Make links thicker, reduce timeout trigger time

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

wip

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

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

bayer/additional_information/__init__.py

@@ -0,0 +1,178 @@
+import enum
+from typing import Optional
+
+from envipy_additional_information import GroupEnum as G
+from envipy_additional_information import SubcategoryEnum as S
+from envipy_additional_information import (
+    register,
+    register_parser_command,
+    EnviPyModel,
+    # EnviPyModelParser,
+    Interval,
+    UIConfig,
+    IntervalConfig,
+    WidgetType,
+    registry,
+)
+
+
+@register(keyname="compoundlabel", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
+class CompoundLabel(EnviPyModel):
+    label: str
+
+    class UI:
+        title = "Compound Label"
+        label = UIConfig(widget=WidgetType.TEXT, label="Label", order=1)
+
+
+# TODO Expose EnviPyModelParser in lib and subclass
+@register_parser_command("compoundlabel")
+class CompoundLabelParser:
+    @staticmethod
+    def from_string(data: str) -> CompoundLabel:
+        return CompoundLabel(label=data)
+
+
+@register(keyname="studywaterstoragecapacity", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
+class StudyWaterStorageCapacity(EnviPyModel):
+    capacity: str
+
+    class UI:
+        title = "Study Water Storage Capacity"
+        capacity = UIConfig(widget=WidgetType.TEXT, label="Study Water Storage Capacity", order=1)
+
+
+# TODO Expose EnviPyModelParser in lib and subclass
+@register_parser_command("studywst")
+class StudyWaterStorageCapacityParser:
+    @staticmethod
+    def from_string(data: str) -> StudyWaterStorageCapacity:
+        return StudyWaterStorageCapacity(capacity=data)
+
+
+class ObservationType(enum.Enum):
+    OBSERVED = "observed"
+    APPLIED = "applied"
+    NA = 'NA'
+
+
+@register(keyname="observation", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
+class Observation(EnviPyModel):
+    type: ObservationType
+    min_value: Optional[float] = None
+    max_value: Optional[float] = None
+
+    class UI:
+        title = "Observation"
+        type = UIConfig(widget=WidgetType.SELECT, label="Observed or Applied", order=1)
+        min_value = UIConfig(widget=WidgetType.NUMBER, label="Min Value", order=2)
+        max_value = UIConfig(widget=WidgetType.NUMBER, label="Max Value", order=3)
+
+
+# TODO Expose EnviPyModelParser in lib and subclass
+@register_parser_command("observation")
+class ObservationParser:
+    @staticmethod
+    def from_string(data: str) -> Observation:
+        parts = data.split(";")
+
+        observation_type = ObservationType(parts[0])
+        min_value = None
+        if parts[1]:
+            try:
+                min_value = float(parts[1])
+            except ValueError:
+                pass
+
+        max_value = None
+        if parts[2]:
+            try:
+                max_value = float(parts[2])
+            except ValueError:
+                pass
+
+        return Observation(type=observation_type, min_value=min_value, max_value=max_value)
+
+
+@register(keyname="kinetics", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
+class Kinetics(EnviPyModel):
+    dt50: Interval[float]
+    normalized_dt50: bool
+    chi2err: Optional[float] = None
+    t_test: Optional[float] = None
+    swarc: Optional[float] = None
+    visual_fit: Optional[int] = None
+    comment: str
+    source: str
+    kinetic_model: str
+    k1: Optional[float] = None
+    k2: Optional[float] = None
+    g: Optional[float] = None
+    tb: Optional[float] = None
+    alpha: Optional[float] = None
+    beta: Optional[float] = None
+
+    class UI:
+        title = "Kinetics"
+
+        # Field config
+        dt50 = IntervalConfig(label="DT50 Range", order=1, unit="d")
+        normalized_dt50 = UIConfig(widget=WidgetType.CHECKBOX, label="Normalized DT50", order=2)
+        chi2err = UIConfig(widget=WidgetType.NUMBER, label="Chi2err", order=3)
+        t_test = UIConfig(widget=WidgetType.NUMBER, label="T-Test", order=4)
+        swarc = UIConfig(widget=WidgetType.NUMBER, label="SWARC", order=5)
+        visual_fit = UIConfig(widget=WidgetType.NUMBER, label="Visual Fit", order=6)
+        comment = UIConfig(widget=WidgetType.TEXTAREA, label="Comments", order=7)
+        source = UIConfig(widget=WidgetType.TEXT, label="Source", order=8)
+        kinetic_model = UIConfig(widget=WidgetType.SELECT, label="Kinetic Model", order=9)
+        k1 = UIConfig(widget=WidgetType.NUMBER, label="K1", order=10)
+        k2 = UIConfig(widget=WidgetType.NUMBER, label="K2", order=11)
+        g = UIConfig(widget=WidgetType.NUMBER, label="G", order=12)
+        tb = UIConfig(widget=WidgetType.NUMBER, label="TB", order=13)
+        alpha = UIConfig(widget=WidgetType.NUMBER, label="Alpha", order=14)
+        beta = UIConfig(widget=WidgetType.NUMBER, label="Beta", order=15)
+
+
+# TODO Expose EnviPyModelParser in lib and subclass
+@register_parser_command("kineticevaluation")
+class KinecticsParser:
+    @staticmethod
+    def from_string(data: str) -> Kinetics:
+        parts = data.split(";")
+        dt50 = registry.get_parser("interval").from_string(parts[0])
+        normalized_dt50 = parts[1] == "true"
+        chi2err = float(parts[2]) if parts[2] else None
+        t_test = float(parts[3]) if parts[3] else None
+        swarc = float(parts[4]) if parts[4] else None
+        visual_fit = int(parts[5]) if parts[5] else None
+        comment = parts[6]
+        source = parts[7]
+        kinetic_model = parts[8]
+        k1 = float(parts[9]) if parts[9] else None
+        k2 = float(parts[10]) if parts[10] else None
+        g = float(parts[11]) if parts[11] else None
+        tb = float(parts[12]) if parts[12] else None
+        alpha = float(parts[13]) if parts[13] else None
+        beta = float(parts[14]) if parts[14] else None
+
+        return Kinetics(
+            dt50=dt50,
+            normalized_dt50=normalized_dt50,
+            chi2err=chi2err,
+            t_test=t_test,
+            swarc=swarc,
+            visual_fit=visual_fit,
+            comment=comment,
+            source=source,
+            kinetic_model=kinetic_model,
+            k1=k1,
+            k2=k2,
+            g=g,
+            tb=tb,
+            alpha=alpha,
+            beta=beta,
+        )
+
+
+if __name__ == '__main__':
+    print(KinecticsParser.from_string("187.0 - 187.0;false;;;;;;;AFO;;;;;;"))

