[Feature] Sync Features from Client Repo (#425)

- New PackageImporter
- Fix persisting Molfile on Structure creation
- Add NonPersistent Prediction
- Pathway View Options
- Edit Node Fix

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#425

Dockerfile

@@ -35,15 +35,13 @@ RUN mkdir -p -m 0700 /root/.ssh \
     && ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts
 
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
-# docker build --ssh default -t envipath/envipy-bayer:1.0 .
+# docker build --ssh default -t envipath/envipy:1.0 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bb4g bb4g
 COPY biotransformer biotransformer
-COPY bayer bayer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi

bayer/additional_information/__init__.py

@@ -1,178 +0,0 @@
-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/admin.py

@@ -1,19 +0,0 @@
-from django.contrib import admin
-
-# Register your models here.
-from .models import (
-    PESCompound,
-    PESStructure
-)
-
-
-class PESCompoundAdmin(admin.ModelAdmin):
-    pass
-
-
-class PESStructureAdmin(admin.ModelAdmin):
-    pass
-
-
-admin.site.register(PESCompound, PESCompoundAdmin)
-admin.site.register(PESStructure, PESStructureAdmin)

bayer/apps.py

@@ -1,6 +0,0 @@
-from django.apps import AppConfig
-
-
-class BayerConfig(AppConfig):
-    default_auto_field = 'django.db.models.BigAutoField'
-    name = 'bayer'

bayer/epdb_hooks.py

@@ -1,40 +0,0 @@
-import logging
-
-from bayer import additional_information  # noqa: F401
-from epdb.template_registry import register_template
-
-logger = logging.getLogger(__name__)
-
-# PES Create
-register_template(
-    "epdb.actions.collections.compound",
-    "actions/collections/new_pes.html",
-)
-register_template(
-    "modals.collections.compound",
-    "modals/collections/new_pes_modal.html",
-)
-register_template(
-    "epdb.actions.objects.pathway.add",
-    "actions/objects/pathway_add_pes.html",
-)
-register_template(
-    "epdb.modals.objects.pathway.add",
-    "modals/objects/add_pathway_pes_node_modal.html"
-)
-
-# PES Viz
-register_template(
-    "epdb.objects.compound.viz",
-    "objects/compound_viz.html",
-)
-
-register_template(
-    "epdb.objects.compound_structure.viz",
-    "objects/compound_structure_viz.html",
-)
-
-register_template(
-    "epdb.objects.node.viz",
-    "objects/node_viz.html",
-)

bayer/migrations/0001_initial.py

@@ -1,35 +0,0 @@
-# Generated by Django 5.2.7 on 2026-03-06 10:51
-
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    initial = True
-
-    dependencies = [
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='Package',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
-                ('classification_level', models.IntegerField(choices=[(0, 'Internal'), (10, 'Restricted'), (20, 'Secret')], default=10)),
-            ],
-            options={
-                'db_table': 'epdb_package',
-            },
-        ),
-    ]

bayer/migrations/0002_initial.py

@@ -1,22 +0,0 @@
-# Generated by Django 5.2.7 on 2026-03-06 10:51
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    initial = True
-
-    dependencies = [
-        ('bayer', '0001_initial'),
-        ('epdb', '0019_remove_scenario_additional_information_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='package',
-            name='license',
-            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License'),
-        ),
-    ]

bayer/migrations/0003_pescompound_pesstructure_package_data_pool.py

@@ -1,41 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-17 21:22
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0002_initial'),
-        ('epdb', '0023_alter_compoundstructure_options_and_more'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='PESCompound',
-            fields=[
-                ('compound_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compound')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.compound',),
-        ),
-        migrations.CreateModel(
-            name='PESStructure',
-            fields=[
-                ('compoundstructure_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compoundstructure')),
-                ('pes_link', models.URLField(verbose_name='PES Link')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.compoundstructure',),
-        ),
-        migrations.AddField(
-            model_name='package',
-            name='data_pool',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
-        ),
-    ]

bayer/models.py

@@ -1,237 +0,0 @@
-from typing import List
-import urllib.parse
-import nh3
-from django.conf import settings as s
-from django.db import models, transaction
-from django.db.models import QuerySet
-from django.urls import reverse
-
-from epdb.models import (
-    EnviPathModel,
-    Compound,
-    CompoundStructure,
-    ParallelRule,
-    SequentialRule,
-    SimpleAmbitRule,
-    SimpleRDKitRule,
-)
-from utilities.chem import FormatConverter
-
-
-class Package(EnviPathModel):
-    reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
-    license = models.ForeignKey(
-        "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
-    )
-
-    class Classification(models.IntegerChoices):
-        INTERNAL = 0, "Internal"
-        RESTRICTED = 10 , "Restricted"
-        SECRET = 20, "Secret"
-
-    classification_level = models.IntegerField(
-        choices=Classification,
-        default=Classification.RESTRICTED,
-    )
-
-    data_pool = models.ForeignKey("epdb.Group", on_delete=models.SET_NULL, blank=True, null=True,
-                                  verbose_name="Data pool", default=None)
-
-    def delete(self, *args, **kwargs):
-        # explicitly handle related Rules
-        for r in self.rules.all():
-            r.delete()
-        super().delete(*args, **kwargs)
-
-    def __str__(self):
-        return f"{self.name} (pk={self.pk})"
-
-    @property
-    def compounds(self) -> QuerySet:
-        return self.compound_set.all()
-
-    @property
-    def rules(self) -> QuerySet:
-        return self.rule_set.all()
-
-    @property
-    def reactions(self) -> QuerySet:
-        return self.reaction_set.all()
-
-    @property
-    def pathways(self) -> QuerySet:
-        return self.pathway_set.all()
-
-    @property
-    def scenarios(self) -> QuerySet:
-        return self.scenario_set.all()
-
-    @property
-    def models(self) -> QuerySet:
-        return self.epmodel_set.all()
-
-    def _url(self):
-        return "{}/package/{}".format(s.SERVER_URL, self.uuid)
-
-    def get_applicable_rules(self) -> List["Rule"]:
-        """
-        Returns a ordered set of rules where the following applies:
-        1. All Composite will be added to result
-        2. All SimpleRules will be added if theres no CompositeRule present using the SimpleRule
-        Ordering is based on "url" field.
-        """
-        rules = []
-        rule_qs = self.rules
-
-        reflected_simple_rules = set()
-
-        for r in rule_qs:
-            if isinstance(r, ParallelRule) or isinstance(r, SequentialRule):
-                rules.append(r)
-                for sr in r.simple_rules.all():
-                    reflected_simple_rules.add(sr)
-
-        for r in rule_qs:
-            if isinstance(r, SimpleAmbitRule) or isinstance(r, SimpleRDKitRule):
-                if r not in reflected_simple_rules:
-                    rules.append(r)
-
-        rules = sorted(rules, key=lambda x: x.url)
-        return rules
-
-    class Meta:
-        db_table = "epdb_package"
-
-
-class PESCompound(Compound):
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
-    ) -> "Compound":
-
-        pes_url = pes_data["pes_url"]
-
-        # Check if we find a direct match for a given pes_link
-        if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
-            # Due to normalization we might end up in having multiple structures
-            # All of them point to the same compound -> pick any
-            return PESStructure.objects.filter(pes_link=pes_url, compound__package=package).first().compound
-
-        # Generate Compound
-        c = PESCompound()
-        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}"
-
-        c.name = name
-
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
-            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        c.save()
-
-        molfile = pes_data.get("representativeStructures", [{}])[0].get("ctab")
-
-        if molfile is None:
-            raise ValueError("PES data does not contain a valid mol file!")
-
-        smiles = FormatConverter.to_smiles(FormatConverter.from_molfile(molfile))
-
-        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
-
-        is_standardized = standardized_smiles == smiles
-
-        if not is_standardized:
-            _ = PESStructure.create(
-                c,
-                pes_url,
-                molfile,
-                standardized_smiles,
-                name="Normalized structure of {}".format(name),
-                description="{} (in its normalized form)".format(description),
-                normalized_structure=True,
-            )
-
-
-        cs = PESStructure.create(
-            c,
-            pes_url,
-            molfile,
-            smiles,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized
-        )
-
-        c.default_structure = cs
-        c.save()
-
-        return c
-
-
-class PESStructure(CompoundStructure):
-    pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-            compound: Compound,
-            pes_link: str,
-            mol_file: str,
-            smiles: str,
-            name: str = None,
-            description: str = None,
-            *args,
-            **kwargs
-    ):
-        if compound.pk is None:
-            raise ValueError("Unpersisted Compound! Persist compound first!")
-
-        cs = PESStructure()
-        # Clean for potential XSS
-        if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if description is not None:
-            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        cs.smiles = smiles
-        cs.mol_file = mol_file
-        cs.pes_link = pes_link
-        cs.compound = compound
-
-        if "normalized_structure" in kwargs:
-            cs.normalized_structure = kwargs["normalized_structure"]
-
-        cs.save()
-
-        return cs
-
-    @transaction.atomic
-    def add_structure(
-        self,
-        smiles: str,
-        name: str = None,
-        description: str = None,
-        default_structure: bool = False,
-        *args,
-        **kwargs,
-    ) -> "CompoundStructure":
-        raise ValueError("Not supported!")
-
-    def d3_json(self):
-        return {
-            "is_pes": True,
-            "pes_link": self.pes_link,
-            # Will overwrite image from Node
-            "image": f"{reverse('depict_pes')}?pesLink={urllib.parse.quote(self.pes_link)}",
-            "image_type": "png",
-        }

