missing import

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

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wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

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Dockerfile

@@ -37,7 +37,7 @@ RUN mkdir -p -m 0700 /root/.ssh \
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
 # docker build --ssh default -t envipath/envipy-bayer:1.0 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable

bayer/models.py

@@ -185,7 +185,7 @@ class PESStructure(CompoundStructure):
     def create(
             compound: Compound,
             pes_link: str,
-            molfile: str,
+            mol_file: str,
             smiles: str,
             name: str = None,
             description: str = None,
@@ -204,7 +204,7 @@ class PESStructure(CompoundStructure):
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.smiles = smiles
-        cs.molfile = molfile
+        cs.mol_file = mol_file
         cs.pes_link = pes_link
         cs.compound = compound
 

bayer/templates/objects/compound_structure_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/compound_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound.default_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/node_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ node.default_node_label.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/views.py

@@ -2,13 +2,14 @@ import base64
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest
+from django.core.exceptions import BadRequest
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
 from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real, error
+from epdb.views import _anonymous_or_real
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
@@ -22,11 +23,7 @@ def create_pes(request, package_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -36,25 +33,25 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -68,11 +65,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -82,18 +75,18 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
@@ -116,7 +109,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -125,9 +118,6 @@ def fetch_pes(request, pes_url) -> dict:
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
-    if token is None:
-        token = pes_url.split('/')[-1] == 'dummy'
-
     if token:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):

bb4g/__init__.py

@@ -89,13 +89,14 @@ class BB4G(Classifier):
         }
 
         started = False
-
-        while not started:
+        retries = 0
+        while not started and retries < 5:
             res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
             logger.info(f"Starting BB4G: {res.status_code}")
             if res.status_code == 200:
                 started = True
             elif res.status_code in [500, 502]:
+                retries += 1
                 import time
                 time.sleep(5)
             else:
@@ -170,7 +171,7 @@ class BB4G(Classifier):
             }
 
             retries = 0
-            while retries < 100:
+            while retries < 5:
                 resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
                                      proxies=s.PROXIES or None)
 
@@ -178,7 +179,7 @@ class BB4G(Classifier):
                     retries += 1
                     logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
                     import time
-                    time.sleep(3)
+                    time.sleep(60)
                     continue
 
                 resp.raise_for_status()

docker-compose.dev.yml

@@ -28,11 +28,22 @@ services:
     image: git.envipath.com/envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
+#  web:
+#    image: envipath/envipy-bayer:1.0
+#    container_name: epdjango
+#    ports:
+#      - "127.0.0.1:8000:8000"
+#    env_file:
+#      - .env
+#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
+#    volumes:
+#      - ep_bayer_data:/opt/enviPy/
+
   celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.2
+    image: git.envipath.com/envipath/envipy-bayer:1.0
     container_name: epcelery
     env_file:
-      - .env
+      - .env.dev
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
       - ep_bayer_data:/opt/enviPy/

envipath/settings.py

@@ -354,7 +354,7 @@ DEFAULT_MODEL_PARAMS = {
     "num_chains": 10,
 }
 
-DEFAULT_MAX_NUMBER_OF_NODES = 9999
+DEFAULT_MAX_NUMBER_OF_NODES = 50
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
 

epdb/exceptions.py

@@ -1,5 +0,0 @@
-class InvalidSMILESException(Exception):
-    pass
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -633,14 +633,9 @@ class CompoundSchema(Schema):
     reviewStatus: str = Field(False, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     structures: List["CompoundStructureSchema"] = []
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
-    def resolve_pes_link(obj: Compound):
-        return getattr(obj.default_structure, "pes_link", None)
-
-    @staticmethod
-    def resolve_review_status(obj: Compound):
+    def resolve_review_status(obj: CompoundStructure):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -714,7 +709,6 @@ class CompoundStructureSchema(Schema):
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smiles: str = Field(None, alias="smiles")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_review_status(obj: CompoundStructure):
@@ -1693,15 +1687,14 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
-    idreact: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="smiles")
+    smiles: str = Field(None, alias="default_node_label.smiles")
     pseudo: bool = Field(False, alias="pseudo")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1714,10 +1707,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -2385,31 +2392,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@router.post("/util", response={200: Any, 403: Error})
-def predict(request, np: Form[NonPersistent]):
-    try:
-        print(request.user)
-        print(np.setting_url)
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-
-        from epdb.logic import SPathway
-
-        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
-        spw.predict()
-
-        return spw.to_json()
-
-    except ValueError:
-        return 403, {
-            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -1078,8 +1078,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1896,12 +1898,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

