[Feature] Modern UI roll out (#236)

This PR moves all the collection pages into the new UI in a rough push.
I did not put the same amount of care into these as into search, index, and predict.

## Major changes

- All modals are now migrated to a state based alpine.js implementation.
- jQuery is no longer present in the base layout; ajax is replace by native fetch api
- most of the pps.js is now obsolte (as I understand it; the code is not referenced any more @jebus  please double check)
- in-memory pagination for large result lists (set to 50; we can make that configurable later; performance degrades at around 1k) stukk a bit rough tracked in #235

## Minor things

- Sarch and index also use alpine now
- The loading spinner is now CSS animated (not sure if it currently gets correctly called)

## Not done

- Ihave not even cheked the admin pages. Not sure If these need migrations
- The temporary migration pages still use the old template. Not sure what is supposed to happen with those? @jebus

## What I did to test

- opend all pages in browse, and user ; plus all pages reachable from there.
- Interacted and tested the functionality of each modal superfically with exception of the API key modal (no functional test).

---
This PR is massive sorry for that; just did not want to push half-brokenn state.
@jebus @liambrydon I would be glad if you could click around and try to break it :)

Finally closes #133

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#236
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

.gitea/workflows/ci.yaml

@@ -8,6 +8,7 @@ on:
 
 jobs:
   test:
+    if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
     runs-on: ubuntu-latest
 
     services:
@@ -99,6 +100,18 @@ 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: |
@@ -110,7 +123,12 @@ 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
+          python manage.py test tests --exclude-tag slow --exclude-tag frontend

.gitignore

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

envipath/settings.py

@@ -49,9 +49,23 @@ 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

@@ -23,12 +23,20 @@ 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

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

epdb/apps.py

@@ -1,4 +1,9 @@
+import logging
+
 from django.apps import AppConfig
+from django.conf import settings
+
+logger = logging.getLogger(__name__)
 
 
 class EPDBConfig(AppConfig):
@@ -7,3 +12,6 @@ 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 .models import Package
+from django.conf import settings as s
 
 
 def package_context(request):
@@ -20,7 +20,7 @@ def package_context(request):
 
     reviewed_package_qs = PackageManager.get_reviewed_packages()
 
-    unreviewed_package_qs = Package.objects.none()
+    unreviewed_package_qs = s.GET_PACKAGE_MODEL().objects.none()
 
     # Only get user-specific packages if user is authenticated
     if current_user.is_authenticated:

epdb/legacy_api.py

@@ -1,27 +1,35 @@
-from typing import List, Dict, Optional, Any
+from typing import Any, Dict, List, Optional
 
+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 Router, Schema, Field, Form
+from ninja import Field, Form, Router, Schema, Query
+from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
-from .logic import PackageManager, UserManager, SettingManager
+from utilities.misc import PackageExporter
+
+from .logic import GroupManager, PackageManager, SettingManager, UserManager, SearchManager
 from .models import (
     Compound,
     CompoundStructure,
-    Package,
+    Edge,
+    EPModel,
+    Node,
+    Pathway,
+    Reaction,
+    Rule,
+    Scenario,
+    SimpleAmbitRule,
     User,
     UserPackagePermission,
-    Rule,
-    Reaction,
-    Scenario,
-    Pathway,
-    Node,
-    Edge,
-    SimpleAmbitRule,
+    ParallelRule,
 )
 
+Package = s.GET_PACKAGE_MODEL()
+
 
 def _anonymous_or_real(request):
     if request.user.is_authenticated and not request.user.is_anonymous:
@@ -29,8 +37,7 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-# router = Router(auth=SessionAuth())
-router = Router()
+router = Router(auth=SessionAuth(csrf=False))
 
 
 class Error(Schema):
@@ -118,13 +125,16 @@ class SimpleEdge(SimpleObject):
     identifier: str = "edge"
 
 
+class SimpleModel(SimpleObject):
+    identifier: str = "relative-reasoning"
+
+
 ################
 # Login/Logout #
 ################
-@router.post("/", response={200: SimpleUser, 403: Error})
+@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
 def login(request, loginusername: Form[str], loginpassword: Form[str]):
-    from django.contrib.auth import authenticate
-    from django.contrib.auth import login
+    from django.contrib.auth import authenticate, login
 
     email = User.objects.get(username=loginusername).email
     user = authenticate(username=email, password=loginpassword)
@@ -167,9 +177,13 @@ 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, whoami: str = None):
-    if whoami:
+def get_users(request, me: Query[Me]):
+    if me.whoami:
         return {"user": [request.user]}
     else:
         return {"user": User.objects.all()}
@@ -186,6 +200,61 @@ 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 #
 ###########
@@ -251,67 +320,110 @@ def get_packages(request):
     }
 
 
-@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema, 403: Error})
-def get_package(request, package_uuid):
+class GetPackage(Schema):
+    exportAsJson: str | None = None
+
+
+@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 403: Error})
+def get_package(request, package_uuid, gp: Query[GetPackage]):
     try:
-        return PackageManager.get_package_by_id(request.user, package_uuid)
+        p = 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, packageName: Form[str], packageDescription: Optional[str] = Form(None)
+    request,
+    p: Form[CreatePackage],
 ):
     try:
-        if packageName.strip() == "":
+        if p.packageName.strip() == "":
             raise ValueError("Package name cannot be empty!")
 
-        new_pacakge = PackageManager.create_package(request.user, packageName, packageDescription)
+        new_pacakge = PackageManager.create_package(
+            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,
-    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),
-):
+def update_package(request, package_uuid, pack: Form[UpdatePackage]):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        if hiddenMethod:
-            if hiddenMethod == "DELETE":
+        if pack.hiddenMethod:
+            if pack.hiddenMethod == "DELETE":
                 p.delete()
 
-        elif packageDescription and packageDescription.strip() != "":
-            p.description = packageDescription
-            p.save()
-            return
-        elif exportAsJson == "true":
-            pack_json = PackageManager.export_package(
-                p, include_models=False, include_external_identifiers=False
-            )
-            return pack_json
-        elif all([permissions, ppsURI, read]):
-            PackageManager.update_permissions
-        elif all([permissions, ppsURI, write]):
-            pass
+        elif pack.packageDescription is not None:
+            description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
 
+            if description:
+                p.description = description
+                p.save()
+                return HttpResponse(status=200)
+            else:
+                raise ValueError("Package description cannot be empty!")
+        elif all([pack.permissions, pack.ppsURI, pack.read]):
+            if "group" in pack.ppsURI:
+                grantee = GroupManager.get_group_lp(pack.ppsURI)
+            else:
+                grantee = UserManager.get_user_lp(pack.ppsURI)
+
+            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 #
 ################################
@@ -509,6 +621,83 @@ 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 #
 #########
@@ -672,6 +861,73 @@ 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}
 )
@@ -721,6 +977,41 @@ 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 #
 ############
@@ -809,6 +1100,82 @@ 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 #
 ############
@@ -823,7 +1190,7 @@ 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")
@@ -874,6 +1241,38 @@ 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 #
 ###########
@@ -1013,46 +1412,67 @@ 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,
-    smilesinput: Form[str],
-    name: Optional[str] = Form(None),
-    description: Optional[str] = Form(None),
-    rootOnly: Optional[str] = Form(None),
-    selectedSetting: Optional[str] = Form(None),
+    pw: Form[CreatePathway],
 ):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        stand_smiles = FormatConverter.standardize(smilesinput.strip())
+        stand_smiles = FormatConverter.standardize(pw.smilesinput.strip())
 
-        pw = Pathway.create(p, stand_smiles, name=name, description=description)
+        new_pw = Pathway.create(p, stand_smiles, name=pw.name, description=pw.description)
 
         pw_mode = "predict"
-        if rootOnly and rootOnly == "true":
+        if pw.rootOnly and pw.rootOnly.strip() == "true":
             pw_mode = "build"
 
-        pw.kv.update({"mode": pw_mode})
-        pw.save()
+        new_pw.kv.update({"mode": pw_mode})
+        new_pw.save()
 
         if pw_mode == "predict":
             setting = request.user.prediction_settings()
 
-            if selectedSetting:
-                setting = SettingManager.get_setting_by_url(request.user, selectedSetting)
+            if pw.selectedSetting:
+                setting = SettingManager.get_setting_by_url(request.user, pw.selectedSetting)
 
-            pw.setting = setting
-            pw.save()
+            new_pw.setting = setting
+            new_pw.save()
 
-            from .tasks import predict
+            from .tasks import dispatch, predict
 
-            predict.delay(pw.pk, setting.pk, limit=-1)
+            dispatch(request.user, predict, new_pw.pk, setting.pk, limit=-1)
 
-        return redirect(pw.url)
+        return redirect(new_pw.url)
     except ValueError as e:
-        print(e)
+        return 400, {"message": str(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!"
+        }
 
 
 ########
@@ -1143,6 +1563,52 @@ 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 #
 ########
@@ -1206,6 +1672,200 @@ 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

@@ -1,39 +1,40 @@
-import re
-import logging
 import json
-from typing import Union, List, Optional, Set, Dict, Any
+import logging
+import re
+from typing import Any, Dict, List, Optional, Set, Union
 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 (
-    User,
-    Package,
-    UserPackagePermission,
-    GroupPackagePermission,
-    Permission,
-    Group,
-    Setting,
-    EPModel,
-    UserSettingPermission,
-    Rule,
-    Pathway,
-    Node,
-    Edge,
     Compound,
-    Reaction,
     CompoundStructure,
+    Edge,
     EnzymeLink,
+    EPModel,
+    Group,
+    GroupPackagePermission,
+    Node,
+    Pathway,
+    Permission,
+    Reaction,
+    Rule,
+    Setting,
+    User,
+    UserPackagePermission,
+    UserSettingPermission,
 )
 from utilities.chem import FormatConverter
-from utilities.misc import PackageImporter, PackageExporter
+from utilities.misc import PackageExporter, PackageImporter
 
 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}"
@@ -578,30 +579,39 @@ 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 uuid import UUID, uuid4
-        from datetime import datetime
         from collections import defaultdict
+        from datetime import datetime
+        from uuid import UUID, uuid4
+
+        from envipy_additional_information import AdditionalInformationConverter
+
         from .models import (
-            Package,
             Compound,
             CompoundStructure,
-            SimpleRule,
-            SimpleAmbitRule,
+            Edge,
+            Node,
             ParallelRule,
+            Pathway,
+            Reaction,
+            Scenario,
             SequentialRule,
             SequentialRuleOrdering,
-            Reaction,
-            Pathway,
-            Node,
-            Edge,
-            Scenario,
+            SimpleAmbitRule,
+            SimpleRule,
         )
-        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

@@ -2,7 +2,9 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import MLRelativeReasoning, EnviFormer, Package
+from epdb.models import EnviFormer, MLRelativeReasoning
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):
@@ -75,11 +77,13 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(f"Creating models: {options['model_names']}\n"
+        print(
+            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"])
@@ -90,7 +94,7 @@ 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']}.",
@@ -101,7 +105,7 @@ 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

@@ -8,7 +8,9 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer, Package
+from epdb.models import EnviFormer
+
+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, Value, TextField, JSONField
-from django.db.models.functions import Replace, Cast
+from django.db.models import F, JSONField, TextField, Value
+from django.db.models.functions import Cast, Replace
 
 from epdb.models import EnviPathModel
 
@@ -23,10 +23,13 @@ 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

@@ -2,40 +2,41 @@ 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 Union, List, Optional, Dict, Tuple, Set, Any
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
 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 GenericRelation, GenericForeignKey
+from django.contrib.contenttypes.fields import GenericForeignKey, GenericRelation
 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 JSONField, Count, Q, QuerySet
+from django.db.models import Count, JSONField, 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 precision_score, recall_score, jaccard_score
+from sklearn.metrics import jaccard_score, precision_score, recall_score
 from sklearn.model_selection import ShuffleSplit
 