bayer/templates/actions/collections/new_pes.html

@@ -1,9 +0,0 @@
-{% if meta.can_edit %}
-    <button
-      type="button"
-      class="btn btn-primary btn-sm"
-      onclick="document.getElementById('new_pes_modal').showModal(); return false;"
-    >
-      New PES
-    </button>
-{% endif %}

bayer/templates/actions/objects/pathway_add_pes.html

@@ -1,8 +0,0 @@
-<li>
-  <a
-    class="button"
-    onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-plus"></i> Add PES</a
-  >
-</li>

bayer/templates/modals/collections/new_package_modal.html

@@ -1,175 +0,0 @@
-{% load static %}
-
-<dialog
-  id="new_package_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    packageClassification: null,
-
-    reset() {
-      this.isSubmitting = false;
-      this.packageClassification = null;
-    },
-
-    setFormData(data) {
-      this.formData = data;
-    },
-
-    get isSecret() {
-      return this.packageClassification === '20';
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">New Package</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-     <form
-        id="new_package_form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
-       {% csrf_token %}
-
-       <!-- Name -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="package-name"
-            class="input input-bordered w-full"
-            name="package-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-       <!-- Description -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="package-description"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Description..."
-            name="package-description"
-          />
-        </div>
-
-       <!-- Classification Level -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-classification">
-            <span class="label-text">Package Classification</span>
-          </label>
-          <select
-            id="package-classification"
-            name="package-classification"
-            class="select select-bordered w-full"
-            x-model="packageClassification"
-            required
-          >
-            <option value="null" disabled selected>Select Classification</option>
-            <option value="0">Internal</option>
-            <option value="10">Restricted</option>
-            <option value="20">Secret</option>
-          </select>
-        </div>
-
-       <!-- Secret Groups -->
-        <div class="form-control mb-3" x-show="isSecret" x-cloak>
-          <label class="label" for="package-data-pool">
-            <span class="label-text">Data Pool for SECRET Package</span>
-          </label>
-          <p>Only users with this role can be granted access to this package</p>
-          <select
-            id="package-data-pool"
-            name="package-data-pool"
-            class="select select-bordered w-full"
-          >
-            <option value="" disabled selected>Select Data Pool</option>
-              {% for obj in meta.secret_groups %}
-                <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-              {% endfor %}
-          </select>
-        </div>
-
-     </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new_package_form')"
-        :disabled="isSubmitting || !selectedType || loadingSchemas"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/modals/collections/new_pes_modal.html

@@ -1,174 +0,0 @@
-{% load static %}
-
-<dialog
-  id="new_pes_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    pesLink: null,
-    pesVizHtml: '',
-
-    reset() {
-      this.isSubmitting = false;
-    },
-
-    get isPESSet() {
-      console.log(this.pesLink);
-      return this.pesLink !== null;
-    },
-
-    updatePesViz() {
-      if (!this.isPESSet) {
-        this.pesVizHtml = '';
-        return;
-      }
-
-      const img = new Image();
-      img.src = '{% url 'depict_pes' %}?pesLink=' + encodeURIComponent(this.pesLink);
-      img.style.width = '100%';
-      img.style.height = '100%';
-      img.style.objectFit = 'cover';
-
-      img.onload = () => {
-        this.pesVizHtml = img.outerHTML;
-      };
-
-      img.onerror = () => {
-        this.pesVizHtml = `
-          <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
-          </div>`;
-      };
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-  <!-- Header -->
-  <h3 class="text-lg font-bold">New PES</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-pes-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'create pes' meta.current_package.uuid %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="compound-name"
-            class="input input-bordered w-full"
-            name="compound-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pes-link">
-            <span class="label-text">Link to PES</span>
-          </label>
-          <input
-            id="pes-link"
-            name="pes-link"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
-            x-model="pesLink"
-            @input="updatePesViz()"
-            required
-          />
-        </div>
-
-        <div id="pes-viz" class="mb-3" x-html="pesVizHtml"></div>
-
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-pes-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

@@ -1,174 +0,0 @@
-{% load static %}
-
-<dialog
-  id="add_pathway_pes_node_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    pesLink: null,
-    pesVizHtml: '',
-
-    reset() {
-      this.isSubmitting = false;
-    },
-
-    get isPESSet() {
-      console.log(this.pesLink);
-      return this.pesLink !== null;
-    },
-
-    updatePesViz() {
-      if (!this.isPESSet) {
-        this.pesVizHtml = '';
-        return;
-      }
-
-      const img = new Image();
-      img.src = '{% url 'depict_pes' %}?pesLink=' + encodeURIComponent(this.pesLink);
-      img.style.width = '100%';
-      img.style.height = '100%';
-      img.style.objectFit = 'cover';
-
-      img.onload = () => {
-        this.pesVizHtml = img.outerHTML;
-      };
-
-      img.onerror = () => {
-        this.pesVizHtml = `
-          <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
-          </div>`;
-      };
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-  <!-- Header -->
-  <h3 class="text-lg font-bold">New PES</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-pes-node-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'create pes node' current_object.package.uuid current_object.uuid  %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="compound-name"
-            class="input input-bordered w-full"
-            name="compound-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pes-link">
-            <span class="label-text">Link to PES</span>
-          </label>
-          <input
-            id="pes-link"
-            name="pes-link"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
-            x-model="pesLink"
-            @input="updatePesViz()"
-            required
-          />
-        </div>
-
-        <div id="pes-viz" class="mb-3" x-html="pesVizHtml"></div>
-
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-pes-node-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/objects/compound_structure_viz.html

@@ -1,21 +0,0 @@
-{% if compound_structure.pes_link %}
-  <!-- PES -->
-  <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">
-      <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-    </div>
-  </div>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/compound_viz.html

@@ -1,21 +0,0 @@
-{% if compound.default_structure.pes_link %}
-  <!-- PES -->
-  <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">
-      <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-    </div>
-  </div>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound.default_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/node_viz.html

@@ -1,19 +0,0 @@
-{% if node.default_node_label.pes_link %}
-  <!-- PES -->
-  <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>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ node.default_node_label.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/package.html

@@ -1,97 +0,0 @@
-{% extends "framework_modern.html" %}
-{% load static %}
-{% block content %}
-
-  {% block action_modals %}
-    {% include "modals/objects/edit_package_modal.html" %}
-    {% include "modals/objects/edit_package_permissions_modal.html" %}
-    {% include "modals/objects/publish_package_modal.html" %}
-    {% include "modals/objects/set_license_modal.html" %}
-    {% include "modals/objects/export_package_modal.html" %}
-    {% include "modals/objects/generic_delete_modal.html" %}
-  {% endblock action_modals %}
-
-  <div class="space-y-2 p-4">
-    <!-- Header Section -->
-    <div class="card bg-base-100">
-      <div class="card-body">
-        <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ package.name }} {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}<img src="{% static 'images/restricted_mid.png' %}" width="100">{% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}<img src="{% static 'images/secret_mid.png' %}" width="60">{% endif %}</h2>
-          <div id="actionsButton" class="dropdown dropdown-e nd hidden">
-            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                width="16"
-                height="16"
-                viewBox="0 0 24 24"
-                fill="none"
-                stroke="currentColor"
-                stroke-width="2"
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                class="lucide lucide-wrench"
-              >
-                <path
-                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
-                />
-              </svg>
-              Actions
-            </div>
-            <ul
-              tabindex="-1"
-              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
-            >
-              {% block actions %}
-                {% include "actions/objects/package.html" %}
-              {% endblock %}
-            </ul>
-          </div>
-        </div>
-        <p class="mt-2">{{ package.description|safe }}</p>
-        <ul class="menu bg-base-200 rounded-box mt-4 w-full">
-          <li>
-            <a href="{{ package.url }}/pathway" class="hover:bg-base-300"
-              >Pathways ({{ package.pathways.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/rule" class="hover:bg-base-300"
-              >Rules ({{ package.rules.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/compound" class="hover:bg-base-300"
-              >Compounds ({{ package.compounds.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/reaction" class="hover:bg-base-300"
-              >Reactions ({{ package.reactions.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/model" class="hover:bg-base-300"
-              >Models ({{ package.models.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/scenario" class="hover:bg-base-300"
-              >Scenarios ({{ package.scenarios.count }})</a
-            >
-          </li>
-        </ul>
-      </div>
-    </div>
-  </div>
-
-  <script>
-    // Show actions button if there are actions
-    document.addEventListener("DOMContentLoaded", function () {
-      const actionsButton = document.getElementById("actionsButton");
-      const actionsList = actionsButton?.querySelector("ul");
-      if (actionsList && actionsList.children.length > 0) {
-        actionsButton?.classList.remove("hidden");
-      }
-    });
-  </script>
-{% endblock content %}