@@ -99,15 +99,11 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner, all_envipath_user_group):
-        p = PackageManager.import_legacy_package(
+    def import_package(self, data, owner):
+        return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
-        PackageManager.grant_read(owner, p, all_envipath_user_group)
-
-        return p
-
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -202,7 +198,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin, g)
+            imported_package = self.import_package(package_data, admin)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0025_auto_20260511_2025.py

@@ -23,7 +23,6 @@ MAPPING = {
     "true": HalfLifeModel.SFO,
     "SFO-SFO": HalfLifeModel.SFO_SFO,
     "DFOP-SFO": HalfLifeModel.DFOP_SFO,
-    "other": HalfLifeModel.OTHER,
 }
 
 

epdb/migrations/0027_alter_compound_aliases_and_more.py

@@ -1,150 +0,0 @@
-# Generated by Django 6.0.3 on 2026-07-01 20:59
-
-import django.contrib.postgres.fields
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0026_auto_20260602_1718"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="compound",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="default_structure",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                related_name="compound_default_structure",
-                to="epdb.compoundstructure",
-                verbose_name="Default Structure",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="edge_label",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                to="epdb.reaction",
-                verbose_name="Edge label",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="medline_references",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(),
-                blank=True,
-                null=True,
-                verbose_name="Medline References",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="rules",
-            field=models.ManyToManyField(
-                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-    ]

epdb/models.py

@@ -31,7 +31,6 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import InvalidSMILESException
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -577,10 +576,6 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
-    def contains_pes(self):
-        from bayer.models import PESStructure
-        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
-            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #
@@ -637,7 +632,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -660,9 +655,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -788,7 +781,7 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.SET_NULL,
+        on_delete=models.CASCADE,
         null=True,
     )
 
@@ -865,17 +858,13 @@ class Compound(
         package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
-            raise InvalidSMILESException("SMILES is required")
+            raise ValueError("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise InvalidSMILESException("Given SMILES is invalid")
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            raise ValueError("Given SMILES is invalid")
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -887,14 +876,7 @@ class Compound(
 
         # Check if we find a direct match for a given SMILES
         if qs.exists():
-            found_structure = qs.first()
-            found_compound = found_structure.compound
-
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
+            return qs.first().compound
 
 
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
@@ -904,19 +886,16 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            found_structure = qs.first()
-            found_compound = found_structure.compound
-
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
+            return qs.first().compound
 
         # Generate Compound
         c = Compound()
         c.package = package
 
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -1167,27 +1146,18 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
+        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ):
-        # Clean for potential XSS
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
-
-            if name:
-                found_cs.add_alias(name)
-
-            return found_cs
+            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-
+        # Clean for potential XSS
         if name is not None:
-            cs.name = name
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1195,10 +1165,6 @@ class CompoundStructure(
         cs.smiles = smiles
         cs.compound = compound
 
-        # Check if molfile is present and valid
-        if molfile is not None and FormatConverter.from_molfile(molfile) is not None:
-            cs.molfile = molfile
-
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
 
@@ -1216,8 +1182,6 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
-        if self.molfile is not None and self.molfile.strip() != "":
-            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1415,9 +1379,6 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1429,17 +1390,14 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-
-            found_rule = query.first()
-
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
+            return query.first()
 
         r = SimpleAmbitRule()
         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}"
 
@@ -1660,15 +1618,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1685,13 +1638,8 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = False,
+        multi_step: bool = True,
     ):
-
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         _educts = []
         _products = []
 
@@ -1746,19 +1694,14 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-
-            found_reaction = existing_reaction_qs.first()
-
-            if name:
-                found_reaction.add_alias(name)
-
-            return found_reaction
+            return existing_reaction_qs.first()
 
         r = Reaction()
         r.package = package
 
-        if r is not None:
-            r.name = name
+        # Clean for potential XSS
+        if name is not None and name.strip() != "":
+            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -2262,12 +2205,10 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         depth_map[0] = list()
         processed = set()
 