-from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
+from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
-    RuleBasedDataset,
     ApplicabilityDomainPCA,
-    EnsembleClassifierChain,
-    RelativeReasoning,
-    EnviFormerDataset,
     Dataset,
+    EnsembleClassifierChain,
+    EnviFormerDataset,
+    RelativeReasoning,
+    RuleBasedDataset,
 )
 
 logger = logging.getLogger(__name__)
@@ -44,8 +45,6 @@ logger = logging.getLogger(__name__)
 ##########################
 # User/Groups/Permission #
 ##########################
-
-
 class User(AbstractUser):
     email = models.EmailField(unique=True)
     uuid = models.UUIDField(
@@ -53,7 +52,10 @@ class User(AbstractUser):
     )
     url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
     default_package = models.ForeignKey(
-        "epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
+        s.EPDB_PACKAGE_MODEL,
+        verbose_name="Default Package",
+        null=True,
+        on_delete=models.SET_NULL,
     )
     default_group = models.ForeignKey(
         "Group",
@@ -243,7 +245,7 @@ class UserPackagePermission(Permission):
     )
     user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -259,7 +261,7 @@ class GroupPackagePermission(Permission):
     )
     group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -728,10 +730,13 @@ 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(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     default_structure = models.ForeignKey(
         "CompoundStructure",
@@ -781,7 +786,7 @@ 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")
@@ -1061,7 +1066,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     # # https://github.com/django-polymorphic/django-polymorphic/issues/229
@@ -1074,6 +1079,10 @@ 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":
@@ -1167,7 +1176,7 @@ class SimpleAmbitRule(SimpleRule):
     @staticmethod
     @transaction.atomic
     def create(
-        package: Package,
+        package: "Package",
         name: str = None,
         description: str = None,
         smirks: str = None,
@@ -1228,6 +1237,9 @@ 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)
 
@@ -1241,7 +1253,7 @@ class SimpleAmbitRule(SimpleRule):
 
     @property
     def related_reactions(self):
-        qs = Package.objects.filter(reviewed=True)
+        qs = s.GET_PACKAGE_MODEL().objects.filter(reviewed=True)
         return self.reaction_rule.filter(package__in=qs).order_by("name")
 
     @property
@@ -1273,6 +1285,9 @@ 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()
@@ -1304,6 +1319,57 @@ 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(
@@ -1313,6 +1379,9 @@ 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()
@@ -1333,7 +1402,7 @@ class SequentialRuleOrdering(models.Model):
 
 class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     educts = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@@ -1355,7 +1424,7 @@ 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,
@@ -1514,7 +1583,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, 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
@@ -2076,7 +2145,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     def _url(self):
@@ -2085,17 +2154,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
 
 class PackageBasedModel(EPModel):
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.EPDB_PACKAGE_MODEL,
         verbose_name="Rule Packages",
         related_name="%(app_label)s_%(class)s_rule_packages",
     )
     data_packages = models.ManyToManyField(
-        "Package",
+        s.EPDB_PACKAGE_MODEL,
         verbose_name="Data Packages",
         related_name="%(app_label)s_%(class)s_data_packages",
     )
     eval_packages = models.ManyToManyField(
-        "Package",
+        s.EPDB_PACKAGE_MODEL,
         verbose_name="Evaluation Packages",
         related_name="%(app_label)s_%(class)s_eval_packages",
     )
@@ -3400,7 +3469,7 @@ class PluginModel(EPModel):
 
 class Scenario(EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.EPDB_PACKAGE_MODEL, 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(
@@ -3555,7 +3624,7 @@ class Setting(EnviPathModel):
     )
 
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.EPDB_PACKAGE_MODEL,
         verbose_name="Setting Rule Packages",
         related_name="setting_rule_packages",
         blank=True,

epdb/tasks.py

@@ -6,14 +6,17 @@ 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, Package, Pathway, Rule, Setting, User
+from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
 
 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:

epdb/urls.py

@@ -142,6 +142,11 @@ 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

@@ -1,58 +1,60 @@
 import json
 import logging
-from typing import List, Dict, Any
+from typing import Any, Dict, List
 
+import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
-from django.shortcuts import render, redirect
+from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
+from django.shortcuts import redirect, render
 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,
-    UserManager,
-    SettingManager,
     SearchManager,
-    EPDBURLParser,
+    SettingManager,
+    UserManager,
 )
 from .models import (
-    Package,
-    GroupPackagePermission,
-    Group,
-    CompoundStructure,
+    APIToken,
     Compound,
+    CompoundStructure,
+    Edge,
+    EnviFormer,
+    EnzymeLink,
+    EPModel,
+    ExternalDatabase,
+    ExternalIdentifier,
+    Group,
+    GroupPackagePermission,
+    JobLog,
+    License,
+    MLRelativeReasoning,
+    Node,
+    Pathway,
+    Permission,
     Reaction,
     Rule,
-    Pathway,
-    Node,
-    EPModel,
-    EnviFormer,
-    MLRelativeReasoning,
     RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
-    APIToken,
-    UserPackagePermission,
-    Permission,
-    License,
     User,
-    Edge,
-    ExternalDatabase,
-    ExternalIdentifier,
-    EnzymeLink,
-    JobLog,
+    UserPackagePermission,
 )
 
 logger = logging.getLogger(__name__)
 
+Package = s.GET_PACKAGE_MODEL()
+
 
 def log_post_params(request):
     if s.DEBUG:
@@ -60,6 +62,26 @@ 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 = {
@@ -74,6 +96,48 @@ 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)
 
@@ -83,8 +147,7 @@ def login(request):
         return render(request, "static/login.html", context)
 
     elif request.method == "POST":
-        from django.contrib.auth import authenticate
-        from django.contrib.auth import login
+        from django.contrib.auth import authenticate, login
 
         username = request.POST.get("username").strip()
         if username != request.POST.get("username"):
@@ -191,8 +254,8 @@ def register(request):
 
 
 def editable(request, user):
-    if user.is_superuser:
-        return True
+    # if user.is_superuser:
+    #     return True
 
     url = request.build_absolute_uri(request.path)
     if PackageManager.is_package_url(url):
@@ -374,6 +437,22 @@ 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)
 
@@ -856,7 +935,7 @@ def package_models(request, package_uuid):
                 request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
             )
 
-        from .tasks import dispatch, build_model
+        from .tasks import build_model, dispatch
 
         dispatch(current_user, build_model, mod.pk)
 
@@ -890,9 +969,10 @@ def package_model(request, package_uuid, model_uuid):
             if classify:
                 from epdb.tasks import dispatch_eager, predict_simple
 
-                res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
+                pred_res = dispatch_eager(
+                    current_user, predict_simple, current_model.pk, stand_smiles
+                )
 
-                pred_res = current_model.predict(stand_smiles)
                 res = []
 
                 for pr in pred_res:
@@ -1052,9 +1132,7 @@ def package(request, package_uuid):
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
-                    PackageManager.update_permissions(
-                        current_user, current_package, g, Permission.READ[0]
-                    )
+                    PackageManager.grant_read(current_user, current_package, g)
                 return redirect(current_package.url)
             elif hidden == "copy":
                 object_to_copy = request.POST.get("object_to_copy")
@@ -2393,9 +2471,9 @@ 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

@@ -1,24 +1,21 @@
-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)
@@ -59,9 +56,7 @@ 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]
             ]
         )
     )
@@ -85,8 +80,7 @@ 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)
 
@@ -142,9 +136,7 @@ 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)
 
@@ -152,8 +144,6 @@ 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)
 
@@ -235,9 +225,7 @@ 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

@@ -45,6 +45,8 @@ 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]
@@ -66,47 +68,31 @@ docstring-code-format = true
 
 [tool.poe.tasks]
 # Main tasks
-setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
-dev = { shell = """
-# Start pnpm CSS watcher in background
-pnpm run dev &
-PNPM_PID=$!
-echo "Started CSS watcher (PID: $PNPM_PID)"
-
-# Cleanup function
-cleanup() {
-    echo "\nShutting down..."
-    if kill -0 $PNPM_PID 2>/dev/null; then
-        kill $PNPM_PID
-        echo "✓ CSS watcher stopped"
-    fi
-    if [ ! -z "${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" }
+setup = { sequence = [
+    "db-up",
+    "migrate",
+    "bootstrap",
+], help = "Complete setup: start database, run migrations, and bootstrap data" }
+dev = { cmd = "uv run python scripts/dev_server.py", 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 = "pnpm install", help = "Install frontend dependencies" }
+js-deps = { cmd = "uv run python scripts/pnpm_wrapper.py install", help = "Install frontend dependencies" }
 
 # Full cleanup tasks
-clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
+clean = { sequence = [
+    "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
@@ -124,6 +110,14 @@ 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 = "pnpm run build", help = "Build frontend assets using pnpm", deps = ["js-deps"] }
-collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = ["build-frontend"] }
+
+build-frontend = { cmd = "uv run python scripts/pnpm_wrapper.py run build", help = "Build frontend assets using pnpm", deps = [
+    "js-deps",
+] } # 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

@@ -0,0 +1,201 @@
+#!/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

@@ -0,0 +1,59 @@
+#!/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

@@ -34,3 +34,30 @@
 }
 
 @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

@@ -0,0 +1,265 @@
+/**
+ * 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

@@ -0,0 +1,133 @@
+/**
+ * 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

@@ -0,0 +1,145 @@
+/**
+ * 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

@@ -63,17 +63,20 @@ class DiscourseAPI {
      * @returns {string} Cleaned excerpt
      */
     extractExcerpt(excerpt) {
-        if (!excerpt) return 'Click to read more';
+        if (!excerpt) return 'No preview available yet';
 
         // Remove HTML tags and clean up; collapse whitespace; do not add manual ellipsis
-        return excerpt
+        const cleaned = 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

@@ -1,14 +1,21 @@
 console.log("loaded pw.js")
 
 function predictFromNode(url) {
-    $.post("", {node: url})
-        .done(function (data) {
+    fetch("", {
+        method: "POST",
+        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;
     })
-        .fail(function (xhr, status, error) {
-            console.error("Error:", xhr.status, xhr.responseText);
-            // show user-friendly message or log error
+    .catch(error => {
+        console.error("Error:", error);
     });
 }
 
@@ -103,6 +110,9 @@ 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;
@@ -117,6 +127,9 @@ 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;
 
@@ -127,6 +140,9 @@ 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
@@ -192,52 +208,153 @@ function draw(pathway, elem) {
         d3.select(t).select("circle").classed("highlighted", !d3.select(t).select("circle").classed("highlighted"));
     }
 
-    // Wait one second before showing popup
+    // Wait before showing popup (ms)
     var popupWaitBeforeShow = 1000;
-    // Keep Popup at least for one second
-    var popushowAtLeast = 1000;
 
-    function pop_show_e(element) {
-        var e = element;
-        setTimeout(function () {
-            if ($(e).is(':hover')) { // if element is still hovered
-                $(e).popover("show");
+    // Custom popover element
+    let popoverTimeout = null;
 