bayer/epdb_hooks.py

@@ -1,5 +1,6 @@
 import logging
 
+from bayer import additional_information  # noqa: F401
 from epdb.template_registry import register_template
 
 logger = logging.getLogger(__name__)
@@ -36,4 +37,4 @@ register_template(
 register_template(
     "epdb.objects.node.viz",
     "objects/node_viz.html",
-)
+)

bayer/models.py

@@ -185,7 +185,7 @@ class PESStructure(CompoundStructure):
     def create(
             compound: Compound,
             pes_link: str,
-            mol_file: str,
+            molfile: 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.mol_file = mol_file
+        cs.molfile = molfile
         cs.pes_link = pes_link
         cs.compound = compound
 

bayer/templates/objects/compound_structure_viz.html

@@ -3,7 +3,11 @@
   <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">{{ compound_structure.pes_link }}</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>
 
   <!-- Image Representation -->

bayer/templates/objects/compound_viz.html

@@ -3,7 +3,11 @@
   <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">{{ compound.default_structure.pes_link }}</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>
 
   <!-- Image Representation -->

bayer/templates/objects/node_viz.html

@@ -3,7 +3,11 @@
   <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">{{ node.default_node_label.pes_link }}</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>
 
   <!-- Image Representation -->

bayer/views.py

@@ -2,14 +2,13 @@ import base64
 
 import requests
 from django.conf import settings as s
-from django.core.exceptions import BadRequest
-from django.http import HttpResponse
+from django.http import HttpResponse, HttpResponseBadRequest
 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
+from epdb.views import _anonymous_or_real, error
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
@@ -23,7 +22,11 @@ def create_pes(request, package_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
+            return error(
+                request,
+                f'Creation of PESs for package {current_package.name} failed!',
+                "Creating PESs for internal packages is not allowed.",
+            )
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -33,21 +36,25 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
+                return HttpResponseBadRequest(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.")
+
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return BadRequest(
+                        return HttpResponseBadRequest(
                             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 BadRequest("Please provide a PES link.")
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -61,7 +68,11 @@ def create_pes_node(request, package_uuid, pathway_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
+            return error(
+                request,
+                f'Creation of PESs for package {current_package.name} failed!',
+                "Creating PESs for internal packages is not allowed.",
+            )
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -71,18 +82,18 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
+                return HttpResponseBadRequest(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 BadRequest("Cannot create PESs for non-secret packages.")
+                    return HttpResponseBadRequest("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 BadRequest(
+                        return HttpResponseBadRequest(
                             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)
@@ -105,7 +116,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return BadRequest("Please provide a PES link.")
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -114,6 +125,9 @@ 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

