fill: none;
-  stroke: currentColor;
-  stroke-width: 2;
-}
-
-@keyframes spin {
-  100% {
-    transform: rotate(360deg);
-  }
-}

static/js/alpine/index.js

@@ -1,265 +0,0 @@
-/**
- * Alpine.js Components for enviPath
- *
- * This module provides reusable Alpine.js data components for modals,
- * form validation, and form submission.
- */
-
-document.addEventListener('alpine:init', () => {
-  /**
-   * Modal Form Component
-   *
-   * Provides form validation using HTML5 Constraint Validation API,
-   * loading states for submission, and error message management.
-   *
-   * Basic Usage:
-   * <dialog x-data="modalForm()" @close="reset()">
-   *   <form id="my-form">
-   *     <input name="field" required>
-   *   </form>
-   *   <button @click="submit('my-form')" :disabled="isSubmitting">Submit</button>
-   * </dialog>
-   *
-   * With Custom State:
-   * <dialog x-data="modalForm({ state: { selectedItem: '', imageUrl: '' } })" @close="reset()">
-   *   <select x-model="selectedItem" @change="updateImagePreview(selectedItem + '?image=svg')">
-   *   <img :src="imageUrl" x-show="imageUrl">
-   * </dialog>
-   *
-   * With AJAX:
-   * <button @click="submitAsync('my-form', { onSuccess: (data) => console.log(data) })">
-   */
-  Alpine.data('modalForm', (options = {}) => ({
-    isSubmitting: false,
-    errors: {},
-    // Spread custom initial state from options
-    ...(options.state || {}),
-
-    /**
-     * Validate a single field using HTML5 Constraint Validation API
-     * @param {HTMLElement} field - The input/select/textarea element
-     */
-    validateField(field) {
-      const name = field.name || field.id;
-      if (!name) return;
-
-      if (!field.validity.valid) {
-        this.errors[name] = field.validationMessage;
-      } else {
-        delete this.errors[name];
-      }
-    },
-
-    /**
-     * Clear error for a field (call on input)
-     * @param {HTMLElement} field - The input element
-     */
-    clearError(field) {
-      const name = field.name || field.id;
-      if (name && this.errors[name]) {
-        delete this.errors[name];
-      }
-    },
-
-    /**
-     * Get error message for a field
-     * @param {string} name - Field name
-     * @returns {string|undefined} Error message or undefined
-     */
-    getError(name) {
-      return this.errors[name];
-    },
-
-    /**
-     * Check if form has any errors
-     * @returns {boolean} True if there are errors
-     */
-    hasErrors() {
-      return Object.keys(this.errors).length > 0;
-    },
-
-    /**
-     * Validate all fields in a form
-     * @param {string} formId - The form element ID
-     * @returns {boolean} True if form is valid
-     */
-    validateAll(formId) {
-      const form = document.getElementById(formId);
-      if (!form) return false;
-
-      this.errors = {};
-      const fields = form.querySelectorAll('input, select, textarea');
-
-      fields.forEach(field => {
-        if (field.name && !field.validity.valid) {
-          this.errors[field.name] = field.validationMessage;
-        }
-      });
-
-      return !this.hasErrors();
-    },
-
-    /**
-     * Validate that two password fields match
-     * @param {string} password1Id - ID of first password field
-     * @param {string} password2Id - ID of second password field
-     * @returns {boolean} True if passwords match
-     */
-    validatePasswordMatch(password1Id, password2Id) {
-      const pw1 = document.getElementById(password1Id);
-      const pw2 = document.getElementById(password2Id);
-
-      if (!pw1 || !pw2) return false;
-
-      if (pw1.value !== pw2.value) {
-        this.errors[pw2.name || password2Id] = 'Passwords do not match';
-        pw2.setCustomValidity('Passwords do not match');
-        return false;
-      }
-
-      delete this.errors[pw2.name || password2Id];
-      pw2.setCustomValidity('');
-      return true;
-    },
-
-    /**
-     * Submit a form with loading state
-     * @param {string} formId - The form element ID
-     */
-    submit(formId) {
-      const form = document.getElementById(formId);
-      if (!form) return;
-
-      // Validate before submit
-      if (!form.checkValidity()) {
-        form.reportValidity();
-        return;
-      }
-
-      // Set action to current URL if empty
-      if (!form.action || form.action === window.location.href + '#') {
-        form.action = window.location.href;
-      }
-
-      // Set loading state and submit
-      this.isSubmitting = true;
-      form.submit();
-    },
-
-    /**
-     * Submit form via AJAX (fetch)
-     * @param {string} formId - The form element ID
-     * @param {Object} options - Options { onSuccess, onError, closeOnSuccess }
-     */
-    async submitAsync(formId, options = {}) {
-      const form = document.getElementById(formId);
-      if (!form) return;
-
-      // Validate before submit
-      if (!form.checkValidity()) {
-        form.reportValidity();
-        return;
-      }
-
-      this.isSubmitting = true;
-
-      try {
-        const formData = new FormData(form);
-        const response = await fetch(form.action || window.location.href, {
-          method: form.method || 'POST',
-          body: formData,
-          headers: {
-            'X-Requested-With': 'XMLHttpRequest',
-          },
-        });
-
-        const data = await response.json().catch(() => ({}));
-
-        if (response.ok) {
-          if (options.onSuccess) {
-            options.onSuccess(data);
-          }
-
-          if (data.redirect || data.success) {
-            window.location.href = data.redirect || data.success;
-          } else if (options.closeOnSuccess) {
-            this.$el.closest('dialog')?.close();
-          }
-        } else {
-          const errorMsg = data.error || data.message || `Error: ${response.status}`;
-          this.errors['_form'] = errorMsg;
-
-          if (options.onError) {
-            options.onError(errorMsg, data);
-          }
-        }
-      } catch (error) {
-        this.errors['_form'] = error.message;
-
-        if (options.onError) {
-          options.onError(error.message);
-        }
-      } finally {
-        this.isSubmitting = false;
-      }
-    },
-
-    /**
-     * Set form action URL dynamically
-     * @param {string} formId - The form element ID
-     * @param {string} url - The URL to set as action
-     */
-    setFormAction(formId, url) {
-      const form = document.getElementById(formId);
-      if (form) {
-        form.action = url;
-      }
-    },
-
-    /**
-     * Update image preview
-     * @param {string} url - Image URL (with query params)
-     * @param {string} targetId - Target element ID for the image
-     */
-    updateImagePreview(url) {
-      // Store URL for reactive binding with :src
-      this.imageUrl = url;
-    },
-
-    /**
-     * Reset form state (call on modal close)
-     * Resets to initial state from options
-     */
-    reset() {
-      this.isSubmitting = false;
-      this.errors = {};
-      this.imageUrl = '';
-
-      // Reset custom state to initial values
-      if (options.state) {
-        Object.keys(options.state).forEach(key => {
-          this[key] = options.state[key];
-        });
-      }
-
-      // Call custom reset handler if provided
-      if (options.onReset) {
-        options.onReset.call(this);
-      }
-    }
-  }));
-
-  /**
-   * Simple Modal Component (no form)
-   *
-   * For modals that don't need form validation.
-   *
-   * Usage:
-   * <dialog x-data="modal()">
-   *   <button @click="$el.closest('dialog').close()">Close</button>
-   * </dialog>
-   */
-  Alpine.data('modal', () => ({
-    // Placeholder for simple modals that may need state later
-  }));
-});

static/js/alpine/pagination.js

@@ -1,133 +0,0 @@
-/**
- * Alpine.js Pagination Component
- *
- * Provides client-side pagination for large lists.
- */
-
-document.addEventListener('alpine:init', () => {
-  Alpine.data('paginatedList', (initialItems = [], options = {}) => ({
-    allItems: initialItems,
-    filteredItems: [],
-    currentPage: 1,
-    perPage: options.perPage || 50,
-    searchQuery: '',
-    isReviewed: options.isReviewed || false,
-    instanceId: options.instanceId || Math.random().toString(36).substring(2, 9),
-
-    init() {
-      this.filteredItems = this.allItems;
-    },
-
-    get totalPages() {
-      return Math.ceil(this.filteredItems.length / this.perPage);
-    },
-
-    get paginatedItems() {
-      const start = (this.currentPage - 1) * this.perPage;
-      const end = start + this.perPage;
-      return this.filteredItems.slice(start, end);
-    },
-
-    get totalItems() {
-      return this.filteredItems.length;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      return Math.min(this.currentPage * this.perPage, this.totalItems);
-    },
-
-    search(query) {
-      this.searchQuery = query.toLowerCase();
-      if (this.searchQuery === '') {
-        this.filteredItems = this.allItems;
-      } else {
-        this.filteredItems = this.allItems.filter(item =>
-          item.name.toLowerCase().includes(this.searchQuery)
-        );
-      }
-      this.currentPage = 1;
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.currentPage++;
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.currentPage--;
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.currentPage = page;
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      // Handle empty case
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        // Show all pages if 7 or fewer
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        // More than 7 pages - show first, last, and sliding window around current
-        // Always show first page
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        // Determine the start and end of the middle range
-        let rangeStart, rangeEnd;
-
-        if (current <= 4) {
-          // Near the beginning: show pages 2-5
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          // Near the end: show last 4 pages before the last page
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          // In the middle: show current page and one on each side
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        // Add ellipsis before range if there's a gap
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        // Add pages in the range
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        // Add ellipsis after range if there's a gap
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        // Always show last page
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  }));
-});

static/js/alpine/search.js

@@ -1,145 +0,0 @@
-/**
- * Search Modal Alpine.js Component
- *
- * Provides package selection, search mode switching, and results display
- * for the search modal.
- */
-
-document.addEventListener('alpine:init', () => {
-  /**
-   * Search Modal Component
-   *
-   * Usage:
-   * <dialog x-data="searchModal()" @close="reset()">
-   *   ...
-   * </dialog>
-   */
-  Alpine.data('searchModal', () => ({
-    // Package selector state
-    selectedPackages: [],
-
-    // Search state
-    searchMode: 'text',
-    searchModeLabel: 'Text',
-    query: '',
-
-    // Results state
-    results: null,
-    isSearching: false,
-    error: null,
-
-    // Initialize on modal open
-    init() {
-      // Load reviewed packages by default
-      this.loadInitialSelection();
-
-      // Watch for modal open to focus searchbar
-      this.$watch('$el.open', (open) => {
-        if (open) {
-          setTimeout(() => {
-            this.$refs.searchbar.focus();
-          }, 320);
-        }
-      });
-    },
-
-    loadInitialSelection() {
-      // Select all reviewed packages by default
-      const menuItems = this.$refs.packageDropdown.querySelectorAll('li');
-
-      for (const item of menuItems) {
-        // Stop at 'Unreviewed Packages' section
-        if (item.classList.contains('menu-title') &&
-            item.textContent.trim() === 'Unreviewed Packages') {
-          break;
-        }
-
-        const packageOption = item.querySelector('.package-option');
-        if (packageOption) {
-          this.selectedPackages.push({
-            url: packageOption.dataset.packageUrl,
-            name: packageOption.dataset.packageName
-          });
-        }
-      }
-    },
-
-    togglePackage(url, name) {
-      const index = this.selectedPackages.findIndex(pkg => pkg.url === url);
-
-      if (index !== -1) {
-        this.selectedPackages.splice(index, 1);
-      } else {
-        this.selectedPackages.push({ url, name });
-      }
-    },
-
-    removePackage(url) {
-      const index = this.selectedPackages.findIndex(pkg => pkg.url === url);
-      if (index !== -1) {
-        this.selectedPackages.splice(index, 1);
-      }
-    },
-
-    isPackageSelected(url) {
-      return this.selectedPackages.some(pkg => pkg.url === url);
-    },
-
-    setSearchMode(mode, label) {
-      this.searchMode = mode;
-      this.searchModeLabel = label;
-      this.$refs.modeDropdown.hidePopover();
-    },
-
-    async performSearch(serverBase) {
-      if (!this.query.trim()) {
-        return;
-      }
-
-      if (this.selectedPackages.length < 1) {
-        this.results = { error: 'no_packages' };
-        return;
-      }
-
-      const params = new URLSearchParams();
-      this.selectedPackages.forEach(pkg => params.append('packages', pkg.url));
-      params.append('search', this.query.trim());
-      params.append('mode', this.searchModeLabel.toLowerCase());
-
-      this.isSearching = true;
-      this.results = null;
-      this.error = null;
-
-      try {
-        const response = await fetch(`${serverBase}/search?${params.toString()}`, {
-          method: 'GET',
-          headers: { 'Accept': 'application/json' }
-        });
-
-        if (!response.ok) {
-          throw new Error('Search request failed');
-        }
-
-        this.results = await response.json();
-      } catch (err) {
-        console.error('Search error:', err);
-        this.error = 'Search failed. Please try again.';
-      } finally {
-        this.isSearching = false;
-      }
-    },
-
-    hasResults() {
-      if (!this.results || this.results.error) return false;
-      const categories = ['Compounds', 'Compound Structures', 'Rules', 'Reactions', 'Pathways'];
-      return categories.some(cat => this.results[cat] && this.results[cat].length > 0);
-    },
-
-    reset() {
-      this.query = '';
-      this.results = null;
-      this.error = null;
-      this.isSearching = false;
-    }
-  }));
-});

static/js/discourse-api.js

@@ -63,20 +63,17 @@ class DiscourseAPI {
      * @returns {string} Cleaned excerpt
      */
     extractExcerpt(excerpt) {
-        if (!excerpt) return 'No preview available yet';
+        if (!excerpt) return 'Click to read more';
 
         // Remove HTML tags and clean up; collapse whitespace; do not add manual ellipsis
-        const cleaned = excerpt
+        return excerpt
             .replace(/<[^>]*>/g, '') // Remove HTML tags
             .replace(/&nbsp;/g, ' ') // Replace &nbsp; with spaces
             .replace(/&amp;/g, '&') // Replace &amp; with &
             .replace(/&lt;/g, '<') // Replace &lt; with <
             .replace(/&gt;/g, '>') // Replace &gt; with >
             .replace(/\s+/g, ' ') // Collapse all whitespace/newlines
-            .trim();
+            .trim()
-
-        // Check if excerpt is empty after cleaning
-        return cleaned || 'No preview available yet';
     }
 
     /**

static/js/pw.js

@@ -1,21 +1,14 @@
 console.log("loaded pw.js")
 
 function predictFromNode(url) {
-    fetch("", {
+    $.post("", {node: url})
-        method: "POST",
+        .done(function (data) {
-        headers: {
-            "Content-Type": "application/x-www-form-urlencoded",
-            "X-CSRFToken": document.querySelector('[name=csrfmiddlewaretoken]')?.value || ''
-        },
-        body: new URLSearchParams({node: url})
-    })
-    .then(response => response.json())
-    .then(data => {
             console.log("Success:", data);
             window.location.href = data.success;
         })
-    .catch(error => {
+        .fail(function (xhr, status, error) {
-        console.error("Error:", error);
+            console.error("Error:", xhr.status, xhr.responseText);
+            // show user-friendly message or log error
         });
 }
 
@@ -110,9 +103,6 @@ function draw(pathway, elem) {
     }
 
     function dragstarted(event, d) {
-        // Prevent zoom pan when dragging nodes
-        event.sourceEvent.stopPropagation();
-
         if (!event.active) simulation.alphaTarget(0.3).restart();
         d.fx = d.x;
         d.fy = d.y;
@@ -127,9 +117,6 @@ function draw(pathway, elem) {
     }
 
     function dragged(event, d) {
-        // Prevent zoom pan when dragging nodes
-        event.sourceEvent.stopPropagation();
-
         d.fx = event.x;
         d.fy = event.y;
 
@@ -140,9 +127,6 @@ function draw(pathway, elem) {
     }
 
     function dragended(event, d) {
-        // Prevent zoom pan when dragging nodes
-        event.sourceEvent.stopPropagation();
-
         if (!event.active) simulation.alphaTarget(0);
 
         // Mark that dragging has ended
@@ -208,153 +192,52 @@ function draw(pathway, elem) {
         d3.select(t).select("circle").classed("highlighted", !d3.select(t).select("circle").classed("highlighted"));
     }
 
-    // Wait before showing popup (ms)
+    // Wait one second before showing popup
     var popupWaitBeforeShow = 1000;
+    // Keep Popup at least for one second
+    var popushowAtLeast = 1000;
 
-    // Custom popover element
+    function pop_show_e(element) {
-    let popoverTimeout = null;
+        var e = element;
+        setTimeout(function () {
+            if ($(e).is(':hover')) { // if element is still hovered
+                $(e).popover("show");
 
-    function createPopover() {
+                // workaround to set fixed positions
-        const popover = document.createElement('div');
+                pop = $(e).attr("aria-describedby")
-        popover.id = 'custom-popover';
+                h = $('#' + pop).height();
-        popover.className = 'fixed z-50';
+                $('#' + pop).attr("style", `position: fixed; top: ${clientY - (h / 2.0)}px; left: ${clientX + 10}px; margin: 0px; max-width: 1000px; display: block;`)
-        popover.style.cssText = `
+                setTimeout(function () {
-            background: #ffffff;
+                    var close = setInterval(function () {
-            border: 1px solid #d1d5db;
+                        if (!$(".popover:hover").length // mouse outside popover
-            box-shadow: 0 10px 15px -3px rgb(0 0 0 / 0.1), 0 4px 6px -4px rgb(0 0 0 / 0.1);
+                            && !$(e).is(':hover')) { // mouse outside element
-            max-width: 320px;
+                            $(e).popover('hide');
-            padding: 0.75rem;
+                            clearInterval(close);
-            border-radius: 0.5rem;
-            opacity: 0;
-            visibility: hidden;
-            transition: opacity 150ms ease-in-out, visibility 150ms ease-in-out;
-            pointer-events: auto;
-        `;
-        popover.setAttribute('role', 'tooltip');
-        popover.innerHTML = `
-            <div class="font-semibold mb-2 popover-title" style="font-weight: 600; margin-bottom: 0.5rem;"></div>
-            <div class="text-sm popover-content" style="font-size: 0.875rem;"></div>
-        `;
-
-        // Add styles for content images
-        const style = document.createElement('style');
-        style.textContent = `
-            #custom-popover img {
-                max-width: 100%;
-                height: auto;
-                display: block;
-                margin: 0.5rem 0;
                         }
-            #custom-popover a {
+                    }, 100);
-                color: #2563eb;
+                }, popushowAtLeast);
-                text-decoration: none;
             }
-            #custom-popover a:hover {
+        }, popupWaitBeforeShow);
-                text-decoration: underline;
-            }
-        `;
-        if (!document.getElementById('popover-styles')) {
-            style.id = 'popover-styles';
-            document.head.appendChild(style);
-        }
-
-        // Keep popover open when hovering over it
-        popover.addEventListener('mouseenter', () => {
-            if (popoverTimeout) {
-                clearTimeout(popoverTimeout);
-                popoverTimeout = null;
-            }
-        });
-
-        popover.addEventListener('mouseleave', () => {
-            hidePopover();
-        });
-
-        document.body.appendChild(popover);
-        return popover;
-    }
-
-    function getPopover() {
-        return document.getElementById('custom-popover') || createPopover();
-    }
-
-    function showPopover(element, title, content) {
-        const popover = getPopover();
-        popover.querySelector('.popover-title').textContent = title;
-        popover.querySelector('.popover-content').innerHTML = content;
-
-        // Make visible to measure
-        popover.style.visibility = 'hidden';
-        popover.style.opacity = '0';
-        popover.style.display = 'block';
-
-        // Smart positioning - avoid viewport overflow
-        const padding = 10;
-        const popoverRect = popover.getBoundingClientRect();
-        const viewportWidth = window.innerWidth;
-        const viewportHeight = window.innerHeight;
-
-        let left = clientX + 15;
-        let top = clientY - (popoverRect.height / 2);
-
-        // Prevent right overflow
-        if (left + popoverRect.width > viewportWidth - padding) {
-            left = clientX - popoverRect.width - 15;
-        }
-
-        // Prevent bottom overflow
-        if (top + popoverRect.height > viewportHeight - padding) {
-            top = viewportHeight - popoverRect.height - padding;
-        }
-
-        // Prevent top overflow
-        if (top < padding) {
-            top = padding;
-        }
-
-        popover.style.top = `${top}px`;
-        popover.style.left = `${left}px`;
-        popover.style.visibility = 'visible';
-        popover.style.opacity = '1';
-
-        currentElement = element;
-    }
-
-    function hidePopover() {
-        const popover = getPopover();
-        popover.style.opacity = '0';
-        popover.style.visibility = 'hidden';
-        currentElement = null;
     }
 
     function pop_add(objects, title, contentFunction) {
-        objects.each(function (d) {
+        objects.attr("id", "pop")
-            const element = this;
+            .attr("data-container", "body")
+            .attr("data-toggle", "popover")
+            .attr("data-placement", "right")
+            .attr("title", title);
 
-            element.addEventListener('mouseenter', () => {
+        objects.each(function (d, i) {
-                if (popoverTimeout) clearTimeout(popoverTimeout);
+            options = {trigger: "manual", html: true, animation: false};
-
+            this_ = this;
-                popoverTimeout = setTimeout(() => {
+            var p = $(this).popover(options).on("mouseenter", function () {
-                    if (element.matches(':hover')) {
+                pop_show_e(this);
-                        const content = contentFunction(d);
-                        showPopover(element, title, content);
-                    }
-                }, popupWaitBeforeShow);
             });
-
+            p.on("show.bs.popover", function (e) {
-            element.addEventListener('mouseleave', () => {
+                // this is to dynamically ajdust the content and bounds of the popup
-                if (popoverTimeout) {
+                p.attr('data-content', contentFunction(d));
-                    clearTimeout(popoverTimeout);
+                p.data("bs.popover").setContent();
-                    popoverTimeout = null;
+                p.data("bs.popover").tip().css({"max-width": "1000px"});
-                }
-
-                // Delay hide to allow moving to popover
-                setTimeout(() => {
-                    const popover = getPopover();
-                    if (!popover.matches(':hover') && !element.matches(':hover')) {
-                        hidePopover();
-                    }
-                }, 100);
             });
         });
     }
@@ -372,7 +255,7 @@ function draw(pathway, elem) {
             }
         }
 
-        popupContent += "<img src='" + n.image + "'><br>"
+        popupContent += "<img src='" + n.image + "' width='" + 20 * nodeRadius + "'><br>"
         if (n.scenarios.length > 0) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of n.scenarios) {
@@ -382,7 +265,7 @@ function draw(pathway, elem) {
 
         var isLeaf = pathway.links.filter(obj => obj.source.id === n.id).length === 0;
         if (pathway.isIncremental && isLeaf) {
-            popupContent += '<br><a class="btn btn-primary btn-sm mt-2" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
+            popupContent += '<br><a class="btn btn-primary" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
         }
 
         return popupContent;
@@ -402,7 +285,7 @@ function draw(pathway, elem) {
             popupContent += adcontent;
         }
 
-        popupContent += "<img src='" + e.image + "'><br>"
+        popupContent += "<img src='" + e.image + "' width='" + 20 * nodeRadius + "'><br>"
         if (e.reaction_probability) {
             popupContent += '<b>Probability:</b><br>' + e.reaction_probability.toFixed(3) + '<br>';
         }
@@ -425,23 +308,6 @@ function draw(pathway, elem) {
     });
 
     const zoomable = d3.select("#zoomable");
-    const svg = d3.select("#pwsvg");
-    const container = d3.select("#vizdiv");
-
-    // Set explicit SVG dimensions for proper zoom behavior
-    svg.attr("width", width)
-       .attr("height", height);
-
-    // Add background rectangle FIRST to enable pan/zoom on empty space
-    // This must be inserted before zoomable group so it's behind everything
-    svg.insert("rect", "#zoomable")
-        .attr("x", 0)
-        .attr("y", 0)
-        .attr("width", width)
-        .attr("height", height)
-        .attr("fill", "transparent")
-        .attr("pointer-events", "all")
-        .style("cursor", "grab");
 
     // Zoom Funktion aktivieren
     const zoom = d3.zoom()
@@ -450,12 +316,7 @@ function draw(pathway, elem) {
             zoomable.attr("transform", event.transform);
         });
 