-                // workaround to set fixed positions
-                pop = $(e).attr("aria-describedby")
-                h = $('#' + pop).height();
-                $('#' + pop).attr("style", `position: fixed; top: ${clientY - (h / 2.0)}px; left: ${clientX + 10}px; margin: 0px; max-width: 1000px; display: block;`)
-                setTimeout(function () {
-                    var close = setInterval(function () {
-                        if (!$(".popover:hover").length // mouse outside popover
-                            && !$(e).is(':hover')) { // mouse outside element
-                            $(e).popover('hide');
-                            clearInterval(close);
+    function createPopover() {
+        const popover = document.createElement('div');
+        popover.id = 'custom-popover';
+        popover.className = 'fixed z-50';
+        popover.style.cssText = `
+            background: #ffffff;
+            border: 1px solid #d1d5db;
+            box-shadow: 0 10px 15px -3px rgb(0 0 0 / 0.1), 0 4px 6px -4px rgb(0 0 0 / 0.1);
+            max-width: 320px;
+            padding: 0.75rem;
+            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;
             }
-                    }, 100);
-                }, popushowAtLeast);
+            #custom-popover a {
+                color: #2563eb;
+                text-decoration: none;
             }
-        }, popupWaitBeforeShow);
+            #custom-popover a:hover {
+                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.attr("id", "pop")
-            .attr("data-container", "body")
-            .attr("data-toggle", "popover")
-            .attr("data-placement", "right")
-            .attr("title", title);
+        objects.each(function (d) {
+            const element = this;
 
-        objects.each(function (d, i) {
-            options = {trigger: "manual", html: true, animation: false};
-            this_ = this;
-            var p = $(this).popover(options).on("mouseenter", function () {
-                pop_show_e(this);
+            element.addEventListener('mouseenter', () => {
+                if (popoverTimeout) clearTimeout(popoverTimeout);
+
+                popoverTimeout = setTimeout(() => {
+                    if (element.matches(':hover')) {
+                        const content = contentFunction(d);
+                        showPopover(element, title, content);
+                    }
+                }, popupWaitBeforeShow);
             });
-            p.on("show.bs.popover", function (e) {
-                // this is to dynamically ajdust the content and bounds of the popup
-                p.attr('data-content', contentFunction(d));
-                p.data("bs.popover").setContent();
-                p.data("bs.popover").tip().css({"max-width": "1000px"});
+
+            element.addEventListener('mouseleave', () => {
+                if (popoverTimeout) {
+                    clearTimeout(popoverTimeout);
+                    popoverTimeout = null;
+                }
+
+                // Delay hide to allow moving to popover
+                setTimeout(() => {
+                    const popover = getPopover();
+                    if (!popover.matches(':hover') && !element.matches(':hover')) {
+                        hidePopover();
+                    }
+                }, 100);
             });
         });
     }
@@ -255,7 +372,7 @@ function draw(pathway, elem) {
             }
         }
 
-        popupContent += "<img src='" + n.image + "' width='" + 20 * nodeRadius + "'><br>"
+        popupContent += "<img src='" + n.image + "'><br>"
         if (n.scenarios.length > 0) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of n.scenarios) {
@@ -265,7 +382,7 @@ 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" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
+            popupContent += '<br><a class="btn btn-primary btn-sm mt-2" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
         }
 
         return popupContent;
@@ -285,7 +402,7 @@ function draw(pathway, elem) {
             popupContent += adcontent;
         }
 
-        popupContent += "<img src='" + e.image + "' width='" + 20 * nodeRadius + "'><br>"
+        popupContent += "<img src='" + e.image + "'><br>"
         if (e.reaction_probability) {
             popupContent += '<b>Probability:</b><br>' + e.reaction_probability.toFixed(3) + '<br>';
         }
@@ -308,6 +425,23 @@ 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()
@@ -316,7 +450,12 @@ function draw(pathway, elem) {
             zoomable.attr("transform", event.transform);
         });
 
-    d3.select("svg").call(zoom);
+    // Apply zoom to the SVG element - this enables wheel 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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_compound_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Compound</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_edge_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Edge</a>
+    <a
+      role="button"
+      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

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

templates/actions/collections/model.html

@@ -1,6 +1,10 @@
 {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_model_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Model</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_node_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Node</a>
+    <a
+      role="button"
+      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

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

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

templates/actions/collections/reaction.html

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_reaction_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Reaction</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_rule_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Rule</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_scenario_modal">
-            <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
+    <a
+      role="button"
+      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

@@ -1,6 +1,10 @@
 {% if meta.can_edit %}
   <li>
-        <a role="button" data-toggle="modal" data-target="#new_setting_modal">
-            <span class="glyphicon glyphicon-plus"></span>New Setting</a>
+    <a
+      role="button"
+      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

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

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

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

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

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

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

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

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

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

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

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

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

templates/admin.html

@@ -1,12 +1,17 @@
 {% 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 id="textarea" class="form-control" rows="10" placeholder="Paste query here" required>
+        <textarea
+          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 {
@@ -15,32 +20,29 @@ 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

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

@@ -1,20 +1,32 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
 
-    {% if object_type != 'package' %}
-        <div>
-            <div id="load-all-error" style="display: none;">
-                <div class="alert alert-danger" role="alert">
-                    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-                    <span class="sr-only">Error:</span>
-                    Getting objects failed!
-                </div>
-            </div>
+  {# 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 #}
 
-            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
-                   style="display: none;">
-            <p></p>
+  {% if object_type != 'package' %}
+    <div class="px-8 py-4">
+      <input
+        type="text"
+        id="object-search"
+        class="input input-bordered hidden w-full max-w-xs"
+        placeholder="Search by name"
+      />
     </div>
   {% endif %}
 
@@ -48,9 +60,12 @@
     {% endif %}
   {% endblock action_modals %}
 
-<div class="panel-group" id="reviewListAccordion">
-    <div class="panel panel-default">
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+  <div class="px-8 py-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <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' %}
@@ -78,13 +93,31 @@
             {% elif object_type == 'group' %}
               Groups
             {% endif %}
-            <div id="actionsButton"
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                     aria-haspopup="true" aria-expanded="false"><span
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-                    style="padding-right:1em"></span></a>
-                <ul id="actionsList" class="dropdown-menu">
+          </h2>
+          <div id="actionsButton" class="dropdown dropdown-end hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <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-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" %}
@@ -115,205 +148,386 @@
             </ul>
           </div>
         </div>
-        <div class="panel-body">
+        <div class="mt-2">
           <!-- Set Text above links -->
           {% if object_type == 'package' %}
-            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-                    more &gt;&gt;</a></p>
+            <p>
+              A package contains pathways, rules, etc. and can reflect specific
+              experimental conditions.
+              <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>A compound stores the structure of a molecule and can include meta-information.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A compound stores the structure of a molecule and can include
+              meta-information.
+              <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>The structures stored in this compound
-                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              The structures stored in this compound
+              <a
+                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>A rule describes a biotransformation reaction template that is defined as SMIRKS.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A rule describes a biotransformation reaction template that is
+              defined as SMIRKS.
+              <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>A reaction is a specific biotransformation from educt compounds to product compounds.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A reaction is a specific biotransformation from educt compounds to
+              product compounds.
+              <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>A pathway displays the (predicted) biodegradation of a compound as graph.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A pathway displays the (predicted) biodegradation of a compound as
+              graph.
+              <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>Nodes represent the (predicted) compounds in a graph.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              Nodes represent the (predicted) compounds in a graph.
+              <a
+                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>Edges represent the links between Nodes in a graph
-                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              Edges represent the links between Nodes in a graph
+              <a
+                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>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
-                <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A scenario contains meta-information that can be attached to other
+              data (compounds, rules, ..).
+              <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>A model applies machine learning to limit the combinatorial explosion.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
-                    more
-                    &gt;&gt;</a></p>
+            <p>
+              A model applies machine learning to limit the combinatorial
+              explosion.
+              <a
+                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>A setting includes configuration parameters for pathway predictions.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              A setting includes configuration parameters for pathway
+              predictions.
+              <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>Register now to create own packages and to submit and manage your data.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              Register now to create own packages and to submit and manage your
+              data.
+              <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>Users can team up in groups to share packages.
-                <a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
-                    &gt;&gt;</a></p>
+            <p>
+              Users can team up in groups to share packages.
+              <a
+                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>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
-                reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
+              <p class="mt-4">
+                Nothing found. There are two possible reasons: <br /><br />1.
+                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 %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            <h4 class="panel-title">
-                <a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
-                   href="#Reviewed">Reviewed</a>
-            </h4>
+          <!-- Reviewed -->
+          <div
+            class="collapse-arrow bg-base-200 collapse order-2 w-full"
+            x-data="paginatedList(window.reviewedObjects || [], { isReviewed: true, instanceId: 'reviewed' })"
+          >
+            <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 id="Reviewed" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item" id="ReviewedContent">
-                {% if object_type == 'package' %}
-                {% for obj in reviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
-                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                          style="float:right" data-toggle="tooltip"
-                          data-placement="top" title="" data-original-title="Reviewed">
+            <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">
+                      <span x-text="obj.name"></span>
+                      <span
+                        class="tooltip tooltip-left ml-auto"
+                        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>
-                {% endfor %}
-                {% else %}
-                {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
-                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                          style="float:right" data-toggle="tooltip"
-                          data-placement="top" title="" data-original-title="Reviewed">
+                  </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>
-                </a>
-                {% endfor %}
-                {% endif %}
+                <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 %}
       {% endif %}
+
       {% if unreviewed_objects %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
-                class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
-                                       href="#Unreviewed">Unreviewed</a></h4></div>
-        <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">
-                {% if object_type == 'package' %}
-                {% for obj in unreviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                {% endfor %}
-                {% else %}
-                {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                {% endfor %}
-                {% endif %}
+        <!-- Unreviewed -->
+        <div
+          class="collapse-arrow bg-base-200 collapse order-1 w-full"
+          x-data="paginatedList(window.unreviewedObjects || [], { isReviewed: false, instanceId: 'unreviewed' })"
+        >
+          <input
+            type="checkbox"
+            {% if reviewed_objects|length == 0 or object_type == 'package' %}checked{% endif %}
+          />
+          <div class="collapse-title text-xl font-medium">
+            Unreviewed
+            <span
+              class="badge badge-sm badge-neutral ml-2"
+              x-text="totalItems"
+            ></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 -->
-        <ul class='list-group'>
+      <div class="card bg-base-100">
+        <div class="card-body">
+          <ul class="menu bg-base-200 rounded-box">
             {% for obj in objects %}
               {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
+                <li>
+                  <a href="{{ obj.url }}" class="hover:bg-base-300"
+                    >{{ obj.username }}</a
+                  >
+                </li>
               {% else %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+                <li>
+                  <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>
-        $(function () {
-
-            $('#object-search').show();
-
-            {% if object_type != 'package' and object_type != 'user' and object_type != 'group' %}
-                {% 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>');
-                                }
+    document.addEventListener("DOMContentLoaded", function () {
+      // Show actions button if there are actions
+      const actionsButton = document.getElementById("actionsButton");
+      const actionsList = actionsButton?.querySelector("ul");
+      if (actionsList && actionsList.children.length > 0) {
+        actionsButton?.classList.remove("hidden");
       }
 
-                            $('#load-all-loading').hide();
-                            $('#load-remaining').hide();
-                        }).fail(function (resp) {
-                            $('#load-all-loading').hide();
-                            $('#load-all-error').show();
+      // Show search input and connect to Alpine pagination
+      const objectSearch = document.getElementById("object-search");
+      if (objectSearch) {
+        objectSearch.classList.remove("hidden");
+        objectSearch.addEventListener("input", function () {
+          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);
+              }
             });
+        });
+      }
 
-                    }, 2500);
-                {% endif %}
-            {% endif %}
-        
-            $('#modal-form-delete-submit').on('click', function (e) {
+      // Delete form submit handler
+      const deleteSubmit = document.getElementById("modal-form-delete-submit");
+      const deleteForm = document.getElementById("modal-form-delete");
+      if (deleteSubmit && deleteForm) {
+        deleteSubmit.addEventListener("click", function (e) {
           e.preventDefault();
-                $('#modal-form-delete').submit();
+          deleteForm.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