@@ -1,12 +1,13 @@
+import enum
 import json
+import logging
 import math
 from datetime import datetime
 from typing import List
-import enum
+
 import requests
 from django.conf import settings as s
-from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
-from envipy_additional_information import register
+from envipy_additional_information import register, EnviPyModel, UIConfig, WidgetType
 
 from bridge.contracts import Classifier  # noqa: I001
 from bridge.dto import (
@@ -17,6 +18,9 @@ from bridge.dto import (
     TransformationProductPrediction,
 )  # noqa: I001
 
+logger = logging.getLogger("epdb")
+
+
 class SamplingAlgorithm(enum.Enum):
     EXACT = "exact"
 
@@ -85,14 +89,13 @@ class BB4G(Classifier):
         }
 
         started = False
-        retries = 0
-        while not started and retries < 5:
-            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
 
+        while not started:
+            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:
@@ -166,18 +169,30 @@ class BB4G(Classifier):
                 "cutoff": self.config.cutoff,
             }
 
-            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
+            retries = 0
+            while retries < 100:
+                resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
+                                     proxies=s.PROXIES or None)
 
-            resp.raise_for_status()
+                if resp.status_code == 418:
+                    retries += 1
+                    logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
+                    import time
+                    time.sleep(3)
+                    continue
 
-            for substrate, predictions in resp.json().items():
-                preds = {}
+                resp.raise_for_status()
 
-                for pred in predictions:
-                    prod = pred["prediction"]
-                    prob = math.exp(pred["log_likelihood"])
-                    preds[prod] = prob
+                for substrate, predictions in resp.json().items():
+                    preds = {}
 
-                result[substrate] = preds
+                    for pred in predictions:
+                        prod = pred["prediction"]
+                        prob = math.exp(pred["log_likelihood"])
+                        preds[prod] = prob
+
+                    result[substrate] = preds
+
+                break
 
         return result

bridge/contracts.py

@@ -261,7 +261,6 @@ class Classifier(Plugin):
             for k, v in data.items():
                 if v != "":
                     cpy[k] = v
-
         return cls.Config(**cpy)
 
     @classmethod

docker-compose.dev.yml

@@ -25,25 +25,14 @@ services:
       - ep_bayer_redis_data:/data
 
   biotransformer3:
-    image: envipath/biotransformer3:1.0
+    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: envipath/envipy-bayer:1.0
+    image: git.envipath.com/envipath/envipy-bayer:1.2
     container_name: epcelery
     env_file:
-      - .env.dev
+      - .env
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
       - ep_bayer_data:/opt/enviPy/

envipath/settings.py

@@ -275,6 +275,12 @@ LOGGING = {
             "filename": os.path.join(LOG_DIR, "debug.log"),
             "formatter": "simple",
         },
+        "auth_file": {
+            "level": "INFO",  # Or higher
+            "class": "logging.FileHandler",
+            "filename": os.path.join(LOG_DIR, "auth.log"),
+            "formatter": "simple",
+        }
     },
     "loggers": {
         # For everything under epdb/ loaded via getlogger(__name__)
@@ -295,6 +301,11 @@ LOGGING = {
             "propagate": True,
             "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
+        "auth": {
+            "handlers": ["auth_file"],
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
+        }
     },
 }
 