-        data_driven_root_nodes = (
-            self.node_set.all()
-            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
-            .filter(prod_cnt=0, educt_cnt__gt=0)
-            .distinct()
-        )
+        data_driven_root_nodes = self.node_set.all().annotate(
+            prod_cnt=Count('edge_products'),
+            educt_cnt=Count('edge_educts')
+        ).filter(prod_cnt=0, educt_cnt__gt=0).distinct()
 
         # Eval QuerySet
         root_nodes_by_depth = list(self.root_nodes)
@@ -2360,12 +2301,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
-                if self.default_node_label.molfile is not None
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
+                self.default_node_label.smiles, width=40, height=40
             ),
             "image_type": "svg",
             "name": self.get_name(),
@@ -2379,7 +2315,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.is_proposed_intermediate(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2420,11 +2355,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     @property
     def as_svg(self):
-        if (
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
-            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
@@ -2453,26 +2383,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return data
 
-    def is_proposed_intermediate(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-                type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"]
-                , scenario__isnull=False
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
-
-            if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = ai.get().importance.value
-
-        return list(collected.values())
-
     def simple_json(self, include_description=False):
         res = super().simple_json()
         name = res.get("name", None)

epdb/views.py

@@ -19,7 +19,6 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -786,11 +785,6 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -803,14 +797,12 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
-
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
+            "EnviFormer": {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
+        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -818,9 +810,6 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
-                    "additional_parameters": v.Config.__name__.lower()
-                    if v.Config.__name__ != ""
-                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -829,6 +818,12 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
+        # Context for paginated template
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -943,12 +938,13 @@ def package_models(request, package_uuid):
                 "requires_data_packages": True,
             },
         }
+
         if s.ENVIFORMER_PRESENT:
             context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1124,11 +1120,6 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
-                        res["pred"] = sorted(
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
-
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1232,7 +1223,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -2368,13 +2361,7 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-
-        try:
-            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        except InvalidSMILESException:
-            return error(
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
 
         return redirect(current_pathway.url)
 
@@ -2482,22 +2469,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.name = new_node_name
-
-            if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.description = new_node_description
-
-            current_node.save()
-            return redirect(current_node.url)
-
-        return error(request, "Node update failed!", "No changes were made to the node")
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -3029,15 +3001,9 @@ def settings(request):
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         # min 2, max s.DEFAULT_MAX_NUMBER_OF_NODES
-        temp_max_nodes = request.POST.get("prediction-setting-max-nodes")
-        if temp_max_nodes is None or temp_max_nodes == "" or int(temp_max_nodes) == -1:
-            temp_max_nodes = s.DEFAULT_MAX_NUMBER_OF_NODES
-        else:
-            temp_max_nodes = int(request.POST.get("prediction-setting-max-nodes", 1))
-
         max_nodes = min(
             max(
-                temp_max_nodes,
+                int(request.POST.get("prediction-setting-max-nodes", 1)),
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -3058,7 +3024,6 @@ def settings(request):
 
             model_uuid = model_url.split("/")[-1]
             params["model"] = EPModel.objects.get(uuid=model_uuid)
-            # TODO Check if removed if request contains "" or not at all
             params["model_threshold"] = request.POST.get(
                 "model-based-prediction-setting-threshold", s.DEFAULT_MODEL_THRESHOLD
             )

migration/views.py

@@ -81,7 +81,6 @@ def migration(request):
         "bt0416-4269",
         "bt0432-4254",
         "bt0337-4117",
-        "bt0322-3393",
     ]
 
     if request.method == "GET":

static/css/input.css

@@ -34,12 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-select.select[multiple] {
-  display: block;
-  white-space: normal;
-}
-
-p a {
-  @apply underline;
-}

static/js/alpine/pagination.js

@@ -5,125 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    }));
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/pw.js

@@ -1,37 +1,5 @@
 console.log("loaded pw.js")
 