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

templates/errors/400_bad_request.html

@@ -1,15 +1,77 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
-
-<div class="alert alert-error" role="alert">
-    <h4 class="alert-heading">Bad Request!</h4>
-    <p>Lorem</p>
-    <hr>
-    <p class="mb-0">
-        You can find out more about permissions in our <a target="_blank"
-                                                          href="https://wiki.envipath.org/index.php/packages"
-                                                          role="button">Wiki &gt;&gt;</a></p>
+  <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 mb-6 shadow-lg">
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          class="h-8 w-8 shrink-0 stroke-current"
+          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">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

@@ -1,15 +1,80 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
-
-<div class="alert alert-error" role="alert">
-    <h4 class="alert-heading">Access Denied!</h4>
-    <p>Access to X denied. </p>
-    <hr>
-    <p class="mb-0">
-        You can find out more about permissions in our <a target="_blank"
-                                                          href="https://wiki.envipath.org/index.php/packages"
-                                                          role="button">Wiki &gt;&gt;</a></p>
+  <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-warning mb-6 shadow-lg">
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          class="h-8 w-8 shrink-0 stroke-current"
+          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">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

@@ -1,15 +1,77 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
-
-<div class="alert alert-error" role="alert">
-    <h4 class="alert-heading">Not Found!</h4>
-    <p>Does not exist</p>
-    <hr>
-    <p class="mb-0">
-        You can find out more about permissions in our <a target="_blank"
-                                                          href="https://wiki.envipath.org/index.php/packages"
-                                                          role="button">Wiki &gt;&gt;</a></p>
+  <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-info mb-6 shadow-lg">
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          class="h-8 w-8 shrink-0 stroke-current"
+          fill="none"
+          viewBox="0 0 24 24"
+        >
+          <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

@@ -1,13 +1,76 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
-
-    <div class="alert alert-danger" role="alert">
-        <h4 class="alert-heading">{{ error_message }}</h4>
-        <hr>
-        <p class="mb-0">
-            {{ error_detail }}
+  <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 mb-6 shadow-lg">
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          class="h-8 w-8 shrink-0 stroke-current"
+          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

@@ -1,12 +1,81 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
 {% block content %}
-
-    <div class="alert alert-danger" role="alert">
-        <h4 class="alert-heading">Your account has not been activated yet!</h4>
-        <p>Your account has not been activated yet. If you have questions <a href="mailto:admin@envipath.org">contact
-            us.</a>
-        </p>
+  <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-warning mb-6 shadow-lg">
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          class="h-8 w-8 shrink-0 stroke-current"
+          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="collapse navbar-collapse collapse-framework navbar-collapse-framework"
+            class="navbar-collapse collapse-framework navbar-collapse-framework collapse"
             id="navbarCollapse"
           >
             <ul class="nav navbar-nav navbar-nav-framework">
@@ -151,11 +151,6 @@
                   >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
@@ -233,15 +228,7 @@
                       >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>
@@ -338,7 +325,7 @@
               >
             </div>
           </div>
-          <div id="license" class="panel-collapse collapse in">
+          <div id="license" class="panel-collapse in collapse">
             <div class="panel-body list-group-item">
               <a target="_blank" href="{{ meta.current_package.license.link }}">
                 <img src="{{ meta.current_package.license.image_link }}" />
@@ -413,10 +400,5 @@
         }
       });
     </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

@@ -21,8 +21,14 @@
       type="text/css"
     />
 
-    {# jQuery - Keep for compatibility with existing JS #}
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
+    {# Alpine.js - For reactive components #}
+    <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
@@ -35,21 +41,10 @@
 
     <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 -->
@@ -80,7 +75,7 @@
       {% block main_content %}
         {# Breadcrumbs - outside main content, optional #}
         {% if breadcrumbs %}
-          <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
+          <div id="bread" class="mx-auto max-w-7xl px-4 py-4">
             <div class="breadcrumbs text-sm">
               <ul>
                 {% for elem in breadcrumbs %}
@@ -113,7 +108,7 @@
 
           {# License - inside paper if present #}
           {% if meta.url_contains_package and meta.current_package.license %}
-            <div class="collapse collapse-arrow bg-base-200 m-8">
+            <div class="collapse-arrow bg-base-200 collapse p-8">
               <input type="checkbox" checked />
               <div class="collapse-title text-xl font-medium">License</div>
               <div class="collapse-content">
@@ -137,7 +132,7 @@
 
     {# Floating Help Tab #}
     {% if not public_mode %}
-      <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
+      <div class="fixed top-1/2 right-0 z-50 -translate-y-1/2">
         <a
           href="https://community.envipath.org/"
           target="_blank"
@@ -171,10 +166,11 @@
     {% endblock %}
 
     <script>
-      $(function () {
-        // Hide actionsbutton if there's no action defined
-        if ($("#actionsButton ul").children().length > 0) {
-          $("#actionsButton").show();
+      document.addEventListener("DOMContentLoaded", function () {
+        // Show actions button if there are actions defined
+        const actionsButtonUl = document.querySelector("#actionsButton ul");
+        if (actionsButtonUl && actionsButtonUl.children.length > 0) {
+          document.getElementById("actionsButton").style.display = "";
         }
       });
 

templates/includes/footer.html

@@ -1,17 +1,20 @@
 {% load static %}
-<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
-
+<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
   <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</a>
-            <a class="link link-hover" href="/search">Search</a>
-            <a class="link link-hover" href="/package">Browse</a>
+        <a class="link link-hover" href="/predict">Predict</a>
+        <a class="link link-hover" href="/package">Packages</a>
         {% if user.is_authenticated %}
           <a class="link link-hover" href="/model">Your Collections</a>
         {% endif %}
-            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
+        <a
+          href="https://wiki.envipath.org/"
+          target="_blank"
+          class="link link-hover"
+          >Documentation</a
+        >
       </nav>
     {% endif %}
     <nav>
@@ -29,39 +32,61 @@
       <a class="link link-hover" href="/cite">Cite enviPath</a>
     </nav>
   </footer>
-  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
-    <div class="flex flex-row justify-between w-full items-start">
+  <footer class="footer border-t-2 border-neutral-300 px-10 py-4">
+    <div class="flex w-full flex-row items-start justify-between">
       <aside class="grid-flow-col items-center">
-          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
+        <svg
+          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-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
+      <aside class="text-base-200 mt-2 text-sm">
+        <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 role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
+          <svg
+            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 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"/>
+            <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"
+            />
           </svg>
         </a>
         <a href="https://community.envipath.org/" target="_blank">
-            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
+          <svg
+            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 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"/>
+            <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"
+            />
           </svg>
         </a>
         <a href="https://www.linkedin.com/company/envipath/" target="_blank">
-            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
+          <img
+            src="{% static "/images/linkedin.png" %}"
+            alt="LinkedIn"
+            class="h-6 w-6"
+          />
         </a>
       </div>
     </nav>

templates/includes/navbar.html

@@ -1,15 +1,44 @@
 {% load static %}
-{# Modern DaisyUI Navbar #}
-<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
+{# Modern DaisyUI Navbar with Mobile Drawer Menu #}
+<div class="drawer drawer-mobile">
+  <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">
-    <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-      <svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
+        {# Hamburger menu button - visible on mobile, hidden on desktop #}
+        {% if not public_mode %}
+          <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"
@@ -18,8 +47,6 @@
             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
@@ -27,9 +54,18 @@
               class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
             >
               <li>
-            <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
+                <a href="{{ meta.server_url }}/package" id="packageLink"
+                  >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
@@ -41,7 +77,9 @@
                 >
               </li>
               <li>
-            <a href="{{ meta.server_url }}/model" id="relative-reasoningLink"
+                <a
+                  href="{{ meta.server_url }}/model"
+                  id="relative-reasoningLink"
                   >Model</a
                 >
               </li>
@@ -59,7 +97,7 @@
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">
             <div
-          class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
+              class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
             >
               <svg
                 xmlns="http://www.w3.org/2000/svg"
@@ -87,7 +125,7 @@
             <div
               tabindex="0"
               role="button"
-          class="btn btn-ghost m-1 btn-circle"
+              class="btn btn-ghost btn-circle m-1"
               id="loggedInButton"
             >
               <svg
@@ -111,7 +149,9 @@
               tabindex="-1"
               class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm"
             >
-          <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
+              <li>
+                <a href="{{ meta.user.url }}" id="accountbutton">Settings</a>
+              </li>
               <li>
                 <form
                   id="logoutForm"
@@ -134,6 +174,96 @@
         {% 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

@@ -2,36 +2,90 @@
 {% load static %}
 {% block main_content %}
   <!-- Hero Section with Logo and Search -->
-  <section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
+  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
     <div
-      class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
+      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
       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 z-10">
-        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
+      <div class="absolute bottom-40 left-1/8 -translate-x-8">
+        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
           Predict Your Pathway
         </h2>
       </div>
     </div>
   </section>
 
-  <div class="shadow-md max-w-5xl mx-auto bg-base-200">
+  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
     <!-- Predict Pathway Section -->
     <div
-      class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
+      class="relative mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
     >
       <div
-        class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out"
+        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl 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">
-          <!-- Input Mode Toggle - Fixed position outside fieldset -->
-          <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-            <div class="flex items-center gap-2">
-              <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
-              <label class="toggle text-base-content toggle-md">
-                <input type="checkbox" />
+          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+            <div class="flex items-center gap-1">
+              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
+                <input type="checkbox" x-model="drawMode" />
+                <span class="swap-on 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="smiles mode"
                       xmlns="http://www.w3.org/2000/svg"
@@ -52,6 +106,13 @@
                         />
                       </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"
@@ -64,57 +125,78 @@
                         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 transition-all duration-300 ease-in-out overflow-hidden"
+            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
+            :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"
-                class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
+                x-show="!drawMode"
+                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 w-full mx-auto">
+                <div class="join mx-auto w-full">
                   <input
                     type="text"
                     id="index-form-text-input"
                     placeholder="canonical SMILES string"
-                    class="input grow input-md join-item"
+                    class="input input-md join-item grow"
+                    x-model="smiles"
                   />
                   <button class="btn btn-neutral join-item">Predict!</button>
                 </div>
-                <div class="label relative w-full mt-1">
+                <div class="label relative mt-1 w-full">
                   <div class="flex gap-2">
                     <a
                       href="#"
-                      class="example-link cursor-pointer hover:text-primary"
-                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+                      class="example-link hover:text-primary cursor-pointer"
                       title="load example"
+                      @click.prevent="loadExample('CN1C=NC2=C1C(=O)N(C(=O)N2C)C', $el)"
                       >Caffeine</a
                     >
                     <a
                       href="#"
-                      class="example-link cursor-pointer hover:text-primary"
-                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
+                      class="example-link hover:text-primary cursor-pointer"
                       title="load example"
+                      @click.prevent="loadExample('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', $el)"
                       >Ibuprofen</a
                     >
                   </div>
-                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
+                  <a
+                    class="absolute top-0 left-[calc(100%-5.4rem)]"
+                    href="/predict"
                     >Advanced</a
                   >
                 </div>
               </div>
               <div
                 id="ketcher-container"
-                class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
+                x-show="drawMode"
+                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"
@@ -124,11 +206,13 @@
                   class="rounded-lg"
                 ></iframe>
                 <button
-                  class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
                 >
                   Predict!
                 </button>
-                <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
+                <div class="mt-1 flex w-full justify-end">
+                  <a class="label justify-end" href="/predict">Advanced</a>
+                </div>
               </div>
               <input
                 type="hidden"
@@ -150,18 +234,18 @@
     </div>
 