bayer/templates/static/login.html

@@ -1,154 +0,0 @@
-{% extends "static/login_base.html" %}
-{% load static %}
-{% block title %}enviPath - Sign In{% endblock %}
-
-{% block extra_styles %}
-  <style>
-    /* Tab styling */
-    .tab-content {
-      display: none;
-    }
-    .tab-content.active {
-      display: block;
-    }
-    input[type="radio"].tab-radio {
-      display: none;
-    }
-    .tab-label {
-      cursor: pointer;
-      padding: 0.75rem 1.5rem;
-      border-bottom: 2px solid transparent;
-      transition: all 0.3s ease;
-    }
-    .tab-label:hover {
-      background-color: rgba(0, 0, 0, 0.05);
-    }
-    input[type="radio"].tab-radio:checked + .tab-label {
-      border-bottom-color: #3b82f6;
-      font-weight: 600;
-    }
-  </style>
-{% endblock %}
-
-{% block content %}
-  <div>
-  <img src="{% static 'images/bayer-logo.svg' %}">
-
-  </div>
-  <div class="flex flex-col space-y-4 ...">
-    <div><p></p></div>
-  <div><p></p></div>
-
-  </div>
-
-  <!-- Tab Navigation -->
-  <div class="border-base-300 mb-6 border-b" hidden>
-    <div class="flex justify-start">
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-sso"
-        class="tab-radio"
-        checked
-      />
-      <label for="tab-sso" class="tab-label">SSO</label>
-
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-signin"
-        class="tab-radio"
-      />
-      <label for="tab-signin" class="tab-label">Local User</label>
-    </div>
-  </div>
-
-  <!-- SSO Tab -->
-  <div id="content-sso" class="tab-content active">
-      <button role="link" onclick="window.location.href='/entra/login'" name="sso" class="btn btn-primary w-full">
-        Login with Microsoft
-      </button>
-  </div>
-
-  <!-- Sign In Tab -->
-  <div id="content-signin" class="tab-content">
-    <form method="post" action="{% url 'login' %}" class="space-y-4">
-      {% csrf_token %}
-      <input type="hidden" name="login" value="true" />
-
-      <div class="form-control">
-        <label class="label" for="username">
-          <span class="label-text">Account</span>
-        </label>
-        <input
-          type="text"
-          id="username"
-          name="username"
-          placeholder="Username or Email"
-          class="input input-bordered w-full"
-          required
-          autocomplete="username"
-        />
-      </div>
-
-      <div class="form-control">
-        <label class="label" for="passwordinput">
-          <span class="label-text">Password</span>
-        </label>
-        <input
-          type="password"
-          id="passwordinput"
-          name="password"
-          placeholder="••••••••"
-          class="input input-bordered w-full"
-          required
-          autocomplete="current-password"
-        />
-      </div>
-
-      <div class="text-right">
-        <a href="{% url 'password_reset' %}" class="link link-primary text-sm"
-          >Forgot password?</a
-        >
-      </div>
-
-      <input type="hidden" name="next" value="{{ next }}" />
-
-      <button type="submit" name="signin" class="btn btn-primary w-full">
-        Sign In
-      </button>
-    </form>
-  </div>
-
-{% endblock %}
-
-{% block extra_scripts %}
-  <script>
-    // Tab switching functionality
-    document.querySelectorAll('input[name="auth-tab"]').forEach((radio) => {
-      radio.addEventListener("change", function () {
-        // Hide all content
-        document.querySelectorAll(".tab-content").forEach((content) => {
-          content.classList.remove("active");
-        });
-
-        // Show selected content
-        const contentId = "content-" + this.id.replace("tab-", "");
-        document.getElementById(contentId).classList.add("active");
-      });
-    });
-
-    // Check for hash in URL to auto-select tab
-    window.addEventListener("DOMContentLoaded", function () {
-      const hash = window.location.hash.substring(1); // Remove the # symbol
-      if (hash === "signup" || hash === "signin") {
-        const tabRadio = document.getElementById("tab-" + hash);
-        if (tabRadio) {
-          tabRadio.checked = true;
-          // Trigger change event to show correct content
-          tabRadio.dispatchEvent(new Event("change"));
-        }
-      }
-    });
-  </script>
-{% endblock %}

bayer/tests.py

@@ -1,3 +0,0 @@
-from django.test import TestCase
-
-# Create your tests here.

bayer/urls.py

@@ -1,19 +0,0 @@
-from django.urls import re_path
-
-from . import views as v
-
-UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
-
-urlpatterns = [
-    re_path(r"^depict_pes$", v.visualize_pes, name="depict_pes"),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pes$",
-        v.create_pes,
-        name="create pes",
-    ),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/pes$",
-        v.create_pes_node,
-        name="create pes node",
-    ),
-]

bayer/views.py

@@ -1,170 +0,0 @@
-import base64
-
-import requests
-from django.conf import settings as s
-from django.core.exceptions import BadRequest
-from django.http import HttpResponse
-from django.shortcuts import redirect
-
-from bayer.models import PESCompound
-from epdb.logic import PackageManager
-from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real
-from utilities.decorators import package_permission_required
-
-Package = s.GET_PACKAGE_MODEL()
-
-
-@package_permission_required()
-def create_pes(request, package_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                pes_data = fetch_pes(request, pes_link)
-            except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return BadRequest("Cannot create PESs for non-secret packages.")
-
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return BadRequest(
-                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
-
-            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
-
-            return redirect(pes.url)
-        else:
-            return BadRequest("Please provide a PES link.")
-    else:
-        pass
-
-
-@package_permission_required()
-def create_pes_node(request, package_uuid, pathway_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                pes_data = fetch_pes(request, pes_link)
-            except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return BadRequest("Cannot create PESs for non-secret packages.")
-
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return BadRequest(
-                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
-
-            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
-
-            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
-            if node_qs.exists():
-                return redirect(current_pathway.url)
-
-            n = Node()
-            n.stereo_removed = False
-            n.pathway = current_pathway
-            n.depth = 0
-
-            n.default_node_label = pes.default_structure
-            n.save()
-
-            n.node_labels.add(pes.default_structure)
-            n.save()
-
-            return redirect(current_pathway.url)
-
-        else:
-            return BadRequest("Please provide a PES link.")
-    else:
-        pass
-
-
-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):
-                pes_id = pes_url.split('/')[-1]
-
-                if pes_id == 'dummy':
-                    import json
-                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
-                    res_data["pes_url"] = pes_url
-                    return res_data
-                else:
-                    headers = {"Authorization": f"Bearer {token['access_token']}"}
-                    params = {"pes_reg_entity_corporate_id": pes_id}
-
-                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
-
-                    try:
-                        res.raise_for_status()
-                        pes_data = res.json()
-
-                        if len(pes_data) == 0:
-                            raise ValueError(f"PES with id {pes_id} not found")
-
-                        res_data = pes_data[0]
-                        res_data["pes_url"] = pes_url
-                        return res_data
-
-                    except requests.exceptions.HTTPError as e:
-                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
-        else:
-            raise ValueError(f"Unknown URL {pes_url}")
-    else:
-        raise ValueError("Could not fetch access token from request.")
-
-
-def visualize_pes(request):
-    pes_link = request.GET.get('pesLink')
-
-    if pes_link:
-        pes_data = fetch_pes(request, pes_link)
-
-        representations = pes_data.get('representations')
-
-        for rep in representations:
-            if rep.get('type') == 'color':
-                image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
-                return HttpResponse(image_data, content_type="image/png")

bb4g/__init__.py

@@ -1,198 +0,0 @@
-import enum
-import json
-import logging
-import math
-from datetime import datetime
-from typing import List
-
-import requests
-from django.conf import settings as s
-from envipy_additional_information import register, EnviPyModel, UIConfig, WidgetType
-
-from bridge.contracts import Classifier  # noqa: I001
-from bridge.dto import (
-    BuildResult,
-    EnviPyDTO,
-    EvaluationResult,
-    RunResult,
-    TransformationProductPrediction,
-)  # noqa: I001
-
-logger = logging.getLogger("epdb")
-
-
-class SamplingAlgorithm(enum.Enum):
-    EXACT = "exact"
-
-
-@register("bb4gconfig")
-class BB4GConfig(EnviPyModel):
-    sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
-    cutoff: int = -5
-
-    class UI:
-        title = "BB4G Configuration"
-        sampling_algorithm = UIConfig(
-            widget=WidgetType.SELECT,
-            label="BB4G Sampling Algorithm",
-            order=1,
-            placeholder="If unset defaults to 'exact'"
-        )
-        cutoff = UIConfig(
-            widget=WidgetType.NUMBER,
-            label="BB4G Cutoff",
-            order=2,
-            placeholder="If unset defaults to -5"
-        )
-
-
-# Once stable these will be exposed by enviPy-plugins lib
-class BB4G(Classifier):
-    Config = BB4GConfig
-
-    def __init__(self, config: BB4GConfig | None = None):
-        super().__init__(config)
-        self.url = f"{s.BB4G_URL}"
-
-        self.token = self.acquire_token()
-        self.header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-    def acquire_token(self):
-        BB4G_TENANT_ID = s.BB4G_TENANT_ID
-        BB4G_CLIENT_ID = s.BB4G_CLIENT_ID
-        BB4G_CLIENT_SECRET = s.BB4G_CLIENT_SECRET
-        BB4G_SCOPE = s.BB4G_SCOPE
-
-        BB4G_TOKEN_URL = f"https://login.microsoftonline.com/{BB4G_TENANT_ID}/oauth2/v2.0/token"
-
-        payload = {
-            "client_id": BB4G_CLIENT_ID,
-            "client_secret": BB4G_CLIENT_SECRET,
-            "scope": BB4G_SCOPE,
-            "grant_type": "client_credentials"
-        }
-
-        # No Proxy required, URL is whitelisted
-        res = requests.post(BB4G_TOKEN_URL, data=payload)
-
-        res.raise_for_status()
-
-        return res.json()["access_token"]
-
-    def start(self):
-        header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-        started = False
-
-        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]:
-                import time
-                time.sleep(5)
-            else:
-                raise ValueError(f"Unexpected status code: {res.status_code}")
-
-    @classmethod
-    def requires_rule_packages(cls) -> bool:
-        return False
-
-    @classmethod
-    def requires_data_packages(cls) -> bool:
-        return False
-
-    @classmethod
-    def identifier(cls) -> str:
-        return "bb4g"
-
-    @classmethod
-    def name(cls) -> str:
-        return "BB4G Template Free Model"
-
-    @classmethod
-    def display(cls) -> str:
-        return "BB4G Template Free Model"
-
-    def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
-        return
-
-    def run(self, eP: EnviPyDTO, *args, **kwargs) -> RunResult:
-
-        # Ensure Service is running
-        self.start()
-
-        smiles = [c.smiles for c in eP.get_compounds()]
-        preds = self._post(smiles)
-
-        results = []
-
-        for substrate in preds.keys():
-            results.append(
-                TransformationProductPrediction(
-                    substrate=substrate,
-                    products=preds[substrate],
-                )
-            )
-
-        return RunResult(
-            producer=eP.get_context().url,
-            description=f"Generated at {datetime.now()}",
-            result=results,
-        )
-
-    def evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
-        pass
-
-    def build_and_evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
-        pass
-
-    def _post(self, smiles: List[str]) -> dict[str, dict[str, float]]:
-        header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-        result = {}
-
-        for smi in smiles:
-            data = {
-                "smiles": smi,
-                "sampling_alg": self.config.sampling_algorithm.value,
-                "cutoff": self.config.cutoff,
-            }
-
-            retries = 0
-            while retries < 100:
-                resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
-                                     proxies=s.PROXIES or None)
-
-                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
-
-                resp.raise_for_status()
-
-                for substrate, predictions in resp.json().items():
-                    preds = {}
-
-                    for pred in predictions:
-                        prod = pred["prediction"]
-                        prob = math.exp(pred["log_likelihood"])
-                        preds[prod] = prob
-
-                    result[substrate] = preds
-
-                break
-
-        return result