-function findPaths(source_idx, links) {
-    const resultLinks = new Set();
-    const visited = new Set();
-    // Helper function for depth-first search
-    function dfs(current) {
-
-        if (visited.has(current)) {
-            return;
-        }
-
-        if (links.filter(link => link.target.id === current).length === 0) {
-            return;
-        }
-
-        visited.add(current);
-        links.forEach(link => {
-            if (
-                link.target.id === current &&
-                !visited.has(link.source.id) &&
-                link.source.id !== link.target.id // Avoid self-loops
-            ) {
-                resultLinks.add(link); // Add link to result
-                dfs(link.source.id);
-            }
-        });
-        visited.delete(current);
-    }
-    // Start DFS
-    dfs(source_idx);
-    return Array.from(resultLinks);
-}
-
 function predictFromNode(url) {
     fetch("", {
         method: "POST",
@@ -67,9 +35,6 @@ function draw(pathway, elem) {
         const horizontalSpacing = 75; // horizontal space between nodes
         const depthMap = new Map();
 
-        // Avoid leaving unconnected Nodes leaving the viewport
-        nodes.forEach(node => {if (node.depth < 0)  node.depth = 0;});
-
         // Sort nodes by depth first to minimize crossings
         const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth);
 
@@ -157,10 +122,6 @@ function draw(pathway, elem) {
         });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
-
-        linkText
-         .attr("x", d => (d.source.x + d.target.x) / 2)
-         .attr("y", d => (d.source.y + d.target.y) / 2);
     }
 
     function dragstarted(event, d) {
@@ -263,7 +224,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 500;
+    var popupWaitBeforeShow = 1000;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -654,68 +615,48 @@ function draw(pathway, elem) {
         .on("tick", ticked);
 
     // Kanten zeichnen
-    const linkGroup = zoomable.append("g")
-      .selectAll("g")
-      .data(links)
-      .enter()
-      .append("g")
-      .attr("class", "link-group");
-
-    const link = linkGroup
-      .append("path")
-      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-      .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)")
-      .attr("fill", "none")
-
-      // Check if target is pseudo and draw marker only if not pseudo
-      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-      .attr("marker-end", d => {
-        if (d.target.pseudo) return '';
-        if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
-          return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
-        }
-      )
-      .attr("fill", "none")
-      .on("click", function(event, d) {
+    const link = zoomable.append("g")
+        .selectAll("path")
+        .data(links)
+        .enter().append("path")
+        // Check if target is pseudo and draw marker only if not pseudo
+        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+        .attr("marker-end", d => {
+            if (d.target.pseudo) return '';
+            if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
+            return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
+        })
+        .attr("fill", "none")
+	.on("click", function(event, d) {
           const wasHighlighted = d3.select(this).classed("highlighted");
-          d3.selectAll("path").classed("highlighted", false);
+
+	  d3.selectAll("path").classed("highlighted", false);
+
           if (!wasHighlighted) {
-            const toHighlight = [];
-            toHighlight.push(d.el);
+              const toHighlight = [];
+              toHighlight.push(d.el);
 
-            if (d.source.pseudo || d.target.pseudo) {
-              if (d.target.pseudo) {
-                d3.selectAll("path").each(e => {
-                  if (e !== undefined && e.source.id === d.target.id) {
-                    toHighlight.push(e.el);
+              if (d.source.pseudo || d.target.pseudo) {
+                  if (d.target.pseudo) {
+                      d3.selectAll("path").each(e => {
+                          if (e !== undefined && e.source.id === d.target.id) {
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  } else {
+                      d3.selectAll("path").each(e => {
+                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                              toHighlight.push(e.el);
+                          }
+                      });
                   }
-                });
-              } else {
-                d3.selectAll("path").each(e => {
-                  if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
-                    toHighlight.push(e.el);
-                  }
-                });
               }
-            }
 
-            for (const e of toHighlight) {
-              d3.select(e).classed("highlighted", true);
-            }
+              for (const e of toHighlight) {
+                  d3.select(e).classed("highlighted", true);
+              }
           }
-        });
-
-    const linkText = linkGroup
-      .append("text")
-      .attr("class", "link-label")
-      .attr("text-anchor", "middle")
-      .attr("dy", -6)
-      .style("font-size", "4px")
-      .style("pointer-events", "none")
-      .style("display", "none")
-      .text(d => d.name)
-      .attr("x", d => (d.source.x + d.target.x) / 2)
-      .attr("y", d => (d.source.y + d.target.y) / 2);
+      })
 