     <!-- Community News Section -->
-    <section class="py-16 bg-base-200 z-10 mx-8">
-      <div class="max-w-7xl mx-auto px-4">
-        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
+    <section class="bg-base-200 z-10 mx-8 py-16">
+      <div class="mx-auto max-w-7xl px-4">
+        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
 
-        <div id="community-news-container" class="flex gap-4 justify-center">
+        <div id="community-news-container" class="flex justify-center gap-4">
           <!-- News cards will be populated here -->
-          <div id="loading" class="flex justify-center w-full">
+          <div id="loading" class="flex w-full justify-center">
             <span class="loading loading-spinner loading-lg"></span>
           </div>
         </div>
 
-        <div class="text-right mt-6">
+        <div class="mt-6 text-right">
           <a
             href="https://community.envipath.org/c/announcements/10"
             target="_blank"
@@ -177,18 +261,18 @@
     </section>
 
     <!-- Mission Statement Section -->
-    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
+    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
       <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="w-full h-full object-contain"
+              class="h-full w-full object-contain"
             />
           </div>
-          <div class="space-y-4 text-left w-2/3 mr-8">
-            <h2 class="h2 font-bold mb-8">About enviPath</h2>
+          <div class="mr-8 w-2/3 space-y-4 text-left">
+            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
             <p class="">
               enviPath is a database and prediction system for the microbial
               biotransformation of organic environmental contaminants. The
@@ -201,7 +285,7 @@
               products. Explore our tools and contribute to advancing
               environmental biotransformation research.
             </p>
-            <div class="flex flex-row gap-4 float-right">
+            <div class="float-right flex flex-row gap-4">
               <a href="/about" class="btn btn-ghost-neutral">Read More</a>
               <a href="/about" class="btn btn-neutral">Publications</a>
             </div>
@@ -211,7 +295,7 @@
     </section>
 
     <!-- Partners Section -->
-    <section class="py-14 sm:py-12 bg-base-100">
+    <section class="bg-base-100 py-14 sm:py-12">
       <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>
@@ -242,6 +326,31 @@
   <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
@@ -264,16 +373,13 @@
       const date = new Date(topic.created_at).toLocaleDateString();
 
       return `
-                <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">
-                        <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
+                <div class="card bg-white shadow-sm hover:shadow-lg transition-shadow duration-300 h-52 w-75 flex-shrink-0">
+                    <div class="card-body flex flex-col h-full justify-between">
+                        <h3 class="card-title leading-tight font-normal tracking-tight mb-2 line-clamp-5 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">
@@ -299,141 +405,20 @@
     // Make render function globally available
     window.renderDiscourseTopics = renderDiscourseTopics;
 
-    // Toggle functionality with smooth animations
-    function toggleInputMode() {
-      const toggle = $('input[type="checkbox"]');
-      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 () {
+    // Ketcher iframe load handler - set up change event to sync SMILES
+    document.addEventListener("DOMContentLoaded", function () {
+      const indexKetcher = document.getElementById("index-ketcher");
+      indexKetcher.addEventListener("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

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

templates/migration_detail.html

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

templates/modals/cite_modal.html

@@ -1,31 +0,0 @@
-<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

@@ -1,42 +1,85 @@
-<div class="modal fade" tabindex="-1" id="import_legacy_package_modal" role="dialog"
-     aria-labelledby="import_legacy_package_modal" aria-hidden="true">
-    <div class="modal-dialog">
-        <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>
+<dialog
+  id="import_legacy_package_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- Header -->
+    <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>
-                <h4 class="modal-title">Import Package from legacy System</h4>
-            </div>
-            <div class="modal-body">
-                <p>Create a Package based on the JSON Export of the legacy system.</p>
-                <form id="import-legacy-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-                      enctype="multipart/form-data">
-                    {% csrf_token %}
-                    <p>
-                        <label class="btn btn-primary" for="legacyJsonFile">
-                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
-                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
-                            Choose JSON File
-                        </label>
-                        <span class="label label-info" id="upload-legacy-file-info"></span>
-                        <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        Create a Package based on the JSON Export of the legacy system.
       </p>
+      <form
+        id="import-legacy-package-modal-form"
+        accept-charset="UTF-8"
+        method="post"
+        enctype="multipart/form-data"
+      >
+        {% csrf_token %}
+        <div class="form-control">
+          <label class="label">
+            <span class="label-text">Legacy JSON File</span>
+          </label>
+          <input
+            type="file"
+            id="legacyJsonFile"
+            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">
-                <a id="import-legacy-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+
+    <!-- Footer -->
+    <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('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>
-</div>
-<script>
-    $(function () {
-        $('#import-legacy-package-modal-form-submit').on('click', function (e) {
-            e.preventDefault();
-            $('#import-legacy-package-modal-form').submit();
-        });
-    });
-</script>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/import_package_modal.html

@@ -1,42 +1,83 @@
-<div class="modal fade" tabindex="-1" id="import_package_modal" role="dialog"
-     aria-labelledby="import_package_modal" aria-hidden="true">
-    <div class="modal-dialog">
-        <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>
+<dialog
+  id="import_package_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- Header -->
+    <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>
-                <h4 class="modal-title">Import Package</h4>
-            </div>
-            <div class="modal-body">
-                <p>Create a Package based on a JSON Export.</p>
-                <form id="import-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-                      enctype="multipart/form-data">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">Create a Package based on a JSON Export.</p>
+      <form
+        id="import-package-modal-form"
+        accept-charset="UTF-8"
+        method="post"
+        enctype="multipart/form-data"
+      >
         {% csrf_token %}
-                    <p>
-                        <label class="btn btn-primary" for="jsonFile">
-                            <input id="jsonFile" name="file" type="file" style="display:none;"
-                                   onchange="$('#upload-file-info').html(this.files[0].name)">
-                            Choose JSON File
+        <div class="form-control">
+          <label class="label">
+            <span class="label-text">JSON File</span>
           </label>
-                        <span class="label label-info" id="upload-file-info"></span>
-                        <input type="hidden" value="import-package-json" name="hidden" readonly="">
-                    </p>
+          <input
+            type="file"
+            id="jsonFile"
+            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">
-                <a id="import-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+
+    <!-- Footer -->
+    <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('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>
-</div>
-<script>
-    $(function () {
-        $('#import-package-modal-form-submit').on('click', function (e) {
-            e.preventDefault();
-            $('#import-package-modal-form').submit();
-        });
-    });
-</script>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/new_compound_modal.html

@@ -1,78 +1,137 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="new_compound_modal" tabindex="-1" aria-labelledby="new_compound_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>
+
+<dialog
+  id="new_compound_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <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>
-                <h4 class="modal-title">Create a new Compound</h4>
-            </div>
-            <div class="modal-body">
-                <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>
+
+    <!-- Body -->
+    <div class="py-4">
+      <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>
-                    <input id="compound-name" class="form-control" name="compound-name" placeholder="Name"/>
-                    <label for="compound-description">Description</label>
-                    <input id="compound-description" class="form-control" name="compound-description" placeholder="Description"/>
-                    <label for="compound-smiles">SMILES</label>
-                    <input type="text" class="form-control" name="compound-smiles" placeholder="SMILES" id="compound-smiles">
-                    <p></p>
-                    <div>
-                        <iframe id="new_compound_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                                height="510"></iframe>
+
+        <div class="form-control mb-3">
+          <label class="label" for="compound-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="compound-name"
+            class="input input-bordered w-full"
+            name="compound-name"
+            placeholder="Name"
+            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">
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+
+    <!-- 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-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>
 
-</div>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>
+
 <script>
-
-function newCompoundModalketcherToNewCompoundModalTextInput() {
-    $('#compound-smiles').val(this.ketcher.getSmiles());
-}
-
-$(function() {
-
-    $('#new_compound_ketcher').on('load', function() {
+  document
+    .getElementById("new_compound_ketcher")
+    .addEventListener("load", function () {
+      const iframe = this;
       const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
+        const win = iframe.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
           win.ketcher.editor.event.change.handlers.push({
             once: false,
             priority: 0,
-                    f: newCompoundModalketcherToNewCompoundModalTextInput,
-                    ketcher: win.ketcher
+            f: function () {
+              document.getElementById("compound-smiles").value =
+                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

@@ -1,45 +1,96 @@
-<div class="modal fade" tabindex="-1" id="new_group_modal" role="dialog" aria-labelledby="new_group_modal"
-     aria-hidden="true">
-    <div class="modal-dialog">
-        <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>
+{% load static %}
+
+<dialog
+  id="new_group_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <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>
-                <h4 class="modal-title">New Group</h4>
-            </div>
-            <div class="modal-body">
-                <p>Create new Group. You can assign users to the group once
-                    it is created. Description can be changed after creation.</p>
-                <form id="new_group_modal_form" accept-charset="UTF-8" action="{{ SERVER_BASE }}/group"
-                      data-remote="true"
-                      method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        Create new Group. You can assign users to the group once it is created.
+        Description can be changed after creation.
+      </p>
+
+      <form
+        id="new-group-modal-form"
+        accept-charset="UTF-8"
+        action="{{ SERVER_BASE }}/group"
+        method="post"
+      >
         {% csrf_token %}
-                    <p>
-                        <label for="name">Name</label>
-                        <input id="name" type="text" name="group-name" class="form-control" placeholder="Name"/>
-                    </p>
-                    <p>
-                        <label for="description">Description</label>
-                        <input id="description" type="text" class="form-control" placeholder="Description..."
-                               name="group-description"/>
-                    </p>
+
+        <div class="form-control mb-3">
+          <label class="label" for="group-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="group-name"
+            class="input input-bordered w-full"
+            name="group-name"
+            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">
-                <a id="new_group_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">
+
+    <!-- Footer -->
+    <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-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>
-</div>
-<script>
-$(function() {
-    $('#new_group_modal_form_submit').on('click', function() {
-        $('#new_group_modal_form').submit();
-    });
-});
-</script>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/new_model_modal.html

@@ -1,188 +1,337 @@
+<dialog
+  id="new_model_modal"
+  class="modal"
+  x-data="{
+    isSubmitting: false,
+    modelType: '',
+    buildAppDomain: false,
 
-<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
-     aria-hidden="true">
-    <div class="modal-dialog modal-lg">
-        <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>
+    reset() {
+      this.isSubmitting = false;
+      this.modelType = '';
+      this.buildAppDomain = false;
+    },
+
+    get showMlrr() {
+      return this.modelType === 'mlrr';
+    },
+
+    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>
-                <h4 class="modal-title">New Model</h4>
-            </div>
-            <div class="modal-body">
-                <form id="new_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-                      data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="new_model_form"
+        accept-charset="UTF-8"
+        action="{{ meta.current_package.url }}/model"
+        method="post"
+      >
         {% csrf_token %}
-                    <div class="jumbotron">Create a new Model to
-                        limit the number of degradation products in the
-                        prediction. You just need to set a name and the packages
-                        you want the object to be based on. There are multiple types of models available.
-                        For additional information have a look at our
-                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
-                            &gt;&gt;</a>
+        <div class="alert alert-info mb-4">
+          <span>
+            Create a new Model to limit the number of degradation products in
+            the prediction. You just need to set a name and the packages you
+            want the object to be based on. There are multiple types of models
+            available. For additional information have a look at our
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/relative-reasoning"
+              class="link"
+              >wiki &gt;&gt;</a
+            >
+          </span>
         </div>
+
         <!-- Name -->
-                    <label for="model-name">Name</label>
-                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
+        <div class="form-control mb-3">
+          <label class="label" for="model-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 -->
-                    <label for="model-description">Description</label>
-                    <input id="model-description" name="model-description" class="form-control"
-                           placeholder="Description"/>
+        <div class="form-control mb-3">
+          <label class="label" for="model-description">
+            <span class="label-text">Description</span>
+          </label>
+          <input
+            id="model-description"
+            name="model-description"
+            class="input input-bordered w-full"
+            placeholder="Description"
+          />
+        </div>
 