docker-compose.dev.yml

@@ -1,43 +1,26 @@
 services:
   db:
     image: postgres:18
-    container_name: eppostgres
+    container_name: envipath-postgres
     environment:
-      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_DB: envipath
     ports:
       - "5432:5432"
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - postgres_data:/var/lib/postgresql
     healthcheck:
-      test: [ "CMD-SHELL", "pg_isready -U postgres" ]
+      test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 5s
       timeout: 5s
       retries: 5
 
   redis:
     image: redis:7-alpine
-    container_name: epredis
+    container_name: envipath-redis
     ports:
       - "6379:6379"
-    volumes:
-      - ep_bayer_redis_data:/data
-
-  biotransformer3:
-    image: git.envipath.com/envipath/biotransformer3:1.0
-    container_name: epbiotransformer3
-
-  celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.2
-    container_name: epcelery
-    env_file:
-      - .env
-    command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
-    volumes:
-      - ep_bayer_data:/opt/enviPy/
 
 volumes:
-  ep_bayer_postgres_data:
+  postgres_data:
-  ep_bayer_redis_data:
-  ep_bayer_data:

docker-compose.yml

@@ -7,7 +7,7 @@ services:
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
       POSTGRES_DB: ${POSTGRES_DB}
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - ep_postgres_data:/var/lib/postgresql
     healthcheck:
       test: [ "CMD-SHELL", "pg_isready -U postgres" ]
       interval: 5s
@@ -18,14 +18,14 @@ services:
     image: redis:7-alpine
     container_name: epredis
     volumes:
-      - ep_bayer_redis_data:/data
+      - ep_redis_data:/data
 
   biotransformer3:
     image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
   web:
-    image: envipath/envipy-bayer:1.0
+    image: envipath/envipy:1.0
     container_name: epdjango
     ports:
       - "127.0.0.1:8000:8000"
@@ -33,18 +33,18 @@ services:
       - .env
     command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
     volumes:
-      - ep_bayer_data:/opt/enviPy/
+      - ep_data:/opt/enviPy/
 
   celery_worker:
-    image: envipath/envipy-bayer:1.0
+    image: envipath/envipy:1.0
     container_name: epcelery
     env_file:
       - .env
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
-      - ep_bayer_data:/opt/enviPy/
+      - ep_data:/opt/enviPy/
 
 volumes:
-  ep_bayer_postgres_data:
+  ep_postgres_data:
-  ep_bayer_redis_data:
+  ep_redis_data:
-  ep_bayer_data:
+  ep_data:

envipath/settings.py

@@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
-import json
+
 import os
 from pathlib import Path
 
@@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -143,12 +143,6 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
         "TEMPLATE": os.environ["TEMPLATE_DB"],
     }
 
-CACHES = {
-    "default": {
-        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
-        "LOCATION": "unique-snowflake",
-    }
-}
 
 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@@ -275,12 +269,6 @@ 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__)
@@ -301,11 +289,6 @@ LOGGING = {
             "propagate": True,
             "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
-        "auth": {
-            "handlers": ["auth_file"],
-            "propagate": True,
-            "level": os.environ.get("LOG_LEVEL", "INFO"),
-        }
     },
 }
 
@@ -354,7 +337,7 @@ DEFAULT_MODEL_PARAMS = {
     "num_chains": 10,
 }
 
-DEFAULT_MAX_NUMBER_OF_NODES = 9999
+DEFAULT_MAX_NUMBER_OF_NODES = 50
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
 
@@ -459,48 +442,3 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
-
-# PES
-PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
-if PES_API_MAPPING:
-    import json
-    PES_API_MAPPING = json.loads(PES_API_MAPPING)
-else:
-    PES_API_MAPPING = {}
-
-# Entra Groups
-ENTRA_GROUPS = os.environ.get("ENTRA_GROUPS", None)
-if ENTRA_GROUPS:
-    import json
-    ENTRA_GROUPS = json.loads(ENTRA_GROUPS)
-else:
-    ENTRA_GROUPS = {}
-
-ENTRA_SECRET_GROUPS = os.environ.get("ENTRA_SECRET_GROUPS", None)
-if ENTRA_SECRET_GROUPS:
-    import json
-    ENTRA_SECRET_GROUPS = json.loads(ENTRA_SECRET_GROUPS)
-else:
-    ENTRA_SECRET_GROUPS = {}
-
-# PES Data Pools vs Entra Mapping
-DATA_POOL_MAPPING = os.environ.get("DATA_POOL_MAPPING", None)
-if DATA_POOL_MAPPING:
-    import json
-    DATA_POOL_MAPPING = json.loads(DATA_POOL_MAPPING)
-else:
-    DATA_POOL_MAPPING = {}
-
-PROXIES = {}
-if os.environ.get("HTTP_PROXY"):
-    PROXIES["http"] = os.environ.get("HTTP_PROXY")
-    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
-
-# BB4g
-BB4G_URL = os.environ.get("BB4G_URL")
-BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
-BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
-BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
-BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
-
-os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

epapi/tests/v1/test_api_permissions.py

@@ -117,25 +117,28 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
+            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
+            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
+            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
+            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
+            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
+            cls.unreviewed_package_no_access,
+            "CCCCCC",
+            name="No Access Compound",
+            description="Test compound",
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
+            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Reviewed Compound {idx:03d}",
+            name=f"Reviewed Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Draft Compound {idx:03d}",
+            name=f"Draft Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
 

epauth/urls.py

@@ -5,5 +5,4 @@ from . import views
 urlpatterns = [
     path("entra/login/", views.entra_login, name="entra_login"),
     path("auth/redirect/", views.entra_callback, name="entra_callback"),
-    path("auth/token/", views.get_token, name="get_token"),
 ]

epauth/views.py

@@ -2,11 +2,9 @@ import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.contrib.auth import login
-from django.http import HttpResponse
 from django.shortcuts import redirect
 
-from epdb.logic import UserManager, GroupManager
+from epdb.logic import UserManager
-from epdb.models import Group
 
 
 def get_msal_app_with_cache(request):
@@ -82,33 +80,6 @@ def entra_callback(request):
 
     login(request, u)
 
-    # EDIT START
-
-    # Ensure groups exists in eP
-    for id, name in s.ENTRA_SECRET_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-        # Ensure its secret
-        g.secret = True
-        g.save()
-
-    for id, name in s.ENTRA_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-
-    for group_uuid in claims.get("groups", []):
-        if Group.objects.filter(uuid=group_uuid).exists():
-            g = Group.objects.get(uuid=group_uuid)
-            g.user_member.add(u)
-
-    # EDIT END
-
     return redirect(s.SERVER_URL)  # Handle errors
 