     // add element to links array
     link.each(function (d) {
@@ -732,41 +673,16 @@ function draw(pathway, elem) {
         .call(d3.drag()
             .on("start", dragstarted)
             .on("drag", dragged)
-            .on("end", dragended)
-        )
+            .on("end", dragended))
         .on("click", function (event, d) {
-          const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
-          d3.selectAll('circle.highlighted').classed('highlighted', false);
-          d3.selectAll("path").classed("inedge", false);
-          d3.selectAll("path").classed("outedge", false);
+            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
 
-          if (!wasHighlighted) {
-            d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            const inEdges = findPaths(d.id, links);
-            const outEdges = []
-            // Colorize out edges green
-            for (const l of links) {
-              if (l.source.id === d.id) {
-                outEdges.push(l);
-                if (l.target.pseudo) {
-                  for (const l2 of links) {
-                    if (l.target.id === l2.source.id) {
-                      outEdges.push(l2);
-                    }
-                  }
-                }
-              }
-            }
+            d3.selectAll('circle.highlighted').classed('highlighted', false);
 
-            for (const e of inEdges) {
-              d3.select(e.el).classed("inedge", true);
+            if (!wasHighlighted) {
+                d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
             }
-
-            for (const e of outEdges) {
-              d3.select(e.el).classed("outedge", true);
-            }
-          }
-        });
+        })
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -840,14 +756,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("path.link").forEach(line => {
+    svgElement.querySelectorAll("line.link").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);
         line.setAttribute("fill", style.fill);
     });
 
-    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

templates/modals/objects/add_pathway_edge_modal.html

@@ -5,7 +5,6 @@
   x-data="{
     isSubmitting: false,
     reactionImageUrl: '',
-    pes: false,
 
     reset() {
       this.isSubmitting = false;
@@ -16,30 +15,20 @@
       const substratesSelect = document.getElementById('add_pathway_edge_substrates');
       const productsSelect = document.getElementById('add_pathway_edge_products');
 
-      const pesLinks = [];
-
       const substrates = [];
       for (const option of substratesSelect.selectedOptions) {
         substrates.push(option.dataset.smiles);
-        if (option.dataset.pes === 'true') {
-          pesLinks.push(option.dataset.pes);
-        }
       }
 
       const products = [];
       for (const option of productsSelect.selectedOptions) {
         products.push(option.dataset.smiles);
-        if (option.dataset.pes === 'true') {
-          pesLinks.push(option.dataset.pes);
-        }
       }
 
       if (substrates.length > 0 && products.length > 0) {
         const reaction = substrates.join('.') + '>>' + products.join('.');
         this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
-        this.pes = pesLinks.length > 0;
       } else {
-        this.pes = false;
         this.reactionImageUrl = '';
       }
     },
@@ -117,7 +106,6 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
-                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -144,7 +132,6 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
-                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -157,9 +144,6 @@
 
         <div class="mb-3" x-show="reactionImageUrl" x-cloak>
           <img :src="reactionImageUrl" class="w-full" alt="Reaction preview" />
-          <div x-show="pes">
-            <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-          </div>
         </div>
       </form>
     </div>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -6,6 +6,7 @@
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
   @modal-opened.window="
    const links = d3.selectAll('path.highlighted');
+
    if (!links.empty()) {
         const el = links.node();
         const selectElement = document.getElementById('delete_pathway_edge_edges');
@@ -17,7 +18,9 @@
                 break;
             }
         }
+
         selectElement.dispatchEvent(new Event('change'));
+
    }
   "
   @close="reset()"

templates/modals/objects/delete_pathway_node_modal.html

@@ -6,14 +6,17 @@
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
   @modal-opened.window="
    const el = d3.select('circle.highlighted').node();
+
    if (el !== null) {
     const selectElement = document.getElementById('delete_pathway_node_nodes');
+
     for (let option of selectElement.options) {
         if (option.value === el.__data__.url) {
             option.selected = true;
             break;
         }
     }
+
     selectElement.dispatchEvent(new Event('change'));
    }
   "

templates/objects/edge.html

@@ -82,9 +82,6 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ edge.edge_label.as_svg|safe }}</div>
       </div>
-      {% if edge.edge_label.contains_pes %}
-        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-      {% endif %}
     </div>
 