@@ -343,7 +354,7 @@ DEFAULT_MODEL_PARAMS = {
     "num_chains": 10,
 }
 
-DEFAULT_MAX_NUMBER_OF_NODES = 50
+DEFAULT_MAX_NUMBER_OF_NODES = 9999
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
 

epdb/exceptions.py

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

epdb/legacy_api.py

@@ -633,9 +633,14 @@ 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_review_status(obj: CompoundStructure):
+    def resolve_pes_link(obj: Compound):
+        return getattr(obj.default_structure, "pes_link", None)
+
+    @staticmethod
+    def resolve_review_status(obj: Compound):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -709,6 +714,7 @@ 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):
@@ -871,6 +877,10 @@ def create_package_compound(
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
+
+                if p.classification_level != Package.Classification.SECRET:
+                    return 400, {"Cannot create PESs for non-secret packages."}
+
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
@@ -1683,14 +1693,15 @@ 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="default_node_label.url")
-    idreact: str = Field(None, alias="default_node_label.url")
+    idcomp: str = Field(None, alias="node_label_id")
+    idreact: str = Field(None, alias="node_label_id")
     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="default_node_label.smiles")
+    smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
+    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1703,24 +1714,10 @@ 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")
@@ -2388,3 +2385,31 @@ 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

@@ -1078,10 +1078,8 @@ 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, add_import_timestamp, trust_reviewed)
+        importer = PackageImporter(data, preserve_uuids)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1898,6 +1896,12 @@ 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

@@ -99,11 +99,15 @@ 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):
-        return PackageManager.import_legacy_package(
+    def import_package(self, data, owner, all_envipath_user_group):
+        p = 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,
@@ -198,7 +202,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin)
+            imported_package = self.import_package(package_data, admin, g)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0025_auto_20260511_2025.py

@@ -23,6 +23,7 @@ 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

@@ -0,0 +1,150 @@
+# 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

@@ -31,6 +31,7 @@ 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,
@@ -576,6 +577,10 @@ 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 #
@@ -632,7 +637,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
     )
 
     @transaction.atomic
@@ -655,7 +660,9 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
+    scenarios = models.ManyToManyField(
+        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
+    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -781,7 +788,7 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.CASCADE,
+        on_delete=models.SET_NULL,
         null=True,
     )
 
@@ -858,13 +865,17 @@ class Compound(
         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")
+            raise InvalidSMILESException("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise ValueError("Given SMILES is invalid")
+            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()
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -876,7 +887,14 @@ class Compound(
 
         # Check if we find a direct match for a given SMILES
         if qs.exists():
-            return qs.first().compound
+            found_structure = qs.first()
+            found_compound = found_structure.compound
+
+            if name:
+                found_structure.add_alias(name)
+                found_compound.add_alias(name)
+
+            return found_compound
 
 
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
@@ -886,16 +904,19 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            return qs.first().compound
+            found_structure = qs.first()
+            found_compound = found_structure.compound
+
+            if name:
+                found_structure.add_alias(name)
+                found_compound.add_alias(name)
+
+            return found_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}"
 
@@ -1146,18 +1167,27 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: 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():
-            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+
+            if name:
+                found_cs.add_alias(name)
+
+            return found_cs
 
         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 = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            cs.name = name
 
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1165,6 +1195,10 @@ 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"]
 
@@ -1182,6 +1216,8 @@ 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
@@ -1379,6 +1415,9 @@ 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() != "":
@@ -1390,14 +1429,17 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-            return query.first()
+
+            found_rule = query.first()
+
+            if name:
+                found_rule.add_alias(name)
+
+            return found_rule
 
         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}"
 
@@ -1618,10 +1660,15 @@ 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")
+    rules = models.ManyToManyField(
+        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
+    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
+        models.TextField(blank=False, null=False),
+        null=True,
+        verbose_name="Medline References",
+        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1638,8 +1685,13 @@ 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 = True,
+        multi_step: bool = False,
     ):
+
+        # Clean for potential XSS
+        if name is not None and name.strip() != "":
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         _educts = []
         _products = []
 
@@ -1694,14 +1746,19 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-            return existing_reaction_qs.first()
+
+            found_reaction = existing_reaction_qs.first()
+
+            if name:
+                found_reaction.add_alias(name)
+
+            return found_reaction
 
         r = Reaction()
         r.package = package
 
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if r is not None:
+            r.name = name
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -2174,7 +2231,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         smiles: str,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        depth: Optional[int] = 0,
+        depth: Optional[int] = -1,
     ):
         return Node.create(self, smiles, depth, name=name, description=description)
 
@@ -2205,7 +2262,25 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         depth_map[0] = list()
         processed = set()
 