 
@@ -162,9 +133,3 @@ def get_access_token_from_request(request, scopes=None):
         return result
 
     return None
-
-
-def get_token(request):
-    token = get_access_token_from_request(request)
-    msg = f"{token}"
-    return HttpResponse(msg, content_type='text/plain')

epdb/exceptions.py

@@ -1,2 +1,10 @@
 class InvalidSMILESException(Exception):
     pass
+
+
+class InvalidMolfileException(Exception):
+    pass
+
+
+class PackageImportException(Exception):
+    pass

epdb/legacy_api.py

@@ -1,20 +1,17 @@
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
-import jwt
 import nh3
-import requests
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
-from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
-from ninja.security import HttpBearer
+from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
+
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -49,26 +46,6 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
-def get_cached_jwks(tenant_id: str, force=False) -> Dict:
-    """Get JWKS using Django cache"""
-    cache_key = f"jwks_{tenant_id}"
-
-    jwks = cache.get(cache_key)
-
-    if jwks is None or force:
-        # Cache miss, fetch new keys
-        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
-        response = requests.get(jwks_uri)
-        response.raise_for_status()
-
-        jwks = response.json()
-
-        # Cache for 1 hour (3600 seconds)
-        cache.set(cache_key, jwks, 3600)
-
-    return jwks
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -82,52 +59,7 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-def validate_token(token: str) -> dict:
+router = Router(auth=SessionAuth(csrf=False))
-    TENANT_ID = s.MS_ENTRA_TENANT_ID
-    CLIENT_ID = s.MS_ENTRA_CLIENT_ID
-
-    jwks = get_cached_jwks(TENANT_ID)
-
-    header = jwt.get_unverified_header(token)
-
-    public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
-        next(k for k in jwks["keys"] if k["kid"] == header["kid"])
-    )
-
-    # Handle V1 and V2 tokens
-    try:
-        claims = jwt.decode(
-            token,
-            public_key,
-            algorithms=["RS256"],
-            audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-            issuer=[
-                f"https://sts.windows.net/{TENANT_ID}/",
-                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
-            ]
-        )
-    except Exception as e:
-        raise ValueError(f"Token verification failed! - {e}")
-
-    return claims
-
-
-class MSBearerTokenAuth(HttpBearer):
-
-    def authenticate(self, request, token):
-        if token is None:
-            return None
-
-        claims = validate_token(token)
-
-        if not User.objects.filter(uuid=claims['oid']).exists():
-            return None
-
-        request.user = User.objects.get(uuid=claims['oid'])
-        return request.user
-
-
-router = Router(auth=MSBearerTokenAuth())
 
 
 class Error(Schema):
@@ -221,6 +153,21 @@ class SimpleModel(SimpleObject):
     identifier: str = "relative-reasoning"
 
 
+################
+# Login/Logout #
+################
+@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
+def login(request, loginusername: Form[str], loginpassword: Form[str]):
+    from django.contrib.auth import authenticate, login
+
+    email = User.objects.get(username=loginusername).email
+    user = authenticate(username=email, password=loginpassword)
+    if user:
+        login(request, user)
+        return user
+    else:
+        return 403, {"message": "Invalid username and/or password"}
+
 
 ########
 # User #
@@ -844,10 +791,10 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
+    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
-    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -858,32 +805,13 @@ def create_package_compound(
 ):
     try:
         p = get_package_for_write(request.user, package_uuid)
-        # inchi is not used atm
-
-        if c.pesLink is not None:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            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:
-                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-
-            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-        else:
         c = Compound.create(
-                p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+            p,
+            c.compoundSmiles,
+            molfile=c.compoundMolFile,
+            name=c.compoundName,
+            description=c.compoundDescription,
+            inchi=c.inchi,
         )
         return redirect(c.url)
     except ValueError as e:
@@ -1707,24 +1635,10 @@ 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")
@@ -1976,70 +1890,36 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
+    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 400: Error, 403: Error},
+    response={200: str | Any, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        # TODO Code Dup from bayer.views
-
-        if n.pesLink:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, n.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
-
-            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:
-                        return 400, {
-                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
-                        }
-
-            c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
-
-            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
-            if node_qs.exists():
-                return redirect(pw.url)
-
-            node = Node()
-            node.stereo_removed = False
-            node.pathway = pw
-            node.depth = 0
-
-            node.default_node_label = c.default_structure
-            node.save()
-
-            node.node_labels.add(c.default_structure)
-            node.save()
-        else:
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-                node_depth = int(n.nodeDepth)
+            node_depth = int(float(n.nodeDepth))
         else:
             node_depth = -1
 
-            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        n = Node.create(
+            pw,
+            n.nodeAsSmiles,
+            node_depth,
+            molfile=n.nodeAsMolFile,
+            name=n.nodeName,
+            description=n.nodeReason,
+        )
 
-        return redirect(node.url)
+        return redirect(n.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -2149,16 +2029,13 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
-        subclasses = CompoundStructure.__subclasses__()
-
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -2169,8 +2046,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -2392,3 +2268,26 @@ 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:
+        from epdb.logic import SPathway
+
+        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
+        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

@@ -7,7 +7,6 @@ import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
-from django.db.models import QuerySet
 from pydantic import ValidationError
 
 from epdb.models import (
@@ -365,14 +364,6 @@ class PackageManager(object):
 
         groups = GroupManager.get_groups(user)
 
-        # EDIT START
-
-        if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
-                return False
-
-        # EDIT END
-
         perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
 
         valid_perms = perms.get(permission)
@@ -415,7 +406,6 @@ class PackageManager(object):
         try:
             p = Package.objects.get(uuid=package_id)
             if PackageManager.readable(user, p):
-                p = PackageManager.check_package_classification(user, p)
                 return p
             else:
                 # FIXME: use custom exception to be translatable to 403 in API
@@ -425,37 +415,6 @@ class PackageManager(object):
         except Package.DoesNotExist:
             raise ValueError("Package with ID {} does not exist!".format(package_id))
 
-    # EDIT START
-
-    @staticmethod
-    def check_package_classification(user, pack: Package):
-        if pack.classification_level == Package.Classification.SECRET:
-            if pack.data_pool.user_member.filter(id=user.id).exists():
-                return pack
-
-            raise ValueError("Package is secret and not accessible to user!")
-
-        else:
-            return pack
-
-
-    @staticmethod
-    def check_package_classifications(user, package_qs: QuerySet[Package]):
-        non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
-        secret = package_qs.filter(classification_level=Package.Classification.SECRET)
-
-        # TODO we should be able to do via the db
-        accessible_secret = []
-
-        for s_package in secret:
-            if s_package.data_pool.user_member.filter(id=user.id).exists():
-                accessible_secret.append(s_package.pk)
-
-        # Cannot combine a unique query with a non-unique query -> we have to call distinct
-        return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
-
-    # EDIT END
-
     @staticmethod
     def get_all_readable_packages(user, include_reviewed=False):
         # UserPermission only exists if at least read is granted...
@@ -482,10 +441,6 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
         return qs
 
     @staticmethod
@@ -532,12 +487,12 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
         return qs
 
+    @staticmethod
+    def get_packages():
+        return Package.objects.all()
+
     @staticmethod
     @transaction.atomic
     def create_package(current_user, name: str, description: str = None):
@@ -641,25 +596,6 @@ class PackageManager(object):
         else:
             pack.reviewed = False
 
-        # EDIT START
-        if data.get("classification"):
-            if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
-
-                if not "datapool" in data:
-                    raise ValueError("Missing datapool in package")
-
-                g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
-                pack.data_pool = g
-            else:
-                raise ValueError(f"Invalid classification {data['classification']}")
-
-        # EDIT END
-
         pack.description = data["description"]
         pack.save()
 
@@ -745,13 +681,7 @@ class PackageManager(object):
             default_structure = None
 
             for structure in compound["structures"]:
-                if structure.get("pesLink"):
-                    from bayer.models import PESStructure
-                    struc = PESStructure()
-                    struc.pes_link = structure["pesLink"]
-                else:
                 struc = CompoundStructure()
-
                 # struc.object_url = Command.get_id(structure, keep_ids)
                 struc.compound = comp
                 struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@@ -1081,7 +1011,7 @@ class PackageManager(object):
         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 +1828,11 @@ 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/migrations/0001_initial.py