-    // Apply zoom to the SVG element - this enables wheel zoom
+    d3.select("svg").call(zoom);
-    svg.call(zoom);
-
-    // Also apply zoom to container to catch events that might not reach SVG
-    // This ensures drag-to-pan works even when clicking on empty space
-    container.call(zoom);
 
     nodes = pathway['nodes'];
     links = pathway['links'];

templates/actions/collections/compound.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_compound_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Compound</a>
-      onclick="document.getElementById('new_compound_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Compound</a
-    >
     </li>
 {% endif %}

templates/actions/collections/compound_structure.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
-      onclick="document.getElementById('new_compound_structure_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a
-    >
     </li>
 {% endif %}

templates/actions/collections/edge.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_edge_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Edge</a>
-      onclick="document.getElementById('new_edge_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Edge</a
-    >
     </li>
 {% endif %}

templates/actions/collections/group.html

@@ -1,8 +1,4 @@
 <li>
-  <a
+    <a role="button" data-toggle="modal" data-target="#new_group_modal">
-    role="button"
+        <span class="glyphicon glyphicon-plus"></span> New Group</a>
-    onclick="document.getElementById('new_group_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-plus"></span> New Group</a
-  >
 </li>

templates/actions/collections/model.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_model_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Model</a>
-      onclick="document.getElementById('new_model_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Model</a
-    >
     </li>
 {% endif %}

templates/actions/collections/node.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_node_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Node</a>
-      onclick="document.getElementById('new_node_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Node</a
-    >
     </li>
 {% endif %}

templates/actions/collections/package.html

@@ -1,25 +1,12 @@
 <li>
-  <a
+    <a role="button" data-toggle="modal" data-target="#new_package_modal">
-    role="button"
+        <span class="glyphicon glyphicon-plus"></span> New Package</a>
-    onclick="document.getElementById('new_package_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-plus"></span> New Package</a
-  >
 </li>
 <li>
-  <a
+    <a role="button" data-toggle="modal" data-target="#import_package_modal">
-    role="button"
+        <span class="glyphicon glyphicon-import"></span> Import Package from JSON</a>
-    onclick="document.getElementById('import_package_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-import"></span> Import Package from JSON</a
-  >
 </li>
 <li>
-  <a
+    <a role="button" data-toggle="modal" data-target="#import_legacy_package_modal">
-    role="button"
+        <span class="glyphicon glyphicon-import"></span> Import Package from legacy JSON</a>
-    onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-import"></span> Import Package from legacy
-    JSON</a
-  >
 </li>

templates/actions/collections/pathway.html

@@ -1,9 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a href="{{ meta.server_url }}/predict">
-      href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
+            <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Pathway</a
-    >
     </li>
 {% endif %}

templates/actions/collections/reaction.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_reaction_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Reaction</a>
-      onclick="document.getElementById('new_reaction_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Reaction</a
-    >
     </li>
 {% endif %}

templates/actions/collections/rule.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_rule_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Rule</a>
-      onclick="document.getElementById('new_rule_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Rule</a
-    >
     </li>
 {% endif %}

templates/actions/collections/scenario.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_scenario_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
-      onclick="document.getElementById('new_scenario_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Scenario</a
-    >
     </li>
 {% endif %}

templates/actions/collections/setting.html

@@ -1,10 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_setting_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span>New Setting</a>
-      onclick="document.getElementById('new_setting_modal').showModal(); return false;"
-    >
-      <span class="glyphicon glyphicon-plus"></span>New Setting</a
-    >
     </li>
 {% endif %}

templates/actions/objects/compound.html

@@ -1,60 +1,32 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
-      onclick="document.getElementById('edit_compound_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#add_structure_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
-      onclick="document.getElementById('add_structure_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Add Structure</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
 {% endif %}
     <li>
-  <a
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    role="button"
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-    onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
-  >
     </li>
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
-    >
     </li>
 {% endif %}

templates/actions/objects/compound_structure.html

@@ -1,42 +1,22 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
-      onclick="document.getElementById('edit_compound_structure_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a
-    >
     </li>
 {% endif %}

templates/actions/objects/edge.html

@@ -1,26 +1,14 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Edge</a
-    >
     </li>
 {% endif %}

templates/actions/objects/group.html

@@ -1,18 +1,10 @@
 {% if meta.can_edit %}
     <li>
-    <a
+    <a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
-      role="button"
+            <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
-      onclick="document.getElementById('edit_group_member_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Group</a
-    >
     </li>
 {% endif %}

templates/actions/objects/model.html

@@ -1,34 +1,18 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_model_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Model</a>
-      onclick="document.getElementById('edit_model_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Model</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
-      role="button"
+            <i class="glyphicon glyphicon-ok"></i> Evaluate Model</a>
-      onclick="document.getElementById('evaluate_model_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-ok"></i> Evaluate Model</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#retrain_model_modal">
-      role="button"
+            <i class="glyphicon glyphicon-repeat"></i> Retrain Model</a>
-      onclick="document.getElementById('retrain_model_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-repeat"></i> Retrain Model</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Model</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Model</a
-    >
     </li>
 {% endif %}

templates/actions/objects/node.html

@@ -1,34 +1,18 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_node_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
-      onclick="document.getElementById('edit_node_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Node</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Node</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Node</a
-    >
     </li>
 {% endif %}

templates/actions/objects/package.html

@@ -1,50 +1,26 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_package_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Package</a>
-      onclick="document.getElementById('edit_package_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Package</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
-      role="button"
+            <i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
-      onclick="document.getElementById('edit_package_permissions_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#publish_package_modal">
-      role="button"
+            <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a>
-      onclick="document.getElementById('publish_package_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#export_package_modal">
-      role="button"
+            <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a>
-      onclick="document.getElementById('export_package_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_license_modal">
-      role="button"
+            <i class="glyphicon glyphicon-duplicate"></i> License</a>
-      onclick="document.getElementById('set_license_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-duplicate"></i> License</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Package</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Package</a
-    >
     </li>
 {% endif %}

templates/actions/objects/pathway.html

@@ -1,104 +1,59 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
-      class="button"
+            <i class="glyphicon glyphicon-plus"></i> Add Compound</a>
-      onclick="document.getElementById('add_pathway_node_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Add Compound</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
-      class="button"
+            <i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
-      onclick="document.getElementById('add_pathway_edge_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
-    >
     </li>
     <li role="separator" class="divider"></li>
 {% endif %}
     <li>
-  <a
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    role="button"
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-    onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
-  >
     </li>
     <li>
-  <a
+        <a class="button" data-toggle="modal" data-target="#download_pathway_csv_modal">
-    class="button"
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a>
-    onclick="document.getElementById('download_pathway_csv_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
-  >
     </li>
     <li>
-  <a
+        <a class="button" data-toggle="modal" data-target="#download_pathway_image_modal">
-    class="button"
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
-    onclick="document.getElementById('download_pathway_image_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
-  >
     </li>
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
-      class="button"
+            <i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
-      onclick="document.getElementById('identify_missing_rules_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-question-sign"></i> Identify Missing
-      Rules</a
-    >
     </li>
     <li role="separator" class="divider"></li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
-      class="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
-      onclick="document.getElementById('edit_pathway_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
+    {#    <li>#}
+    {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
+    {#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
+    {#    </li>#}
     <li role="separator" class="divider"></li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
-      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
-      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a
-    >
     </li>
 {% endif %}

templates/actions/objects/reaction.html

@@ -1,52 +1,28 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
-      onclick="document.getElementById('edit_reaction_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
 {% endif %}
     <li>
-  <a
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    role="button"
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-    onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
-  >
     </li>
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
-    >
     </li>
 {% endif %}

templates/actions/objects/rule.html

@@ -1,44 +1,24 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
-      onclick="document.getElementById('edit_rule_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Rule</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-      onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-      onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    >
     </li>
 {% endif %}
     <li>
-  <a
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    role="button"
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-    onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
-  >
     </li>
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Rule</a
-    >
     </li>
 {% endif %}

templates/actions/objects/scenario.html

@@ -1,26 +1,14 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#add_additional_information_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a>
-      onclick="document.getElementById('add_additional_information_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#update_scenario_additional_information_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Set Additional Information</a>
-      onclick="document.getElementById('update_scenario_additional_information_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Set Additional Information</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Scenario</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Scenario</a
-    >
     </li>
 {% endif %}

templates/actions/objects/user.html

@@ -1,38 +1,22 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_user_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Update</a>
-      onclick="document.getElementById('edit_user_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Update</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_password_modal">
-      role="button"
+            <i class="glyphicon glyphicon-lock"></i> Update Password</a>
-      onclick="document.getElementById('edit_password_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-lock"></i> Update Password</a
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
-      onclick="document.getElementById('new_prediction_setting_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
-    >
     </li>
 {#    <li>#}
 {#        <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
 {#            <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
 {#    </li>#}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
-      onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Account</a
-    >
     </li>
 {% endif %}

templates/admin.html

@@ -1,17 +1,12 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div id="searchContent">
+
+<div id=searchContent>
     <form id="admin-form" action="{{ SERVER_BASE }}/admin" method="post">
         <div class="form-group">
             <label for="textarea">Query</label>
-        <textarea
+            <textarea id="textarea" class="form-control" rows="10" placeholder="Paste query here" required>
-          id="textarea"
-          class="form-control"
-          rows="10"
-          placeholder="Paste query here"
-          required
-        >
 PREFIX pps: <http://localhost:8080/vocabulary#>
 SELECT ?name (count(?objId) as ?xcnt)
 WHERE {
@@ -20,29 +15,32 @@ WHERE {
     ?packageId pps:reviewStatus 'reviewed' .
     ?packageId pps:pathway ?objId .
 } GROUP BY ?name
-            </textarea
+            </textarea>
-        >
         </div>
         <button id="submit" type="button" class="btn btn-primary">Submit</button>
     </form>
     <p></p>
 </div>
-  <div id="results"></div>
+<div id="results">
+</div>
 <div id="loading"></div>
+</div>
 <script>
 $(function() {
-      $("#submit").on("click", function () {
+    $('#submit').on('click', function() {
+
         makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
 
         data = {
-          query: $("#textarea").val(),
+            "query": $("#textarea").val()
-        };
+        }
 
         $.post("{{ SERVER_BASE }}/expire", data, function(result) {
             $("#loading").empty();
             queryResultToTable("results", result);
+        })
     });
-      });
+})
-    });
 </script>
+
 {% endblock content %}

templates/collections/joblog.html

@@ -1,52 +1,48 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
-  <div class="space-y-2 p-4">
+
-    <!-- Header Section -->
+    <div class="panel-group" id="reviewListAccordion">
-    <div class="card bg-base-100">
+        <div class="panel panel-default">
-      <div class="card-body">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        <h2 class="card-title text-2xl">User Prediction Jobs</h2>
+                Jobs
-        <p class="mt-2">Job Logs Desc</p>
             </div>
+            <div class="panel-body">
+                <p>
+                    Job Logs Desc
+                </p>
+
             </div>
 
-    <!-- Jobs -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-    <div class="collapse-arrow bg-base-200 collapse">
+                <h4 class="panel-title">
-      <input type="checkbox" checked />
+                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
-      <div class="collapse-title text-xl font-medium">Recent Jobs</div>
+                        Jobs
-      <div class="collapse-content" id="job-content">
+                    </a>
-        <div class="overflow-x-auto">
+                </h4>
-          <table class="table-zebra table">
+            </div>
-            <thead>
+            <div id="jobs"
-              <tr>
+                 class="panel-collapse collapse in">
-                <th>ID</th>
+                <div class="panel-body list-group-item" id="job-content">
-                <th>Name</th>
+                    <table class="table table-bordered table-hover">
-                <th>Status</th>
+                        <tr style="background-color: rgba(0, 0, 0, 0.08);">
-                <th>Queued</th>
+                            <th scope="col">ID</th>
-                <th>Done</th>
+                            <th scope="col">Name</th>
-                <th>Result</th>
+                            <th scope="col">Status</th>
+                            <th scope="col">Queued</th>
+                            <th scope="col">Done</th>
+                            <th scope="col">Result</th>
                         </tr>
-            </thead>
                         <tbody>
                         {% for job in jobs %}
                             <tr>
-                  {% if meta.user.is_superuser %}
-                    <td>
-                      <a href="{{ job.user.url }}">{{ job.user.username }}</a>
-                    </td>
-                  {% endif %}
                                 <td>{{ job.task_id }}</td>
                                 <td>{{ job.job_name }}</td>
                                 <td>{{ job.status }}</td>
                                 <td>{{ job.created }}</td>
                                 <td>{{ job.done_at }}</td>
                                 {% if job.task_result and job.task_result|is_url == True %}
-                    <td>
+                                    <td><a href="{{ job.task_result }}">Result</a></td>
-                      <a href="{{ job.task_result }}" class="link link-primary"
-                        >Result</a
-                      >
-                    </td>
                                 {% elif job.task_result %}
                                     <td>{{ job.task_result|slice:"40" }}...</td>
                                 {% else %}
@@ -58,31 +54,17 @@
                     </table>
                 </div>
             </div>
-    </div>
 
-    {% if objects %}
             <!-- Unreviewable objects such as User / Group / Setting -->
-      <div class="card bg-base-100 shadow-xl">
+            <ul class='list-group'>
-        <div class="card-body">
-          <ul class="menu bg-base-200 rounded-box">
                 {% for obj in objects %}
                     {% if object_type == 'user' %}
-                <li>
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
-                  <a href="{{ obj.url }}" class="hover:bg-base-300"
-                    >{{ obj.username }}</a
-                  >
-                </li>
                     {% else %}
-                <li>
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
-                  <a href="{{ obj.url }}" class="hover:bg-base-300"
-                    >{{ obj.name }}</a
-                  >
-                </li>
                     {% endif %}
                 {% endfor %}
             </ul>
         </div>
     </div>
-    {% endif %}
-  </div>
 {% endblock content %}

templates/collections/objects_list.html

@@ -1,32 +1,20 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
 
-  {# Serialize objects data for Alpine pagination #}
-  {# prettier-ignore-start #}
-  {# FIXME: This is a hack to get the objects data into the JavaScript code. #}
-  <script>
-    window.reviewedObjects = [
-      {% for obj in reviewed_objects %}
-        { "name": "{{ obj.name|escapejs }}", "url": "{{ obj.url }}" }{% if not forloop.last %},{% endif %}
-      {% endfor %}
-    ];
-    window.unreviewedObjects = [
-      {% for obj in unreviewed_objects %}
-        { "name": "{{ obj.name|escapejs }}", "url": "{{ obj.url }}" }{% if not forloop.last %},{% endif %}
-      {% endfor %}
-    ];
-  </script>
-  {# prettier-ignore-end #}
-
     {% if object_type != 'package' %}
-    <div class="px-8 py-4">
+        <div>
-      <input
+            <div id="load-all-error" style="display: none;">
-        type="text"
+                <div class="alert alert-danger" role="alert">
-        id="object-search"
+                    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-        class="input input-bordered hidden w-full max-w-xs"
+                    <span class="sr-only">Error:</span>
-        placeholder="Search by name"
+                    Getting objects failed!
-      />
+                </div>
+            </div>
+
+            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
+                   style="display: none;">
+            <p></p>
         </div>
     {% endif %}
 
@@ -60,12 +48,9 @@
         {% endif %}
     {% endblock action_modals %}
 
-  <div class="px-8 py-4">
+<div class="panel-group" id="reviewListAccordion">
-    <!-- Header Section -->
+    <div class="panel panel-default">
-    <div class="card bg-base-100">
+        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-      <div class="card-body px-0 py-4">
-        <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">
             {% if object_type == 'package' %}
             Packages
             {% elif object_type == 'compound' %}
@@ -93,31 +78,13 @@
             {% elif object_type == 'group' %}
             Groups
             {% endif %}
-          </h2>
+            <div id="actionsButton"
-          <div id="actionsButton" class="dropdown dropdown-end hidden">
+                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-              <svg
+                                     aria-haspopup="true" aria-expanded="false"><span
-                xmlns="http://www.w3.org/2000/svg"
+                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                width="16"
+                    style="padding-right:1em"></span></a>
-                height="16"
+                <ul id="actionsList" class="dropdown-menu">
-                viewBox="0 0 24 24"
-                fill="none"
-                stroke="currentColor"
-                stroke-width="2"
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                class="lucide lucide-wrench"
-              >
-                <path
-                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
-                />
-              </svg>
-              Actions
-            </div>
-            <ul
-              tabindex="-1"
-              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
-            >
                     {% block actions %}
                         {% if object_type == 'package' %}
                             {% include "actions/collections/package.html" %}
@@ -148,386 +115,205 @@
                 </ul>
             </div>
         </div>
-        <div class="mt-2">
+        <div class="panel-body">
             <!-- Set Text above links -->
             {% if object_type == 'package' %}
-            <p>
+            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-              A package contains pathways, rules, etc. and can reflect specific
+                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-              experimental conditions.
+                    more &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/packages"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'compound' %}
-            <p>
+            <p>A compound stores the structure of a molecule and can include meta-information.
-              A compound stores the structure of a molecule and can include
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-              meta-information.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/compounds"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'structure' %}
-            <p>
+            <p>The structures stored in this compound
-              The structures stored in this compound
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-              <a
+                    &gt;&gt;</a></p>
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/compounds"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'rule' %}
-            <p>
+            <p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
-              A rule describes a biotransformation reaction template that is
+                <a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
-              defined as SMIRKS.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/Rules"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'reaction' %}
-            <p>
+            <p>A reaction is a specific biotransformation from educt compounds to product compounds.
-              A reaction is a specific biotransformation from educt compounds to
+                <a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
-              product compounds.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/reactions"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'pathway' %}
-            <p>
+            <p>A pathway displays the (predicted) biodegradation of a compound as graph.
-              A pathway displays the (predicted) biodegradation of a compound as
+                <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
-              graph.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/pathways"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'node' %}
-            <p>
+            <p>Nodes represent the (predicted) compounds in a graph.
-              Nodes represent the (predicted) compounds in a graph.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
-              <a
+                    &gt;&gt;</a></p>
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/nodes"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'edge' %}
-            <p>
+            <p>Edges represent the links between Nodes in a graph
-              Edges represent the links between Nodes in a graph
+                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
-              <a
+                    &gt;&gt;</a></p>
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/edges"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'scenario' %}
-            <p>
+            <p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
-              A scenario contains meta-information that can be attached to other
+                <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
-              data (compounds, rules, ..).
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/scenarios"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'model' %}
-            <p>
+            <p>A model applies machine learning to limit the combinatorial explosion.
-              A model applies machine learning to limit the combinatorial
+                <a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
-              explosion.
+                    more
-              <a
+                    &gt;&gt;</a></p>
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/relative_reasoning"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'setting' %}
-            <p>
+            <p>A setting includes configuration parameters for pathway predictions.
-              A setting includes configuration parameters for pathway
+                <a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
-              predictions.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/settings"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'user' %}
-            <p>
+            <p>Register now to create own packages and to submit and manage your data.
-              Register now to create own packages and to submit and manage your
+                <a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
-              data.
+                    &gt;&gt;</a></p>
-              <a
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/users"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% elif object_type == 'group' %}
-            <p>
+            <p>Users can team up in groups to share packages.
-              Users can team up in groups to share packages.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
-              <a
+                    &gt;&gt;</a></p>
-                target="_blank"
-                href="https://wiki.envipath.org/index.php/groups"
-                class="link link-primary"
-                >Learn more &gt;&gt;</a
-              >
-            </p>
             {% endif %}
 
             <!-- If theres nothing to show extend the text above -->
             {% if reviewed_objects and unreviewed_objects %}
             {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
-              <p class="mt-4">
+            <p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
-                Nothing found. There are two possible reasons: <br /><br />1.
+                reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
-                There is no content yet.<br />2. You have no reading
-                permissions.<br /><br />Please be sure you have at least reading
-                permissions.
-              </p>
             {% endif %}
             {% endif %}
         </div>
-      </div>
-    </div>
-
-    <!-- Lists Container - Full Width with Reviewed on Right -->
-    <div class="w-full">
         {% if reviewed_objects %}
         {% if reviewed_objects|length > 0 %}
-          <!-- Reviewed -->
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-          <div
+            <h4 class="panel-title">
-            class="collapse-arrow bg-base-200 collapse order-2 w-full"
+                <a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
-            x-data="paginatedList(window.reviewedObjects || [], { isReviewed: true, instanceId: 'reviewed' })"
+                   href="#Reviewed">Reviewed</a>
-          >
+            </h4>
-            <input type="checkbox" checked />
-            <div class="collapse-title text-xl font-medium">
-              Reviewed
-              <span
-                class="badge badge-sm badge-neutral ml-2"
-                x-text="totalItems"
-              ></span>
         </div>
-            <div class="collapse-content w-full">
+        <div id="Reviewed" class="panel-collapse collapse in">
-              <ul class="menu bg-base-100 rounded-box w-full">
+            <div class="panel-body list-group-item" id="ReviewedContent">
-                <template x-for="obj in paginatedItems" :key="obj.url">
+                {% if object_type == 'package' %}
-                  <li>
+                {% for obj in reviewed_objects %}
-                    <a :href="obj.url" class="hover:bg-base-200">
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
-                      <span x-text="obj.name"></span>
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                      <span
+                          style="float:right" data-toggle="tooltip"
-                        class="tooltip tooltip-left ml-auto"
+                          data-placement="top" title="" data-original-title="Reviewed">
-                        data-tip="Reviewed"
-                      >
-                        <svg
-                          xmlns="http://www.w3.org/2000/svg"
-                          width="16"
-                          height="16"
-                          viewBox="0 0 24 24"
-                          fill="none"
-                          stroke="currentColor"
-                          stroke-width="2"
-                          stroke-linecap="round"
-                          stroke-linejoin="round"
-                          class="lucide lucide-star"
-                        >
-                          <polygon
-                            points="12 2 15.09 8.26 22 9.27 17 14.14 18.18 21.02 12 17.77 5.82 21.02 7 14.14 2 9.27 8.91 8.26 12 2"
-                          />
-                        </svg>
                         </span>
                 </a>
-                  </li>
+                {% endfor %}
-                </template>
+                {% else %}
-              </ul>
+                {% for obj in reviewed_objects|slice:":50" %}
-              <!-- Pagination Controls -->
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
-              <div
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                x-show="totalPages > 1"
+                          style="float:right" data-toggle="tooltip"
-                class="mt-4 flex items-center justify-between px-2"
+                          data-placement="top" title="" data-original-title="Reviewed">
-              >
-                <span class="text-base-content/70 text-sm">
-                  Showing <span x-text="showingStart"></span>-<span
-                    x-text="showingEnd"
-                  ></span>
-                  of <span x-text="totalItems"></span>
                         </span>
-                <div class="join">
+                </a>
-                  <button
+                {% endfor %}
-                    class="join-item btn btn-sm"
+                {% endif %}
-                    :disabled="currentPage === 1"
-                    @click="prevPage()"
-                  >
-                    «
-                  </button>
-                  <template x-for="item in pageNumbers" :key="item.key">
-                    <button
-                      class="join-item btn btn-sm"
-                      :class="{ 'btn-active': item.page === currentPage }"
-                      :disabled="item.isEllipsis"
-                      @click="!item.isEllipsis && goToPage(item.page)"
-                      x-text="item.page"
-                    ></button>
-                  </template>
-                  <button
-                    class="join-item btn btn-sm"
-                    :disabled="currentPage === totalPages"
-                    @click="nextPage()"
-                  >
-                    »
-                  </button>
-                </div>
-              </div>
             </div>
         </div>
         {% endif %}
         {% endif %}
-
         {% if unreviewed_objects %}
-        <!-- Unreviewed -->
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
-        <div
+                class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
-          class="collapse-arrow bg-base-200 collapse order-1 w-full"
+                                       href="#Unreviewed">Unreviewed</a></h4></div>
-          x-data="paginatedList(window.unreviewedObjects || [], { isReviewed: false, instanceId: 'unreviewed' })"
+        <div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
-        >
+            <div class="panel-body list-group-item" id="UnreviewedContent">
-          <input
+                {% if object_type == 'package' %}
-            type="checkbox"
+                {% for obj in unreviewed_objects %}
-            {% if reviewed_objects|length == 0 or object_type == 'package' %}checked{% endif %}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-          />
+                {% endfor %}
-          <div class="collapse-title text-xl font-medium">
+                {% else %}
-            Unreviewed
+                {% for obj in unreviewed_objects|slice:":50" %}
-            <span
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-              class="badge badge-sm badge-neutral ml-2"
+                {% endfor %}
-              x-text="totalItems"
+                {% endif %}
-            ></span>
-          </div>
-          <div class="collapse-content w-full">
-            <ul class="menu bg-base-100 rounded-box w-full">
-              <template x-for="obj in paginatedItems" :key="obj.url">
-                <li>
-                  <a
-                    :href="obj.url"
-                    class="hover:bg-base-200"
-                    x-text="obj.name"
-                  ></a>
-                </li>
-              </template>
-            </ul>
-            <!-- Pagination Controls -->
-            <div
-              x-show="totalPages > 1"
-              class="mt-4 flex items-center justify-between px-2"
-            >
-              <span class="text-base-content/70 text-sm">
-                Showing <span x-text="showingStart"></span>-<span
-                  x-text="showingEnd"
-                ></span>
-                of <span x-text="totalItems"></span>
-              </span>
-              <div class="join">
-                <button
-                  class="join-item btn btn-sm"
-                  :disabled="currentPage === 1"
-                  @click="prevPage()"
-                >
-                  «
-                </button>
-                <template x-for="item in pageNumbers" :key="item.key">
-                  <button
-                    class="join-item btn btn-sm"
-                    :class="{ 'btn-active': item.page === currentPage }"
-                    :disabled="item.isEllipsis"
-                    @click="!item.isEllipsis && goToPage(item.page)"
-                    x-text="item.page"
-                  ></button>
-                </template>
-                <button
-                  class="join-item btn btn-sm"
-                  :disabled="currentPage === totalPages"
-                  @click="nextPage()"
-                >
-                  »
-                </button>
-              </div>
-            </div>
             </div>
         </div>
         {% endif %}
-    </div>
-
         {% if objects %}
         <!-- Unreviewable objects such as User / Group / Setting -->
-      <div class="card bg-base-100">
+        <ul class='list-group'>
-        <div class="card-body">
-          <ul class="menu bg-base-200 rounded-box">
             {% for obj in objects %}
             {% if object_type == 'user' %}
-                <li>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
-                  <a href="{{ obj.url }}" class="hover:bg-base-300"
-                    >{{ obj.username }}</a
-                  >
-                </li>
             {% else %}
-                <li>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                  <a href="{{ obj.url }}" class="hover:bg-base-300"
-                    >{{ obj.name }}</a
-                  >
-                </li>
             {% endif %}
             {% endfor %}
         </ul>
-        </div>
-      </div>
         {% endif %}
     </div>
+    <style>
+        .spinner-widget {
+            position: fixed; /* stays in place on scroll */
+            bottom: 20px; /* distance from bottom */
+            right: 20px; /* distance from right */
+            z-index: 9999; /* above most elements */
+            width: 60px; /* adjust to gif size */
+            height: 60px;
+        }
 
+        .spinner-widget img {
+            width: 100%;
+            height: auto;
+        }
+    </style>
+
+    <div id="load-all-loading" class="spinner-widget" style="display: none">
+        <img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
+    </div>
+
+</div>
     <script>
-    document.addEventListener("DOMContentLoaded", function () {
+        $(function () {
-      // Show actions button if there are actions
+
-      const actionsButton = document.getElementById("actionsButton");
+            $('#object-search').show();
-      const actionsList = actionsButton?.querySelector("ul");
+
-      if (actionsList && actionsList.children.length > 0) {
+            {% if object_type != 'package' and object_type != 'user' and object_type != 'group' %}
-        actionsButton?.classList.remove("hidden");
+                {% if reviewed_objects|length > 50 or unreviewed_objects|length > 50 %}
+                    $('#load-all-loading').show()
+
+                    setTimeout(function () {
+                        $('#load-all-error').hide();
+
+                        $.getJSON('?all=true', function (resp) {
+                            $('#ReviewedContent').empty();
+                            $('#UnreviewedContent').empty();
+
+                            for (o in resp.objects) {
+                                obj = resp.objects[o];
+                                if (obj.reviewed) {
+                                    $('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + ' <span class="glyphicon glyphicon-star" aria-hidden="true" style="float:right" data-toggle="tooltip" data-placement="top" title="" data-original-title="Reviewed"></span></a>');
+                                } else {
+                                    $('#UnreviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
+                                }
                             }
 