-        for n in self.root_nodes:
+        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)
+
+        data_driven_root_nodes.update(depth=0)
+        root_nodes = [n for n in data_driven_root_nodes]
+
+        for n in root_nodes_by_depth:
+            if n not in root_nodes:
+                if len(n.edge_products.all()) == 0:
+                    root_nodes.append(n)
+
+        for n in root_nodes:
             depth_map[0].append(n)
 
         # At most depth len(nodes) is possible
@@ -2285,7 +2360,12 @@ 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.smiles, width=40, height=40
+                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,
             ),
             "image_type": "svg",
             "name": self.get_name(),
@@ -2299,6 +2379,7 @@ 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,
         }
@@ -2339,12 +2420,17 @@ 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):
         for ai in self.additional_information.all():
-            if ai.__class__.__name__ == "OECD301FTimeSeries":
-                return ai.model_dump(mode="json")
+            if ai.type == "OECD301FTimeSeries":
+                return ai.get().model_dump(mode="json")
 
         return None
 
@@ -2367,6 +2453,26 @@ 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)
@@ -2381,7 +2487,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"

epdb/views.py

@@ -19,6 +19,7 @@ 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,
@@ -785,6 +786,11 @@ 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": {
@@ -797,12 +803,14 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-            "EnviFormer": {
+        }
+
+        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():
@@ -810,6 +818,9 @@ 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()] = {
@@ -818,12 +829,6 @@ 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":
@@ -938,13 +943,12 @@ 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():
@@ -1120,6 +1124,11 @@ 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:
@@ -1223,9 +1232,7 @@ 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, include_models=False, include_external_identifiers=False
-            )
+            pack_json = PackageManager.export_package(current_package)
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -2361,7 +2368,13 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+
+        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"
+            )
 
         return redirect(current_pathway.url)
 
@@ -2469,7 +2482,22 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        return HttpResponseBadRequest()
+        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")
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -3001,9 +3029,15 @@ 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(
-                int(request.POST.get("prediction-setting-max-nodes", 1)),
+                temp_max_nodes,
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -3024,6 +3058,7 @@ 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

@@ -65,6 +65,25 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
+    accepted_diffs = [
+        "bt0055-3469.1",
+        "bt0056-2685",
+        "bt0193-4263",
+        "bt0231-1871.1",
+        "bt0242-3803",
+        "bt0254-4224.1",
+        "bt0254-4224.2",
+        "bt0291-1129",
+        "bt0337-3543",
+        "bt0391-4285",
+        "bt0402-3576",
+        "bt0404-3928",
+        "bt0416-4269",
+        "bt0432-4254",
+        "bt0337-4117",
+        "bt0322-3393",
+    ]
+
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -109,11 +128,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res,
+                        "status": res or r.name in accepted_diffs,
                     }
                 )
 
-                if res:
+                if res or r.name in accepted_diffs:
                     success += 1
                 else:
                     error += 1
@@ -135,7 +154,16 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
+            if r["name"] in accepted_diffs:
+                r["status"] = True
 
+        migration_status["results"] = sorted(
+            migration_status["results"], key=lambda x: (x["status"], x["name"])
+        )
+
+        num_success = sum([int(x["status"]) for x in migration_status["results"]])
+        migration_status["success"] = num_success
+        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

static/css/input.css

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

static/js/alpine/pagination.js

@@ -5,6 +5,125 @@
  */
 
 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

@@ -1,5 +1,37 @@
 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",
@@ -23,6 +55,7 @@ function predictFromNode(url) {
 // elem = 'vizdiv'
 function draw(pathway, elem) {
 
+    const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -34,6 +67,9 @@ 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);
 
@@ -63,7 +99,7 @@ function draw(pathway, elem) {
                 node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
             }
 
-            node.fy = node.depth * levelSpacing + 50;
+            node.fy = (node.depth + initialzoom + 0.5) * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
@@ -101,12 +137,30 @@ function draw(pathway, elem) {
         // Update pseudo node positions first
         updatePseudoNodePositions();
 
-        link.attr("x1", d => d.source.x)
-            .attr("y1", d => d.source.y)
-            .attr("x2", d => d.target.x)
-            .attr("y2", d => d.target.y);
+        link.attr("d", d => {
+            // Check if it's a self-loop (source equals target)
+            if (d.source.id === d.target.id) {
+                // Create a bezier curve for self-loops
+                const x = d.source.x;
+                const y = d.source.y;
+                const loopRadius = nodeRadius * 2; // Adjust size of the loop
+
+                // Create a circular path to the left of the node
+                return `M ${x},${y - nodeRadius}
+                        C ${x - loopRadius},${y - nodeRadius - loopRadius}
+                          ${x - loopRadius},${y + nodeRadius + loopRadius}
+                          ${x},${y + nodeRadius}`;
+            } else {
+                // Regular straight line for normal edges
+                return `M ${d.source.x},${d.source.y} L ${d.target.x},${d.target.y}`;
+            }
+        });
 