@@ -0,0 +1,594 @@
+# Generated by Django 5.2.1 on 2025-07-22 20:58
+
+import datetime
+import django.contrib.auth.models
+import django.contrib.auth.validators
+import django.contrib.postgres.fields
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('auth', '0012_alter_user_first_name_max_length'),
+        ('contenttypes', '0002_remove_content_type_name'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Compound',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='EPModel',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+        ),
+        migrations.CreateModel(
+            name='Permission',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='License',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('link', models.URLField(verbose_name='link')),
+                ('image_link', models.URLField(verbose_name='Image link')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Rule',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+        ),
+        migrations.CreateModel(
+            name='User',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('password', models.CharField(max_length=128, verbose_name='password')),
+                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
+                ('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
+                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
+                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
+                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
+                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
+                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
+                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
+                ('email', models.EmailField(max_length=254, unique=True)),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
+                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
+            ],
+            options={
+                'verbose_name': 'user',
+                'verbose_name_plural': 'users',
+                'abstract': False,
+            },
+            managers=[
+                ('objects', django.contrib.auth.models.UserManager()),
+            ],
+        ),
+        migrations.CreateModel(
+            name='APIToken',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('hashed_key', models.CharField(max_length=128, unique=True)),
+                ('created', models.DateTimeField(auto_now_add=True)),
+                ('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
+                ('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='CompoundStructure',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('smiles', models.TextField(verbose_name='SMILES')),
+                ('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
+                ('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
+                ('normalized_structure', models.BooleanField(default=False)),
+                ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='default_structure',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
+        ),
+        migrations.CreateModel(
+            name='Edge',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+        ),
+        migrations.CreateModel(
+            name='EnviFormer',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='PluginModel',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='RuleBaseRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='Group',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(verbose_name='Group name')),
+                ('public', models.BooleanField(default=False, verbose_name='Public Group')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
+                ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='default_group',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
+        ),
+        migrations.CreateModel(
+            name='Node',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('depth', models.IntegerField(verbose_name='Node depth')),
+                ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
+                ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
+                ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='end_nodes',
+            field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='start_nodes',
+            field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
+        ),
+        migrations.CreateModel(
+            name='Package',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
+                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='epmodel',
+            name='package',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='package',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='default_package',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
+        ),
+        migrations.CreateModel(
+            name='SequentialRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.CreateModel(
+            name='SimpleRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='package',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='polymorphic_ctype',
+            field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
+        ),
+        migrations.CreateModel(
+            name='Pathway',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='node',
+            name='pathway',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='pathway',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
+        ),
+        migrations.CreateModel(
+            name='Reaction',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
+                ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
+                ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
+                ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='edge_label',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
+        ),
+        migrations.CreateModel(
+            name='Scenario',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('scenario_date', models.CharField(default='No date', max_length=256)),
+                ('scenario_type', models.CharField(default='Not specified', max_length=256)),
+                ('additional_information', models.JSONField(verbose_name='Additional Information')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='reaction',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='pathway',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='node',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='compoundstructure',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.CreateModel(
+            name='Setting',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('public', models.BooleanField(default=False)),
+                ('global_default', models.BooleanField(default=False)),
+                ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
+                ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
+                ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
+                ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='pathway',
+            name='setting',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='default_setting',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
+        ),
+        migrations.CreateModel(
+            name='MLRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='ApplicabilityDomain',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('num_neighbours', models.FloatField(default=5)),
+                ('reliability_threshold', models.FloatField(default=0.5)),
+                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
+                ('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='SimpleAmbitRule',
+            fields=[
+                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
+                ('smirks', models.TextField(verbose_name='SMIRKS')),
+                ('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
+                ('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.simplerule',),
+        ),
+        migrations.CreateModel(
+            name='SimpleRDKitRule',
+            fields=[
+                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
+                ('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.simplerule',),
+        ),
+        migrations.CreateModel(
+            name='SequentialRuleOrdering',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('order_index', models.IntegerField()),
+                ('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
+                ('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='sequentialrule',
+            name='simple_rules',
+            field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
+        ),
+        migrations.CreateModel(
+            name='ParallelRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+                ('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.AlterUniqueTogether(
+            name='compound',
+            unique_together={('uuid', 'package')},
+        ),
+        migrations.CreateModel(
+            name='GroupPackagePermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
+            ],
+            options={
+                'unique_together': {('package', 'group')},
+            },
+            bases=('epdb.permission',),
+        ),
+        migrations.CreateModel(
+            name='UserPackagePermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
+            ],
+            options={
+                'unique_together': {('package', 'user')},
+            },
+            bases=('epdb.permission',),
+        ),
+        migrations.CreateModel(
+            name='UserSettingPermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
+            ],
+            options={
+                'unique_together': {('setting', 'user')},
+            },
+            bases=('epdb.permission',),
+        ),
+    ]

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

@@ -0,0 +1,128 @@
+# Generated by Django 5.2.1 on 2025-08-25 18:07
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('contenttypes', '0002_remove_content_type_name'),
+        ('epdb', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ExternalDatabase',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
+                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
+                ('description', models.TextField(blank=True, verbose_name='Description')),
+                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
+                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
+                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
+            ],
+            options={
+                'verbose_name': 'External Database',
+                'verbose_name_plural': 'External Databases',
+                'db_table': 'epdb_external_database',
+                'ordering': ['name'],
+            },
+        ),
+        migrations.AlterModelOptions(
+            name='apitoken',
+            options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
+        ),
+        migrations.AlterModelOptions(
+            name='edge',
+            options={},
+        ),
+        migrations.RemoveField(
+            model_name='edge',
+            name='polymorphic_ctype',
+        ),
+        migrations.AddField(
+            model_name='apitoken',
+            name='is_active',
+            field=models.BooleanField(default=True, help_text='Whether this token is active'),
+        ),
+        migrations.AddField(
+            model_name='apitoken',
+            name='modified',
+            field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
+        ),
+        migrations.AddField(
+            model_name='applicabilitydomain',
+            name='functional_groups',
+            field=models.JSONField(blank=True, default=dict, null=True),
+        ),
+        migrations.AddField(
+            model_name='mlrelativereasoning',
+            name='app_domain',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
+        ),
+        migrations.AlterField(
+            model_name='apitoken',
+            name='created',
+            field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
+        ),
+        migrations.AlterField(
+            model_name='apitoken',
+            name='expires_at',
+            field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
+        ),
+        migrations.AlterField(
+            model_name='apitoken',
+            name='hashed_key',
+            field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
+        ),
+        migrations.AlterField(
+            model_name='apitoken',
+            name='name',
+            field=models.CharField(help_text='Descriptive name for this token', max_length=100),
+        ),
+        migrations.AlterField(
+            model_name='apitoken',
+            name='user',
+            field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
+        ),
+        migrations.AlterField(
+            model_name='applicabilitydomain',
+            name='num_neighbours',
+            field=models.IntegerField(default=5),
+        ),
+        migrations.AlterModelTable(
+            name='apitoken',
+            table='epdb_api_token',
+        ),
+        migrations.CreateModel(
+            name='ExternalIdentifier',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ('object_id', models.IntegerField()),
+                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
+                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
+                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
+                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
+                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
+            ],
+            options={
+                'verbose_name': 'External Identifier',
+                'verbose_name_plural': 'External Identifiers',
+                'db_table': 'epdb_external_identifier',
+                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
+                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
+            },
+        ),
+    ]

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

@@ -0,0 +1,228 @@
+# Generated by Django 5.2.1 on 2025-08-26 17:05
+
+from django.db import migrations, models
+
+
+def populate_url(apps, schema_editor):
+    MODELS = [
+        'User',
+        'Group',
+        'Package',
+        'Compound',
+        'CompoundStructure',
+        'Pathway',
+        'Edge',
+        'Node',
+        'Reaction',
+        'SimpleAmbitRule',
+        'SimpleRDKitRule',
+        'ParallelRule',
+        'SequentialRule',
+        'Scenario',
+        'Setting',
+        'MLRelativeReasoning',
+        'EnviFormer',
+        'ApplicabilityDomain',
+    ]
+    for model in MODELS:
+        obj_cls = apps.get_model("epdb", model)
+        for obj in obj_cls.objects.all():
+            obj.url = assemble_url(obj)
+            if obj.url is None:
+                raise ValueError(f"Could not assemble url for {obj}")
+            obj.save()
+
+
+def assemble_url(obj):
+    from django.conf import settings as s
+    match obj.__class__.__name__:
+        case 'User':
+            return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
+        case 'Group':
+            return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
+        case 'Package':
+            return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
+        case 'Compound':
+            return '{}/compound/{}'.format(obj.package.url, obj.uuid)
+        case 'CompoundStructure':
+            return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
+        case 'SimpleAmbitRule':
+            return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
+        case 'SimpleRDKitRule':
+            return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
+        case 'ParallelRule':
+            return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
+        case 'SequentialRule':
+            return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
+        case 'Reaction':
+            return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
+        case 'Pathway':
+            return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
+        case 'Node':
+            return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
+        case 'Edge':
+            return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
+        case 'MLRelativeReasoning':
+            return '{}/model/{}'.format(obj.package.url, obj.uuid)
+        case 'EnviFormer':
+            return '{}/model/{}'.format(obj.package.url, obj.uuid)
+        case 'ApplicabilityDomain':
+            return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
+        case 'Scenario':
+            return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
+        case 'Setting':
+            return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
+        case _:
+            raise ValueError(f"Unknown model {obj.__class__.__name__}")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='applicabilitydomain',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='compoundstructure',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='epmodel',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='group',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='node',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='package',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='pathway',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='reaction',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='scenario',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='setting',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='url',
+            field=models.TextField(null=True, unique=False, verbose_name='URL'),
+        ),
+
+        migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
+
+        migrations.AlterField(
+            model_name='applicabilitydomain',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='compound',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='compoundstructure',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='edge',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='epmodel',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='group',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='node',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='package',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='pathway',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='reaction',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='rule',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='scenario',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='setting',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+        migrations.AlterField(
+            model_name='user',
+            name='url',
+            field=models.TextField(null=True, unique=True, verbose_name='URL'),
+        ),
+    ]

epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py

@@ -0,0 +1,55 @@
+# Generated by Django 5.2.1 on 2025-09-09 09:21
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='mlrelativereasoning',
+            options={},
+        ),
+        migrations.AlterField(
+            model_name='mlrelativereasoning',
+            name='data_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
+        ),
+        migrations.AlterField(
+            model_name='mlrelativereasoning',
+            name='eval_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
+        ),
+        migrations.AlterField(
+            model_name='mlrelativereasoning',
+            name='rule_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
+        ),
+        migrations.CreateModel(
+            name='RuleBasedRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('min_count', models.IntegerField(default=10)),
+                ('max_count', models.IntegerField(default=0)),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.DeleteModel(
+            name='RuleBaseRelativeReasoning',
+        ),
+    ]

epdb/migrations/0005_alter_group_group_member.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.1 on 2025-09-11 06:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='group',
+            name='group_member',
+            field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
+        ),
+    ]

epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.2.1 on 2025-09-18 06:42
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0005_alter_group_group_member'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='mlrelativereasoning',
+            name='multigen_eval',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='rulebasedrelativereasoning',
+            name='multigen_eval',
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py