-      // Show search input and connect to Alpine pagination
+                            $('#load-all-loading').hide();
-      const objectSearch = document.getElementById("object-search");
+                            $('#load-remaining').hide();
-      if (objectSearch) {
+                        }).fail(function (resp) {
-        objectSearch.classList.remove("hidden");
+                            $('#load-all-loading').hide();
-        objectSearch.addEventListener("input", function () {
+                            $('#load-all-error').show();
-          const query = this.value;
-          // Dispatch search to all paginatedList components
-          document
-            .querySelectorAll('[x-data*="paginatedList"]')
-            .forEach((el) => {
-              if (el._x_dataStack && el._x_dataStack[0]) {
-                el._x_dataStack[0].search(query);
-              }
                         });
-        });
-      }
 
-      // Delete form submit handler
+                    }, 2500);
-      const deleteSubmit = document.getElementById("modal-form-delete-submit");
+                {% endif %}
-      const deleteForm = document.getElementById("modal-form-delete");
+            {% endif %}
-      if (deleteSubmit && deleteForm) {
+        
-        deleteSubmit.addEventListener("click", function (e) {
+            $('#modal-form-delete-submit').on('click', function (e) {
                 e.preventDefault();
-          deleteForm.submit();
+                $('#modal-form-delete').submit();
             });
-      }
+
+            $('#object-search').on('keyup', function () {
+                let query = $(this).val().toLowerCase();
+                $('a.list-group-item').each(function () {
+                    let text = $(this).text().toLowerCase();
+                    $(this).toggle(text.indexOf(query) !== -1);
+                });
+            });
+
         });
     </script>
 {% endblock content %}

templates/compare.html

@@ -4,32 +4,16 @@
     <div>
         <form action="" method="post">
             {% csrf_token %}
-      <input
+            <input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
-        type="text"
+                   value="{{ smiles }}"/>
-        class="form-control"
+            <input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
-        id="smiles"
+                   value="{{ smirks }}"/>
-        name="smiles"
-        placeholder="SMILES"
-        value="{{ smiles }}"
-      />
-      <input
-        type="text"
-        class="form-control"
-        id="smiles"
-        name="smirks"
-        placeholder="SMIRKS"
-        value="{{ smirks }}"
-      />
             <button type="submit" class="btn btn-primary">Test</button>
         </form>
     </div>
     {% if result %}
-    {{ smiles }}
+        {{ smiles }}<p></p>
-    <p></p>
+        <img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
-    <img
-      width="400"
-      src="{% url 'depict' %}?smiles={{ smiles|urlencode }}"
-    /><br />
         <p></p>
         {% if rule %}
             {{ smirks }}
@@ -38,7 +22,9 @@
             <p></p>
             {{ rule.products_smarts }}
             <p></p>
-      <div>{{ rule.as_svg|safe }}</div>
+            <div>
+                {{ rule.as_svg|safe }}
+            </div>
         {% endif %}
         <h2>Diff</h2>
         {% if diff %}
@@ -52,22 +38,16 @@
             <div class="col-md-6">
                 <h2>Ambit</h2>
                 {% for p in ambit_res %}
-          {{ p }}<br />
+                    {{ p }}<br>
-          <img
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
-            width="400"
-            src="{% url 'depict' %}?smiles={{ p|urlencode }}"
-          /><br />
                 {% endfor %}
             </div>
 
             <div class="col-md-6">
                 <h2>RDKit</h2>
                 {% for p in rdkit_res %}
-          {{ p }}<br />
+                    {{ p }}<br>
-          <img
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
-            width="400"
-            src="{% url 'depict' %}?smiles={{ p|urlencode }}"
-          /><br />
                 {% endfor %}
             </div>
         </div>

templates/errors/400_bad_request.html

@@ -1,77 +1,15 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
+
-    <div class="w-full max-w-2xl">
+<div class="alert alert-error" role="alert">
-      <div class="alert alert-error mb-6 shadow-lg">
+    <h4 class="alert-heading">Bad Request!</h4>
-        <svg
+    <p>Lorem</p>
-          xmlns="http://www.w3.org/2000/svg"
+    <hr>
-          class="h-8 w-8 shrink-0 stroke-current"
+    <p class="mb-0">
-          fill="none"
+        You can find out more about permissions in our <a target="_blank"
-          viewBox="0 0 24 24"
+                                                          href="https://wiki.envipath.org/index.php/packages"
-        >
+                                                          role="button">Wiki &gt;&gt;</a></p>
-          <path
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            stroke-width="2"
-            d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
-          />
-        </svg>
-        <div class="flex flex-col">
-          <h3 class="text-lg font-bold">Bad Request</h3>
-          <p class="text-sm">The request you sent was invalid or malformed.</p>
-        </div>
 </div>
 
-      <div class="card bg-base-100 shadow-xl">
-        <div class="card-body">
-          <h2 class="card-title mb-4 text-2xl">What happened?</h2>
-          <p class="text-base-content/70 mb-4">
-            The server couldn't process your request because it contains invalid
-            data or parameters.
-          </p>
-          <div class="card-actions mt-6 justify-end">
-            <a href="/" class="btn btn-primary">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
-                />
-              </svg>
-              Go Home
-            </a>
-            <a
-              href="https://wiki.envipath.org/index.php/packages"
-              target="_blank"
-              class="btn btn-outline"
-            >
-              Learn More
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="ml-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
-                />
-              </svg>
-            </a>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 {% endblock content %}

templates/errors/403_access_denied.html

@@ -1,80 +1,15 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
+
-    <div class="w-full max-w-2xl">
+<div class="alert alert-error" role="alert">
-      <div class="alert alert-warning mb-6 shadow-lg">
+    <h4 class="alert-heading">Access Denied!</h4>
-        <svg
+    <p>Access to X denied. </p>
-          xmlns="http://www.w3.org/2000/svg"
+    <hr>
-          class="h-8 w-8 shrink-0 stroke-current"
+    <p class="mb-0">
-          fill="none"
+        You can find out more about permissions in our <a target="_blank"
-          viewBox="0 0 24 24"
+                                                          href="https://wiki.envipath.org/index.php/packages"
-        >
+                                                          role="button">Wiki &gt;&gt;</a></p>
-          <path
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            stroke-width="2"
-            d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
-          />
-        </svg>
-        <div class="flex flex-col">
-          <h3 class="text-lg font-bold">Access Denied</h3>
-          <p class="text-sm">
-            You don't have permission to access this resource.
-          </p>
-        </div>
 </div>
 
-      <div class="card bg-base-100 shadow-xl">
-        <div class="card-body">
-          <h2 class="card-title mb-4 text-2xl">Permission Required</h2>
-          <p class="text-base-content/70 mb-4">
-            You need the appropriate permissions to access this content. If you
-            believe this is an error, please contact the package owner or
-            administrator.
-          </p>
-          <div class="card-actions mt-6 justify-end">
-            <a href="/" class="btn btn-primary">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
-                />
-              </svg>
-              Go Home
-            </a>
-            <a
-              href="https://wiki.envipath.org/index.php/packages"
-              target="_blank"
-              class="btn btn-outline"
-            >
-              Learn More
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="ml-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
-                />
-              </svg>
-            </a>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 {% endblock content %}

templates/errors/404_not_found.html

@@ -1,77 +1,15 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
+
-    <div class="w-full max-w-2xl">
+<div class="alert alert-error" role="alert">
-      <div class="alert alert-info mb-6 shadow-lg">
+    <h4 class="alert-heading">Not Found!</h4>
-        <svg
+    <p>Does not exist</p>
-          xmlns="http://www.w3.org/2000/svg"
+    <hr>
-          class="h-8 w-8 shrink-0 stroke-current"
+    <p class="mb-0">
-          fill="none"
+        You can find out more about permissions in our <a target="_blank"
-          viewBox="0 0 24 24"
+                                                          href="https://wiki.envipath.org/index.php/packages"
-        >
+                                                          role="button">Wiki &gt;&gt;</a></p>
-          <path
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            stroke-width="2"
-            d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
-          />
-        </svg>
-        <div class="flex flex-col">
-          <h3 class="text-lg font-bold">Page Not Found</h3>
-          <p class="text-sm">The page you're looking for doesn't exist.</p>
-        </div>
 </div>
 
-      <div class="card bg-base-100 shadow-xl">
-        <div class="card-body">
-          <h2 class="card-title mb-4 text-2xl">404 Error</h2>
-          <p class="text-base-content/70 mb-4">
-            The page or resource you requested could not be found. It may have
-            been moved, deleted, or the URL might be incorrect.
-          </p>
-          <div class="card-actions mt-6 justify-end">
-            <a href="/" class="btn btn-primary">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
-                />
-              </svg>
-              Go Home
-            </a>
-            <a
-              href="https://wiki.envipath.org/index.php/packages"
-              target="_blank"
-              class="btn btn-outline"
-            >
-              Learn More
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="ml-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
-                />
-              </svg>
-            </a>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 {% endblock content %}

templates/errors/error.html

@@ -1,76 +1,13 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
+
-    <div class="w-full max-w-2xl">
+    <div class="alert alert-danger" role="alert">
-      <div class="alert alert-error mb-6 shadow-lg">
+        <h4 class="alert-heading">{{ error_message }}</h4>
-        <svg
+        <hr>
-          xmlns="http://www.w3.org/2000/svg"
+        <p class="mb-0">
-          class="h-8 w-8 shrink-0 stroke-current"
+            {{ error_detail }}
-          fill="none"
-          viewBox="0 0 24 24"
-        >
-          <path
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            stroke-width="2"
-            d="M10 14l2-2m0 0l2-2m-2 2l-2-2m2 2l2 2m7-2a9 9 0 11-18 0 9 9 0 0118 0z"
-          />
-        </svg>
-        <div class="flex flex-col">
-          <h3 class="text-lg font-bold">
-            {{ error_message|default:"An Error Occurred" }}
-          </h3>
-          <p class="text-sm">
-            {{ error_detail|default:"Something went wrong. Please try again later." }}
         </p>
     </div>
-      </div>
 
-      <div class="card bg-base-100 shadow-xl">
-        <div class="card-body">
-          <h2 class="card-title mb-4 text-2xl">Oops! Something went wrong</h2>
-          <p class="text-base-content/70 mb-4">
-            {{ error_description|default:"We encountered an unexpected error while processing your request. Our team has been notified and is working to resolve the issue." }}
-          </p>
-          <div class="card-actions mt-6 justify-end">
-            <a href="/" class="btn btn-primary">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
-                />
-              </svg>
-              Go Home
-            </a>
-            <button onclick="window.history.back()" class="btn btn-outline">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M10 19l-7-7m0 0l7-7m-7 7h18"
-                />
-              </svg>
-              Go Back
-            </button>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 {% endblock content %}

templates/errors/user_account_inactive.html

@@ -1,81 +1,12 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
+
-    <div class="w-full max-w-2xl">
+    <div class="alert alert-danger" role="alert">
-      <div class="alert alert-warning mb-6 shadow-lg">
+        <h4 class="alert-heading">Your account has not been activated yet!</h4>
-        <svg
+        <p>Your account has not been activated yet. If you have questions <a href="mailto:admin@envipath.org">contact
-          xmlns="http://www.w3.org/2000/svg"
+            us.</a>
-          class="h-8 w-8 shrink-0 stroke-current"
+        </p>
-          fill="none"
-          viewBox="0 0 24 24"
-        >
-          <path
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            stroke-width="2"
-            d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
-          />
-        </svg>
-        <div class="flex flex-col">
-          <h3 class="text-lg font-bold">Account Not Activated</h3>
-          <p class="text-sm">Your account is pending activation.</p>
-        </div>
     </div>
 
-      <div class="card bg-base-100 shadow-xl">
-        <div class="card-body">
-          <h2 class="card-title mb-4 text-2xl">Account Activation Required</h2>
-          <p class="text-base-content/70 mb-4">
-            Your account has not been activated yet. An administrator needs to
-            approve your account before you can access all features. This
-            process typically takes 24-48 hours.
-          </p>
-          <div class="divider"></div>
-          <p class="text-base-content/70 mb-4">
-            If you have questions or believe this is an error, please
-            <a href="mailto:admin@envipath.org" class="link link-primary"
-              >contact us</a
-            >.
-          </p>
-          <div class="card-actions mt-6 justify-end">
-            <a href="/" class="btn btn-primary">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
-                />
-              </svg>
-              Go Home
-            </a>
-            <a href="mailto:admin@envipath.org" class="btn btn-outline">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                class="mr-2 h-5 w-5"
-                fill="none"
-                viewBox="0 0 24 24"
-                stroke="currentColor"
-              >
-                <path
-                  stroke-linecap="round"
-                  stroke-linejoin="round"
-                  stroke-width="2"
-                  d="M3 8l7.89 5.26a2 2 0 002.22 0L21 8M5 19h14a2 2 0 002-2V7a2 2 0 00-2-2H5a2 2 0 00-2 2v10a2 2 0 002 2z"
-                />
-              </svg>
-              Contact Admin
-            </a>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 {% endblock content %}

templates/framework.html

@@ -124,7 +124,7 @@
 
           <!-- Collect the nav links, forms, and other content for toggling -->
           <div
-            class="navbar-collapse collapse-framework navbar-collapse-framework collapse"
+            class="collapse navbar-collapse collapse-framework navbar-collapse-framework"
             id="navbarCollapse"
           >
             <ul class="nav navbar-nav navbar-nav-framework">
@@ -151,6 +151,11 @@
                   >Package</a
                 >
               </li>
+              <li>
+                <a href="{{ meta.server_url }}/search" id="searchLink"
+                  >Search</a
+                >
+              </li>
               <li>
                 <a href="{{ meta.server_url }}/model" id="modelLink"
                   >Modelling</a
@@ -228,7 +233,15 @@
                       >Documentation Wiki</a
                     >
                   </li>
-
+                  <li>
+                    <a
+                      href="#"
+                      id="citeButton"
+                      data-toggle="modal"
+                      data-target="#citemodal"
+                      >How to cite enviPath</a
+                    >
+                  </li>
                   <li class="divider"></li>
                   <li><a>Version: {{ meta.version }}</a></li>
                 </ul>
@@ -325,7 +338,7 @@
               >
             </div>
           </div>
-          <div id="license" class="panel-collapse in collapse">
+          <div id="license" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
               <a target="_blank" href="{{ meta.current_package.license.link }}">
                 <img src="{{ meta.current_package.license.image_link }}" />
@@ -400,5 +413,10 @@
         }
       });
     </script>
+    {% block modals %}
+      {% include "modals/cite_modal.html" %}
+      {% include "modals/predict_modal.html" %}
+      {% include "modals/batch_predict_modal.html" %}
+    {% endblock %}
   </body>
 </html>

templates/framework_modern.html

@@ -21,14 +21,8 @@
       type="text/css"
     />
 
-    {# Alpine.js - For reactive components #}
+    {# jQuery - Keep for compatibility with existing JS #}
-    <script
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
-      defer
-      src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"
-    ></script>
-    <script src="{% static 'js/alpine/index.js' %}"></script>
-    <script src="{% static 'js/alpine/search.js' %}"></script>
-    <script src="{% static 'js/alpine/pagination.js' %}"></script>
 
     {# Font Awesome #}
     <link
@@ -41,10 +35,21 @@
 
     <script>
       const csrftoken = document.querySelector("[name=csrf-token]").content;
+
+      // Setup CSRF header for all jQuery AJAX requests
+      $.ajaxSetup({
+        beforeSend: function (xhr, settings) {
+          if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+            xhr.setRequestHeader("X-CSRFToken", csrftoken);
+          }
+        },
+      });
     </script>
 
     {# General EP JS #}
     <script src="{% static 'js/pps.js' %}"></script>
+    {# Modal Steps for Stepwise Modal Wizards #}
+    <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
 
     {% if not debug %}
       <!-- Matomo -->
@@ -75,7 +80,7 @@
       {% block main_content %}
         {# Breadcrumbs - outside main content, optional #}
         {% if breadcrumbs %}
-          <div id="bread" class="mx-auto max-w-7xl px-4 py-4">
+          <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
             <div class="breadcrumbs text-sm">
               <ul>
                 {% for elem in breadcrumbs %}
@@ -108,7 +113,7 @@
 
           {# License - inside paper if present #}
           {% if meta.url_contains_package and meta.current_package.license %}
-            <div class="collapse-arrow bg-base-200 collapse p-8">
+            <div class="collapse collapse-arrow bg-base-200 m-8">
               <input type="checkbox" checked />
               <div class="collapse-title text-xl font-medium">License</div>
               <div class="collapse-content">
@@ -132,7 +137,7 @@
 
     {# Floating Help Tab #}
     {% if not public_mode %}
-      <div class="fixed top-1/2 right-0 z-50 -translate-y-1/2">
+      <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
         <a
           href="https://community.envipath.org/"
           target="_blank"
@@ -166,31 +171,13 @@
     {% endblock %}
 
     <script>
-      document.addEventListener("DOMContentLoaded", function () {
+      $(function () {
-        // Show actions button if there are actions defined
+        // Hide actionsbutton if there's no action defined
-        const actionsButtonUl = document.querySelector("#actionsButton ul");
+        if ($("#actionsButton ul").children().length > 0) {
-        if (actionsButtonUl && actionsButtonUl.children.length > 0) {
+          $("#actionsButton").show();
-          document.getElementById("actionsButton").style.display = "";
         }
       });
 
-      // Open search modal function
-      function openSearchModal() {
-        const searchModal = document.getElementById("search_modal");
-        if (searchModal) {
-          searchModal.showModal();
-        }
-      }
-
-      // Click handler for search badge
-      const searchTrigger = document.getElementById("search-trigger");
-      if (searchTrigger) {
-        searchTrigger.addEventListener("click", function (event) {
-          event.preventDefault();
-          openSearchModal();
-        });
-      }
-
       // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
       document.addEventListener("keydown", function (event) {
         // Check if user is typing in an input field
@@ -211,7 +198,7 @@
 
         if (isCorrectModifier && event.key === "k") {
           event.preventDefault();
-          openSearchModal();
+          search_modal.showModal();
         }
       });
     </script>

templates/includes/footer.html

@@ -1,20 +1,17 @@
 {% load static %}
-<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
+<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
+
     <footer class="footer sm:footer-horizontal p-10">
         {% if not public_mode %}
         <nav>
             <h6 class="footer-title">Services</h6>
-        <a class="link link-hover" href="/predict">Predict</a>
+            <a class="link link-hover" href="/">Predict</a>
-        <a class="link link-hover" href="/package">Packages</a>
+            <a class="link link-hover" href="/search">Search</a>
+            <a class="link link-hover" href="/package">Browse</a>
             {% if user.is_authenticated %}
             <a class="link link-hover" href="/model">Your Collections</a>
             {% endif %}
-        <a
+            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
-          href="https://wiki.envipath.org/"
-          target="_blank"
-          class="link link-hover"
-          >Documentation</a
-        >
     </nav>
         {% endif %}
     <nav>
@@ -32,61 +29,39 @@
       <a class="link link-hover" href="/cite">Cite enviPath</a>
     </nav>
   </footer>
-  <footer class="footer border-t-2 border-neutral-300 px-10 py-4">
+  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
-    <div class="flex w-full flex-row items-start justify-between">
+    <div class="flex flex-row justify-between w-full items-start">
       <aside class="grid-flow-col items-center">
-        <svg
+          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
-          class="fill-neutral-content m-2 h-14 flex-shrink-0"
-          viewbox="0 0 65 65"
-        >
               <use
                 href="{% static "/images/logo-square.svg" %}#ep-logo-square"
-          ></use>
+              >
+              </use>
             </svg>
 
           enviPath Ltd.
           <br />
           Biodegredation prediction since 2015.
+        </p>
       </aside>
-      <aside class="text-base-200 mt-2 text-sm">
+      <aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
-        <span class="text-xs tracking-tight">Version</span>
-        <span class="text-base font-bold">{{ meta.version }}</span>
-      </aside>
     </div>
     <nav class="md:place-self-center md:justify-self-end">
       <div class="grid grid-flow-col gap-4">
         <a href="https://www.youtube.com/@envipath7231" target="_blank">
-          <svg
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-            role="img"
-            viewBox="0 0 24 24"
-            xmlns="http://www.w3.org/2000/svg"
-            class="h-6 w-6 fill-current"
-          >
                 <title>YouTube</title>
-            <path
+                <path d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"/>
-              d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"
-            />
             </svg>
         </a>
         <a href="https://community.envipath.org/" target="_blank">
-          <svg
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-            role="img"
-            viewBox="0 0 24 24"
-            xmlns="http://www.w3.org/2000/svg"
-            class="h-6 w-6 fill-current"
-          >
                 <title>Discourse</title>
-            <path
+                <path d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"/>
-              d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"
-            />
             </svg>
         </a>
         <a href="https://www.linkedin.com/company/envipath/" target="_blank">
-          <img
+            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
-            src="{% static "/images/linkedin.png" %}"
-            alt="LinkedIn"
-            class="h-6 w-6"
-          />
         </a>
       </div>
     </nav>

templates/includes/navbar.html

@@ -1,44 +1,15 @@
 {% load static %}
-{# Modern DaisyUI Navbar with Mobile Drawer Menu #}
+{# Modern DaisyUI Navbar #}
-<div class="drawer drawer-mobile">
+<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
-  <input id="drawer-toggle" type="checkbox" class="drawer-toggle" />
-  <div class="drawer-content flex flex-col">
-    {# Navbar #}
-    <div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
   <div class="navbar-start">
-        {# Hamburger menu button - visible on mobile, hidden on desktop #}
+    <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-        {% if not public_mode %}
+      <svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
-          <label
-            for="drawer-toggle"
-            class="btn btn-square btn-ghost drawer-button lg:hidden"
-          >
-            <svg
-              xmlns="http://www.w3.org/2000/svg"
-              fill="none"
-              viewBox="0 0 24 24"
-              class="inline-block h-5 w-5 stroke-current"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                stroke-width="2"
-                d="M4 6h16M4 12h16M4 18h16"
-              ></path>
-            </svg>
-          </label>
-        {% endif %}
-        <a
-          href="{{ meta.server_url }}"
-          class="btn btn-ghost text-xl normal-case"
-        >
-          <svg class="fill-base-content h-8" viewBox="0 0 104 26" role="img">
         <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
       </svg>
     </a>
   </div>
 
   {% if not public_mode %}
-        {# Desktop menu - hidden on mobile, visible on desktop #}
     <div class="navbar-center hidden lg:flex">
       <a
         href="{{ meta.server_url }}/predict"
@@ -47,6 +18,8 @@
         id="predictLink"
         >Predict</a
       >
+      <!-- <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li> -->
+      <!--<li><a href="{{ meta.server_url }}/browse" id="browseLink">Browse</a></li>-->
       <div class="dropdown dropdown-center">
         <div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
         <ul
@@ -54,18 +27,9 @@
           class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
         >
           <li>
-                <a href="{{ meta.server_url }}/package" id="packageLink"
+            <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
-                  >Package</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/pathway" id="pathwayLink"
-                  >Pathway</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
           </li>
+          <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
           <li>
             <a href="{{ meta.server_url }}/compound" id="compoundLink"
               >Compound</a
@@ -77,9 +41,7 @@
             >
           </li>
           <li>
-                <a
+            <a href="{{ meta.server_url }}/model" id="relative-reasoningLink"
-                  href="{{ meta.server_url }}/model"
-                  id="relative-reasoningLink"
               >Model</a
             >
           </li>
@@ -95,9 +57,9 @@
 
   <div class="navbar-end">
     {% if not public_mode %}
-          <a id="search-trigger" role="button" class="cursor-pointer">
+      <a href="/search" role="button">
         <div
-              class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
+          class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
         >
           <svg
             xmlns="http://www.w3.org/2000/svg"
@@ -125,7 +87,7 @@
         <div
           tabindex="0"
           role="button"
-              class="btn btn-ghost btn-circle m-1"
+          class="btn btn-ghost m-1 btn-circle"
           id="loggedInButton"
         >
           <svg
@@ -149,9 +111,7 @@
           tabindex="-1"
           class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm"
         >
-              <li>
+          <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
-                <a href="{{ meta.user.url }}" id="accountbutton">Settings</a>
-              </li>
           <li>
             <form
               id="logoutForm"
@@ -174,96 +134,6 @@
     {% endif %}
   </div>
 </div>
-  </div>
-  {# Mobile drawer menu - slides in from the left #}
-  <div class="drawer-side">
-    <label for="drawer-toggle" class="drawer-overlay"></label>
-    <ul class="menu min-h-full w-80 bg-base-200 p-4 text-base-content">
-      {# Drawer header with close button #}
-      <li class="mb-4">
-        <div class="flex items-center justify-between">
-          <span class="font-bold text-lg">Menu</span>
-          <label
-            for="drawer-toggle"
-            class="btn btn-sm btn-circle btn-ghost"
-            aria-label="Close menu"
-          >
-            <svg
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-6 w-6"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                stroke-width="2"
-                d="M6 18L18 6M6 6l12 12"
-              />
-            </svg>
-          </label>
-        </div>
-      </li>
-      {% if not public_mode %}
-        {# Predict link #}
-        <li>
-          <a
-            href="{{ meta.server_url }}/predict"
-            class="text-lg"
-            id="predictLinkMobile"
-            >Predict</a
-          >
-        </li>
-        {# Browse menu with submenu #}
-        <li>
-          <details>
-            <summary class="text-lg">Browse</summary>
-            <ul>
-              <li>
-                <a href="{{ meta.server_url }}/package" id="packageLinkMobile"
-                  >Package</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/pathway" id="pathwayLinkMobile"
-                  >Pathway</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/rule" id="ruleLinkMobile"
-                  >Rule</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/compound" id="compoundLinkMobile"
-                  >Compound</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/reaction" id="reactionLinkMobile"
-                  >Reaction</a
-                >
-              </li>
-              <li>
-                <a
-                  href="{{ meta.server_url }}/model"
-                  id="relative-reasoningLinkMobile"
-                  >Model</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/scenario" id="scenarioLinkMobile"
-                  >Scenario</a
-                >
-              </li>
-            </ul>
-          </details>
-        </li>
-      {% endif %}
-    </ul>
-  </div>
-</div>
 