         <!-- Model Type -->
-                    <label for="model-type">Model Type</label>
-                    <select id="model-type" name="model-type" class="form-control" data-width='100%'>
-                        <option disabled selected>Select Model Type</option>
+        <div class="form-control mb-3">
+          <label class="label" for="model-type">
+            <span class="label-text">Model Type</span>
+          </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 -->
-                    <div id="rule-packages" class="ep-model-param mlrr rbrr">
-                        <label for="model-rule-packages">Rule Packages</label>
-                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
-                                class="form-control" multiple data-width='100%'>
-                            <option disabled>Reviewed Packages</option>
+        <!-- Rule Packages (MLRR, RBRR) -->
+        <div class="form-control mb-3" x-show="showMlrr || showRbrr" x-cloak>
+          <label class="label" for="model-rule-packages">
+            <span class="label-text">Rule Packages</span>
+          </label>
+          <select
+            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 %}
-
-                            <option disabled>Unreviewed Packages</option>
+            </optgroup>
+            <optgroup label="Unreviewed Packages">
               {% 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 -->
-                    <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
-                        <label for="model-data-packages">Data Packages</label>
-                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
-                                class="form-control" multiple data-width='100%'>
-                            <option disabled>Reviewed Packages</option>
+        <!-- Data Packages (MLRR, RBRR, Enviformer) -->
+        <div
+          class="form-control mb-3"
+          x-show="showMlrr || showRbrr || showEnviformer"
+          x-cloak
+        >
+          <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 %}
-
-                            <option disabled>Unreviewed Packages</option>
+            </optgroup>
+            <optgroup label="Unreviewed Packages">
               {% 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 -->
-                    <div id="fingerprinter" class="ep-model-param mlrr">
-                        <label for="model-fingerprinter">Fingerprinter</label>
-                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
-                                class="form-control" multiple data-width='100%'>
+        <!-- Fingerprinter (MLRR) -->
+        <div class="form-control mb-3" x-show="showMlrr" x-cloak>
+          <label class="label" for="model-fingerprinter">
+            <span class="label-text">Fingerprinter</span>
+          </label>
+          <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 %}
-                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
+              <optgroup label="Additional Fingerprinter / Descriptor">
                 {% for k, v in additional_descriptors.items %}
                   <option value="{{ v }}">{{ k }}</option>
                 {% endfor %}
+              </optgroup>
             {% endif %}
           </select>
-                    </div>
-
-                    <!-- Threshold -->
-                    <div id="threshold" class="ep-model-param mlrr enviformer">
-                        <label for="model-threshold">Threshold</label>
-                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
-                               name="model-threshold" class="form-control">
-                    </div>
-
-                    <div id="appdomain" class="ep-model-param mlrr">
-                        {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
-                            <!-- Build AD? -->
-                            <div class="checkbox">
-                                <label>
-                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
-                                    Applicability Domain?
+          <label class="label">
+            <span class="label-text-alt">Hold Ctrl/Cmd to select multiple</span>
           </label>
         </div>
-                            <div id="ad-params" style="display:none">
-                                <!-- Num Neighbors -->
-                                <label for="num-neighbors">Number of Neighbors</label>
-                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
-                                       value="5"
-                                       step="1" min="0" max="10">
-                                <!-- Local Compatibility -->
-                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
+
+        <!-- Threshold (MLRR, Enviformer) -->
+        <div
+          class="form-control mb-3"
+          x-show="showMlrr || showEnviformer"
+          x-cloak
+        >
+          <label class="label" for="model-threshold">
+            <span class="label-text">Threshold</span>
+          </label>
+          <input
             type="number"
-                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                                <!-- Reliability -->
-                                <label for="reliability-threshold">Reliability Threshold</label>
-                                <input id="reliability-threshold" name="reliability-threshold" type="number"
-                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
+            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) -->
+        {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
+          <div x-show="showMlrr" x-cloak>
+            <div class="form-control mb-3">
+              <label class="label cursor-pointer justify-start gap-3">
+                <input
+                  type="checkbox"
+                  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 x-show="buildAppDomain" x-cloak class="ml-4 space-y-3">
+              <div class="form-control">
+                <label class="label" for="num-neighbors">
+                  <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"
+                  min="0"
+                  max="10"
+                />
+              </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"
+                  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">
-                <a id="new_model_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-            </div>
-        </div>
+
+    <!-- Footer -->
+    <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_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>
 
-<script>
-    $(function () {
-        // Built in Model Types
-        var nativeModelTypes = [
-            "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>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/new_package_modal.html

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

templates/modals/collections/new_pathway_modal.html

@@ -1,302 +0,0 @@
-
-{% 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

@@ -1,109 +1,260 @@
-
 {% load static %}
 
-<div id="new_prediction_setting_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Create a Prediction Setting</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+<dialog
+  id="new_prediction_setting_modal"
+  class="modal"
+  x-data="{
+    isSubmitting: false,
+    tpMethod: '',
+
+    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>
-            </div>
-            <div class="modal-body">
-                <p>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="" data-remote="true"
-                      method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        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 %}
 
-                    <label for="prediction-setting-name">Name</label>
-                    <input id="prediction-setting-name" name="prediction-setting-name" class="form-control" placeholder="Name"/>
-                    <label for="prediction-setting-description">Description</label>
-                    <input id="prediction-setting-description" name="prediction-setting-description" class="form-control"
-                           placeholder="Description"/>
+        <div class="form-control mb-3">
+          <label class="label" for="prediction-setting-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="prediction-setting-name"
+            name="prediction-setting-name"
+            class="input input-bordered w-full"
+            placeholder="Name"
+            required
+          />
+        </div>
 
-                    <label for="prediction-setting-max-nodes">Max #Nodes</label>
-                    <input id="prediction-setting-max-nodes" type="number" class="form-control" name="prediction-setting-max-nodes" value="30" min="1" max="50" step="1">
-                    <label for="prediction-setting-max-depth">Max Depth</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">
+        <div class="form-control mb-3">
+          <label class="label" for="prediction-setting-description">
+            <span class="label-text">Description</span>
+          </label>
+          <input
+            id="prediction-setting-description"
+            name="prediction-setting-description"
+            class="input input-bordered w-full"
+            placeholder="Description"
+          />
+        </div>
 
-                    <label for="tp-generation-method">TP Generation Method</label>
-                    <select id="tp-generation-method" name="tp-generation-method" class="form-control" data-width='100%'>
-                        <option disabled selected>Select how TPs are generated</option>
+        <div class="form-control mb-3">
+          <label class="label" for="prediction-setting-max-nodes">
+            <span class="label-text">Max #Nodes</span>
+          </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 id="rule-based-prediction-setting-specific-form">
-                        <!-- Rule Packages -->
-                        <label>Rule Packages</label><br>
-                        <select id="rule-based-prediction-setting-packages" name="rule-based-prediction-setting-packages"
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
-                            <option disabled>Reviewed Packages</option>
+        </div>
+
+        <!-- Rule Based Settings -->
+        <div x-show="tpMethod === 'rule-based-prediction-setting'" x-cloak>
+          <div class="form-control mb-3">
+            <label class="label">
+              <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 %}
-
-                            <option disabled>Unreviewed Packages</option>
+              </optgroup>
+              <optgroup label="Unreviewed Packages">
                 {% 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 id="model-based-prediction-setting-specific-form">
-                        <label>Select Model</label><br>
-                        <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
-                        <option disabled selected>Select the model</option>
+        </div>
+
+        <!-- Model Based Settings -->
+        <div x-show="tpMethod === 'model-based-prediction-setting'" x-cloak>
+          <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>
 
-                    <input class="form-check-input" type="checkbox" value="on" id="prediction-setting-new-default" name="prediction-setting-new-default">
-                    <label class="form-check-label" for="prediction-setting-new-default">Set this setting as new default</label>
+          <div class="form-control mb-3">
+            <label class="label" for="model-based-prediction-setting-threshold">
+              <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">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="new-prediction-setting-modal-submit">Create</button>
+
+    <!-- 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">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() {
 
-        // Initially hide all "specific" forms
-        $("div[id$='-specific-form']").each( function() {
-            $(this).hide();
-        });
-
-        $("#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>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/new_reaction_modal.html

@@ -1,50 +1,105 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="new_reaction_modal" tabindex="-1" aria-labelledby="new_reaction_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>
+
+<dialog
+  id="new_reaction_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <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>
-                <h4 class="modal-title">Create a new Reaction</h4>
-            </div>
-            <div class="modal-body">
-                <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>
+
+    <!-- Body -->
+    <div class="py-4">
+      <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>
-                    <input id="reaction-name" class="form-control" name="reaction-name" placeholder="Name"/>
-                    <label for="reaction-description">Description</label>
-                    <input id="reaction-description" class="form-control" name="reaction-description" placeholder="Description"/>
-                    <p></p>
-                    <div>
-                        <iframe id="new_reaction_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                                height="510"></iframe>
+
+        <div class="form-control mb-3">
+          <label class="label" for="reaction-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="reaction-name"
+            class="input input-bordered w-full"
+            name="reaction-name"
+            placeholder="Name"
+            required
+          />
         </div>
-                    <input type="hidden" name="reaction-smirks" id="reaction-smirks">
-                    <p></p>
+
+        <div class="form-control mb-3">
+          <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">
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+
+    <!-- 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="
+          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>
 
-</div>
-<script>
-$(function() {
-    $('#new_reaction_modal_form_submit').on('click', function(e) {
-        e.preventDefault();
-        $(this).prop("disabled",true);
-
-        k = getKetcher('new_reaction_ketcher');
-        $('#reaction-smirks').val(k.getSmiles());
-
-        // submit form
-        $('#new_reaction_modal_form').submit();
-    });
-});
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/collections/new_rule_modal.html

@@ -1,72 +1,140 @@
 {% 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>
 
-</div>
-<script>
-$(function() {
-
-    $('#rule-smirks').on('input', function(e) {
-        $('#rule-smirks-viz').empty()
-
-        smirks = $('#rule-smirks').val()
+<dialog
+  id="new_rule_modal"
+  class="modal"
+  x-data="{
+    ...modalForm(),
+    smirksVizHtml: '',
+    updateSmirksViz() {
+      const smirks = document.getElementById('rule-smirks').value;
+      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 = function () {
-            $('#rule-smirks-viz').append(img);
+      img.onload = () => {
+        this.smirksVizHtml = img.outerHTML;
       };
 
-        img.onerror = function () {
-            error_tpl = `
-                <div class="alert alert-error" role="alert">
-                    <h4 class="alert-heading">Could not render SMIRKS!</h4>
-                    <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</a>
-                    </p>
-                </div>`
-            $('#rule-smirks-viz').append(error_tpl);
+      img.onerror = () => {
+        this.smirksVizHtml = `
+          <div class='alert alert-error' role='alert'>
+            <h4 class='alert-heading'>Could not render SMIRKS!</h4>
+            <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</p>
+          </div>`;
       };
-    });
+    }
+  }"
+  @close="reset(); smirksVizHtml = ''"
+>
+  <div class="modal-box max-w-3xl">
+    <!-- Header -->
+    <h3 class="font-bold text-lg">Create a new Rule</h3>
 