     <!-- Reaction Description -->
@@ -95,7 +92,7 @@
         <div class="flex flex-wrap items-center justify-center gap-4">
           {% for educt in edge.start_nodes.all %}
             <a href="{{ educt.url }}" class="btn btn-outline btn-sm"
-              >{{ educt.get_name }}</a
+              >{{ educt.name }}</a
             >
           {% endfor %}
           <svg
@@ -115,7 +112,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.get_name }}</a
+              >{{ product.name }}</a
             >
           {% endfor %}
         </div>

templates/objects/group.html

@@ -56,10 +56,8 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a
-                href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}"
-                class="hover:bg-base-300"
-                >{{ um.username }}
+                <a href="{% if not user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
+                  >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >
             </li>

templates/objects/node.html

@@ -55,15 +55,6 @@
       </div>
     </div>
 
-    <!-- Description -->
-    {% if node.description and node.description != "no description" %}
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Description</div>
-        <div class="collapse-content">{{ node.description }}</div>
-      </div>
-    {% endif %}
-
     {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
 
     {% for tpl in viz_templates %}

templates/objects/pathway.html

@@ -21,7 +21,6 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
-      stroke-width: 1.5px;
       /* marker-end: url(#arrow); */
     }
 
@@ -73,15 +72,6 @@
       stroke: red;
       stroke-width: 3px;
     }
-
-    .inedge {
-      stroke: red;
-      stroke-width: 3px;
-    }
-    .outedge {
-      stroke: green;
-      stroke-width: 3px;
-    }
   </style>
   <script src="{% static 'js/pw.js' %}"></script>
 
@@ -121,7 +111,7 @@
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
       </div>
-      <div class="collapse-content">
+      <div class="collapse-content ">
         <div class="bg-base-100 mb-2 rounded-lg p-2">
           <div class="navbar bg-base-100 rounded-lg">
             <div class="flex-1">
@@ -178,52 +168,6 @@
                   tabindex="0"
                   class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2"
                 >
-                  <li>
-                    <a id="compound-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="compound-names-icon"
-                          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-eye"
-                        >
-                          <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
-                          <circle cx="12" cy="12" r="3" />
-                        </svg>
-                      Compound Names
-                    </a>
-                  </li>
-                  <li>
-                    <a id="reaction-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="reaction-names-icon"
-                          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-eye"
-                        >
-                          <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
-                          <circle cx="12" cy="12" r="3" />
-                        </svg>
-                      Reaction Names
-                    </a>
-                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -249,7 +193,6 @@
                       </a>
                     </li>
                   {% endif %}
-                  {% if 1 == 0 %}
                   <li>
                     <a id="timeseries-toggle-button" class="cursor-pointer">
                       <svg
@@ -300,7 +243,6 @@
                       Show Predicted Properties
                     </a>
                   </li>
-                  {% endif %}
                 </ul>
               </div>
             </div>
@@ -544,10 +486,6 @@
   {{ pathway.d3_json|json_script:"pathway" }}
 
   <script>
-    // Global switch for compound names view
-    var compoundNamesViewEnabled = false;
-    // Gloabl switch for reaction names view
-    var reactionNamesViewEnabled = false;
     // Global switch for app domain view
     var appDomainViewEnabled = false;
     // Global switch for timeseries view
@@ -583,67 +521,6 @@
         descContent.innerHTML = newDesc;
       }
 