@@ -0,0 +1,53 @@
+# Generated by Django 5.2.1 on 2025-10-07 08:19
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='enviformer',
+            options={},
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='app_domain',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='data_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='eval_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='eval_results',
+            field=models.JSONField(blank=True, default=dict, null=True),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='model_status',
+            field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='multigen_eval',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='rule_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
+        ),
+    ]

epdb/migrations/0008_enzymelink.py

@@ -0,0 +1,64 @@
+# Generated by Django 5.2.7 on 2025-10-10 06:58
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="EnzymeLink",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "uuid",
+                    models.UUIDField(
+                        default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
+                    ),
+                ),
+                ("name", models.TextField(default="no name", verbose_name="Name")),
+                (
+                    "description",
+                    models.TextField(default="no description", verbose_name="Descriptions"),
+                ),
+                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
+                ("kv", models.JSONField(blank=True, default=dict, null=True)),
+                ("ec_number", models.TextField(verbose_name="EC Number")),
+                ("classification_level", models.IntegerField(verbose_name="Classification Level")),
+                ("linking_method", models.TextField(verbose_name="Linking Method")),
+                ("edge_evidence", models.ManyToManyField(to="epdb.edge")),
+                ("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
+                (
+                    "rule",
+                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

epdb/migrations/0009_joblog.py

@@ -0,0 +1,66 @@
+# Generated by Django 5.2.7 on 2025-10-27 09:39
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0008_enzymelink"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="JobLog",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                ("task_id", models.UUIDField(unique=True)),
+                ("job_name", models.TextField()),
+                (
+                    "status",
+                    models.CharField(
+                        choices=[
+                            ("INITIAL", "Initial"),
+                            ("SUCCESS", "Success"),
+                            ("FAILURE", "Failure"),
+                            ("REVOKED", "Revoked"),
+                            ("IGNORED", "Ignored"),
+                        ],
+                        default="INITIAL",
+                        max_length=20,
+                    ),
+                ),
+                ("done_at", models.DateTimeField(blank=True, default=None, null=True)),
+                ("task_result", models.TextField(blank=True, default=None, null=True)),
+                (
+                    "user",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

epdb/migrations/0010_license_cc_string.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.7 on 2025-11-11 14:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0009_joblog"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="license",
+            name="cc_string",
+            field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
+            preserve_default=False,
+        ),
+    ]

epdb/migrations/0011_auto_20251111_1413.py

@@ -0,0 +1,59 @@
+# Generated by Django 5.2.7 on 2025-11-11 14:13
+
+import re
+
+from django.contrib.postgres.aggregates import ArrayAgg
+from django.db import migrations
+from django.db.models import Min
+
+
+def set_cc(apps, schema_editor):
+    License = apps.get_model("epdb", "License")
+
+    # For all existing licenses extract cc_string from link
+    for license in License.objects.all():
+        pattern = r"/licenses/([^/]+)/4\.0"
+        match = re.search(pattern, license.link)
+        if match:
+            license.cc_string = match.group(1)
+            license.save()
+        else:
+            raise ValueError(f"Could not find license for {license.link}")
+
+    # Ensure we have all licenses
+    cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+    for cc_string in cc_strings:
+        if not License.objects.filter(cc_string=cc_string).exists():
+            new_license = License()
+            new_license.cc_string = cc_string
+            new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+            new_license.save()
+
+    # As we might have existing Licenses representing the same License,
+    # get min pk and all pks as a list
+    license_lookup_qs = License.objects.values("cc_string").annotate(
+        lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
+    )
+
+    license_lookup = {
+        row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
+    }
+
+    Packages = apps.get_model("epdb", "Package")
+
+    for k, v in license_lookup.items():
+        # Set min pk to all packages pointing to any of the duplicates
+        Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
+        # remove the min pk from "other" pks as we use them for deletion
+        v[1].remove(v[0])
+        # Delete redundant License objects
+        License.objects.filter(pk__in=v[1]).delete()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0010_license_cc_string"),
+    ]
+
+    operations = [migrations.RunPython(set_cc)]

epdb/migrations/0012_node_stereo_removed_pathway_predicted.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.2.7 on 2025-12-02 13:09
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0011_auto_20251111_1413"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="node",
+            name="stereo_removed",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="pathway",
+            name="predicted",
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/migrations/0013_setting_expansion_schema.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.2.7 on 2025-12-14 11:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0012_node_stereo_removed_pathway_predicted"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="setting",
+            name="expansion_schema",
+            field=models.CharField(
+                choices=[
+                    ("BFS", "Breadth First Search"),
+                    ("DFS", "Depth First Search"),
+                    ("GREEDY", "Greedy"),
+                ],
+                default="BFS",
+                max_length=20,
+            ),
+        ),
+    ]

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.7 on 2025-12-14 16:02
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0013_setting_expansion_schema"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="setting",
+            old_name="expansion_schema",
+            new_name="expansion_scheme",
+        ),
+    ]

epdb/migrations/0015_user_is_reviewer.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.7 on 2026-01-19 19:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="user",
+            name="is_reviewer",
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/migrations/0016_remove_enviformer_model_status_and_more.py

@@ -0,0 +1,179 @@
+# Generated by Django 5.2.7 on 2026-02-12 09:38
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0015_user_is_reviewer"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="enviformer",
+            name="model_status",
+        ),
+        migrations.RemoveField(
+            model_name="mlrelativereasoning",
+            name="model_status",
+        ),
+        migrations.RemoveField(
+            model_name="rulebasedrelativereasoning",
+            name="model_status",
+        ),
+        migrations.AddField(
+            model_name="epmodel",
+            name="model_status",
+            field=models.CharField(
+                choices=[
+                    ("INITIAL", "Initial"),
+                    ("INITIALIZING", "Model is initializing."),
+                    ("BUILDING", "Model is building."),
+                    (
+                        "BUILT_NOT_EVALUATED",
+                        "Model is built and can be used for predictions, Model is not evaluated yet.",
+                    ),
+                    ("EVALUATING", "Model is evaluating"),
+                    ("FINISHED", "Model has finished building and evaluation."),
+                    ("ERROR", "Model has failed."),
+                ],
+                default="INITIAL",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="enviformer",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="enviformer",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="mlrelativereasoning",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="mlrelativereasoning",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rulebasedrelativereasoning",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rulebasedrelativereasoning",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to=settings.EPDB_PACKAGE_MODEL,
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.CreateModel(
+            name="PropertyPluginModel",
+            fields=[
+                (
+                    "epmodel_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="epdb.epmodel",
+                    ),
+                ),
+                ("threshold", models.FloatField(default=0.5)),
+                ("eval_results", models.JSONField(blank=True, default=dict, null=True)),
+                ("multigen_eval", models.BooleanField(default=False)),
+                ("plugin_identifier", models.CharField(max_length=255)),
+                (
+                    "app_domain",
+                    models.ForeignKey(
+                        blank=True,
+                        default=None,
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        to="epdb.applicabilitydomain",
+                    ),
+                ),
+                (
+                    "data_packages",
+                    models.ManyToManyField(
+                        blank=True,
+                        related_name="%(app_label)s_%(class)s_data_packages",
+                        to=settings.EPDB_PACKAGE_MODEL,
+                        verbose_name="Data Packages",
+                    ),
+                ),
+                (
+                    "eval_packages",
+                    models.ManyToManyField(
+                        blank=True,
+                        related_name="%(app_label)s_%(class)s_eval_packages",
+                        to=settings.EPDB_PACKAGE_MODEL,
+                        verbose_name="Evaluation Packages",
+                    ),
+                ),
+                (
+                    "rule_packages",
+                    models.ManyToManyField(
+                        blank=True,
+                        related_name="%(app_label)s_%(class)s_rule_packages",
+                        to=settings.EPDB_PACKAGE_MODEL,
+                        verbose_name="Rule Packages",
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+            bases=("epdb.epmodel",),
+        ),
+        migrations.AddField(
+            model_name="setting",
+            name="property_models",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="settings",
+                to="epdb.propertypluginmodel",
+                verbose_name="Setting Property Models",
+            ),
+        ),
+        migrations.DeleteModel(
+            name="PluginModel",
+        ),
+    ]

epdb/migrations/0017_additionalinformation.py

@@ -0,0 +1,93 @@
+# Generated by Django 5.2.7 on 2026-02-20 12:02
+
+import django.db.models.deletion
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("contenttypes", "0002_remove_content_type_name"),
+        ("epdb", "0016_remove_enviformer_model_status_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="AdditionalInformation",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
+                ("kv", models.JSONField(blank=True, default=dict, null=True)),
+                ("type", models.TextField(verbose_name="Additional Information Type")),
+                ("data", models.JSONField(blank=True, default=dict, null=True)),
+                ("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
+                (
+                    "content_type",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="contenttypes.contenttype",
+                    ),
+                ),
+                (
+                    "package",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to=settings.EPDB_PACKAGE_MODEL,
+                        verbose_name="Package",
+                    ),
+                ),
+                (
+                    "scenario",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="scenario_additional_information",
+                        to="epdb.scenario",
+                    ),
+                ),
+            ],
+            options={
+                "indexes": [
+                    models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
+                    models.Index(
+                        fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
+                    ),
+                    models.Index(
+                        fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
+                    ),
+                    models.Index(
+                        fields=["scenario", "content_type", "object_id"],
+                        name="epdb_additi_scenari_ef2bf5_idx",
+                    ),
+                ],
+                "constraints": [
+                    models.CheckConstraint(
+                        condition=models.Q(
+                            models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
+                            models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
+                            _connector="OR",
+                        ),
+                        name="ck_addinfo_gfk_pair",
+                    ),
+                    models.CheckConstraint(
+                        condition=models.Q(
+                            ("scenario__isnull", False),
+                            ("content_type__isnull", False),
+                            _connector="OR",
+                        ),
+                        name="ck_addinfo_not_both_null",
+                    ),
+                ],
+            },
+        ),
+    ]