 <script>
   // OS-aware search shortcut display

templates/index/index.html

@@ -2,90 +2,36 @@
 {% load static %}
 {% block main_content %}
   <!-- Hero Section with Logo and Search -->
-  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
+  <section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
     <div
-      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
+      class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
       style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
     >
       <div class="hero-overlay"></div>
       <!-- Predict Pathway text over the image -->
-      <div class="absolute bottom-40 left-1/8 -translate-x-8">
+      <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
+        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
           Predict Your Pathway
         </h2>
       </div>
     </div>
   </section>
 
-  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
+  <div class="shadow-md max-w-5xl mx-auto bg-base-200">
     <!-- Predict Pathway Section -->
     <div
-      class="relative mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
+      class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
     >
       <div
-        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
+        class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out"
-        x-data="{
-          drawMode: false,
-          smiles: '',
-          loadExample(smilesStr, linkEl) {
-            if (this.drawMode && window.indexKetcher && window.indexKetcher.setMolecule) {
-              window.indexKetcher.setMolecule(smilesStr);
-            } else {
-              this.smiles = smilesStr;
-            }
-            const original = linkEl.textContent;
-            linkEl.textContent = 'loaded!';
-            setTimeout(() => linkEl.textContent = original, 1000);
-          },
-          syncFromKetcher() {
-            const ketcher = getKetcherInstance('index-ketcher');
-            if (ketcher && ketcher.getSmiles) {
-              try {
-                const s = ketcher.getSmiles();
-                if (s && s.trim()) this.smiles = s;
-              } catch (err) {
-                console.error('Failed to sync from Ketcher:', err);
-              }
-            }
-          },
-          submitForm() {
-            let finalSmiles = '';
-            if (this.drawMode) {
-              const ketcher = getKetcherInstance('index-ketcher');
-              if (ketcher && ketcher.getSmiles) {
-                try {
-                  finalSmiles = ketcher.getSmiles().trim();
-                } catch (err) {
-                  console.error('Failed to get SMILES from Ketcher:', err);
-                  alert('Unable to extract structure. Please try again or switch to SMILES input.');
-                  return;
-                }
-              } else {
-                alert('The drawing editor is still loading. Please wait and try again.');
-                return;
-              }
-            } else {
-              finalSmiles = this.smiles.trim();
-            }
-            if (!finalSmiles) {
-              alert('Please enter a SMILES string or draw a structure.');
-              return;
-            }
-            document.getElementById('index-form-smiles').value = finalSmiles;
-            document.getElementById('index-form').submit();
-          }
-        }"
-        x-init="$watch('drawMode', value => { if (!value) syncFromKetcher(); })"
       >
         <div class="card-body">
-          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+          <!-- Input Mode Toggle - Fixed position outside fieldset -->
-            <div class="flex items-center gap-1">
+          <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
+            <div class="flex items-center gap-2">
-                <input type="checkbox" x-model="drawMode" />
+              <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
-                <span class="swap-on flex items-center gap-1">
+              <label class="toggle text-base-content toggle-md">
-                  <div
+                <input type="checkbox" />
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  >
                 <svg
                   aria-label="smiles mode"
                   xmlns="http://www.w3.org/2000/svg"
@@ -106,13 +52,6 @@
                     />
                   </g>
                 </svg>
-                  </div>
-                  <span class="ext-xs">SMILES</span>
-                </span>
-                <span class="swap-off flex items-center gap-1">
-                  <div
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  >
                 <svg
                   aria-label="draw mode"
                   xmlns="http://www.w3.org/2000/svg"
@@ -125,78 +64,57 @@
                     d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
                   />
                 </svg>
-                  </div>
-                  <span class="text-base/50 text-xs">Draw</span>
-                </span>
               </label>
             </div>
           </div>
 
           <fieldset
-            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
+            class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
-            :class="drawMode ? 'p-4' : 'p-8'"
           >
             <form
               id="index-form"
               action="{{ meta.current_package.url }}/pathway"
               method="POST"
-              @submit.prevent="submitForm()"
             >
               {% csrf_token %}
               <div
                 id="text-input-container"
-                x-show="!drawMode"
+                class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
-                x-transition:enter="transition ease-out duration-300"
-                x-transition:enter-start="opacity-0 scale-95"
-                x-transition:enter-end="opacity-100 scale-100"
-                x-transition:leave="transition ease-in duration-300"
-                x-transition:leave-start="opacity-100 scale-100"
-                x-transition:leave-end="opacity-0 scale-95"
               >
-                <div class="join mx-auto w-full">
+                <div class="join w-full mx-auto">
                   <input
                     type="text"
                     id="index-form-text-input"
                     placeholder="canonical SMILES string"
-                    class="input input-md join-item grow"
+                    class="input grow input-md join-item"
-                    x-model="smiles"
                   />
                   <button class="btn btn-neutral join-item">Predict!</button>
                 </div>
-                <div class="label relative mt-1 w-full">
+                <div class="label relative w-full mt-1">
                   <div class="flex gap-2">
                     <a
                       href="#"
-                      class="example-link hover:text-primary cursor-pointer"
+                      class="example-link cursor-pointer hover:text-primary"
+                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
                       title="load example"
-                      @click.prevent="loadExample('CN1C=NC2=C1C(=O)N(C(=O)N2C)C', $el)"
                       >Caffeine</a
                     >
                     <a
                       href="#"
-                      class="example-link hover:text-primary cursor-pointer"
+                      class="example-link cursor-pointer hover:text-primary"
+                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
                       title="load example"
-                      @click.prevent="loadExample('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', $el)"
                       >Ibuprofen</a
                     >
                   </div>
-                  <a
+                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
-                    class="absolute top-0 left-[calc(100%-5.4rem)]"
-                    href="/predict"
                     >Advanced</a
                   >
                 </div>
               </div>
               <div
                 id="ketcher-container"
-                x-show="drawMode"
+                class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
-                x-transition:enter="transition ease-out duration-300"
-                x-transition:enter-start="opacity-0 scale-95"
-                x-transition:enter-end="opacity-100 scale-100"
-                x-transition:leave="transition ease-in duration-300"
-                x-transition:leave-start="opacity-100 scale-100"
-                x-transition:leave-end="opacity-0 scale-95"
-                class="w-full"
               >
                 <iframe
                   id="index-ketcher"
@@ -206,13 +124,11 @@
                   class="rounded-lg"
                 ></iframe>
                 <button
-                  class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
                 >
                   Predict!
                 </button>
-                <div class="mt-1 flex w-full justify-end">
+                <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
-                  <a class="label justify-end" href="/predict">Advanced</a>
-                </div>
               </div>
               <input
                 type="hidden"
@@ -234,18 +150,18 @@
     </div>
 
     <!-- Community News Section -->
-    <section class="bg-base-200 z-10 mx-8 py-16">
+    <section class="py-16 bg-base-200 z-10 mx-8">
-      <div class="mx-auto max-w-7xl px-4">
+      <div class="max-w-7xl mx-auto px-4">
-        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
+        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
 
-        <div id="community-news-container" class="flex justify-center gap-4">
+        <div id="community-news-container" class="flex gap-4 justify-center">
           <!-- News cards will be populated here -->
-          <div id="loading" class="flex w-full justify-center">
+          <div id="loading" class="flex justify-center w-full">
             <span class="loading loading-spinner loading-lg"></span>
           </div>
         </div>
 
-        <div class="mt-6 text-right">
+        <div class="text-right mt-6">
           <a
             href="https://community.envipath.org/c/announcements/10"
             target="_blank"
@@ -261,18 +177,18 @@
     </section>
 
     <!-- Mission Statement Section -->
-    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
+    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
       <div class="mx-auto px-8 md:px-12">
         <div class="flex flex-row gap-4">
           <div class="w-1/3">
             <img
               src="{% static "/images/ep-rule-artwork.png" %}"
               alt="rule-based iterative tree greneration"
-              class="h-full w-full object-contain"
+              class="w-full h-full object-contain"
             />
           </div>
-          <div class="mr-8 w-2/3 space-y-4 text-left">
+          <div class="space-y-4 text-left w-2/3 mr-8">
-            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
+            <h2 class="h2 font-bold mb-8">About enviPath</h2>
             <p class="">
               enviPath is a database and prediction system for the microbial
               biotransformation of organic environmental contaminants. The
@@ -285,7 +201,7 @@
               products. Explore our tools and contribute to advancing
               environmental biotransformation research.
             </p>
-            <div class="float-right flex flex-row gap-4">
+            <div class="flex flex-row gap-4 float-right">
               <a href="/about" class="btn btn-ghost-neutral">Read More</a>
               <a href="/about" class="btn btn-neutral">Publications</a>
             </div>
@@ -295,7 +211,7 @@
     </section>
 
     <!-- Partners Section -->
-    <section class="bg-base-100 py-14 sm:py-12">
+    <section class="py-14 sm:py-12 bg-base-100">
       <div class="mx-auto px-6 lg:px-8">
         <div class="divider">
           <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
@@ -326,31 +242,6 @@
   <script language="javascript">
     var currentPackage = "{{ meta.current_package.url }}";
 
-    // Helper function to safely get Ketcher instance from iframe
-    function getKetcherInstance(iframeId) {
-      const ketcherFrame = document.getElementById(iframeId);
-      if (!ketcherFrame) {
-        console.error("Ketcher iframe not found:", iframeId);
-        return null;
-      }
-
-      try {
-        if (
-          "contentWindow" in ketcherFrame &&
-          ketcherFrame.contentWindow.ketcher
-        ) {
-          return ketcherFrame.contentWindow.ketcher;
-        }
-      } catch (err) {
-        console.error(
-          "Cannot access Ketcher iframe - possible CORS issue:",
-          err,
-        );
-      }
-
-      return null;
-    }
-
     // Discourse API integration is now handled by discourse-api.js
 
     // Function to render Discourse topics into cards
@@ -373,13 +264,16 @@
       const date = new Date(topic.created_at).toLocaleDateString();
 
       return `
-                <div class="card bg-white shadow-sm hover:shadow-lg transition-shadow duration-300 h-52 w-75 flex-shrink-0">
+                <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
-                    <div class="card-body flex flex-col h-full justify-between">
+                    <div class="card-body flex flex-col h-full">
-                        <h3 class="card-title leading-tight font-normal tracking-tight mb-2 line-clamp-5 overflow-hidden">
+                        <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
                             <a href="${topic.url}" target="_blank" class="hover:text-primary">
                                 ${topic.title}
                             </a>
                         </h3>
+                        <div class="text-sm line-clamp-4 break-words" >
+                            ${topic.excerpt}
+                        </div>
 
                         <div class="flex flex-row items-center justify-between">
                             <div class="flex items-center gap-2">
@@ -405,20 +299,141 @@
     // Make render function globally available
     window.renderDiscourseTopics = renderDiscourseTopics;
 
-    // Ketcher iframe load handler - set up change event to sync SMILES
+    // Toggle functionality with smooth animations
-    document.addEventListener("DOMContentLoaded", function () {
+    function toggleInputMode() {
-      const indexKetcher = document.getElementById("index-ketcher");
+      const toggle = $('input[type="checkbox"]');
-      indexKetcher.addEventListener("load", function () {
+      const textContainer = $("#text-input-container");
+      const ketcherContainer = $("#ketcher-container");
+      const formCard = $(".card");
+      const fieldset = $(".fieldset");
+
+      if (toggle.is(":checked")) {
+        // Draw mode - show Ketcher, hide text input
+        textContainer.addClass("opacity-0 transform scale-95");
+        textContainer.removeClass("opacity-100 transform scale-100");
+
+        // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
+        fieldset.removeClass("p-8");
+        fieldset.addClass("p-4");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          textContainer.addClass("hidden");
+          ketcherContainer.removeClass("hidden opacity-0 transform scale-95");
+          ketcherContainer.addClass("opacity-100 transform scale-100");
+
+          // Force re-evaluation of iframe size
+          const iframe = document.getElementById("index-ketcher");
+          if (iframe) {
+            iframe.style.height = "400px";
+          }
+        }, 300);
+      } else {
+        // SMILES mode - show text input, hide Ketcher
+        ketcherContainer.addClass("opacity-0 transform scale-95");
+        ketcherContainer.removeClass("opacity-100 transform scale-100");
+
+        // Restore fieldset padding for text input mode
+        fieldset.removeClass("p-4");
+        fieldset.addClass("p-8");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          ketcherContainer.addClass("hidden");
+          textContainer.removeClass("hidden opacity-0 transform scale-95");
+          textContainer.addClass("opacity-100 transform scale-100");
+        }, 300);
+
+        // Transfer SMILES from Ketcher to text input if available
+        if (window.indexKetcher && window.indexKetcher.getSmiles) {
+          const smiles = window.indexKetcher.getSmiles();
+          if (smiles && smiles.trim() !== "") {
+            $("#index-form-text-input").val(smiles);
+          }
+        }
+      }
+    }
+
+    // Ketcher integration
+    function indexKetcherToTextInput() {
+      $("#index-form-smiles").val(this.ketcher.getSmiles());
+    }
+
+    $(function () {
+      // Initialize fieldset with proper padding
+      $(".fieldset").addClass("p-8");
+
+      // Toggle event listener
+      $('input[type="checkbox"]').on("change", toggleInputMode);
+
+      // Ketcher iframe load handler
+      $("#index-ketcher").on("load", function () {
         const checkKetcherReady = () => {
           const win = this.contentWindow;
           if (win.ketcher && "editor" in win.ketcher) {
             window.indexKetcher = win.ketcher;
+            win.ketcher.editor.event.change.handlers.push({
+              once: false,
+              priority: 0,
+              f: indexKetcherToTextInput,
+              ketcher: win.ketcher,
+            });
           } else {
             setTimeout(checkKetcherReady, 100);
           }
         };
         checkKetcherReady();
       });
+
+      // Handle example link clicks
+      $(".example-link").on("click", function (e) {
+        e.preventDefault();
+        const smiles = $(this).data("smiles");
+        const title = $(this).attr("title");
+
+        // Check if we're in Ketcher mode or text input mode
+        if ($('input[type="checkbox"]').is(":checked")) {
+          // In Ketcher mode - set the SMILES in Ketcher
+          if (window.indexKetcher && window.indexKetcher.setMolecule) {
+            window.indexKetcher.setMolecule(smiles);
+          }
+        } else {
+          // In text input mode - set the SMILES in the text input
+          $("#index-form-text-input").val(smiles);
+        }
+
+        // Show a brief feedback
+        const originalText = $(this).text();
+        $(this).text(`loaded!`);
+        setTimeout(() => {
+          $(this).text(originalText);
+        }, 1000);
+      });
+
+      // Handle form submission on Enter
+      $("#index-form").on("submit", function (e) {
+        e.preventDefault();
+
+        var textSmiles = "";
+
+        // Check if we're in Ketcher mode and extract SMILES
+        if ($('input[type="checkbox"]').is(":checked") && window.indexKetcher) {
+          textSmiles = window.indexKetcher.getSmiles().trim();
+        } else {
+          textSmiles = $("#index-form-text-input").val().trim();
+        }
+
+        if (textSmiles === "") {
+          return;
+        }
+
+        $("#index-form-smiles").val(textSmiles);
+        $("#index-form").attr("action", currentPackage + "/pathway");
+        $("#index-form").attr("method", "POST");
+        this.submit();
+      });
+
+      // Discourse topics are now loaded automatically by discourse-api.js
     });
   </script>
 {% endblock main_content %}

templates/migration.html

@@ -3,11 +3,7 @@
 {% block content %}
 <div class="panel-group" id="migration-detail">
     <div class="panel panel-default">
-      <div
+        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
             Migration Status BT Rules
         </div>
         <div class="panel-body">
@@ -16,56 +12,33 @@
         </div>
 
         {% for obj in results %}
-        <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
             {% if obj.status %}
-            <span
+            <span class="glyphicon glyphicon-ok" aria-hidden="true"
-              class="glyphicon glyphicon-ok"
+                  style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                  data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
             </span>
             {% else %}
-            <span
+            <span class="glyphicon glyphicon-remove" aria-hidden="true"
-              class="glyphicon glyphicon-remove"
+                  style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                  data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
             </span>
             {% endif %}
             <h4 class="panel-title">
-            <a
+                <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-              id="{{ obj.id }}-link"
+                   href="#{{ obj.id }}">{{ obj.name|safe }}</a>
-              data-toggle="collapse"
-              data-parent="#migration-detail"
-              href="#{{ obj.id }}"
-              >{{ obj.name|safe }}</a
-            >
             </h4>
         </div>
-        <div
+        <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-          id="{{ obj.id }}"
-          class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
-        >
             <div class="panel-body list-group-item">
-            <a class="list-group-item" href="{{ obj.detail_url }}"
+                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name|safe }} Migration Detail Page</a>
-              >{{ obj.name|safe }} Migration Detail Page</a
-            >
             </div>
         </div>
         {% endfor %}
     </div>
 </div>
 
-  <script></script>
+<script>
+
+</script>
 {% endblock content %}

templates/migration_detail.html

@@ -3,68 +3,34 @@
 {% block content %}
     <div class="panel-group" id="migration-detail">
         <div class="panel panel-default">
-      <div
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
                 Migration Status for {{ bt_rule_name }}
             </div>
             <div class="panel-body">
-        <p>
+                <p>A package contains pathways, rules, etc. and can reflect specific experimental
-          A package contains pathways, rules, etc. and can reflect specific
+                    conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-          experimental conditions.
+                        more &gt;&gt;</a></p>
-          <a
-            target="_blank"
-            href="https://wiki.envipath.org/index.php/packages"
-            role="button"
-            >Learn more &gt;&gt;</a
-          >
-        </p>
             </div>
 
             {% for obj in results %}
-        <div
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
                     {% if obj.status %}
-            <span
+                        <span class="glyphicon glyphicon-ok" aria-hidden="true"
-              class="glyphicon glyphicon-ok"
+                              style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                              data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
                         </span>
                     {% else %}
-            <span
+                        <span class="glyphicon glyphicon-remove" aria-hidden="true"
-              class="glyphicon glyphicon-remove"
+                              style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                              data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
                         </span>
                     {% endif %}
                     <h4 class="panel-title">
-            <a
+                        <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-              id="{{ obj.id }}-link"
+                           href="#{{ obj.id }}">{{ obj.name|safe }}</a>
-              data-toggle="collapse"
-              data-parent="#migration-detail"
-              href="#{{ obj.id }}"
-              >{{ obj.name|safe }}</a
-            >
                     </h4>
                 </div>
-        <div
+                <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-          id="{{ obj.id }}"
-          class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
-        >
                     <div class="panel-body list-group-item">
                         <pre>{{ obj.detail }}</pre>
                     </div>
@@ -73,5 +39,7 @@
         </div>
     </div>
 
-  <script></script>
+    <script>
+
+    </script>
 {% endblock content %}

templates/modals/cite_modal.html

@@ -0,0 +1,31 @@
+<div class="modal fade bs-modal-lg" id="citemodal" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel"
+     aria-hidden="true">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3>How to cite enviPath</h3>
+            </div>
+            <div class="modal-body">
+                <ol class="list-group list-group-numbered">
+                    <li class="list-group-item">
+                        Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
+                        <cite>Advancements in biotransformation pathway prediction: enhancements, datasets, and novel
+                            functionalities in enviPath.</cite>
+                        <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank">J Cheminform 16, 93
+                            (2024)</a>
+                    </li>
+                    <li class="list-group-item">
+                        Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., Fenner, K.
+                        <cite>enviPath - The environmental contaminant biotransformation pathway resource</cite>
+                        <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank">
+                            Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D502-D508
+                        </a>
+                    </li>
+                </ol>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+            </div>
+        </div>
+    </div>
+</div>

templates/modals/collections/import_legacy_package_modal.html

@@ -1,85 +1,42 @@
-<dialog
+<div class="modal fade" tabindex="-1" id="import_legacy_package_modal" role="dialog"
-  id="import_legacy_package_modal"
+     aria-labelledby="import_legacy_package_modal" aria-hidden="true">
-  class="modal"
+    <div class="modal-dialog">
-  x-data="modalForm()"
+        <div class="modal-content">
-  @close="reset()"
+            <div class="modal-header">
->
+                <button type="button" class="close" data-dismiss="modal">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
+                    <span class="sr-only">Close</span>
-    <h3 class="text-lg font-bold">Import Package from Legacy System</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Import Package from legacy System</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <p>Create a Package based on the JSON Export of the legacy system.</p>
-      <p class="mb-4">
+                <form id="import-legacy-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-        Create a Package based on the JSON Export of the legacy system.
+                      enctype="multipart/form-data">
-      </p>
-      <form
-        id="import-legacy-package-modal-form"
-        accept-charset="UTF-8"
-        method="post"
-        enctype="multipart/form-data"
-      >
                     {% csrf_token %}
-        <div class="form-control">
+                    <p>
-          <label class="label">
+                        <label class="btn btn-primary" for="legacyJsonFile">
-            <span class="label-text">Legacy JSON File</span>
+                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
+                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
+                            Choose JSON File
                         </label>
-          <input
+                        <span class="label label-info" id="upload-legacy-file-info"></span>
-            type="file"
+                        <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
-            id="legacyJsonFile"
+                    </p>
-            name="file"
-            class="file-input file-input-bordered w-full"
-            accept=".json"
-            required
-          />
-        </div>
-        <input
-          type="hidden"
-          value="import-legacy-package-json"
-          name="hidden"
-          readonly
-        />
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="import-legacy-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-    <div class="modal-action">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('import-legacy-package-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Importing...</span>
-      </button>
             </div>
         </div>
-
+    </div>
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
+<script>
-    <button :disabled="isSubmitting">close</button>
+    $(function () {
-  </form>
+        $('#import-legacy-package-modal-form-submit').on('click', function (e) {
-</dialog>
+            e.preventDefault();
+            $('#import-legacy-package-modal-form').submit();
+        });
+    });
+</script>

templates/modals/collections/import_package_modal.html

@@ -1,83 +1,42 @@
-<dialog
+<div class="modal fade" tabindex="-1" id="import_package_modal" role="dialog"
-  id="import_package_modal"
+     aria-labelledby="import_package_modal" aria-hidden="true">
-  class="modal"
+    <div class="modal-dialog">
-  x-data="modalForm()"
+        <div class="modal-content">
-  @close="reset()"
+            <div class="modal-header">
->
+                <button type="button" class="close" data-dismiss="modal">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
+                    <span class="sr-only">Close</span>
-    <h3 class="text-lg font-bold">Import Package</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Import Package</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <p>Create a Package based on a JSON Export.</p>
-      <p class="mb-4">Create a Package based on a JSON Export.</p>
+                <form id="import-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-      <form
+                      enctype="multipart/form-data">
-        id="import-package-modal-form"
-        accept-charset="UTF-8"
-        method="post"
-        enctype="multipart/form-data"
-      >
                     {% csrf_token %}
-        <div class="form-control">
+                    <p>
-          <label class="label">
+                        <label class="btn btn-primary" for="jsonFile">
-            <span class="label-text">JSON File</span>
+                            <input id="jsonFile" name="file" type="file" style="display:none;"
+                                   onchange="$('#upload-file-info').html(this.files[0].name)">
+                            Choose JSON File
                         </label>
-          <input
+                        <span class="label label-info" id="upload-file-info"></span>
-            type="file"
+                        <input type="hidden" value="import-package-json" name="hidden" readonly="">
-            id="jsonFile"
+                    </p>
-            name="file"
-            class="file-input file-input-bordered w-full"
-            accept=".json"
-            required
-          />
-        </div>
-        <input
-          type="hidden"
-          value="import-package-json"
-          name="hidden"
-          readonly
-        />
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="import-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-    <div class="modal-action">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('import-package-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Importing...</span>
-      </button>
             </div>
         </div>
-
+    </div>
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
+<script>
-    <button :disabled="isSubmitting">close</button>
+    $(function () {
-  </form>
+        $('#import-package-modal-form-submit').on('click', function (e) {
-</dialog>
+            e.preventDefault();
+            $('#import-package-modal-form').submit();
+        });
+    });
+</script>

templates/modals/collections/new_compound_modal.html

@@ -1,137 +1,78 @@
 {% load static %}
-
+<div class="modal fade bs-modal-lg" id="new_compound_modal" tabindex="-1" aria-labelledby="new_compound_modal" aria-modal="true"
-<dialog
+     role="dialog">
-  id="new_compound_modal"
+    <div class="modal-dialog modal-lg">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
->
+                    <span aria-hidden="true">×</span>
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Create a new Compound</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Create a new Compound</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="new_compound_modal_form" accept-charset="UTF-8" action="{% url 'package compound list' meta.current_package.uuid %}" data-remote="true" method="post">
-      <form
-        id="new-compound-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'package compound list' meta.current_package.uuid %}"
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <label for="compound-name">Name</label>
-        <div class="form-control mb-3">
+                    <input id="compound-name" class="form-control" name="compound-name" placeholder="Name"/>
-          <label class="label" for="compound-name">
+                    <label for="compound-description">Description</label>
-            <span class="label-text">Name</span>
+                    <input id="compound-description" class="form-control" name="compound-description" placeholder="Description"/>
-          </label>
+                    <label for="compound-smiles">SMILES</label>
-          <input
+                    <input type="text" class="form-control" name="compound-smiles" placeholder="SMILES" id="compound-smiles">
-            id="compound-name"
+                    <p></p>
-            class="input input-bordered w-full"
+                    <div>
-            name="compound-name"
+                        <iframe id="new_compound_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-            placeholder="Name"
+                                height="510"></iframe>
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-smiles">
-            <span class="label-text">SMILES</span>
-          </label>
-          <input
-            type="text"
-            class="input input-bordered w-full"
-            name="compound-smiles"
-            placeholder="SMILES"
-            id="compound-smiles"
-          />
-        </div>
-
-        <div class="mb-3">
-          <iframe
-            id="new_compound_ketcher"
-            src="{% static '/js/ketcher2/ketcher.html' %}"
-            width="100%"
-            height="510"
-          ></iframe>
                     </div>
+                    <p></p>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-compound-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
                 </button>
+                <button type="button" class="btn btn-primary" id="new_compound_modal_form_submit">Submit</button>
+            </div>
         </div>
     </div>
 