-      const compoundNamesBtn = document.getElementById("compound-names-toggle-button");
-      if (compoundNamesBtn) {
-        compoundNamesBtn.addEventListener("click", function () {
-          compoundNamesViewEnabled = !compoundNamesViewEnabled;
-          const icon = document.getElementById("compound-names-icon");
-
-          if (compoundNamesViewEnabled) {
-            // Change to eye-off icon
-            icon.innerHTML =
-              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
-            nodes.forEach((x) => {
-              if (x.name) {
-                d3.select(x.el)
-                  .append("text")
-                  .text(d => d.name)
-                  .attr("text-anchor", "middle")
-                  .attr("y", -20)
-                  .style("font-size", "4px");
-              }
-            });
-          } else {
-            // Change back to eye icon
-            icon.innerHTML =
-              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
-            nodes.forEach((x) => {
-              d3.select(x.el)
-                .select("text")
-                .remove()
-            })
-          }
-        });
-      }
-
-      const reactionNamesBtn = document.getElementById("reaction-names-toggle-button");
-      if (reactionNamesBtn) {
-        reactionNamesBtn.addEventListener("click", function () {
-          reactionNamesViewEnabled = !reactionNamesViewEnabled;
-          const icon = document.getElementById("reaction-names-icon");
-
-          if (reactionNamesViewEnabled) {
-            // Change to eye-off icon
-            icon.innerHTML =
-              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
-              d3.selectAll(".link-label")
-                .style("display", null);
-
-          } else {
-            // Change back to eye icon
-            icon.innerHTML =
-              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
-            d3.selectAll(".link-label")
-                .style("display", "none");
-
-          }
-        });
-      }
-
       // App domain toggle
       const appDomainBtn = document.getElementById("app-domain-toggle-button");
       if (appDomainBtn) {

templates/objects/reaction.html

@@ -79,9 +79,6 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ reaction.as_svg|safe }}</div>
       </div>
-      {% if reaction.contains_pes %}
-        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-      {% endif %}
     </div>
 
     <!-- Reaction Description -->

templates/objects/setting_template.html

@@ -24,76 +24,6 @@
         <td>Setting Name</td>
         <td>{{ setting_to_render.name }}</td>
       </tr>
-      <tr>
-        <td>Setting URL</td>
-        <td>
-          <a href="{{ setting_to_render.url }}" class="link link-primary">{{ setting_to_render.url }}</a>
-          <div
-            x-data="{
-              value: '{{ setting_to_render.url }}',
-              copied: false,
-
-              async copy() {
-                await navigator.clipboard.writeText(this.value)
-                this.copied = true
-
-                setTimeout(() => {
-                  this.copied = false
-                }, 1500)
-              }
-            }"
-            class="join"
-          >
-          <button
-            type="button"
-            class="btn btn-ghost"
-            :data-tip="copied ? 'Copied!' : 'Copy'"
-            @click="copy"
-            aria-label="Copy to clipboard"
-          >
-            <svg
-              x-show="!copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M8 16H6a2 2 0 01-2-2V6a2 2 0 012-2h8a2 2 0 012 2v2"
-              />
-              <rect
-                width="12"
-                height="12"
-                x="8"
-                y="8"
-                rx="2"
-                ry="2"
-              />
-            </svg>
-
-            <svg
-              x-show="copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M5 13l4 4L19 7"
-              />
-            </svg>
-            </button>
-          </div>
-        </td>
-      </tr>
       {% if setting_to_render.description %}
         <tr>
           <td>Setting Description</td>

templates/predict_pathway.html

@@ -212,13 +212,7 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-
-        // Set text depending on mode
-        if (document.getElementById("predict-submit-button").innerText === "Build") {
-          button.textContent = "Building...";
-        } else {
-          button.textContent = "Predicting...";
-        }
+        button.textContent = "Predicting...";
 
         // Get SMILES from either input or Ketcher
         const smilesInput = document.getElementById("predict-smiles");

tests/test_compound_model.py

@@ -1,7 +1,5 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
-
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -35,13 +33,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -98,7 +96,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(
                 self.package,
                 smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",

tests/test_reaction_model.py

@@ -1,7 +1,6 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
@@ -164,7 +163,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_model_views.py

@@ -46,14 +46,6 @@ class ModelViewTest(TestCase):
         )
 
         expected = [
-            {
-                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
-                "probability": 0.75,
-                "btrule": {
-                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
-                    "name": "bt0001-3568",
-                },
-            },
             {
                 "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
@@ -70,6 +62,14 @@ class ModelViewTest(TestCase):
                     "name": "bt0243-4301",
                 },
             },
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
         ]
 
         actual = response.json()["pred"]

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#ad825570480bbe2f1a35c04923fede756c450751" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
 dependencies = [
     { name = "pydantic" },
 ]