-    $('#new_rule_modal_form_submit').on('click', function(e) {
-        e.preventDefault();
-        $(this).prop("disabled",true);
-        // submit form
-        $('#new_rule_modal_form').submit();
-    });
-});
-</script>
+    <!-- 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">
+      <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

@@ -1,102 +1,177 @@
-<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="new_scenario_modal"
-     aria-hidden="true">
-    <div class="modal-dialog modal-lg">
-        <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>
+{% load static %}
+
+<dialog
+  id="new_scenario_modal"
+  class="modal"
+  x-data="{
+    ...modalForm(),
+    scenarioType: 'empty',
+    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>
-                <h4 class="modal-title">New Scenario</h4>
-            </div>
-            <div class="modal-body">
-                <form id="new_scenario_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/scenario"
-                      data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        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
-                        associated to the data, not the current date. For example, this 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" role="button">wiki
-                            &gt;&gt;</a>
+
+        <div class="alert alert-info mb-4">
+          <span>
+            Please enter name, description, and date of scenario. Date should be
+            associated to the data, not the current date. For example, this
+            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>
-                    <input id="scenario-name" name="scenario-name" class="form-control" placeholder="Name"/>
-                    <label for="scenario-description">Description</label>
-                    <input id="scenario-description" name="scenario-description" class="form-control"
-                           placeholder="Description"/>
-                    <label id="dateField" for="dateYear">Date</label>
-                    <table>
-                        <tr>
-                            <th>
-                                <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
-                                       placeholder="YYYY" max="{% now "Y" %}">
-                            </th>
-                            <th>
-                                <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
-                                       class="form-control" placeholder="MM" >
-                            </th>
-                            <th>
-                                <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
-                                       placeholder="DD">
-                            </th>
-                        </tr>
-                    </table>
-                    <label for="scenario-type">Scenario Type</label>
-                    <select id="scenario-type" name="scenario-type" class="form-control" data-width='100%'>
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="scenario-name"
+            name="scenario-name"
+            class="input input-bordered w-full"
+            placeholder="Name"
+            required
+          />
+        </div>
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-description">
+            <span class="label-text">Description</span>
+          </label>
+          <input
+            id="scenario-description"
+            name="scenario-description"
+            class="input input-bordered w-full"
+            placeholder="Description"
+          />
+        </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 id="{{ type.name }}-specific-inputs">
+          <div
+            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">
-                <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-            </div>
-        </div>
+
+    <!-- Footer -->
+    <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-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>
 
-<script>
-    $(function () {
-        // Initially hide all "specific" forms
-        $("div[id$='-specific-inputs']").each(function () {
-            $(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>
-
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/add_additional_information_modal.html

@@ -1,61 +1,117 @@
 {% load static %}
 <!-- Add Additional Information -->
-<div id="add_additional_information_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+<dialog
+  id="add_additional_information_modal"
+  class="modal"
+  x-data="{
+    isSubmitting: false,
+    selectedType: '',
+
+    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>
-                <h3 class="modal-title">Add Additional Information</h3>
-            </div>
-            <div class="modal-body">
-                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
-                    <option selected disabled>Select the type to add</option>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <div class="form-control">
+        <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 }}">{{ add_inf.display_name }}</option>
+            <option value="{{ add_inf.name }}">
+              {{ add_inf.display_name }}
+            </option>
           {% endfor %}
         </select>
+      </div>
+
       {% for add_inf in available_additional_information %}
-                    <div class="aiform {{ add_inf.name }}" style="display: none;">
-                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
-                              action="" data-remote="true" method="post">
+        <div
+          class="mt-4"
+          x-show="selectedType === '{{ add_inf.name }}'"
+          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 type="hidden" name="hidden" value="add-additional-information">
+            <input
+              type="hidden"
+              name="hidden"
+              value="add-additional-information"
+            />
           </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="add-additional-information-modal-submit">Add
+
+    <!-- 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 || !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() {
 
-    $('#select-additional-information-type').change(function(e){
-        var selectedType = $("#select-additional-information-type :selected").val();
-        $('.aiform').hide();
-        $('.' + selectedType).show();
-    })
-
-    $('#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>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,127 +1,181 @@
-
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_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">&times;</span>
+<dialog
+  id="add_pathway_edge_modal"
+  class="modal"
+  x-data="{
+    isSubmitting: false,
+    reactionImageUrl: '',
+
+    reset() {
+      this.isSubmitting = false;
+      this.reactionImageUrl = '';
+    },
+
+    updateReactionImage() {
+      const substratesSelect = document.getElementById('add_pathway_edge_substrates');
+      const productsSelect = document.getElementById('add_pathway_edge_products');
+
+      const substrates = [];
+      for (const option of substratesSelect.selectedOptions) {
+        substrates.push(option.dataset.smiles);
+      }
+
+      const products = [];
+      for (const option of productsSelect.selectedOptions) {
+        products.push(option.dataset.smiles);
+      }
+
+      if (substrates.length > 0 && products.length > 0) {
+        const reaction = substrates.join('.') + '>>' + products.join('.');
+        this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
+      } else {
+        this.reactionImageUrl = '';
+      }
+    },
+
+    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) -->
+    <form method="dialog">
+      <button
+        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
+        :disabled="isSubmitting"
+      >
+        ✕
       </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"
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <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">
+        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 class="form-control mb-3">
+          <label class="label" for="edge-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="edge-name"
+            type="text"
+            class="input input-bordered w-full"
+            name="edge-name"
+            placeholder="Name"
+          />
         </div>
-                        <div class="col-xs-2">
 
+        <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="col-xs-5">
-                            <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%'>
+
+        <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 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>
+                  <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">
-
+          <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>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+
+    <!-- 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>
-                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
-            </div>
     </div>
   </div>
 
-</div>
-<script>
-
-    function reactionImage() {
-        var substrates = [];
-        $('#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) {
-            reaction = substrates.join('.') + ">>" + products.join('.');
-            $('#reaction_image').empty();
-            $('#reaction_image').append(
-                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
-            );
-        }
-    }
-
-    $(function () {
-        $("#add_pathway_edge_substrates").selectpicker();
-        $("#add_pathway_edge_products").selectpicker();
-
-        $("#add_pathway_edge_substrates").on('change', function (e) {
-            reactionImage();
-        })
-
-        $("#add_pathway_edge_products").on('change', function (e) {
-            reactionImage();
-        })
-
-        $(function () {
-            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
-                e.preventDefault();
-                $(this).prop("disabled", true);
-
-
-                // submit form
-                $('#add_pathway_edge_modal_form').submit();
-            });
-        });
-
-    });
-
-</script>
-
-
-
-
-
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/add_pathway_node_modal.html

@@ -1,78 +1,137 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_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">&times;</span>
+<dialog
+  id="add_pathway_node_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box max-w-4xl">
+    <!-- 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>
-                <h4 class="modal-title">Add a Node</h4>
-            </div>
-            <div class="modal-body">
-                <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>
+
+    <!-- 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"
+      >
         {% csrf_token %}
-                    <label for="node-name">Name</label>
-                    <input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
-                    <label for="node-description">Description</label>
-                    <input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
-                    <label for="node-smiles">SMILES</label>
-                    <input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
-                    <p></p>
-                    <div>
-                        <iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                                height="510"></iframe>
+        <div class="form-control mb-3">
+          <label class="label" for="node-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="node-name"
+            type="text"
+            class="input input-bordered w-full"
+            name="node-name"
+            placeholder="Name"
+          />
+        </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">
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+
+    <!-- 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('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>
 
-</div>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>
+
 <script>
-
-function newStructureModalketcherToNewStructureModalTextInput() {
-    $('#node-smiles').val(this.ketcher.getSmiles());
-}
-
-$(function() {
-
-    $('#add_node_ketcher').on('load', function() {
+  document
+    .getElementById("add_node_ketcher")
+    .addEventListener("load", function () {
+      const iframe = this;
       const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
+        const win = iframe.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
           win.ketcher.editor.event.change.handlers.push({
             once: false,
             priority: 0,
-                    f: newStructureModalketcherToNewStructureModalTextInput,
-                    ketcher: win.ketcher
+            f: function () {
+              document.getElementById("node-smiles").value =
+                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

@@ -1,78 +1,137 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_structure_modal" tabindex="-1" aria-labelledby="add_structure_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>
+<dialog
+  id="add_structure_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box max-w-4xl">
+    <!-- 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>
-                <h4 class="modal-title">Create a new Structure</h4>
-            </div>
-            <div class="modal-body">
-                <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>
+
+    <!-- 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"
+      >
         {% csrf_token %}
-                    <label for="structure-name">Name</label>
-                    <input id="structure-name" class="form-control" name="structure-name" placeholder="Name"/>
-                    <label for="structure-description">Description</label>
-                    <input id="structure-description" class="form-control" name="structure-description" placeholder="Description"/>
-                    <label for="structure-smiles">SMILES</label>
-                    <input type="text" class="form-control" name="structure-smiles" placeholder="SMILES" id="structure-smiles">
-                    <p></p>
-                    <div>
-                        <iframe id="add_structure_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-                                height="510"></iframe>
+        <div class="form-control mb-3">
+          <label class="label" for="structure-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="structure-name"
+            type="text"
+            class="input input-bordered w-full"
+            name="structure-name"
+            placeholder="Name"
+          />
+        </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">
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+
+    <!-- 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('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>
 
-</div>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>
+
 <script>
-
-function newStructureModalketcherToNewStructureModalTextInput() {
-    $('#structure-smiles').val(this.ketcher.getSmiles());
-}
-
-$(function() {
-
-    $('#add_structure_ketcher').on('load', function() {
+  document
+    .getElementById("add_structure_ketcher")
+    .addEventListener("load", function () {
+      const iframe = this;
       const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
+        const win = iframe.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
           win.ketcher.editor.event.change.handlers.push({
             once: false,
             priority: 0,
-                    f: newStructureModalketcherToNewStructureModalTextInput,
-                    ketcher: win.ketcher
+            f: function () {
+              document.getElementById("structure-smiles").value =
+                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

@@ -1,66 +1,94 @@
-
 {% load static %}
 <!-- Delete Edge -->
-<div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Edge</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+<dialog
+  id="delete_pathway_edge_modal"
+  class="modal"
+  x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
         Deletes the Edge. Nodes referenced by this edge will remain.
-                <p></p>
-                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-                      method="post">
+      </p>
+      <form
+        id="delete-pathway-edge-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
         {% csrf_token %}
-                    <select id="delete_pathway_edge_edges" name="edge-url"
-                            data-actions-box='true' class="form-control" data-width='100%'>
-                        <option value="" disabled selected>Select Reaction to delete</option>
+        <div class="form-control">
+          <label class="label" for="delete_pathway_edge_edges">
+            <span class="label-text">Select Reaction to delete</span>
+          </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>
+
+      <!-- Image Preview -->
+      <div class="mt-4" x-show="imageUrl" x-cloak>
+        <img :src="imageUrl" class="w-full" alt="Edge preview" />
       </div>
     </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-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>
-<script>
-    $(function () {
-        $("#delete_pathway_edge_edges").selectpicker();
 
-        $("#delete_pathway_edge_edges").on('change', function (e) {
-            edge_url = $('#delete_pathway_edge_edges option:selected').val()
-
-            if (edge_url !== "") {
-                $('#delete_pathway_edge_image').empty();
-                $('#delete_pathway_edge_image').append(
-                    "<img width='100%' src='" + edge_url + "?image=svg'>"
-                );
-            }
-        })
-
-        $('#delete-pathway-edge-modal-submit').click(function (e) {
-            e.preventDefault();
-            edge_url = $('#delete_pathway_edge_edges option:selected').val()
-
-            if (edge_url === "") {
-                return;
-            }
-
-            $('#delete-pathway-edge-modal-form').attr('action', edge_url)
-            $('#delete-pathway-edge-modal-form').submit();
-        });
-
-    })
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/delete_pathway_node_modal.html