         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) {
@@ -209,7 +263,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 1000;
+    var popupWaitBeforeShow = 500;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -563,6 +617,8 @@ function draw(pathway, elem) {
     // Apply zoom to the SVG element - this enables wheel zoom
     svg.call(zoom);
 
+    svg.call(zoom.scaleBy, initialzoom);
+
     // 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);
@@ -598,43 +654,68 @@ function draw(pathway, elem) {
         .on("tick", ticked);
 
     // Kanten zeichnen
-    const link = zoomable.append("g")
-        .selectAll("line")
-        .data(links)
-        .enter().append("line")
-        // 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 => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
+    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 wasHighlighted = d3.select(this).classed("highlighted");
-
-          d3.selectAll("line").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("line").each(e => {
-                          if (e !== undefined && e.source.id === d.target.id) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  } else {
-                      d3.selectAll("line").each(e => {
-                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.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);
+                  }
+                });
               }
+            }
 
-              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) {
@@ -651,16 +732,41 @@ 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");
+          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);
 
-            d3.selectAll('circle.highlighted').classed('highlighted', false);
-
-            if (!wasHighlighted) {
-                d3.select(this).select("circle").classed("highlighted", !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);
+                    }
+                  }
+                }
+              }
             }
-        })
+
+            for (const e of inEdges) {
+              d3.select(e.el).classed("inedge", true);
+            }
+
+            for (const e of outEdges) {
+              d3.select(e.el).classed("outedge", true);
+            }
+          }
+        });
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -734,14 +840,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("line.link").forEach(line => {
+    svgElement.querySelectorAll("path.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("line.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

templates/collections/packages_paginated.html

@@ -3,73 +3,73 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-    <div class="flex items-center gap-2">
-      <button
-        type="button"
-        class="btn btn-primary btn-sm"
-        id="new-package-button"
-        onclick="document.getElementById('new_package_modal').showModal(); return false;"
+  <div class="flex items-center gap-2">
+    <button
+      type="button"
+      class="btn btn-primary btn-sm"
+      id="new-package-button"
+      onclick="document.getElementById('new_package_modal').showModal(); return false;"
+    >
+      <svg
+        xmlns="http://www.w3.org/2000/svg"
+        width="24"
+        height="24"
+        viewBox="0 0 24 24"
+        fill="none"
+        stroke="currentColor"
+        stroke-width="2"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
+        <path d="M12 10v6" />
+        <path d="M9 13h6" />
+        <path
+          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+        />
+      </svg>
+    </button>
+    <div class="dropdown dropdown-end">
+      <div tabindex="0" role="button" class="btn btn-sm">
+        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="24"
-          height="24"
+          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-folder-plus-icon lucide-folder-plus"
+          class="lucide lucide-chevron-down ml-1"
         >
-          <path d="M12 10v6" />
-          <path d="M9 13h6" />
-          <path
-            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-          />
+          <path d="m6 9 6 6 6-6" />
         </svg>
-      </button>
-      <div class="dropdown dropdown-end">
-        <div tabindex="0" role="button" class="btn btn-sm">
-          Import
-          <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-chevron-down ml-1"
-          >
-            <path d="m6 9 6 6 6-6" />
-          </svg>
-        </div>
-        <ul
-          tabindex="-1"
-          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-        >
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_package_modal').showModal(); return false;"
-            >
-              Import Package from JSON
-            </a>
-          </li>
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-            >
-              Import Package from legacy JSON
-            </a>
-          </li>
-        </ul>
       </div>
+      <ul
+        tabindex="-1"
+        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+      >
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_package_modal').showModal(); return false;"
+          >
+            Import Package from JSON
+          </a>
+        </li>
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+          >
+            Import Package from legacy JSON
+          </a>
+        </li>
+      </ul>
     </div>
+  </div>
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/scenarios_paginated.html

@@ -11,7 +11,7 @@
 {% endblock action_modals %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package  %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/modals/collections/new_model_modal.html