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>
-
 <script>
-  document
+
-    .getElementById("new_compound_ketcher")
+function newCompoundModalketcherToNewCompoundModalTextInput() {
-    .addEventListener("load", function () {
+    $('#compound-smiles').val(this.ketcher.getSmiles());
-      const iframe = this;
+}
+
+$(function() {
+
+    $('#new_compound_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        const win = iframe.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
-            f: function () {
+                    f: newCompoundModalketcherToNewCompoundModalTextInput,
-              document.getElementById("compound-smiles").value =
+                    ketcher: win.ketcher
-                this.ketcher.getSmiles();
-            },
-            ketcher: win.ketcher,
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
             }
         };
+
         checkKetcherReady();
+    })
+
+    $(function() {
+        $('#new_compound_modal_form_submit').on('click', function(e) {
+            e.preventDefault();
+            $(this).prop("disabled",true);
+
+
+
+            // submit form
+            $('#new_compound_modal_form').submit();
         });
+    });
+
+});
+
 </script>

templates/modals/collections/new_group_modal.html

@@ -1,96 +1,45 @@
-{% load static %}
+<div class="modal fade" tabindex="-1" id="new_group_modal" role="dialog" aria-labelledby="new_group_modal"
-
+     aria-hidden="true">
-<dialog
+    <div class="modal-dialog">
-  id="new_group_modal"
+        <div class="modal-content">
-  class="modal"
+            <div class="modal-header">
-  x-data="modalForm()"
+                <button type="button" class="close" data-dismiss="modal">
-  @close="reset()"
+                    <span aria-hidden="true">&times;</span>
->
+                    <span class="sr-only">Close</span>
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">New Group</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">New Group</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <p>Create new Group. You can assign users to the group once
-      <p class="mb-4">
+                    it is created. Description can be changed after creation.</p>
-        Create new Group. You can assign users to the group once it is created.
+                <form id="new_group_modal_form" accept-charset="UTF-8" action="{{ SERVER_BASE }}/group"
-        Description can be changed after creation.
+                      data-remote="true"
-      </p>
+                      method="post">
-
-      <form
-        id="new-group-modal-form"
-        accept-charset="UTF-8"
-        action="{{ SERVER_BASE }}/group"
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="name">Name</label>
-          <label class="label" for="group-name">
+                        <input id="name" type="text" name="group-name" class="form-control" placeholder="Name"/>
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="description">Description</label>
-            id="group-name"
+                        <input id="description" type="text" class="form-control" placeholder="Description..."
-            class="input input-bordered w-full"
+                               name="group-description"/>
-            name="group-name"
+                    </p>
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="group-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="group-description"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Description..."
-            name="group-description"
-          />
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="new_group_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-    <div class="modal-action">
+                <button type="button" class="btn btn-default" data-dismiss="modal">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
                     Cancel
                 </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-group-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
             </div>
         </div>
-
+    </div>
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
+<script>
-    <button :disabled="isSubmitting">close</button>
+$(function() {
-  </form>
+    $('#new_group_modal_form_submit').on('click', function() {
-</dialog>
+        $('#new_group_modal_form').submit();
+    });
+});
+</script>

templates/modals/collections/new_model_modal.html

@@ -1,337 +1,188 @@
-<dialog
-  id="new_model_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    modelType: '',
-    buildAppDomain: false,
 
-    reset() {
+<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
-      this.isSubmitting = false;
+     aria-hidden="true">
-      this.modelType = '';
+    <div class="modal-dialog modal-lg">
-      this.buildAppDomain = false;
+        <div class="modal-content">
-    },
+            <div class="modal-header">
-
+                <button type="button" class="close" data-dismiss="modal">
-    get showMlrr() {
+                    <span aria-hidden="true">&times;</span>
-      return this.modelType === 'mlrr';
+                    <span class="sr-only">Close</span>
-    },
-
-    get showRbrr() {
-      return this.modelType === 'rbrr';
-    },
-
-    get showEnviformer() {
-      return this.modelType === 'enviformer';
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">New Model</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">New Model</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="new_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-      <form
+                      data-remote="true" method="post">
-        id="new_model_form"
-        accept-charset="UTF-8"
-        action="{{ meta.current_package.url }}/model"
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="alert alert-info mb-4">
+                    <div class="jumbotron">Create a new Model to
-          <span>
+                        limit the number of degradation products in the
-            Create a new Model to limit the number of degradation products in
+                        prediction. You just need to set a name and the packages
-            the prediction. You just need to set a name and the packages you
+                        you want the object to be based on. There are multiple types of models available.
-            want the object to be based on. There are multiple types of models
+                        For additional information have a look at our
-            available. For additional information have a look at our
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
-            <a
+                            &gt;&gt;</a>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/relative-reasoning"
-              class="link"
-              >wiki &gt;&gt;</a
-            >
-          </span>
                     </div>
-
                     <!-- Name -->
-        <div class="form-control mb-3">
+                    <label for="model-name">Name</label>
-          <label class="label" for="model-name">
+                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="model-name"
-            name="model-name"
-            class="input input-bordered w-full"
-            placeholder="Name"
-            required
-          />
-        </div>
 
                     <!-- Description -->
-        <div class="form-control mb-3">
+                    <label for="model-description">Description</label>
-          <label class="label" for="model-description">
+                    <input id="model-description" name="model-description" class="form-control"
-            <span class="label-text">Description</span>
+                           placeholder="Description"/>
-          </label>
-          <input
-            id="model-description"
-            name="model-description"
-            class="input input-bordered w-full"
-            placeholder="Description"
-          />
-        </div>
 
                     <!-- Model Type -->
-        <div class="form-control mb-3">
+                    <label for="model-type">Model Type</label>
-          <label class="label" for="model-type">
+                    <select id="model-type" name="model-type" class="form-control" data-width='100%'>
-            <span class="label-text">Model Type</span>
+                        <option disabled selected>Select Model Type</option>
-          </label>
-          <select
-            id="model-type"
-            name="model-type"
-            class="select select-bordered w-full"
-            x-model="modelType"
-            required
-          >
-            <option value="" disabled selected>Select Model Type</option>
                         {% for k, v in model_types.items %}
                             <option value="{{ v }}">{{ k }}</option>
                         {% endfor %}
                     </select>
-        </div>
 
-        <!-- Rule Packages (MLRR, RBRR) -->
+                    <!-- Rule Packages -->
-        <div class="form-control mb-3" x-show="showMlrr || showRbrr" x-cloak>
+                    <div id="rule-packages" class="ep-model-param mlrr rbrr">
-          <label class="label" for="model-rule-packages">
+                        <label for="model-rule-packages">Rule Packages</label>
-            <span class="label-text">Rule Packages</span>
+                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
-          </label>
+                                class="form-control" multiple data-width='100%'>
-          <select
+                            <option disabled>Reviewed Packages</option>
-            id="model-rule-packages"
-            name="model-rule-packages"
-            class="select select-bordered w-full h-32"
-            multiple
-          >
-            <optgroup label="Reviewed Packages">
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
                                     <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
-            </optgroup>
+
-            <optgroup label="Unreviewed Packages">
+                            <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
                                     <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
-            </optgroup>
                         </select>
-          <label class="label">
-            <span class="label-text-alt">Hold Ctrl/Cmd to select multiple</span>
-          </label>
                     </div>
 
-        <!-- Data Packages (MLRR, RBRR, Enviformer) -->
+                    <!-- Data Packages -->
-        <div
+                    <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
-          class="form-control mb-3"
+                        <label for="model-data-packages">Data Packages</label>
-          x-show="showMlrr || showRbrr || showEnviformer"
+                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
-          x-cloak
+                                class="form-control" multiple data-width='100%'>
-        >
+                            <option disabled>Reviewed Packages</option>
-          <label class="label" for="model-data-packages">
-            <span class="label-text">Data Packages</span>
-          </label>
-          <select
-            id="model-data-packages"
-            name="model-data-packages"
-            class="select select-bordered w-full h-32"
-            multiple
-          >
-            <optgroup label="Reviewed Packages">
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
                                     <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
-            </optgroup>
+
-            <optgroup label="Unreviewed Packages">
+                            <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
                                     <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
-            </optgroup>
                         </select>
-          <label class="label">
-            <span class="label-text-alt">Hold Ctrl/Cmd to select multiple</span>
-          </label>
                     </div>
 
-        <!-- Fingerprinter (MLRR) -->
+                    <!-- Fingerprinter -->
-        <div class="form-control mb-3" x-show="showMlrr" x-cloak>
+                    <div id="fingerprinter" class="ep-model-param mlrr">
-          <label class="label" for="model-fingerprinter">
+                        <label for="model-fingerprinter">Fingerprinter</label>
-            <span class="label-text">Fingerprinter</span>
+                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
-          </label>
+                                class="form-control" multiple data-width='100%'>
-          <select
-            id="model-fingerprinter"
-            name="model-fingerprinter"
-            class="select select-bordered w-full h-32"
-            multiple
-          >
                             <option value="MACCS" selected>MACCS Fingerprinter</option>
                             {% if meta.enabled_features.PLUGINS and additional_descriptors %}
-              <optgroup label="Additional Fingerprinter / Descriptor">
+                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
                                 {% for k, v in additional_descriptors.items %}
                                     <option value="{{ v }}">{{ k }}</option>
                                 {% endfor %}
-              </optgroup>
                             {% endif %}
                         </select>
-          <label class="label">
-            <span class="label-text-alt">Hold Ctrl/Cmd to select multiple</span>
-          </label>
                     </div>
 
-        <!-- Threshold (MLRR, Enviformer) -->
+                    <!-- Threshold -->
-        <div
+                    <div id="threshold" class="ep-model-param mlrr enviformer">
-          class="form-control mb-3"
+                        <label for="model-threshold">Threshold</label>
-          x-show="showMlrr || showEnviformer"
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
-          x-cloak
+                               name="model-threshold" class="form-control">
-        >
-          <label class="label" for="model-threshold">
-            <span class="label-text">Threshold</span>
-          </label>
-          <input
-            type="number"
-            min="0"
-            max="1"
-            step="0.05"
-            value="0.5"
-            id="model-threshold"
-            name="model-threshold"
-            class="input input-bordered w-full"
-          />
                     </div>
 
-        <!-- Applicability Domain (MLRR) -->
+                    <div id="appdomain" class="ep-model-param mlrr">
                         {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
-          <div x-show="showMlrr" x-cloak>
+                            <!-- Build AD? -->
-            <div class="form-control mb-3">
+                            <div class="checkbox">
-              <label class="label cursor-pointer justify-start gap-3">
+                                <label>
-                <input
+                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
-                  type="checkbox"
+                                    Applicability Domain?
-                  id="build-app-domain"
-                  name="build-app-domain"
-                  class="checkbox"
-                  x-model="buildAppDomain"
-                />
-                <span class="label-text"
-                  >Also build an Applicability Domain?</span
-                >
                                 </label>
                             </div>
-
+                            <div id="ad-params" style="display:none">
-            <div x-show="buildAppDomain" x-cloak class="ml-4 space-y-3">
+                                <!-- Num Neighbors -->
-              <div class="form-control">
+                                <label for="num-neighbors">Number of Neighbors</label>
-                <label class="label" for="num-neighbors">
+                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
-                  <span class="label-text">Number of Neighbors</span>
-                </label>
-                <input
-                  id="num-neighbors"
-                  name="num-neighbors"
-                  type="number"
-                  class="input input-bordered w-full"
                                        value="5"
-                  step="1"
+                                       step="1" min="0" max="10">
-                  min="0"
+                                <!-- Local Compatibility -->
-                  max="10"
+                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                />
+                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
-              </div>
-
-              <div class="form-control">
-                <label class="label" for="local-compatibility-threshold">
-                  <span class="label-text">Local Compatibility Threshold</span>
-                </label>
-                <input
-                  id="local-compatibility-threshold"
-                  name="local-compatibility-threshold"
                                        type="number"
-                  class="input input-bordered w-full"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                  value="0.5"
+                                <!-- Reliability -->
-                  step="0.01"
+                                <label for="reliability-threshold">Reliability Threshold</label>
-                  min="0"
+                                <input id="reliability-threshold" name="reliability-threshold" type="number"
-                  max="1"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                />
-              </div>
-
-              <div class="form-control">
-                <label class="label" for="reliability-threshold">
-                  <span class="label-text">Reliability Threshold</span>
-                </label>
-                <input
-                  id="reliability-threshold"
-                  name="reliability-threshold"
-                  type="number"
-                  class="input input-bordered w-full"
-                  value="0.5"
-                  step="0.01"
-                  min="0"
-                  max="1"
-                />
-              </div>
-            </div>
                             </div>
                         {% endif %}
+                    </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="new_model_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-    <div class="modal-action">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-      <button
+            </div>
-        type="button"
+        </div>
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new_model_form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
     </div>
 </div>
 
-  <!-- Backdrop -->
+<script>
-  <form method="dialog" class="modal-backdrop">
+    $(function () {
-    <button :disabled="isSubmitting">close</button>
+        // Built in Model Types
-  </form>
+        var nativeModelTypes = [
-</dialog>
+            "mlrr",
+            "rbrr",
+            "enviformer",
+        ]
+
+        // Initially hide all "specific" forms
+        $(".ep-model-param").each(function () {
+            $(this).hide();
+        });
+
+        $('#model-type').selectpicker();
+        $("#model-fingerprinter").selectpicker();
+        $("#model-rule-packages").selectpicker();
+        $("#model-data-packages").selectpicker();
+
+        $("#build-app-domain").change(function () {
+            if ($(this).is(":checked")) {
+                $('#ad-params').show();
+            } else {
+                $('#ad-params').hide();
+            }
+        });
+
+        // On change hide all and show only selected
+        $("#model-type").change(function () {
+            $('.ep-model-param').hide();
+            var modelType = $('#model-type').val();
+            if (nativeModelTypes.indexOf(modelType) !== -1) {
+                $('.' + modelType).show();
+            } else {
+                // do nothing
+            }
+        });
+
+        $('#new_model_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#new_model_form').submit();
+        });
+
+    });
+</script>

templates/modals/collections/new_package_modal.html

@@ -1,93 +1,62 @@
-{% load static %}
+<div class="modal fade"
-
+     tabindex="-1"
-<dialog
      id="new_package_modal"
-  class="modal"
+     role="dialog"
-  x-data="modalForm()"
+     aria-labelledby="new_package_modal"
-  @close="reset()"
+     aria-hidden="true">
->
+    <div class="modal-dialog">
-  <div class="modal-box">
+        <div class="modal-content">
-    <!-- Header -->
+            <div class="modal-header">
-    <h3 class="font-bold text-lg">New Package</h3>
+                <button type="button"
-
+                        class="close"
-    <!-- Close button (X) -->
+                        data-dismiss="modal">
-    <form method="dialog">
+                    <span aria-hidden="true">&times;</span>
-      <button
+                    <span class="sr-only">Close</span>
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">New Package</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <p>Create new package. Description can be changed later.</p>
-      <p class="mb-4">Create new package. Description can be changed later.</p>
+                <form id="new_package_modal_form"
-
-      <form
-        id="new-package-modal-form"
                       accept-charset="UTF-8"
                       action=""
-        method="post"
+                      data-remote="true"
-      >
+                      method="post">
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="name">Name</label>
-          <label class="label" for="package-name">
+                        <input id="name" class="form-control"
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="package-name"
-            class="input input-bordered w-full"
                                name="package-name"
-            placeholder="Name"
+                               placeholder="Name"/>
-            required
+                    </p>
-          />
+                    <p>
-        </div>
+                        <label for="description">Description</label>
-
+                        <input id="description"
-        <div class="form-control mb-3">
-          <label class="label" for="package-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="package-description"
                                type="text"
-            class="input input-bordered w-full"
+                               rows="3"
+                               class="form-control"
                                placeholder="Description..."
-            name="package-description"
+                               name="package-description"/>
-          />
+                    </p>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="new_package_modal_form_submit"
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
                    class="btn btn-primary"
-        @click="submit('new-package-modal-form')"
+                   href="#">Submit</a>
-        :disabled="isSubmitting"
+                <button type="button"
-      >
+                        class="btn btn-default"
-        <span x-show="!isSubmitting">Submit</span>
+                        data-dismiss="modal">Cancel
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
                 </button>
             </div>
         </div>
-
+    </div>
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
+<script>
-    <button :disabled="isSubmitting">close</button>
+$(function() {
-  </form>
+    $('#new_package_modal_form_submit').on('click', function (e) {
-</dialog>
+        e.preventDefault();
+        $('#new_package_modal_form').submit();
+    });
+});
+</script>

templates/modals/collections/new_pathway_modal.html

@@ -0,0 +1,302 @@
+
+{% load static %}
+<div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
+     aria-hidden="true" style="overflow-y: auto;">
+    <!-- FIXME: make width dynamic-->
+    <div class="modal-dialog" id="new_pathway_modal_dialog" style="width:900px">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal">
+                    <span aria-hidden="true">&times;</span> <span class="sr-only">Close</span>
+                </button>
+                <h4 class="js-title-step"></h4>
+            </div>
+            <div class="modal-body hide" data-step="1" data-title="New Pathway">
+                <div class="jumbotron">Create a new pathway by entering
+                    the root compound and a name. Then select if you want to
+                    use the prediction engine to generate a predicted pathway or
+                    create an empty pathway that you fill in by yourself. If
+                    you choose to predict a pathway, you can modify the
+                    settings for the prediction, or use the default settings
+                    and just click Submit.
+                </div>
+                <div class="modal-body">
+                    {% if current_user.name == 'anonymous' %}
+                    <div class="alert alert-warning">
+                        You are currently logged in as Anonymous. Please note:
+                        Pathways entered or predicted as anonymous user will be deleted after 30 days.
+                        Please log in to save your results.
+                    </div>
+                    {% endif %}
+                </div>
+                <div class="row">
+                    <div class="col-md-6">
+                        <label for="name">Name</label>
+                        <input id="name" class="form-control" name="name" placeholder="Name"/>
+                        <label for="description">Description</label>
+                        <input id="description" class="form-control" name="description" placeholder="no description"/>
+                    </div>
+
+                    <div class="col-md-6">
+                        <label for="predict">Predict pathway or build yourself?</label>
+                        <div class="radio" id="predict">
+                            <p>
+                                <label>
+                                    <input type="radio" name="predict" id="radioPredict" value="predict" checked/>Predict pathway
+                                </label>
+                            </p>
+                            <p>
+                                <label>
+                                    <input type="radio" name="predict" id="radioIncremental"value="incremental"/>Incremental prediction
+                                </label>
+                            </p>
+                            <p>
+                                <label>
+                                    <input type="radio" name="predict" id="radioBuild" value="build"/>Build pathway
+                                </label>
+                            </p>
+                        </div>
+                    </div>
+                </div>
+                <label for="smilesinput">SMILES</label>
+                <table style="width: 100%">
+                    <colgroup>
+                        <col span="1" style="width: 90%;">
+                        <col span="1" style="width: 10%;">
+                    </colgroup>
+                    <tr>
+                        <td>
+                            <input id="smilesinput" class="form-control" name="smilesinput" placeholder="C1CCCCC1"
+                                   autocapitalize="none"/>
+                        </td>
+                        <td>
+                            <button type="button" class="btn btn-default" id="render-button">
+                                Render
+                            </button>
+                        </td>
+                    </tr>
+                </table>
+                <p id="ketcher_container"></p>
+                <div>
+                    <iframe id="ifKetcher" src="{% static '/js/ketcher/ketcher.html' %}" width="850"
+                            height="510"></iframe>
+                </div>
+            </div>
+            <div class="modal-body hide" data-step="2" data-title="New Pathway - Advanced Settings">
+                <div class="jumbotron">Choose if you want to use an existing
+                    setting, or create a new one for this pathway
+                    prediction. Then click Submit to use the specified setting,
+                    or click next to set the parameters.
+                </div>
+                <div id="settings">
+                    <div class="radio" id="settingRadio">
+                        <p>
+                            <label>
+                                <input type="radio" name="existing" id="radioDefault" value="exisiting" checked/>
+                                Use Default
+                            </label>
+                        </p>
+                        <p>
+                            <label>
+                                <input type="radio" name="existing" id="radioExists" value="exisiting"/>
+                                Select Existing
+                            </label>
+                        </p>
+                        <p>
+                            <label>
+                                <input type="radio" name="existing" id="radioNew" value="temporary"/>
+                                Create New
+                            </label>
+                        </p>
+                    </div>
+
+                    <select id="settingSelect" name="settingSelect" class="form-control">
+                        {% for setting in available_settings %}
+                        <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
+                        {% endfor %}
+                    </select>
+                    <p></p>
+                </div>
+            </div>
+            {% with step_offset=1 %}
+            {% include "templates/modals/collections/new_setting_modal_body.html" %}
+            {% endwith %}
+            <div class="modal-footer">
+                <button type="button" class="btn btn-default js-btn-step pull-left" data-orientation="cancel"
+                        onclick="reset()" data-dismiss="modal"></button>
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="previous"
+                        id="backbutton"></button>
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="next"
+                        id="nextbutton"></button>
+                <a id="modal-form-submit" class="btn btn-primary" href="#">Submit</a>
+            </div>
+        </div>
+    </div>
+</div>
+
+<script>
+s = new Setting(
+    'settingName',
+    'package_multi_select',
+    'modelSelect',
+    'cutoff',
+    'evalType',
+    'availableTS',
+    'forms',
+    'truncatorTable',
+    'summaryTable',
+);
+
+$(function() {
+    // hide all forms
+    $('#forms').children().hide()
+
+    $("#render-button").on("click", function() {
+        syncKetcherAndTextInput('text', "ifKetcher", "smilesinput");
+    });
+
+    // If theres a change in the in '#smilesinput' sync the value to ketcher
+    $('#smilesinput').on('input', function() {
+        syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
+    });
+
+    // If theres an update in ketcher sync it to textinput
+    setInterval(function() {
+        syncKetcherAndTextInput('ketcher', 'ifKetcher', 'smilesinput');
+    }, 250);
+
+    $("#smilesinput").on("blur", function() {
+        syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
+    });
+
+    $("#smilesinput").on("keypress", function(event) {
+        if (event.keyCode == 13) {
+            syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
+        }
+    });
+
+    // Show forms depending on the selected TS
+    $('#availableTS').on('change', function(e) {
+        e.preventDefault();
+
+        var type = $(this).val();
+        // hide current content
+        $('#forms').children().hide()
+
+        if(type === '') {
+            return;
+        }
+
+        $('#' + type + '_form').show()
+    });
+
+    $("#modelSelect").on("change", function() {
+        setCutoff = function (thresh) {
+            $("#cutoff").val(thresh);
+        }
+
+        var modelUri = $("#modelSelect :selected").val();
+        fillPRCurve(modelUri, setCutoff);
+    });
+
+    // Add a TS to the setting
+    $('#add-ts-button').on('click', function(e) {
+        e.preventDefault();
+        s.addTruncator();
+    });
+
+    $('input[type=radio][name=predict]').change(function() {
+        if (this.id == 'radioBuild') {
+          $("#nextbutton").prop("disabled", true);
+        } else {
+          $("#nextbutton").prop("disabled", false);
+        }
+    });
+
+    $('input[type=radio][name=existing]').change(function() {
+        if (this.id == 'radioDefault' || this.id == 'radioExists') {
+          if(this.id == 'radioDefault') {
+            $("#settingSelect").prop("disabled", true);
+          } else {
+            $("#settingSelect").prop("disabled", false);
+          }
+          $("#nextbutton").prop("disabled", true);
+        } else {
+          // build...
+	  	  $("#settingSelect").prop("disabled", true);
+          $("#nextbutton").prop("disabled", false);
+        }
+    });
+
+    var pwStep1 = function() {
+        console.log("pw step 1");
+        // Make "Next" to "Advanced"
+        $('#nextbutton').val("Advanced");
+    }
+
+    var pwStep2 = function() {
+        console.log("pw step 2");
+        // Make "Advanced" to "Next"
+        $('#nextbutton').val("Next");
+        // As "Use default is preselected" disable "Next" button
+        $("#nextbutton").prop("disabled",true);
+        // Disable setting dropdown as long as the correspndonding radio isnt checked
+        $("#settingSelect").prop("disabled",true);
+        // Show submit button
+        $("#modal-form-submit").show();
+    }
+
+    var settingStep1 = function (){
+        // First step sets name and packages
+        s.extractName();
+        s.extractSelectedPackages();
+    }
+
+    var settingStep2 = function (){
+        // Seconds step gathers relative reasoning params
+        s.extractRelativeReasoning();
+        s.extractCutoff();
+        s.extractEvaluationType();
+    }
+
+    var settingStep3 = function() {
+        s.updateTable();
+        s.updateSummaryTable();
+        // hide duplicate submit...
+        $("#nextbutton").hide();
+    }
+
+    var postPathway = function(){
+        console.log("Complete!");
+        console.log(s.tsParams);
+        console.log("Getting SMILES");
+    }
+
+    function dummy() {
+        console.log("dummy");
+    }
+
+    $('#new_pathway_modal').modalSteps({
+      btnCancelHtml: 'Cancel',
+      btnPreviousHtml: 'Back',
+      btnNextHtml: 'Next',
+      btnLastStepHtml: 'Submit',
+      disableNextButton: false,
+      completeCallback: postPathway,
+      callbacks: {
+        '1': pwStep1,
+        '2' : pwStep2,
+        '3' : dummy,
+        '4' : settingStep1,
+        '5' : settingStep2,
+        '6' : settingStep3,
+      }
+    });
+
+   $('#modal-form-submit').on('click', function() {
+      e.preventDefault();
+      postPathway();
+   });
+});
+
+</script>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,260 +1,109 @@
+
 {% load static %}
 