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

templates/modals/objects/download_pathway_csv_modal.html

@@ -1,36 +1,69 @@
 {% load static %}
-<!-- Download Pathway -->
-<div id="download_pathway_csv_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Download Pathway as CSV</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="download_pathway_csv_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
-                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
-                <form id="download-pathway-csv-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
-                      data-remote="true" method="GET">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p>
+        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">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="download-pathway-csv-modal-submit">Download</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function () {
 
-        $('#download-pathway-csv-modal-submit').click(function (e) {
-            e.preventDefault();
-            $('#download-pathway-csv-modal-form').submit();
-            $('#download_pathway_csv_modal').modal('hide');
-        });
+    <!-- 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('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>
 
-    })
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/download_pathway_image_modal.html

@@ -1,32 +1,57 @@
 {% load static %}
-<!-- Download Pathway -->
-<div id="download_pathway_image_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Download Pathway as Image</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="download_pathway_image_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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 () {
 
-        $('#download-pathway-image-modal-submit').click(function (e) {
-            e.preventDefault();
-            downloadSVG($('#pwsvg')[0], '{{ pathway.name.split|join:"_" }}.svg')
-            $('#download_pathway_image_modal').modal('hide');
-        });
-
-    })
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_compound_modal.html

@@ -1,47 +1,91 @@
-
 {% load static %}
-<!-- Edit Compound -->
-<div id="edit_compound_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Edit Compound</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="edit_compound_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
-                <p>Edit Compound.</p>
-                <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-compound-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
         {% csrf_token %}
-                    <p>
-                        <label for="compound-name">Name</label>
-                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
-                    </p>
-                    <p>
-                        <label for="compound-description">Description</label>
-                        <input id="compound-description" type="text" class="form-control"
+
+        <div class="form-control mb-3">
+          <label class="label" for="compound-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="compound-name"
+            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">
-                    </p>
+            name="compound-description"
+          />
+        </div>
       </form>
     </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-compound-modal-submit">Update</button>
+
+    <!-- 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('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() {
 
-    $('#edit-compound-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-compound-modal-form').submit();
-    });
-
-});
-
-
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_compound_structure_modal.html

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

templates/modals/objects/edit_group_member_modal.html

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

templates/modals/objects/edit_model_modal.html

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

templates/modals/objects/edit_node_modal.html

@@ -1,47 +1,91 @@
-
 {% load static %}
-<!-- Edit Node -->
-<div id="edit_node_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Edit Node</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="edit_node_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
-                <p>Edit Node.</p>
-                <form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-node-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
         {% csrf_token %}
-                    <p>
-                        <label for="node-name">Name</label>
-                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
-                    </p>
-                    <p>
-                        <label for="node-description">Description</label>
-                        <input id="node-description" type="text" class="form-control"
+
+        <div class="form-control mb-3">
+          <label class="label" for="node-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="node-name"
+            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">
-                    </p>
+            name="node-description"
+          />
+        </div>
       </form>
     </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-node-modal-submit">Create</button>
+
+    <!-- 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('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() {
 
-    $('#edit-node-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-node-modal-form').submit();
-    });
-
-});
-
-
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_package_modal.html

@@ -1,45 +1,91 @@
-
 {% load static %}
-<!-- Edit Package -->
-<div id="edit_package_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Update Package</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="edit_package_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
-                <p>Edit a Package.</p>
-                <form id="edit-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-package-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
         {% csrf_token %}
-                    <p>
-                        <label for="package-name">Name</label>
-                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
-                    </p>
-                    <p>
-                        <label for="package-description">Description</label>
-                        <input id="package-description" type="text" class="form-control"
+
+        <div class="form-control mb-3">
+          <label class="label" for="package-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="package-name"
+            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">
-                    </p>
+            name="package-description"
+          />
+        </div>
       </form>
     </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() {
 
-    $('#edit-package-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-package-modal-form').submit();
-    });
+    <!-- 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('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>
 
-})
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,183 +1,271 @@
-
 {% load static %}
-<!-- Edit Package Permission -->
-<div id="edit_package_permissions_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Grant or Revoke Permissions</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+<!-- Edit Package Permissions -->
+<dialog
+  id="edit_package_permissions_modal"
+  class="modal"
+  x-data="{
+    updatePermissions(checkbox) {
+      const parts = checkbox.id.split('_');
+      const perm = parts[0];
+      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>
-            </div>
-            <div class="modal-body">
-                <p>
-                    Modify permissions for this package. Note that if you give <code>write</code>
-                    permissions to a user or group, <code>read</code> permissions will be granted automatically.
-                    <br>
-                    To allow users to perform destructive actions, such as deleting the package, <code>owner</code>
-                    permissions must be granted.
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        Modify permissions for this package. Note that if you give
+        <code class="badge badge-ghost">write</code> permissions to a user or
+        group, <code class="badge badge-ghost">read</code> permissions will be
+        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>
 
-                <div class="row">
-					<div class="col-xs-4">
-						<legend>User or Group</legend>
-					</div>
-					<div class="col-xs-2">
-						<legend>Read</legend>
-					</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">
+      <!-- Add New Permission -->
+      <form
+        id="modal-form-permissions"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+        class="mb-4"
+      >
         {% csrf_token %}
-                        <div class="col-xs-4">
-                            <select id="select_grantee" name="grantee" data-actions-box='true'
-                                    class="selPackages" data-width='100%'>
-                                <option disabled selected>User</option>
+        <div class="grid grid-cols-12 gap-2 items-end">
+          <div class="col-span-5">
+            <label class="label">
+              <span class="label-text">User or Group</span>
+            </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 %}
-                                <option disabled>Groups</option>
+              </optgroup>
+              <optgroup label="Groups">
                 {% for g in groups %}
                   <option value="{{ g.url }}">{{ g.name|safe }}</option>
                 {% endfor %}
+              </optgroup>
             </select>
           </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="read" id="read_new"/>
+          <div class="col-span-2 text-center">
+            <label class="label justify-center">
+              <span class="label-text">Read</span>
+            </label>
+            <input
+              type="checkbox"
+              name="read"
+              id="read_new"
+              class="checkbox"
+              @click="updatePermissions($el)"
+            />
           </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="write" id="write_new"/>
+          <div class="col-span-2 text-center">
+            <label class="label justify-center">
+              <span class="label-text">Write</span>
+            </label>
+            <input
+              type="checkbox"
+              name="write"
+              id="write_new"
+              class="checkbox"
+              @click="updatePermissions($el)"
+            />
           </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_new"/>
+          <div class="col-span-2 text-center">
+            <label class="label justify-center">
+              <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">
+            <button type="submit" class="btn btn-primary btn-sm">+</button>
           </div>
-                        <div class="col-xs-2">
-                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                                <span class="glyphicon glyphicon-plus"></span>
-                            </button>
         </div>
       </form>
-                </div>
-                <p></p>
+
+      <!-- User Permissions -->
+      {% if user_permissions %}
+        <div class="divider">User Permissions</div>
+        <div class="space-y-2">
           {% 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">
+            <form
+              id="modal-form-permissions_{{ up.user.uuid }}"
+              accept-charset="UTF-8"
+              action=""
+              method="post"
+            >
               {% csrf_token %}
-                        <div class="col-xs-4">
+              <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 }}"/>
+                  <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 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-xs-2">
-                            <input type="checkbox" name="write" id="write_{{ up.user.uuid }}" {% if up.has_write %} checked {% endif %}/>
+                <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($el)"
+                  />
                 </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_{{ up.user.uuid }}" {% if up.has_all %} checked {% endif %}/>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="owner"
+                    id="owner_{{ up.user.uuid }}"
+                    class="checkbox"
+                    {% if up.has_all %}checked{% endif %}
+                    @click="updatePermissions($el)"
+                  />
+                </div>
+                <div class="col-span-1">
+                  <button type="submit" class="btn btn-sm btn-ghost">✓</button>
                 </div>
-                        <div 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>
+        </div>
+      {% endif %}
+
+      <!-- Group Permissions -->
+      {% if group_permissions %}
+        <div class="divider">Group Permissions</div>
+        <div class="space-y-2">
           {% 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">
+            <form
+              id="modal-form-permissions_{{ gp.group.uuid }}"
+              accept-charset="UTF-8"
+              action=""
+              method="post"
+            >
               {% csrf_token %}
-                        <div class="col-xs-4">
+              <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 }}"/>
+                  <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 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($el)"
+                  />
                 </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="write" id="write_{{ gp.group.uuid }}" {% if gp.has_write %} checked {% endif %}/>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="write"
+                    id="write_{{ gp.group.uuid }}"
+                    class="checkbox"
+                    {% if gp.has_write %}checked{% endif %}
+                    @click="updatePermissions($el)"
+                  />
                 </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_{{ gp.group.uuid }}" {% if gp.has_all %} checked {% endif %}/>
+                <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 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>
+      {% endif %}
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+      >
+        Close
+      </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>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button>close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_password_modal.html

@@ -1,46 +1,119 @@
 {% load static %}
-<!-- Edit Package -->
-<div id="edit_password_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h5 class="modal-title">Update your Password</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="edit_password_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- 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>
-            </div>
-            <div class="modal-body">
-                <p>To change your password please fill out the following inputs</p>
-                <form id="edit-password-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <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 %}
-                    <p>
-                        <label for="old-password">Old Password</label>
-                        <input id="old-password" class="form-control" name="old-password" type="password" autocomplete="current-password">
-                    </p>
-                    <p>
-                        <label for="new-password">New Password</label>
-                        <input id="new-password" class="form-control" name="new-password" type="password", autocomplete="new-password">
-                    </p>
-                    <p>
-                        <label for="new-password-repeat">Repeat New Password</label>
-                        <input id="new-password-repeat" class="form-control" name="new-password-repeat" type="password" autocomplete="new-password">
-                    </p>
+        <input type="hidden" name="hidden" value="update-password" />
+
+        <div class="form-control mb-3">
+          <label class="label" for="old-password">
+            <span class="label-text">Old Password</span>
+          </label>
+          <input
+            id="old-password"
+            class="input input-bordered w-full"
+            name="old-password"
+            type="password"
+            autocomplete="current-password"
+            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">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="edit-password-modal-submit">Update</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-$(function() {
 
-    $('#edit-password-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-password-modal-form').submit();
-    });
+    <!-- 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="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>
 
-})
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/edit_pathway_modal.html

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

templates/modals/objects/edit_prediction_setting_modal.html

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

templates/modals/objects/edit_reaction_modal.html

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

templates/modals/objects/edit_rule_modal.html

@@ -1,45 +1,91 @@
-
 {% load static %}
-<!-- Edit Rule -->
-<div id="edit_rule_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
+
+<dialog
+  id="edit_rule_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <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>
-                <h3 class="modal-title">Update Rule</h3>
-            </div>
-            <div class="modal-body">
-                <form id="edit-rule-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-rule-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
         {% csrf_token %}
-                    <p>
-                        <label for="rule-name">Name</label>
-                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
-                    </p>
-                    <p>
-                        <label for="rule-description">Description</label>
-                        <input id="rule-description" type="text" class="form-control"
-                               value="{{ rule.description|safe }}" name="rule-description">
-                    </p>
+
+        <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"
+            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">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="edit-rule-modal-submit">Update</button>
+
+    <!-- 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('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() {
 
-    $('#edit-rule-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-rule-modal-form').submit();
-    });
-
-});
-
-
-</script>
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>