@@ -65,11 +65,11 @@
     },
 
     get showMlrr() {
-      return this.selectedType === 'mlrr';
+      return this.selectedType === 'ml-relative-reasoning';
     },
 
     get showRbrr() {
-      return this.selectedType === 'rbrr';
+      return this.selectedType === 'rule-based-relative-reasoning';
     },
 
     get showEnviformer() {

templates/modals/objects/add_pathway_edge_modal.html

@@ -5,6 +5,7 @@
   x-data="{
     isSubmitting: false,
     reactionImageUrl: '',
+    pes: false,
 
     reset() {
       this.isSubmitting = false;
@@ -15,20 +16,30 @@
       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 = '';
       }
     },
@@ -106,6 +117,7 @@
                 {% 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 }}
@@ -132,6 +144,7 @@
                 {% 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 }}
@@ -144,6 +157,9 @@
 
         <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

@@ -5,8 +5,7 @@
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
   @modal-opened.window="
-   const links = d3.selectAll('line.highlighted');
-  console.log(links);
+   const links = d3.selectAll('path.highlighted');
    if (!links.empty()) {
         const el = links.node();
         const selectElement = document.getElementById('delete_pathway_edge_edges');
@@ -18,9 +17,7 @@
                 break;
             }
         }
-
         selectElement.dispatchEvent(new Event('change'));
-
    }
   "
   @close="reset()"

templates/modals/objects/delete_pathway_node_modal.html

@@ -6,17 +6,14 @@
   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

@@ -82,6 +82,9 @@
       <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 -->
@@ -92,7 +95,7 @@
         <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.name }}</a
+              >{{ educt.get_name }}</a
             >
           {% endfor %}
           <svg
@@ -112,7 +115,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.name }}</a
+              >{{ product.get_name }}</a
             >
           {% endfor %}
         </div>

templates/objects/group.html

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

@@ -55,6 +55,15 @@
       </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

@@ -21,6 +21,7 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
+      stroke-width: 1.5px;
       /* marker-end: url(#arrow); */
     }
 
@@ -72,6 +73,15 @@
       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>
 
@@ -111,7 +121,7 @@
       <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">
@@ -168,6 +178,52 @@
                   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">
@@ -193,6 +249,7 @@
                       </a>
                     </li>
                   {% endif %}
+                  {% if 1 == 0 %}
                   <li>
                     <a id="timeseries-toggle-button" class="cursor-pointer">
                       <svg
@@ -243,6 +300,7 @@
                       Show Predicted Properties
                     </a>
                   </li>
+                  {% endif %}
                 </ul>
               </div>
             </div>
@@ -367,6 +425,18 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
+              <marker
+                id="curve-arrow"
+                viewBox="0 0 10 10"
+                refX="10"
+                refY="5"
+                markerWidth="6"
+                markerHeight="6"
+                orient="auto"
+                markerUnits="strokeWidth"
+              >
+                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
+              </marker>
               <marker
                 id="doublearrow"
                 viewBox="0 0 20 30"
@@ -474,6 +544,10 @@
   {{ 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
@@ -509,6 +583,67 @@
         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

@@ -79,6 +79,9 @@
       <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

@@ -24,6 +24,76 @@
         <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

@@ -158,7 +158,6 @@
         document.getElementById("predict-submit-button").innerText = "Predict";
       }
     }
-
     const radioButtons = document.querySelectorAll('input[name="predict"]');
     radioButtons.forEach(radio => {
       radio.addEventListener('change', radioChange);
@@ -213,7 +212,13 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-        button.textContent = "Predicting...";
+
+        // Set text depending on mode
+        if (document.getElementById("predict-submit-button").innerText === "Build") {
+          button.textContent = "Building...";
+        } else {
+          button.textContent = "Predicting...";
+        }
 
         // Get SMILES from either input or Ketcher
         const smilesInput = document.getElementById("predict-smiles");

tests/test_compound_model.py

@@ -1,5 +1,7 @@
 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
 
@@ -33,13 +35,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -96,7 +98,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = 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

@@ -1,6 +1,7 @@
 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
 
@@ -163,7 +164,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_model_views.py

@@ -46,6 +46,14 @@ 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,
@@ -62,14 +70,6 @@ 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#f2f251e0214f016760348730c45e56183d961201" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#ad825570480bbe2f1a35c04923fede756c450751" }
 dependencies = [
     { name = "pydantic" },
 ]