-<dialog
+<div id="new_prediction_setting_modal" class="modal" tabindex="-1">
-  id="new_prediction_setting_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="{
+            <div class="modal-header">
-    isSubmitting: false,
+                <h5 class="modal-title">Create a Prediction Setting</h5>
-    tpMethod: '',
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-
+                    <span aria-hidden="true">&times;</span>
-    reset() {
-      this.isSubmitting = false;
-      this.tpMethod = '';
-    },
-
-    async submit() {
-      const form = document.getElementById('new-prediction-setting-modal-form');
-      if (!form.checkValidity()) {
-        form.reportValidity();
-        return;
-      }
-
-      this.isSubmitting = true;
-      const formData = new FormData(form);
-
-      try {
-        const response = await fetch('/setting', {
-          method: 'POST',
-          body: new URLSearchParams(formData)
-        });
-        if (response.ok) {
-          location.reload();
-        }
-      } catch (error) {
-        console.error('Error creating setting:', error);
-      } finally {
-        this.isSubmitting = false;
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Create a Prediction Setting</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>To create a Prediction Setting fill the form below and click "Create"</p>
-    <div class="py-4">
+                <form id="new-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-      <p class="mb-4">
+                      method="post">
-        To create a Prediction Setting fill the form below and click "Create"
-      </p>
-      <form
-        id="new-prediction-setting-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
 
-        <div class="form-control mb-3">
+                    <label for="prediction-setting-name">Name</label>
-          <label class="label" for="prediction-setting-name">
+                    <input id="prediction-setting-name" name="prediction-setting-name" class="form-control" placeholder="Name"/>
-            <span class="label-text">Name</span>
+                    <label for="prediction-setting-description">Description</label>
-          </label>
+                    <input id="prediction-setting-description" name="prediction-setting-description" class="form-control"
-          <input
+                           placeholder="Description"/>
-            id="prediction-setting-name"
-            name="prediction-setting-name"
-            class="input input-bordered w-full"
-            placeholder="Name"
-            required
-          />
-        </div>
 
-        <div class="form-control mb-3">
+                    <label for="prediction-setting-max-nodes">Max #Nodes</label>
-          <label class="label" for="prediction-setting-description">
+                    <input id="prediction-setting-max-nodes" type="number" class="form-control" name="prediction-setting-max-nodes" value="30" min="1" max="50" step="1">
-            <span class="label-text">Description</span>
+                    <label for="prediction-setting-max-depth">Max Depth</label>
-          </label>
+                    <input id="prediction-setting-max-depth" type="number" class="form-control" name="prediction-setting-max-depth" value="5" min="1" max="8" step="1">
-          <input
-            id="prediction-setting-description"
-            name="prediction-setting-description"
-            class="input input-bordered w-full"
-            placeholder="Description"
-          />
-        </div>
 
-        <div class="form-control mb-3">
+                    <label for="tp-generation-method">TP Generation Method</label>
-          <label class="label" for="prediction-setting-max-nodes">
+                    <select id="tp-generation-method" name="tp-generation-method" class="form-control" data-width='100%'>
-            <span class="label-text">Max #Nodes</span>
+                        <option disabled selected>Select how TPs are generated</option>
-          </label>
-          <input
-            id="prediction-setting-max-nodes"
-            type="number"
-            class="input input-bordered w-full"
-            name="prediction-setting-max-nodes"
-            value="30"
-            min="1"
-            max="50"
-            step="1"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="prediction-setting-max-depth">
-            <span class="label-text">Max Depth</span>
-          </label>
-          <input
-            id="prediction-setting-max-depth"
-            type="number"
-            class="input input-bordered w-full"
-            name="prediction-setting-max-depth"
-            value="5"
-            min="1"
-            max="8"
-            step="1"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="tp-generation-method">
-            <span class="label-text">TP Generation Method</span>
-          </label>
-          <select
-            id="tp-generation-method"
-            name="tp-generation-method"
-            class="select select-bordered w-full"
-            x-model="tpMethod"
-            required
-          >
-            <option value="" disabled selected>
-              Select how TPs are generated
-            </option>
                         <option value="rule-based-prediction-setting">Rule Based</option>
                         <option value="model-based-prediction-setting">Model Based</option>
                     </select>
-        </div>
+                    <div id="rule-based-prediction-setting-specific-form">
-
+                        <!-- Rule Packages -->
-        <!-- Rule Based Settings -->
+                        <label>Rule Packages</label><br>
-        <div x-show="tpMethod === 'rule-based-prediction-setting'" x-cloak>
+                        <select id="rule-based-prediction-setting-packages" name="rule-based-prediction-setting-packages"
-          <div class="form-control mb-3">
+                                data-actions-box='true' class="form-control" multiple data-width='100%'>
-            <label class="label">
+                            <option disabled>Reviewed Packages</option>
-              <span class="label-text">Rule Packages</span>
-            </label>
-            <select
-              id="rule-based-prediction-setting-packages"
-              name="rule-based-prediction-setting-packages"
-              class="select select-bordered w-full h-32"
-              multiple
-            >
-              <optgroup label="Reviewed Packages">
                             {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
                             <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
-              </optgroup>
+
-              <optgroup label="Unreviewed Packages">
+                            <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
                             <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
-              </optgroup>
                         </select>
-            <label class="label">
-              <span class="label-text-alt"
-                >Hold Ctrl/Cmd to select multiple</span
-              >
-            </label>
                     </div>
-        </div>
+                    <div id="model-based-prediction-setting-specific-form">
-
+                        <label>Select Model</label><br>
-        <!-- Model Based Settings -->
+                        <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
-        <div x-show="tpMethod === 'model-based-prediction-setting'" x-cloak>
+                        <option disabled selected>Select the model</option>
-          <div class="form-control mb-3">
-            <label class="label" for="model-based-prediction-setting-model">
-              <span class="label-text">Select Model</span>
-            </label>
-            <select
-              id="model-based-prediction-setting-model"
-              name="model-based-prediction-setting-model"
-              class="select select-bordered w-full"
-            >
-              <option value="" disabled selected>Select the model</option>
                         {% for m in models %}
                         <option value="{{ m.url }}">{{ m.name|safe }}</option>
                         {% endfor %}
                         </select>
+                        <label for="model-based-prediction-setting-threshold">Threshold</label>
+                        <input id="model-based-prediction-setting-threshold" name="model-based-prediction-setting-threshold" class="form-control" placeholder="0.25" type="number"/>
                     </div>
 
-          <div class="form-control mb-3">
+                    <input class="form-check-input" type="checkbox" value="on" id="prediction-setting-new-default" name="prediction-setting-new-default">
-            <label class="label" for="model-based-prediction-setting-threshold">
+                    <label class="form-check-label" for="prediction-setting-new-default">Set this setting as new default</label>
-              <span class="label-text">Threshold</span>
-            </label>
-            <input
-              id="model-based-prediction-setting-threshold"
-              name="model-based-prediction-setting-threshold"
-              class="input input-bordered w-full"
-              placeholder="0.25"
-              type="number"
-              min="0"
-              max="1"
-              step="0.05"
-            />
-          </div>
-        </div>
 
-        <div class="form-control">
-          <label class="label cursor-pointer justify-start gap-3">
-            <input
-              type="checkbox"
-              class="checkbox"
-              value="on"
-              id="prediction-setting-new-default"
-              name="prediction-setting-new-default"
-            />
-            <span class="label-text">Set this setting as new default</span>
-          </label>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="new-prediction-setting-modal-submit">Create</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit()"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Create</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+    $(function() {
 
-  <!-- Backdrop -->
+        // Initially hide all "specific" forms
-  <form method="dialog" class="modal-backdrop">
+        $("div[id$='-specific-form']").each( function() {
-    <button :disabled="isSubmitting">close</button>
+            $(this).hide();
-  </form>
+        });
-</dialog>
+
+        $("#rule-based-prediction-setting-packages").selectpicker();
+
+        // On change hide all and show only selected
+        $("#tp-generation-method").change(function() {
+            $("div[id$='-specific-form']").each( function() {
+                $(this).hide();
+            });
+            val = $('option:selected', this).val();
+            $("#" + val + "-specific-form").show();
+        });
+
+        $('#new-prediction-setting-modal-submit').click(function(e){
+            e.preventDefault();
+            // $('#new-prediction-setting-modal-form').submit();
+
+            const formData = $('#new-prediction-setting-modal-form').serialize();
+            $.post('/setting', formData, function(response) {
+                location.reload();
+            });
+        });
+    })
+</script>

templates/modals/collections/new_reaction_modal.html

@@ -1,105 +1,50 @@
 {% load static %}
-
+<div class="modal fade bs-modal-lg" id="new_reaction_modal" tabindex="-1" aria-labelledby="new_reaction_modal" aria-modal="true"
-<dialog
+     role="dialog">
-  id="new_reaction_modal"
+    <div class="modal-dialog modal-lg">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
->
+                    <span aria-hidden="true">×</span>
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Create a new Reaction</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Create a new Reaction</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="new_reaction_modal_form" accept-charset="UTF-8" action="{% url 'package reaction list' meta.current_package.uuid %}" data-remote="true" method="post">
-      <form
-        id="new-reaction-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'package reaction list' meta.current_package.uuid %}"
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <label for="reaction-name">Name</label>
-        <div class="form-control mb-3">
+                    <input id="reaction-name" class="form-control" name="reaction-name" placeholder="Name"/>
-          <label class="label" for="reaction-name">
+                    <label for="reaction-description">Description</label>
-            <span class="label-text">Name</span>
+                    <input id="reaction-description" class="form-control" name="reaction-description" placeholder="Description"/>
-          </label>
+                    <p></p>
-          <input
+                    <div>
-            id="reaction-name"
+                        <iframe id="new_reaction_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-            class="input input-bordered w-full"
+                                height="510"></iframe>
-            name="reaction-name"
-            placeholder="Name"
-            required
-          />
                     </div>
-
+                    <input type="hidden" name="reaction-smirks" id="reaction-smirks">
-        <div class="form-control mb-3">
+                    <p></p>
-          <label class="label" for="reaction-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="reaction-description"
-            class="input input-bordered w-full"
-            name="reaction-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="mb-3">
-          <iframe
-            id="new_reaction_ketcher"
-            src="{% static '/js/ketcher2/ketcher.html' %}"
-            width="100%"
-            height="510"
-          ></iframe>
-        </div>
-
-        <input type="hidden" name="reaction-smirks" id="reaction-smirks" />
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="
-          const k = getKetcher('new_reaction_ketcher');
-          document.getElementById('reaction-smirks').value = k.getSmiles();
-          submit('new-reaction-modal-form');
-        "
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
                 </button>
+                <button type="button" class="btn btn-primary" id="new_reaction_modal_form_submit">Submit</button>
+            </div>
         </div>
     </div>
 
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
+<script>
-    <button :disabled="isSubmitting">close</button>
+$(function() {
-  </form>
+    $('#new_reaction_modal_form_submit').on('click', function(e) {
-</dialog>
+        e.preventDefault();
+        $(this).prop("disabled",true);
+
+        k = getKetcher('new_reaction_ketcher');
+        $('#reaction-smirks').val(k.getSmiles());
+
+        // submit form
+        $('#new_reaction_modal_form').submit();
+    });
+});
+</script>

templates/modals/collections/new_rule_modal.html

@@ -1,140 +1,72 @@
 {% load static %}
+<div class="modal fade bs-modal-lg" id="new_rule_modal" tabindex="-1" aria-labelledby="new_rule_modal" aria-modal="true"
+     role="dialog">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">×</span>
+                </button>
+                <h4 class="modal-title">Create a new Rule</h4>
+            </div>
+            <div class="modal-body">
+                <form id="new_rule_modal_form" accept-charset="UTF-8" action="{% url 'package rule list' meta.current_package.uuid %}" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="rule-name">Name</label>
+                    <input id="rule-name" class="form-control" name="rule-name" placeholder="Name"/>
+                    <label for="rule-description">Description</label>
+                    <input id="rule-description" class="form-control" name="rule-description" placeholder="Description"/>
+                    <label for="rule-smirks">SMIRKS</label>
+                    <input id="rule-smirks" class="form-control" name="rule-smirks" placeholder="SMIRKS"/>
+                    <p></p>
+                    <div id="rule-smirks-viz"></div>
+                    <input type="hidden" name="rule-type" id="rule-type" value="SimpleAmbitRule">
+                    <p></p>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+                </button>
+                <button type="button" class="btn btn-primary" id="new_rule_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
 
-<dialog
+</div>
-  id="new_rule_modal"
+<script>
-  class="modal"
+$(function() {
-  x-data="{
+
-    ...modalForm(),
+    $('#rule-smirks').on('input', function(e) {
-    smirksVizHtml: '',
+        $('#rule-smirks-viz').empty()
-    updateSmirksViz() {
+
-      const smirks = document.getElementById('rule-smirks').value;
+        smirks = $('#rule-smirks').val()
-      if (!smirks) {
-        this.smirksVizHtml = '';
-        return;
-      }
 
         const img = new Image();
-      img.src = '{% url 'depict' %}?is_query_smirks=true&smirks=' + encodeURIComponent(smirks);
+        img.src = "{% url 'depict' %}?is_query_smirks=true&smirks=" + encodeURIComponent(smirks);
         img.style.width = '100%';
         img.style.height = '100%';
         img.style.objectFit = 'cover';
 
-      img.onload = () => {
+        img.onload = function () {
-        this.smirksVizHtml = img.outerHTML;
+            $('#rule-smirks-viz').append(img);
         };
 
-      img.onerror = () => {
+        img.onerror = function () {
-        this.smirksVizHtml = `
+            error_tpl = `
-          <div class='alert alert-error' role='alert'>
+                <div class="alert alert-error" role="alert">
-            <h4 class='alert-heading'>Could not render SMIRKS!</h4>
+                    <h4 class="alert-heading">Could not render SMIRKS!</h4>
-            <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</p>
+                    <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</a>
-          </div>`;
+                    </p>
+                </div>`
+            $('#rule-smirks-viz').append(error_tpl);
         };
-    }
+    });
-  }"
-  @close="reset(); smirksVizHtml = ''"
->
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Create a new Rule</h3>
 
-    <!-- Close button (X) -->
+    $('#new_rule_modal_form_submit').on('click', function(e) {
-    <form method="dialog">
+        e.preventDefault();
-      <button
+        $(this).prop("disabled",true);
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
+        // submit form
-        :disabled="isSubmitting"
+        $('#new_rule_modal_form').submit();
-      >
+    });
-        ✕
+});
-      </button>
+</script>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-rule-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'package rule list' meta.current_package.uuid %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="rule-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="rule-name"
-            class="input input-bordered w-full"
-            name="rule-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="rule-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="rule-description"
-            class="input input-bordered w-full"
-            name="rule-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="rule-smirks">
-            <span class="label-text">SMIRKS</span>
-          </label>
-          <input
-            id="rule-smirks"
-            class="input input-bordered w-full"
-            name="rule-smirks"
-            placeholder="SMIRKS"
-            @input="updateSmirksViz()"
-          />
-        </div>
-
-        <div id="rule-smirks-viz" class="mb-3" x-html="smirksVizHtml"></div>
-
-        <input
-          type="hidden"
-          name="rule-type"
-          id="rule-type"
-          value="SimpleAmbitRule"
-        />
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-rule-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

templates/modals/collections/new_scenario_modal.html

@@ -1,177 +1,102 @@
-{% load static %}
+<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="new_scenario_modal"
-
+     aria-hidden="true">
-<dialog
+    <div class="modal-dialog modal-lg">
-  id="new_scenario_modal"
+        <div class="modal-content">
-  class="modal"
+            <div class="modal-header">
-  x-data="{
+                <button type="button" class="close" data-dismiss="modal">
-    ...modalForm(),
+                    <span aria-hidden="true">&times;</span>
-    scenarioType: 'empty',
+                    <span class="sr-only">Close</span>
-    validateYear(el) {
-      if (el.value && el.value.length < 4) {
-        el.value = new Date().getFullYear();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">New Scenario</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">New Scenario</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="new_scenario_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/scenario"
-      <form
+                      data-remote="true" method="post">
-        id="new-scenario-modal-form"
-        accept-charset="UTF-8"
-        action="{{ meta.current_package.url }}/scenario"
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <div class="jumbotron">Please enter name, description, and date of scenario. Date should be
-        <div class="alert alert-info mb-4">
+                        associated to the data, not the current date. For example, this could reflect the publishing
-          <span>
+                        date of a study. You can leave all fields but the name empty and fill them in later.
-            Please enter name, description, and date of scenario. Date should be
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/scenario" role="button">wiki
-            associated to the data, not the current date. For example, this
+                            &gt;&gt;</a>
-            could reflect the publishing date of a study. You can leave all
-            fields but the name empty and fill them in later.
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/scenario"
-              class="link"
-              >wiki &gt;&gt;</a
-            >
-          </span>
                     </div>
-
+                    <label for="scenario-name">Name</label>
-        <div class="form-control mb-3">
+                    <input id="scenario-name" name="scenario-name" class="form-control" placeholder="Name"/>
-          <label class="label" for="scenario-name">
+                    <label for="scenario-description">Description</label>
-            <span class="label-text">Name</span>
+                    <input id="scenario-description" name="scenario-description" class="form-control"
-          </label>
+                           placeholder="Description"/>
-          <input
+                    <label id="dateField" for="dateYear">Date</label>
-            id="scenario-name"
+                    <table>
-            name="scenario-name"
+                        <tr>
-            class="input input-bordered w-full"
+                            <th>
-            placeholder="Name"
+                                <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
-            required
+                                       placeholder="YYYY" max="{% now "Y" %}">
-          />
+                            </th>
-        </div>
+                            <th>
-
+                                <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
-        <div class="form-control mb-3">
+                                       class="form-control" placeholder="MM" >
-          <label class="label" for="scenario-description">
+                            </th>
-            <span class="label-text">Description</span>
+                            <th>
-          </label>
+                                <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
-          <input
+                                       placeholder="DD">
-            id="scenario-description"
+                            </th>
-            name="scenario-description"
+                        </tr>
-            class="input input-bordered w-full"
+                    </table>
-            placeholder="Description"
+                    <label for="scenario-type">Scenario Type</label>
-          />
+                    <select id="scenario-type" name="scenario-type" class="form-control" data-width='100%'>
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label">
-            <span class="label-text">Date</span>
-          </label>
-          <div class="flex gap-2">
-            <input
-              type="number"
-              id="dateYear"
-              name="scenario-date-year"
-              class="input input-bordered w-24"
-              placeholder="YYYY"
-              max="{% now 'Y' %}"
-              @blur="validateYear($el)"
-            />
-            <input
-              type="number"
-              id="dateMonth"
-              name="scenario-date-month"
-              min="1"
-              max="12"
-              class="input input-bordered w-20"
-              placeholder="MM"
-            />
-            <input
-              type="number"
-              id="dateDay"
-              name="scenario-date-day"
-              min="1"
-              max="31"
-              class="input input-bordered w-20"
-              placeholder="DD"
-            />
-          </div>
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="scenario-type">
-            <span class="label-text">Scenario Type</span>
-          </label>
-          <select
-            id="scenario-type"
-            name="scenario-type"
-            class="select select-bordered w-full"
-            x-model="scenarioType"
-          >
                         <option value="empty" selected>Empty Scenario</option>
                         {% for k, v in scenario_types.items %}
                             <option value="{{ v.name }}">{{ k }}</option>
                         {% endfor %}
                     </select>
-        </div>
 
                     {% for type in scenario_types.values %}
-          <div
+                        <div id="{{ type.name }}-specific-inputs">
-            id="{{ type.name }}-specific-inputs"
-            x-show="scenarioType === '{{ type.name }}'"
-            x-cloak
-          >
                             {% for widget in type.widgets %}
                                 {{ widget|safe }}
                             {% endfor %}
                         </div>
                     {% endfor %}
+
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-    <div class="modal-action">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-      <button
+            </div>
-        type="button"
+        </div>
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-scenario-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
     </div>
 </div>
 
-  <!-- Backdrop -->
+<script>
-  <form method="dialog" class="modal-backdrop">
+    $(function () {
-    <button :disabled="isSubmitting">close</button>
+        // Initially hide all "specific" forms
-  </form>
+        $("div[id$='-specific-inputs']").each(function () {
-</dialog>
+            $(this).hide();
+        });
+
+        // On change hide all and show only selected
+        $("#scenario-type").change(function () {
+            $("div[id$='-specific-inputs']").each(function () {
+                $(this).hide();
+            });
+            val = $('option:selected', this).val();
+            $("#" + val + "-specific-inputs").show();
+        });
+
+        $('#new_scenario_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#new_scenario_form').submit();
+        });
+
+        var dateYear = document.getElementById("dateYear");
+        dateYear.addEventListener("change", () => {
+            console.log("Final value after editing:", dateYear.value);
+            if (dateYear.value.length < 4) {
+                dateYear.value = {% now "Y" %};
+            }
+        });
+
+    });
+
+</script>
+

templates/modals/objects/add_additional_information_modal.html

@@ -1,117 +1,61 @@
 {% load static %}
 <!-- Add Additional Information-->
-<dialog
+<div id="add_additional_information_modal" class="modal" tabindex="-1">
-  id="add_additional_information_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="{
+            <div class="modal-header">
-    isSubmitting: false,
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-    selectedType: '',
+                    <span aria-hidden="true">&times;</span>
-
-    reset() {
-      this.isSubmitting = false;
-      this.selectedType = '';
-    },
-
-    submit() {
-      if (!this.selectedType) return;
-
-      const form = document.getElementById('add_' + this.selectedType + '_add-additional-information-modal-form');
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Add Additional Information</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h3 class="modal-title">Add Additional Information</h3>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
-      <div class="form-control">
+                    <option selected disabled>Select the type to add</option>
-        <label class="label" for="select-additional-information-type">
-          <span class="label-text">Select the type to add</span>
-        </label>
-        <select
-          id="select-additional-information-type"
-          class="select select-bordered w-full"
-          x-model="selectedType"
-        >
-          <option value="" selected disabled>Select the type to add</option>
                     {% for add_inf in available_additional_information %}
-            <option value="{{ add_inf.name }}">
+                        <option value="{{ add_inf.name }}">{{ add_inf.display_name }}</option>
-              {{ add_inf.display_name }}
-            </option>
                     {% endfor %}
                 </select>
-      </div>
-
                 {% for add_inf in available_additional_information %}
-        <div
+                    <div class="aiform {{ add_inf.name }}" style="display: none;">
-          class="mt-4"
+                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
-          x-show="selectedType === '{{ add_inf.name }}'"
+                              action="" data-remote="true" method="post">
-          x-cloak
-        >
-          <form
-            id="add_{{ add_inf.name }}_add-additional-information-modal-form"
-            accept-charset="UTF-8"
-            action=""
-            method="post"
-          >
                             {% csrf_token %}
                             {{ add_inf.widget|safe }}
-            <input
+                            <input type="hidden" name="hidden" value="add-additional-information">
-              type="hidden"
-              name="hidden"
-              value="add-additional-information"
-            />
                         </form>
                     </div>
                 {% endfor %}
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="add-additional-information-modal-submit">Add
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit()"
-        :disabled="isSubmitting || !selectedType"
-      >
-        <span x-show="!isSubmitting">Add</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Adding...</span>
                 </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#select-additional-information-type').change(function(e){
-  <form method="dialog" class="modal-backdrop">
+        var selectedType = $("#select-additional-information-type :selected").val();
-    <button :disabled="isSubmitting">close</button>
+        $('.aiform').hide();
-  </form>
+        $('.' + selectedType).show();
-</dialog>
+    })
+
+    $('#add-additional-information-modal-submit').click(function(e){
+        e.preventDefault();
+
+        var selectedType = $("#select-additional-information-type :selected").val();
+        console.log(selectedType);
+        if (selectedType !== null && selectedType !== undefined && selectedType !== '') {
+            $('.' + selectedType + ' >form').submit();
+        }
+
+    });
+
+});
+
+
+</script>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,181 +1,127 @@
+
 {% load static %}
-<dialog
+<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
-  id="add_pathway_edge_modal"
+     aria-modal="true"
-  class="modal"
+     role="dialog">
-  x-data="{
+    <div class="modal-dialog modal-lg">
-    isSubmitting: false,
+        <div class="modal-content">
-    reactionImageUrl: '',
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h4 class="modal-title">Add a Reaction</h4>
+            </div>
+            <div class="modal-body">
+                <form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
+                      action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="edge-name">Name</label>
+                    <input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
+                    <label for="edge-description">Description</label>
+                    <input id="edge-description" class="form-control" name="edge-description" placeholder="Description"/>
+                    <p></p>
+                    <div class="row">
+                        <div class="col-xs-5">
+                            <legend>Substrate(s)</legend>
+                        </div>
+                        <div class="col-xs-2">
 
-    reset() {
+                        </div>
-      this.isSubmitting = false;
+                        <div class="col-xs-5">
-      this.reactionImageUrl = '';
+                            <legend>Product(s)</legend>
-    },
+                        </div>
+                    </div>
+                    <div class="row">
+                        <div class="col-xs-5">
+                            <select id="add_pathway_edge_substrates" name="edge-substrates"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
+                                {% for n in pathway.nodes %}
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+                                {% endfor %}
+                            </select>
+                        </div>
+                        <div class="col-xs-2" style="display: flex; justify-content: center; align-items: center;">
+                            <i class="glyphicon glyphicon-arrow-right"></i>
+                        </div>
+                        <div class="col-xs-5">
+                            <select id="add_pathway_edge_products" name="edge-products"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
+                                {% for n in pathway.nodes %}
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+                                {% endfor %}
+                            </select>
+                        </div>
+                    </div>
+                    <div class="row">
+                        <p></p>
+                        <div class="col-xs-12" id="reaction_image">
 
-    updateReactionImage() {
+                        </div>
-      const substratesSelect = document.getElementById('add_pathway_edge_substrates');
+                    </div>
-      const productsSelect = document.getElementById('add_pathway_edge_products');
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+                </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
 
-      const substrates = [];
+</div>
-      for (const option of substratesSelect.selectedOptions) {
+<script>
-        substrates.push(option.dataset.smiles);
-      }
 
-      const products = [];
+    function reactionImage() {
-      for (const option of productsSelect.selectedOptions) {
+        var substrates = [];
-        products.push(option.dataset.smiles);
+        $('#add_pathway_edge_substrates option:selected').each(function () {
-      }
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
+          substrates.push(smiles);
+        });
+
+        var products = []
+        $('#add_pathway_edge_products option:selected').each(function () {
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
+          products.push(smiles);
+        });
 
         if (substrates.length > 0 && products.length > 0) {
-        const reaction = substrates.join('.') + '>>' + products.join('.');
+            reaction = substrates.join('.') + ">>" + products.join('.');
-        this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
+            $('#reaction_image').empty();
-      } else {
+            $('#reaction_image').append(
-        this.reactionImageUrl = '';
+                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
+            );
         }
-    },
-
-    submit() {
-      this.isSubmitting = true;
-      document.getElementById('add_pathway_edge_modal_form').submit();
     }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-4xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Add a Reaction</h3>
 
-    <!-- Close button (X) -->
+    $(function () {
-    <form method="dialog">
+        $("#add_pathway_edge_substrates").selectpicker();
-      <button
+        $("#add_pathway_edge_products").selectpicker();
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
 
-    <!-- Body -->
+        $("#add_pathway_edge_substrates").on('change', function (e) {
-    <div class="py-4">
+            reactionImage();
-      <form
+        })
-        id="add_pathway_edge_modal_form"
+
-        accept-charset="UTF-8"
+        $("#add_pathway_edge_products").on('change', function (e) {
-        action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
+            reactionImage();
-        data-remote="true"
+        })
-        method="post"
+
-      >
+        $(function () {
-        {% csrf_token %}
+            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
-        <div class="form-control mb-3">
+                e.preventDefault();
-          <label class="label" for="edge-name">
+                $(this).prop("disabled", true);
-            <span class="label-text">Name</span>
+
-          </label>
+
-          <input
+                // submit form
-            id="edge-name"
+                $('#add_pathway_edge_modal_form').submit();
-            type="text"
+            });
-            class="input input-bordered w-full"
+        });
-            name="edge-name"
+
-            placeholder="Name"
+    });
-          />
+
-        </div>
+</script>
 
-        <div class="form-control mb-3">
-          <label class="label" for="edge-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="edge-description"
-            type="text"
-            class="input input-bordered w-full"
-            name="edge-description"
-            placeholder="Description"
-          />
-        </div>
 
-        <div class="mb-3 grid grid-cols-11 gap-2">
-          <div class="col-span-5">
-            <div class="form-control">
-              <label class="label">
-                <span class="label-text font-semibold">Substrate(s)</span>
-              </label>
-              <select
-                id="add_pathway_edge_substrates"
-                name="edge-substrates"
-                class="select select-bordered h-32 w-full"
-                multiple
-                @change="updateReactionImage()"
-              >
-                {% for n in pathway.nodes %}
-                  <option
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
-                {% endfor %}
-              </select>
-            </div>
-          </div>
-          <div class="col-span-1 flex items-center justify-center">
-            <span class="text-2xl">→</span>
-          </div>
-          <div class="col-span-5">
-            <div class="form-control">
-              <label class="label">
-                <span class="label-text font-semibold">Product(s)</span>
-              </label>
-              <select
-                id="add_pathway_edge_products"
-                name="edge-products"
-                class="select select-bordered h-32 w-full"
-                multiple
-                @change="updateReactionImage()"
-              >
-                {% for n in pathway.nodes %}
-                  <option
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
-                {% endfor %}
-              </select>
-            </div>
-          </div>
-        </div>
 
-        <div class="mb-3" x-show="reactionImageUrl" x-cloak>
-          <img :src="reactionImageUrl" class="w-full" alt="Reaction preview" />
-        </div>
-      </form>
-    </div>
 
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit()"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Submitting...</span>
-      </button>
-    </div>
-  </div>
 
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

templates/modals/objects/add_pathway_node_modal.html

@@ -1,137 +1,78 @@
 {% load static %}
-<dialog
+<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_modal" aria-modal="true"
-  id="add_pathway_node_modal"
+     role="dialog">
-  class="modal"
+    <div class="modal-dialog modal-lg">
-  x-data="modalForm()"
+        <div class="modal-content">
-  @close="reset()"
+            <div class="modal-header">
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box max-w-4xl">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Add a Node</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Add a Node</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="add_pathway_node_modal_form" accept-charset="UTF-8" action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}" data-remote="true" method="post">
-      <form
-        id="add_pathway_node_modal_form"
-        accept-charset="UTF-8"
-        action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}"
-        data-remote="true"
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="form-control mb-3">
+                    <label for="node-name">Name</label>
-          <label class="label" for="node-name">
+                    <input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
-            <span class="label-text">Name</span>
+                    <label for="node-description">Description</label>
-          </label>
+                    <input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
-          <input
+                    <label for="node-smiles">SMILES</label>
-            id="node-name"
+                    <input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
-            type="text"
+                    <p></p>
-            class="input input-bordered w-full"
+                    <div>
-            name="node-name"
+                        <iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-            placeholder="Name"
+                                height="510"></iframe>
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="node-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="node-description"
-            type="text"
-            class="input input-bordered w-full"
-            name="node-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="node-smiles">
-            <span class="label-text">SMILES</span>
-          </label>
-          <input
-            type="text"
-            class="input input-bordered w-full"
-            name="node-smiles"
-            placeholder="SMILES"
-            id="node-smiles"
-          />
-        </div>
-
-        <div class="mb-3">
-          <iframe
-            id="add_node_ketcher"
-            src="{% static '/js/ketcher2/ketcher.html' %}"
-            width="100%"
-            height="510"
-          ></iframe>
                     </div>
+                    <p></p>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('add_pathway_node_modal_form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Submitting...</span>
                 </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_node_modal_form_submit">Submit</button>
+            </div>
         </div>
     </div>
 
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>
-
 <script>
-  document
+
-    .getElementById("add_node_ketcher")
+function newStructureModalketcherToNewStructureModalTextInput() {
-    .addEventListener("load", function () {
+    $('#node-smiles').val(this.ketcher.getSmiles());
-      const iframe = this;
+}
+
+$(function() {
+
+    $('#add_node_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        const win = iframe.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
-            f: function () {
+                    f: newStructureModalketcherToNewStructureModalTextInput,
-              document.getElementById("node-smiles").value =
+                    ketcher: win.ketcher
-                this.ketcher.getSmiles();
-            },
-            ketcher: win.ketcher,
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
             }
         };
+
         checkKetcherReady();
+    })
+
+    $(function() {
+        $('#add_pathway_node_modal_form_submit').on('click', function(e) {
+            e.preventDefault();
+            $(this).prop("disabled",true);
+
+
+
+            // submit form
+            $('#add_pathway_node_modal_form').submit();
         });
+    });
+
+});
+
 </script>

templates/modals/objects/add_structure_modal.html

@@ -1,137 +1,78 @@
 {% load static %}
-<dialog
+<div class="modal fade bs-modal-lg" id="add_structure_modal" tabindex="-1" aria-labelledby="add_structure_modal" aria-modal="true"
-  id="add_structure_modal"
+     role="dialog">
-  class="modal"
+    <div class="modal-dialog modal-lg">
-  x-data="modalForm()"
+        <div class="modal-content">
-  @close="reset()"
+            <div class="modal-header">
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box max-w-4xl">
+                    <span aria-hidden="true">×</span>
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Create a new Structure</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h4 class="modal-title">Create a new Structure</h4>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="add_structure_modal_form" accept-charset="UTF-8" action="{% url 'package compound structure list' meta.current_package.uuid compound.uuid %}" data-remote="true" method="post">
-      <form
-        id="add_structure_modal_form"
-        accept-charset="UTF-8"
-        action="{% url 'package compound structure list' meta.current_package.uuid compound.uuid %}"
-        data-remote="true"
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="form-control mb-3">
+                    <label for="structure-name">Name</label>
-          <label class="label" for="structure-name">
+                    <input id="structure-name" class="form-control" name="structure-name" placeholder="Name"/>
-            <span class="label-text">Name</span>
+                    <label for="structure-description">Description</label>
-          </label>
+                    <input id="structure-description" class="form-control" name="structure-description" placeholder="Description"/>
-          <input
+                    <label for="structure-smiles">SMILES</label>
-            id="structure-name"
+                    <input type="text" class="form-control" name="structure-smiles" placeholder="SMILES" id="structure-smiles">
-            type="text"
+                    <p></p>
-            class="input input-bordered w-full"
+                    <div>
-            name="structure-name"
+                        <iframe id="add_structure_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-            placeholder="Name"
+                                height="510"></iframe>
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="structure-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="structure-description"
-            type="text"
-            class="input input-bordered w-full"
-            name="structure-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="structure-smiles">
-            <span class="label-text">SMILES</span>
-          </label>
-          <input
-            type="text"
-            class="input input-bordered w-full"
-            name="structure-smiles"
-            placeholder="SMILES"
-            id="structure-smiles"
-          />
-        </div>
-
-        <div class="mb-3">
-          <iframe
-            id="add_structure_ketcher"
-            src="{% static '/js/ketcher2/ketcher.html' %}"
-            width="100%"
-            height="510"
-          ></iframe>
                     </div>
+                    <p></p>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('add_structure_modal_form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Submitting...</span>
                 </button>
+                <button type="button" class="btn btn-primary" id="add_structure_modal_form_submit">Submit</button>
+            </div>
         </div>
     </div>
 
-  <!-- Backdrop -->
+</div>
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>
-
 <script>
-  document
+
-    .getElementById("add_structure_ketcher")
+function newStructureModalketcherToNewStructureModalTextInput() {
-    .addEventListener("load", function () {
+    $('#structure-smiles').val(this.ketcher.getSmiles());
-      const iframe = this;
+}
+
+$(function() {
+
+    $('#add_structure_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        const win = iframe.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
-            f: function () {
+                    f: newStructureModalketcherToNewStructureModalTextInput,
-              document.getElementById("structure-smiles").value =
+                    ketcher: win.ketcher
-                this.ketcher.getSmiles();
-            },
-            ketcher: win.ketcher,
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
             }
         };
+
         checkKetcherReady();
+    })
+
+    $(function() {
+        $('#add_structure_modal_form_submit').on('click', function(e) {
+            e.preventDefault();
+            $(this).prop("disabled",true);
+
+
+
+            // submit form
+            $('#add_structure_modal_form').submit();
         });
+    });
+
+});
+
 </script>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,94 +1,66 @@
+
 {% load static %}
 <!-- Delete Edge -->
-<dialog
+<div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
-  id="delete_pathway_edge_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
+            <div class="modal-header">
-  @close="reset()"
+                <h3 class="modal-title">Delete Edge</h3>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Delete Edge</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
-    <div class="py-4">
-      <p class="mb-4">
                 Deletes the Edge. Nodes referenced by this edge will remain.
-      </p>
+                <p></p>
-      <form
+                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-        id="delete-pathway-edge-modal-form"
+                      method="post">
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="form-control">
+                    <select id="delete_pathway_edge_edges" name="edge-url"
-          <label class="label" for="delete_pathway_edge_edges">
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            <span class="label-text">Select Reaction to delete</span>
+                        <option value="" disabled selected>Select Reaction to delete</option>
-          </label>
-          <select
-            id="delete_pathway_edge_edges"
-            name="edge-url"
-            class="select select-bordered w-full"
-            x-model="selectedEdge"
-            @change="imageUrl = selectedEdge ? selectedEdge + '?image=svg' : ''"
-            required
-          >
-            <option value="" disabled selected>
-              Select Reaction to delete
-            </option>
                         {% for e in pathway.edges %}
                             <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
                         {% endfor %}
                     </select>
-        </div>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>
                 </form>
+                <p></p>
+                <div id="delete_pathway_edge_image"></div>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-pathway-edge-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+        $("#delete_pathway_edge_edges").selectpicker();
 
-      <!-- Image Preview -->
+        $("#delete_pathway_edge_edges").on('change', function (e) {
-      <div class="mt-4" x-show="imageUrl" x-cloak>
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
-        <img :src="imageUrl" class="w-full" alt="Edge preview" />
-      </div>
-    </div>
 
-    <!-- Footer -->
+            if (edge_url !== "") {
-    <div class="modal-action">
+                $('#delete_pathway_edge_image').empty();
-      <button
+                $('#delete_pathway_edge_image').append(
-        type="button"
+                    "<img width='100%' src='" + edge_url + "?image=svg'>"
-        class="btn"
+                );
-        onclick="this.closest('dialog').close()"
+            }
-        :disabled="isSubmitting"
+        })
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-error"
-        @click="setFormAction('delete-pathway-edge-modal-form', selectedEdge); submit('delete-pathway-edge-modal-form')"
-        :disabled="isSubmitting || !selectedEdge"
-      >
-        <span x-show="!isSubmitting">Delete</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Deleting...</span>
-      </button>
-    </div>
-  </div>
 
-  <!-- Backdrop -->
+        $('#delete-pathway-edge-modal-submit').click(function (e) {
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
-  </form>
+
-</dialog>
+            if (edge_url === "") {
+                return;
+            }
+
+            $('#delete-pathway-edge-modal-form').attr('action', edge_url)
+            $('#delete-pathway-edge-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/delete_pathway_node_modal.html

@@ -1,97 +1,66 @@
 {% load static %}
+
 <!-- Delete Node -->
-<dialog
+<div id="delete_pathway_node_modal" class="modal" tabindex="-1">
-  id="delete_pathway_node_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
+            <div class="modal-header">
-  @close="reset()"
+                <h3 class="modal-title">Delete Node</h3>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Delete Node</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
-    <div class="py-4">
+                <p></p>
-      <p class="mb-4">
+                <form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-        Deletes the Node. Edges having this Node as Substrate or Product will be
+                      method="post">
-        removed as well.
-      </p>
-      <form
-        id="delete-pathway-node-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="form-control">
+                    <select id="delete_pathway_node_nodes" name="node-url"
-          <label class="label" for="delete_pathway_node_nodes">
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            <span class="label-text">Select Compound to delete</span>
+                        <option value="" disabled selected>Select Compound to delete</option>
-          </label>
-          <select
-            id="delete_pathway_node_nodes"
-            name="node-url"
-            class="select select-bordered w-full"
-            x-model="selectedNode"
-            @change="imageUrl = selectedNode ? selectedNode + '?image=svg' : ''"
-            required
-          >
-            <option value="" disabled selected>
-              Select Compound to delete
-            </option>
                         {% for n in pathway.nodes %}
-              <option value="{{ n.url }}">
+                            <option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                {{ n.default_node_label.name|safe }}
-              </option>
                         {% endfor %}
                     </select>
-        </div>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>
                 </form>
+                <p></p>
+                <div id="delete_pathway_node_image"></div>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="delete-pathway-node-modal-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+        $("#delete_pathway_node_nodes").selectpicker();
 
-      <!-- Image Preview -->
+        $("#delete_pathway_node_nodes").on('change', function (e) {
-      <div class="mt-4" x-show="imageUrl" x-cloak>
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
-        <img :src="imageUrl" class="w-full" alt="Node preview" />
-      </div>
-    </div>
 
-    <!-- Footer -->
+            if (node_url !== "") {
-    <div class="modal-action">
+                $('#delete_pathway_node_image').empty();
-      <button
+                $('#delete_pathway_node_image').append(
-        type="button"
+                    "<img width='100%' src='" + node_url + "?image=svg'>"
-        class="btn"
+                );
-        onclick="this.closest('dialog').close()"
+            }
-        :disabled="isSubmitting"
+        })
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-error"
-        @click="setFormAction('delete-pathway-node-modal-form', selectedNode); submit('delete-pathway-node-modal-form')"
-        :disabled="isSubmitting || !selectedNode"
-      >
-        <span x-show="!isSubmitting">Delete</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Deleting...</span>
-      </button>
-    </div>
-  </div>
 
-  <!-- Backdrop -->
+        $('#delete-pathway-node-modal-submit').click(function (e) {
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
-  </form>
+
-</dialog>
+            if (node_url === "") {
+                return;
+            }
+
+            $('#delete-pathway-node-modal-form').attr('action', node_url)
+            $('#delete-pathway-node-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/download_pathway_csv_modal.html

@@ -1,69 +1,36 @@
 {% load static %}
-
+<!-- Download Pathway -->
-<dialog
+<div id="download_pathway_csv_modal" class="modal" tabindex="-1">
-  id="download_pathway_csv_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h3 class="modal-title">Download Pathway as CSV</h3>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Download Pathway as CSV</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
-    <div class="py-4">
+                <form id="download-pathway-csv-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
-      <p>
+                      data-remote="true" method="GET">
-        By clicking on Download the Pathway will be converted into a CSV and
-        directly downloaded.
-      </p>
-
-      <form
-        id="download-pathway-csv-modal-form"
-        accept-charset="UTF-8"
-        action="{{ pathway.url }}"
-        method="GET"
-      >
                     <input type="hidden" name="download" value="true"/>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="download-pathway-csv-modal-submit">Download</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('download-pathway-csv-modal-form'); $el.closest('dialog').close();"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Download</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+    $(function () {
 
-  <!-- Backdrop -->
+        $('#download-pathway-csv-modal-submit').click(function (e) {
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            $('#download-pathway-csv-modal-form').submit();
-  </form>
+            $('#download_pathway_csv_modal').modal('hide');
-</dialog>
+        });
+
+    })
+</script>

templates/modals/objects/download_pathway_image_modal.html

@@ -1,57 +1,32 @@
 {% load static %}
-
+<!-- Download Pathway -->
-<dialog
+<div id="download_pathway_image_modal" class="modal" tabindex="-1">
-  id="download_pathway_image_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h3 class="modal-title">Download Pathway as Image</h3>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Download Pathway as Image</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <p>By clicking on Download the Pathway will be saved as SVG.</p>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="isSubmitting = true; downloadSVG(document.getElementById('pwsvg'), '{{ pathway.name.split|join:'_' }}.svg'); $el.closest('dialog').close();"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Download</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
                 </button>
             </div>
+            <div class="modal-body">
+                By clicking on Download the Pathway will be saved as SVG.
             </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="download-pathway-image-modal-submit">Download</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
 
-  <!-- Backdrop -->
+        $('#download-pathway-image-modal-submit').click(function (e) {
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            downloadSVG($('#pwsvg')[0], '{{ pathway.name.split|join:"_" }}.svg')
-  </form>
+            $('#download_pathway_image_modal').modal('hide');
-</dialog>
+        });
+
+    })
+</script>

templates/modals/objects/edit_compound_modal.html

@@ -1,91 +1,47 @@
+
 {% load static %}
-
+<!-- Edit Compound -->
-<dialog
+<div id="edit_compound_modal" class="modal" tabindex="-1">
-  id="edit_compound_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Edit Compound</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Edit Compound</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>Edit Compound.</p>
-    <div class="py-4">
+                <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-compound-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="compound-name">Name</label>
-          <label class="label" for="compound-name">
+                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="compound-description">Description</label>
-            id="compound-name"
+                        <input id="compound-description" type="text" class="form-control"
-            class="input input-bordered w-full"
-            name="compound-name"
-            value="{{ compound.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            type="text"
-            class="input input-bordered w-full"
                                value="{{ compound.description|safe }}"
-            name="compound-description"
+                               name="compound-description">
-          />
+                    </p>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-compound-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-compound-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-compound-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+});
+
+
+</script>

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,91 +1,46 @@
+
 {% load static %}
-
+<!-- Edit Compound -->
-<dialog
+<div id="edit_compound_structure_modal" class="modal" tabindex="-1">
-  id="edit_compound_structure_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Create a Compound</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Edit Compound Structure</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>Edit a Compound Structure.</p>
-    <div class="py-4">
+                <form id="edit-compound-structure-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-compound-structure-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="compound-structure-name">Name</label>
-          <label class="label" for="compound-structure-name">
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="compound-structure-description">Description</label>
-            id="compound-structure-name"
+                        <input id="compound-structure-description" type="text" class="form-control"
-            class="input input-bordered w-full"
+                               value="{{ compound_structure.description|safe }}" name="compound-structure-description">
-            name="compound-structure-name"
+                    </p>
-            value="{{ compound_structure.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-structure-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-structure-description"
-            type="text"
-            class="input input-bordered w-full"
-            value="{{ compound_structure.description|safe }}"
-            name="compound-structure-description"
-          />
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-compound-structure-modal-submit">Create</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-compound-structure-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-compound-structure-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-compound-structure-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+});
+
+
+</script>

templates/modals/objects/edit_group_member_modal.html

@@ -1,150 +1,121 @@
+
 {% load static %}
-<!-- Edit Group Member -->
+<!-- Edit Package Permission -->
-<dialog
+<div id="edit_group_member_modal" class="modal" tabindex="-1">
-  id="edit_group_member_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="{
+            <div class="modal-header">
-    isSubmitting: false,
+                <h5 class="modal-title">Add or Remove Group Member</h5>
-
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-    reset() {
+                    <span aria-hidden="true">&times;</span>
-      this.isSubmitting = false;
-    },
-
-    submitForm(form) {
-      if (form && form.checkValidity()) {
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Add or Remove Group Member</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>
-    <div class="py-4">
+                    To add member (either User or entire Groups) to this group select the entity you want to add below
-      <p class="mb-4">
+                    and click the check mark.
-        To add member (either User or entire Groups) to this group select the
+                    <br>
-        entity you want to add below and click the check mark.
+                    To remove member simply click the <code>X</code> next to the member.
-        <br />
-        To remove member simply click the X button next to the member.
                 </p>
 
-      <!-- Add Member Form -->
+                <div class="row">
-      <form
+					<div class="col-xs-8">
-        id="modal-form-group-member"
+						<legend>User or Group</legend>
-        accept-charset="UTF-8"
+					</div>
-        action=""
+					<div class="col-xs-4">
-        method="post"
+						<legend>Add/Remove</legend>
-        class="mb-4"
+					</div>
-      >
+				</div>
+
+                <div class="row">
+                    <form id="modal-form-group-member" class="form-inline" role="form" accept-charset="UTF-8" action=""
+                          data-remote="true" method="post">
                         {% csrf_token %}
-        <div class="flex gap-2 items-end">
+                        <div class="col-xs-8">
-          <div class="form-control flex-1">
+                            <select id="select_member" name="member" data-actions-box='true'
-            <label class="label">
+                                    class="selPackages" data-width='100%'>
-              <span class="label-text">User or Group</span>
+                                <option disabled selected>User</option>
-            </label>
-            <select
-              id="select_member"
-              name="member"
-              class="select select-bordered w-full"
-              required
-            >
-              <optgroup label="Users">
                                 {% for u in users %}
                                 <option value="{{ u.url }}">{{ u.username }}</option>
                                 {% endfor %}
-              </optgroup>
+                                <option disabled>Groups</option>
-              <optgroup label="Groups">
                                 {% for g in groups %}
                                 <option value="{{ g.url }}">{{ g.name|safe }}</option>
                                 {% endfor %}
-              </optgroup>
                             </select>
-            <input type="hidden" name="action" value="add" />
+                            <input type="hidden" name="action" value="add">
                         </div>
-          <button type="submit" class="btn btn-primary">Add</button>
+                        <div class="col-xs-2">
+                        </div>
+                        <div class="col-xs-2">
+                            <button type="submit" style="width:60%;" class="btn col-xs-2">
+                                <span class="glyphicon glyphicon-ok"></span>
+                            </button>
                         </div>
                     </form>
-
+                </div>
-      <!-- User Members -->
+                <p></p>
-      {% if group.user_member.all %}
-        <div class="divider">User Members</div>
-        <div class="space-y-2">
                 {% for u in group.user_member.all %}
-            <form
+                <div class="row">
-              id="modal-form-group-member_{{ u.uuid }}"
+                    <form id="modal-form-group-member_{{ u.uuid }}" class="form-inline" role="form"
-              accept-charset="UTF-8"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              action=""
-              method="post"
-            >
                         {% csrf_token %}
-              <div class="flex items-center gap-2">
+                        <div class="col-xs-8">
-                <span class="flex-1">{{ u.username }}</span>
+                            {{ u.username }}
                             <input type="hidden" name="member" value="{{ u.url }}"/>
-                <input type="hidden" name="action" value="remove" />
+                            <input type="hidden" name="action" value="remove">
-                <button type="submit" class="btn btn-error btn-sm">
+                        </div>
-                  Remove
+                        <div class="col-xs-2">
+                        </div>
+                        <div class="col-xs-2">
+                            <button type="submit" style="width:60%;" class="btn col-xs-2">
+                                <span class="glyphicon glyphicon-trash"></span>
                             </button>
                         </div>
                     </form>
-          {% endfor %}
                 </div>
-      {% endif %}
+                {% endfor %}
-
+                <p></p>
-      <!-- Group Members -->
-      {% if group.group_member.all %}
-        <div class="divider">Group Members</div>
-        <div class="space-y-2">
                 {% for g in group.group_member.all %}
-            <form
+                <div class="row">
-              id="modal-form-group-member_{{ g.uuid }}"
+                    <form id="modal-form-group-member_{{ g.uuid }}" class="form-inline" role="form"
-              accept-charset="UTF-8"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              action=""
-              method="post"
-            >
                         {% csrf_token %}
-              <div class="flex items-center gap-2">
+                        <div class="col-xs-8">
-                <span class="flex-1">{{ g.name|safe }}</span>
+                            {{ g.name|safe }}
                             <input type="hidden" name="member" value="{{ g.url }}"/>
-                <input type="hidden" name="action" value="remove" />
+                            <input type="hidden" name="action" value="remove">
-                <button type="submit" class="btn btn-error btn-sm">
+                        </div>
-                  Remove
+                        <div class="col-xs-2">
+                        </div>
+                        <div class="col-xs-2">
+                            <button type="submit" style="width:60%;" class="btn col-xs-2">
+                                <span class="glyphicon glyphicon-trash"></span>
                             </button>
                         </div>
                     </form>
+                </div>
                 {% endfor %}
-        </div>
-      {% endif %}
-    </div>
 
-    <!-- Footer -->
+            </div>
-    <div class="modal-action">
+            <div class="modal-footer">
-      <button
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-        type="button"
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-        class="btn"
-        onclick="this.closest('dialog').close()"
-      >
-        Close
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
 
-  <!-- Backdrop -->
+
-  <form method="dialog" class="modal-backdrop">
+$(function() {
-    <button>close</button>
+
-  </form>
+    $('#edit-package-modal-submit').click(function(e){
-</dialog>
+        e.preventDefault();
+        $('#edit-package-modal-form').submit();
+    });
+
+    $("#select_member").selectpicker();
+
+})
+</script>

templates/modals/objects/edit_model_modal.html

@@ -1,94 +1,45 @@
+
 {% load static %}
-
+<!-- Edit Model -->
-<dialog
+<div id="edit_model_modal" class="modal" tabindex="-1">
-  id="edit_model_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
->
+                    <span aria-hidden="true">&times;</span>
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Update Model</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h3 class="modal-title">Update Model</h3>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <p>Alter Name and Description of the Model.</p>
-      <p class="mb-4">Alter Name and Description of the Model.</p>
+                <form id="edit-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-
-      <form
-        id="edit-model-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="model-name">Name</label>
-          <label class="label" for="model-name">
+                        <input id="model-name" type="text" class="form-control" name="model-name"
-            <span class="label-text">Name</span>
+                               value="{{ model.name|safe }}">
-          </label>
+                    </p>
-          <input
+                    <p>
-            id="model-name"
+                        <label for="model-description">Description</label>
-            type="text"
+                        <input id="model-description" type="text" class="form-control" name="model-description"
-            class="input input-bordered w-full"
+                               value="{{ model.description|safe }}">
-            name="model-name"
+                    </p>
-            value="{{ model.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="model-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="model-description"
-            type="text"
-            class="input input-bordered w-full"
-            name="model-description"
-            value="{{ model.description|safe }}"
-          />
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-model-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-model-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+    $(function () {
 
-  <!-- Backdrop -->
+        $('#edit-model-modal-submit').click(function (e) {
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            $('#edit-model-modal-form').submit();
-  </form>
+        });
-</dialog>
+
+    })
+</script>

templates/modals/objects/edit_node_modal.html

@@ -1,91 +1,47 @@
+
 {% load static %}
-
+<!-- Edit Node -->
-<dialog
+<div id="edit_node_modal" class="modal" tabindex="-1">
-  id="edit_node_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Edit Node</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Edit Node</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>Edit Node.</p>
-    <div class="py-4">
+                <form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-node-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="node-name">Name</label>
-          <label class="label" for="node-name">
+                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="node-description">Description</label>
-            id="node-name"
+                        <input id="node-description" type="text" class="form-control"
-            class="input input-bordered w-full"
-            name="node-name"
-            value="{{ node.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="node-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="node-description"
-            type="text"
-            class="input input-bordered w-full"
                                value="{{ node.description|safe }}"
-            name="node-description"
+                               name="node-description">
-          />
+                    </p>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-node-modal-submit">Create</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-node-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-node-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-node-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+});
+
+
+</script>

templates/modals/objects/edit_package_modal.html

@@ -1,91 +1,45 @@
+
 {% load static %}
-
+<!-- Edit Package -->
-<dialog
+<div id="edit_package_modal" class="modal" tabindex="-1">
-  id="edit_package_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Update Package</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Update Package</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>Edit a Package.</p>
-    <div class="py-4">
+                <form id="edit-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-package-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="package-name">Name</label>
-          <label class="label" for="package-name">
+                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="package-description">Description</label>
-            id="package-name"
+                        <input id="package-description" type="text" class="form-control"
-            class="input input-bordered w-full"
-            name="package-name"
-            value="{{ package.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="package-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="package-description"
-            type="text"
-            class="input input-bordered w-full"
                                value="{{ package.description|safe }}"
-            name="package-description"
+                               name="package-description">
-          />
+                    </p>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-package-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-package-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-package-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+})
+</script>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,271 +1,183 @@
+
 {% load static %}
-<!-- Edit Package Permissions -->
+<!-- Edit Package Permission -->
-<dialog
+<div id="edit_package_permissions_modal" class="modal" tabindex="-1">
-  id="edit_package_permissions_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="{
+            <div class="modal-header">
-    updatePermissions(checkbox) {
+                <h5 class="modal-title">Grant or Revoke Permissions</h5>
-      const parts = checkbox.id.split('_');
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-      const perm = parts[0];
+                    <span aria-hidden="true">&times;</span>
-      const id = parts[1];
-
-      const readBox = document.getElementById('read_' + id);
-      const writeBox = document.getElementById('write_' + id);
-      const ownerBox = document.getElementById('owner_' + id);
-
-      if (perm === 'read' && !readBox.checked) {
-        writeBox.checked = false;
-        ownerBox.checked = false;
-      }
-
-      if (perm === 'write') {
-        if (writeBox.checked) {
-          readBox.checked = true;
-        } else {
-          ownerBox.checked = false;
-        }
-      }
-
-      if (perm === 'owner' && ownerBox.checked) {
-        readBox.checked = true;
-        writeBox.checked = true;
-      }
-    }
-  }"
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Grant or Revoke Permissions</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2">
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>
-    <div class="py-4">
+                    Modify permissions for this package. Note that if you give <code>write</code>
-      <p class="mb-4">
+                    permissions to a user or group, <code>read</code> permissions will be granted automatically.
-        Modify permissions for this package. Note that if you give
+                    <br>
-        <code class="badge badge-ghost">write</code> permissions to a user or
+                    To allow users to perform destructive actions, such as deleting the package, <code>owner</code>
-        group, <code class="badge badge-ghost">read</code> permissions will be
+                    permissions must be granted.
-        granted automatically.
-        <br />
-        To allow users to perform destructive actions, such as deleting the
-        package, <code class="badge badge-ghost">owner</code> permissions must
-        be granted.
                 </p>
 
-      <!-- Add New Permission -->
+                <div class="row">
-      <form
+					<div class="col-xs-4">
-        id="modal-form-permissions"
+						<legend>User or Group</legend>
-        accept-charset="UTF-8"
+					</div>
-        action=""
+					<div class="col-xs-2">
-        method="post"
+						<legend>Read</legend>
-        class="mb-4"
+					</div>
-      >
+					<div class="col-xs-2">
+						<legend>Write</legend>
+					</div>
+					<div class="col-xs-2">
+						<legend>Owner</legend>
+					</div>
+				</div>
+
+                <div class="row">
+                    <form id="modal-form-permissions" class="form-inline" role="form" accept-charset="UTF-8" action=""
+                          data-remote="true" method="post">
                         {% csrf_token %}
-        <div class="grid grid-cols-12 gap-2 items-end">
+                        <div class="col-xs-4">
-          <div class="col-span-5">
+                            <select id="select_grantee" name="grantee" data-actions-box='true'
-            <label class="label">
+                                    class="selPackages" data-width='100%'>
-              <span class="label-text">User or Group</span>
+                                <option disabled selected>User</option>
-            </label>
-            <select
-              id="select_grantee"
-              name="grantee"
-              class="select select-bordered w-full select-sm"
-              required
-            >
-              <optgroup label="Users">
                                 {% for u in users %}
                                 <option value="{{ u.url }}">{{ u.username }}</option>
                                 {% endfor %}
-              </optgroup>
+                                <option disabled>Groups</option>
-              <optgroup label="Groups">
                                 {% for g in groups %}
                                 <option value="{{ g.url }}">{{ g.name|safe }}</option>
                                 {% endfor %}
-              </optgroup>
                             </select>
                         </div>
-          <div class="col-span-2 text-center">
+                        <div class="col-xs-2">
-            <label class="label justify-center">
+                            <input type="checkbox" name="read" id="read_new"/>
-              <span class="label-text">Read</span>
-            </label>
-            <input
-              type="checkbox"
-              name="read"
-              id="read_new"
-              class="checkbox"
-              @click="updatePermissions($el)"
-            />
                         </div>
-          <div class="col-span-2 text-center">
+                        <div class="col-xs-2">
-            <label class="label justify-center">
+                            <input type="checkbox" name="write" id="write_new"/>
-              <span class="label-text">Write</span>
-            </label>
-            <input
-              type="checkbox"
-              name="write"
-              id="write_new"
-              class="checkbox"
-              @click="updatePermissions($el)"
-            />
                         </div>
-          <div class="col-span-2 text-center">
+                        <div class="col-xs-2">
-            <label class="label justify-center">
+                            <input type="checkbox" name="owner" id="owner_new"/>
-              <span class="label-text">Owner</span>
-            </label>
-            <input
-              type="checkbox"
-              name="owner"
-              id="owner_new"
-              class="checkbox"
-              @click="updatePermissions($el)"
-            />
                         </div>
-          <div class="col-span-1">
+                        <div class="col-xs-2">
-            <button type="submit" class="btn btn-primary btn-sm">+</button>
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-          </div>
+                                <span class="glyphicon glyphicon-plus"></span>
-        </div>
-      </form>
-
-      <!-- User Permissions -->
-      {% if user_permissions %}
-        <div class="divider">User Permissions</div>
-        <div class="space-y-2">
-          {% for up in user_permissions %}
-            <form
-              id="modal-form-permissions_{{ up.user.uuid }}"
-              accept-charset="UTF-8"
-              action=""
-              method="post"
-            >
-              {% csrf_token %}
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ up.user.username }}
-                  <input
-                    type="hidden"
-                    name="grantee"
-                    value="{{ up.user.url }}"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_read %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_write %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_all %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-1">
-                  <button type="submit" class="btn btn-sm btn-ghost">✓</button>
-                </div>
-              </div>
-            </form>
-          {% endfor %}
-        </div>
-      {% endif %}
-
-      <!-- Group Permissions -->
-      {% if group_permissions %}
-        <div class="divider">Group Permissions</div>
-        <div class="space-y-2">
-          {% for gp in group_permissions %}
-            <form
-              id="modal-form-permissions_{{ gp.group.uuid }}"
-              accept-charset="UTF-8"
-              action=""
-              method="post"
-            >
-              {% csrf_token %}
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ gp.group.name|safe }}
-                  <input
-                    type="hidden"
-                    name="grantee"
-                    value="{{ gp.group.url }}"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_read %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_write %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_all %}checked{% endif %}
-                    @click="updatePermissions($el)"
-                  />
-                </div>
-                <div class="col-span-1">
-                  <button type="submit" class="btn btn-sm btn-ghost">✓</button>
-                </div>
-              </div>
-            </form>
-          {% endfor %}
-        </div>
-      {% endif %}
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-      >
-        Close
                             </button>
                         </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button>close</button>
                     </form>
-</dialog>
+                </div>
+                <p></p>
+                {% for up in user_permissions %}
+                <div class="row">
+                    <form id="modal-form-permissions_{{ up.user.uuid }}" class="form-inline" role="form"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
+                        {% csrf_token %}
+                        <div class="col-xs-4">
+                            {{ up.user.username }}
+                            <input type="hidden" name="grantee" value="{{ up.user.url }}"/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="read" id="read_{{ up.user.uuid }}" {% if up.has_read %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="write" id="write_{{ up.user.uuid }}" {% if up.has_write %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="owner" id="owner_{{ up.user.uuid }}" {% if up.has_all %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
+                                <span class="glyphicon glyphicon-ok"></span>
+                            </button>
+                        </div>
+                    </form>
+                </div>
+                {% endfor %}
+                <p></p>
+                {% for gp in group_permissions %}
+                <div class="row">
+                    <form id="modal-form-permissions_{{ gp.user.uuid }}" class="form-inline" role="form"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
+                        {% csrf_token %}
+                        <div class="col-xs-4">
+                            {{ gp.group.name|safe }}
+                            <input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="read" id="read_{{ gp.group.uuid }}" {% if gp.has_read %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="write" id="write_{{ gp.group.uuid }}" {% if gp.has_write %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <input type="checkbox" name="owner" id="owner_{{ gp.group.uuid }}" {% if gp.has_all %} checked {% endif %}/>
+                        </div>
+                        <div class="col-xs-2">
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
+                                <span class="glyphicon glyphicon-ok"></span>
+                            </button>
+                        </div>
+                    </form>
+                </div>
+                {% endfor %}
+
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+
+function checkboxClick() {
+    // id looks like read_3cadef24-220e-4587-9fa5-0e9a17aca2da
+    parts = this.id.split('_');
+    perm = parts[0];
+    id = parts[1];
+
+    readbox = '#read_' + id;
+    writebox = '#write_' + id;
+    ownerbox = '#owner_' + id;
+
+
+    if (perm == 'read' && !$(readbox).prop("checked")) {
+        $(writebox).prop("checked", false);
+        $(ownerbox).prop("checked", false);
+    }
+
+    if (perm == 'write') {
+        if ($(writebox).prop("checked")) {
+            $(readbox).prop("checked", true);
+        }
+        if (!$(writebox).prop("checked")) {
+            $(ownerbox).prop("checked", false);
+        }
+    }
+
+    if (perm == 'owner') {
+        if ($(ownerbox).prop("checked")) {
+            $(readbox).prop("checked", true);
+            $(writebox).prop("checked", true);
+        }
+    }
+}
+
+$(function() {
+
+    $('#edit-package-modal-submit').click(function(e){
+        e.preventDefault();
+        $('#edit-package-modal-form').submit();
+    });
+
+    $("#select_grantee").selectpicker();
+
+    // Add click functions to permission checkboxes
+    $('[id^="read_"]').on('click', checkboxClick);
+    $('[id^="write_"]').on('click', checkboxClick);
+    $('[id^="owner_"]').on('click', checkboxClick);
+
+})
+</script>

templates/modals/objects/edit_password_modal.html

@@ -1,119 +1,46 @@
 {% load static %}
-
+<!-- Edit Package -->
-<dialog
+<div id="edit_password_modal" class="modal" tabindex="-1">
-  id="edit_password_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Update your Password</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Update your Password</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>To change your password please fill out the following inputs</p>
-    <div class="py-4">
+                <form id="edit-password-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <p class="mb-4">
-        To change your password please fill out the following inputs
-      </p>
-
-      <form
-        id="edit-password-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-        <input type="hidden" name="hidden" value="update-password" />
+                    <p>
-
+                        <label for="old-password">Old Password</label>
-        <div class="form-control mb-3">
+                        <input id="old-password" class="form-control" name="old-password" type="password" autocomplete="current-password">
-          <label class="label" for="old-password">
+                    </p>
-            <span class="label-text">Old Password</span>
+                    <p>
-          </label>
+                        <label for="new-password">New Password</label>
-          <input
+                        <input id="new-password" class="form-control" name="new-password" type="password", autocomplete="new-password">
-            id="old-password"
+                    </p>
-            class="input input-bordered w-full"
+                    <p>
-            name="old-password"
+                        <label for="new-password-repeat">Repeat New Password</label>
-            type="password"
+                        <input id="new-password-repeat" class="form-control" name="new-password-repeat" type="password" autocomplete="new-password">
-            autocomplete="current-password"
+                    </p>
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="new-password">
-            <span class="label-text">New Password</span>
-          </label>
-          <input
-            id="new-password"
-            class="input input-bordered w-full"
-            name="new-password"
-            type="password"
-            autocomplete="new-password"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="new-password-repeat">
-            <span class="label-text">Repeat New Password</span>
-          </label>
-          <input
-            id="new-password-repeat"
-            class="input input-bordered w-full"
-            name="new-password-repeat"
-            type="password"
-            autocomplete="new-password"
-            required
-            @input="validatePasswordMatch('new-password', 'new-password-repeat')"
-          />
-          <label class="label" x-show="errors['new-password-repeat']">
-            <span
-              class="label-text-alt text-error"
-              x-text="errors['new-password-repeat']"
-            ></span>
-          </label>
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-password-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="if (validatePasswordMatch('new-password', 'new-password-repeat')) submit('edit-password-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-password-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-password-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+})
+</script>

templates/modals/objects/edit_pathway_modal.html

@@ -1,92 +1,44 @@
+
 {% load static %}
-
+<!-- Edit Pathway -->
-<dialog
+<div id="edit_pathway_modal" class="modal" tabindex="-1">
-  id="edit_pathway_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Edit Pathway</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Edit Pathway</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>Edit Pathway.</p>
-    <div class="py-4">
+                <form id="edit-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-pathway-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="pathway-name">Name</label>
-          <label class="label" for="pathway-name">
+                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name|safe }}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="pathway-description">Description</label>
-            id="pathway-name"
+                        <textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
-            class="input input-bordered w-full"
+                                  rows="10">{{ pathway.description|safe }}</textarea>
-            name="pathway-name"
+                    </p>
-            value="{{ pathway.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pathway-description">
-            <span class="label-text">Description</span>
-          </label>
-          <textarea
-            id="pathway-description"
-            class="textarea textarea-bordered w-full"
-            name="pathway-description"
-            rows="10"
-          >
-{{ pathway.description|safe }}</textarea
-          >
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-pathway-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-pathway-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-pathway-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-pathway-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+})
+</script>

templates/modals/objects/edit_prediction_setting_modal.html

@@ -1,156 +1,106 @@
 {% load static %}
-<!-- Edit Prediction Setting -->
+<!-- Edit Package -->
-<dialog
+<div id="update_prediction_settings_modal" class="modal" tabindex="-1">
-  id="update_prediction_settings_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <h5 class="modal-title">Update Prediction Setting</h5>
->
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-  <div class="modal-box max-w-3xl">
+                    <span aria-hidden="true">&times;</span>
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Update Prediction Setting</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+            </div>
-
+            <div class="modal-body">
-    <!-- Body -->
+                <p>To update your prediction setting modify parameters in the form below und click "Update"</p>
-    <div class="py-4">
+                <form id="edit-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <p class="mb-4">
-        To update your prediction setting modify parameters in the form below
-        and click "Update"
-      </p>
-      <form
-        id="edit-prediction-setting-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-        <div class="overflow-x-auto">
+                    <div id="prediction-setting" class="panel-collapse collapse in">
-          <table class="table table-zebra w-full">
+                        <div class="panel-body list-group-item">
-            <thead>
+
-              <tr>
+                            <table class="table table-bordered table-hover">
-                <th class="w-1/5">Parameter</th>
+                                <tr style="background-color: rgba(0, 0, 0, 0.08);">
-                <th class="w-4/5">Value</th>
+                                    <th scope="col" width="20%">Parameter</th>
+                                    <th scope="col" width="80%">Value</th>
                                 </tr>
-            </thead>
                                 <tbody>
                                 {% if 'model' in user.prediction_settings %}
                                 <tr>
-                  <td>Model</td>
+                                    <td width="20%">Model</td>
-                  <td>
+                                    <td width="80%">
-                    <div class="form-control">
+                                        <table width="100%" class="table table-bordered table-hover">
-                      <select
+                                            <tbody>
-                        id="model"
+                                            <tr>
-                        name="model"
+                                                <td colspan="2">
-                        class="select select-bordered w-full"
+                                                    <select id="model" name="model" class="form-control" data-width='100%'>
-                      >
                                                     {% for m in models %}
-                          <option
+                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name|safe }}</option>
-                            value="{{ m.id }}"
-                            {% if user.prediction_settings.model.url == m.url %}selected{% endif %}
-                          >
-                            {{ m.name|safe }}
-                          </option>
                                                     {% endfor %}
                                                     </select>
-                    </div>
-                    {% for k, v in user.prediction_settings.model_parameters.items %}
-                      {% if k == 'threshold' %}
-                        <div class="form-control mt-2">
-                          <label class="label">
-                            <span class="label-text">Threshold</span>
-                          </label>
-                          <input
-                            type="number"
-                            class="input input-bordered w-full"
-                            name="{{ k }}"
-                            value="{{ v }}"
-                            min="0"
-                            max="1"
-                            step="0.05"
-                          />
-                        </div>
-                      {% endif %}
-                    {% endfor %}
                                                 </td>
                                             </tr>
-              {% endif %}
+                                            {% for k, v in user.prediction_settings.model_parameters.items %}
-              {% for k, v in user.prediction_settings.truncator.items %}
                                             <tr>
-                  <td>
+                                                <th width="20%">Model Parameter</th>
-                    {% if k == 'max_nodes' %}
+                                                <th width="80%">Parameter Value</th>
-                      Max Nodes
+                                            </tr>
-                    {% elif k == 'max_depth' %}
+                                            <tr>
-                      Max Depth
+                                                <td width="20%">
+                                                    {% if k == 'threshold' %}
+                                                    Threshold
                                                     {% endif %}
                                                 </td>
-                  <td>
+                                                <td width="80%">
-                    {% if k == 'max_nodes' %}
+                                                    {% if k == 'threshold' %}
-                      <input
+                                                    <input type="number" class="form-control" name="{{k}}" value="{{v}}"
-                        type="number"
+                                                           min="0" max="1" step="0.05">
-                        class="input input-bordered w-full"
-                        name="{{ k }}"
-                        value="{{ v }}"
-                        min="1"
-                        max="50"
-                        step="1"
-                      />
-                    {% elif k == 'max_depth' %}
-                      <input
-                        type="number"
-                        class="input input-bordered w-full"
-                        name="{{ k }}"
-                        value="{{ v }}"
-                        min="1"
-                        max="8"
-                        step="1"
-                      />
                                                     {% endif %}
                                                 </td>
                                             </tr>
                                             {% endfor %}
                                             </tbody>
                                         </table>
+                                    </td>
+                                </tr>
+                                {% endif %}
+                                {% for k, v in user.prediction_settings.truncator.items %}
+                                <tr>
+                                    <td><p>
+                                        {% if k == 'max_nodes' %}
+                                        Max Nodes
+                                        {% elif k == 'max_depth' %}
+                                        Max Depth
+                                        {% endif %}
+                                    </p></td>
+                                    <td><p>
+                                        {% if k == 'max_nodes' %}
+                                        <input type="number" class="form-control" name="{{k}}" value="{{v}}" min="1"
+                                               max="50" step="1">
+                                        {% elif k == 'max_depth' %}
+                                        <input type="number" class="form-control" name="{{k}}" value="{{v}}" min="1"
+                                               max="8" step="1">
+                                        {% endif %}
+                                    </p></td>
+                                </tr>
+                                {% endfor %}
+                                </tbody>
+                            </table>
+                        </div>
                     </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-prediction-setting-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-prediction-setting-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+    $(function() {
 
-  <!-- Backdrop -->
+        $('#edit-prediction-setting-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+            e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+            $('#edit-prediction-setting-modal-form').submit();
-  </form>
+        });
-</dialog>
+
+    })
+</script>

templates/modals/objects/edit_reaction_modal.html

@@ -1,91 +1,45 @@
+
 {% load static %}
-
+<!-- Edit Reaction -->
-<dialog
+<div id="edit_reaction_modal" class="modal" tabindex="-1">
-  id="edit_reaction_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
->
+                    <span aria-hidden="true">&times;</span>
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Update Reaction</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h3 class="modal-title">Update Reaction</h3>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="edit-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-reaction-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="reaction-name">Name</label>
-          <label class="label" for="reaction-name">
+                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name|safe }}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="reaction-description">Description</label>
-            id="reaction-name"
+                        <input id="reaction-description" type="text" class="form-control"
-            class="input input-bordered w-full"
+                               value="{{ reaction.description|safe }}" name="reaction-description">
-            name="reaction-name"
+                    </p>
-            value="{{ reaction.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="reaction-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="reaction-description"
-            type="text"
-            class="input input-bordered w-full"
-            value="{{ reaction.description|safe }}"
-            name="reaction-description"
-          />
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-reaction-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-reaction-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-reaction-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-reaction-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+});
+
+
+</script>

templates/modals/objects/edit_rule_modal.html

@@ -1,91 +1,45 @@
+
 {% load static %}
-
+<!-- Edit Rule -->
-<dialog
+<div id="edit_rule_modal" class="modal" tabindex="-1">
-  id="edit_rule_modal"
+    <div class="modal-dialog">
-  class="modal"
+        <div class="modal-content">
-  x-data="modalForm()"
+            <div class="modal-header">
-  @close="reset()"
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
->
+                    <span aria-hidden="true">&times;</span>
-  <div class="modal-box">
-    <!-- Header -->
-    <h3 class="font-bold text-lg">Update Rule</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
-        :disabled="isSubmitting"
-      >
-        ✕
                 </button>
-    </form>
+                <h3 class="modal-title">Update Rule</h3>
-
+            </div>
-    <!-- Body -->
+            <div class="modal-body">
-    <div class="py-4">
+                <form id="edit-rule-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-      <form
-        id="edit-rule-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
                     {% csrf_token %}
-
+                    <p>
-        <div class="form-control mb-3">
+                        <label for="rule-name">Name</label>
-          <label class="label" for="rule-name">
+                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
-            <span class="label-text">Name</span>
+                    </p>
-          </label>
+                    <p>
-          <input
+                        <label for="rule-description">Description</label>
-            id="rule-name"
+                        <input id="rule-description" type="text" class="form-control"
-            class="input input-bordered w-full"
+                               value="{{ rule.description|safe }}" name="rule-description">
-            name="rule-name"
+                    </p>
-            value="{{ rule.name|safe }}"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="rule-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="rule-description"
-            type="text"
-            class="input input-bordered w-full"
-            value="{{ rule.description|safe }}"
-            name="rule-description"
-          />
-        </div>
                 </form>
             </div>
-
+            <div class="modal-footer">
-    <!-- Footer -->
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-    <div class="modal-action">
+                <button type="button" class="btn btn-primary" id="edit-rule-modal-submit">Update</button>
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('edit-rule-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Update</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Updating...</span>
-      </button>
             </div>
         </div>
+    </div>
+</div>
+<script>
+$(function() {
 
-  <!-- Backdrop -->
+    $('#edit-rule-modal-submit').click(function(e){
-  <form method="dialog" class="modal-backdrop">
+        e.preventDefault();
-    <button :disabled="isSubmitting">close</button>
+        $('#edit-rule-modal-form').submit();
-  </form>
+    });
-</dialog>
+
+});
+
+
+</script>