epdb/migrations/0018_auto_20260220_1203.py

@@ -0,0 +1,132 @@
+# Generated by Django 5.2.7 on 2026-02-20 12:03
+
+from django.db import migrations
+
+
+def get_additional_information(scenario):
+    from envipy_additional_information import registry
+    from envipy_additional_information.parsers import TypeOfAerationParser
+
+    for k, vals in scenario.additional_information.items():
+        if k == "enzyme":
+            continue
+
+        if k == "SpikeConentration":
+            k = "SpikeConcentration"
+
+        if k == "AerationType":
+            k = "TypeOfAeration"
+
+        for v in vals:
+            # Per default additional fields are ignored
+            MAPPING = {c.__name__: c for c in registry.list_models().values()}
+            try:
+                inst = MAPPING[k](**v)
+            except Exception:
+                if k == "TypeOfAeration":
+                    toa = TypeOfAerationParser()
+                    inst = toa.from_string(v["type"])
+
+            # Add uuid to uniquely identify objects for manipulation
+            if "uuid" in v:
+                inst.__dict__["uuid"] = v["uuid"]
+
+            yield inst
+
+
+def forward_func(apps, schema_editor):
+    Scenario = apps.get_model("epdb", "Scenario")
+    ContentType = apps.get_model("contenttypes", "ContentType")
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    bulk = []
+    related = []
+    ctype = {o.model: o for o in ContentType.objects.all()}
+    parents = Scenario.objects.prefetch_related(
+        "compound_set",
+        "compoundstructure_set",
+        "reaction_set",
+        "rule_set",
+        "pathway_set",
+        "node_set",
+        "edge_set",
+    ).filter(parent__isnull=True)
+
+    for i, scenario in enumerate(parents):
+        print(f"{i + 1}/{len(parents)}", end="\r")
+        if scenario.parent is not None:
+            related.append(scenario.parent)
+            continue
+
+        for ai in get_additional_information(scenario):
+            bulk.append(
+                AdditionalInformation(
+                    package=scenario.package,
+                    scenario=scenario,
+                    type=ai.__class__.__name__,
+                    data=ai.model_dump(mode="json"),
+                )
+            )
+
+    print("\n", len(bulk))
+
+    related = Scenario.objects.prefetch_related(
+        "compound_set",
+        "compoundstructure_set",
+        "reaction_set",
+        "rule_set",
+        "pathway_set",
+        "node_set",
+        "edge_set",
+    ).filter(parent__isnull=False)
+
+    for i, scenario in enumerate(related):
+        print(f"{i + 1}/{len(related)}", end="\r")
+        parent = scenario.parent
+        # Check to which objects this scenario is attached to
+        for ai in get_additional_information(scenario):
+            rel_objs = [
+                "compound",
+                "compoundstructure",
+                "reaction",
+                "rule",
+                "pathway",
+                "node",
+                "edge",
+            ]
+            for rel_obj in rel_objs:
+                for o in getattr(scenario, f"{rel_obj}_set").all():
+                    bulk.append(
+                        AdditionalInformation(
+                            package=scenario.package,
+                            scenario=parent,
+                            type=ai.__class__.__name__,
+                            data=ai.model_dump(mode="json"),
+                            content_type=ctype[rel_obj],
+                            object_id=o.pk,
+                        )
+                    )
+
+    print("Start creating additional information objects...")
+    AdditionalInformation.objects.bulk_create(bulk)
+    print("Done!")
+    print(len(bulk))
+
+    Scenario.objects.filter(parent__isnull=False).delete()
+    # Call ai save to fix urls
+    ais = AdditionalInformation.objects.all()
+    total = ais.count()
+
+    for i, ai in enumerate(ais):
+        print(f"{i + 1}/{total}", end="\r")
+        ai.save()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0017_additionalinformation"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/migrations/0019_remove_scenario_additional_information_and_more.py

@@ -1,741 +1,20 @@
-# Generated by Django 5.2.7 on 2026-03-06 10:51
+# Generated by Django 5.2.7 on 2026-02-23 08:45
 
-import django.contrib.auth.models
+from django.db import migrations
-import django.contrib.auth.validators
-import django.contrib.postgres.fields
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
-    initial = True
-
     dependencies = [
-        ('auth', '0012_alter_user_first_name_max_length'),
+        ("epdb", "0018_auto_20260220_1203"),
-        ('contenttypes', '0002_remove_content_type_name'),
-        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
-        migrations.CreateModel(
+        migrations.RemoveField(
-            name='ApplicabilityDomain',
+            model_name="scenario",
-            fields=[
+            name="additional_information",
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('num_neighbours', models.IntegerField(default=5)),
-                ('reliability_threshold', models.FloatField(default=0.5)),
-                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
-                ('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
-            ],
-            options={
-                'abstract': False,
-            },
         ),
-        migrations.CreateModel(
+        migrations.RemoveField(
-            name='Edge',
+            model_name="scenario",
-            fields=[
+            name="parent",
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='EPModel',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='ExternalDatabase',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
-                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
-                ('description', models.TextField(blank=True, verbose_name='Description')),
-                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
-                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
-                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
-            ],
-            options={
-                'verbose_name': 'External Database',
-                'verbose_name_plural': 'External Databases',
-                'db_table': 'epdb_external_database',
-                'ordering': ['name'],
-            },
-        ),
-        migrations.CreateModel(
-            name='Permission',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
-            ],
-        ),
-        migrations.CreateModel(
-            name='License',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('cc_string', models.TextField(verbose_name='CC string')),
-                ('link', models.URLField(verbose_name='link')),
-                ('image_link', models.URLField(verbose_name='Image link')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='Rule',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='User',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('password', models.CharField(max_length=128, verbose_name='password')),
-                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
-                ('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
-                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
-                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
-                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
-                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
-                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
-                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
-                ('email', models.EmailField(max_length=254, unique=True)),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('is_reviewer', models.BooleanField(default=False)),
-                ('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
-                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
-                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
-            ],
-            options={
-                'verbose_name': 'user',
-                'verbose_name_plural': 'users',
-                'abstract': False,
-            },
-            managers=[
-                ('objects', django.contrib.auth.models.UserManager()),
-            ],
-        ),
-        migrations.CreateModel(
-            name='APIToken',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
-                ('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
-                ('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
-                ('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
-                ('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
-            ],
-            options={
-                'verbose_name': 'API Token',
-                'verbose_name_plural': 'API Tokens',
-                'db_table': 'epdb_api_token',
-                'ordering': ['-created'],
-            },
-        ),
-        migrations.CreateModel(
-            name='Compound',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='CompoundStructure',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('smiles', models.TextField(verbose_name='SMILES')),
-                ('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
-                ('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
-                ('normalized_structure', models.BooleanField(default=False)),
-                ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='default_structure',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
-        ),
-        migrations.CreateModel(
-            name='PropertyPluginModel',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('plugin_identifier', models.CharField(max_length=255)),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='Group',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('name', models.TextField(verbose_name='Group name')),
-                ('public', models.BooleanField(default=False, verbose_name='Public Group')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
-                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
-                ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_group',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
-        ),
-        migrations.CreateModel(
-            name='JobLog',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('task_id', models.UUIDField(unique=True)),
-                ('job_name', models.TextField()),
-                ('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
-                ('done_at', models.DateTimeField(blank=True, default=None, null=True)),
-                ('task_result', models.TextField(blank=True, default=None, null=True)),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='Package',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
-                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
-            ],
-            options={
-                'swappable': 'EPDB_PACKAGE_MODEL',
-            },
-        ),
-        migrations.CreateModel(
-            name='Node',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('depth', models.IntegerField(verbose_name='Node depth')),
-                ('stereo_removed', models.BooleanField(default=False)),
-                ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
-                ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
-                ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='end_nodes',
-            field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='start_nodes',
-            field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
-        ),
-        migrations.CreateModel(
-            name='SequentialRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.CreateModel(
-            name='Pathway',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('predicted', models.BooleanField(default=False)),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.CreateModel(
-            name='Reaction',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
-                ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
-                ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
-                ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='EnzymeLink',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('ec_number', models.TextField(verbose_name='EC Number')),
-                ('classification_level', models.IntegerField(verbose_name='Classification Level')),
-                ('linking_method', models.TextField(verbose_name='Linking Method')),
-                ('edge_evidence', models.ManyToManyField(to='epdb.edge')),
-                ('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
-                ('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='edge_label',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
-        ),
-        migrations.CreateModel(
-            name='Scenario',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('scenario_date', models.CharField(default='No date', max_length=256)),
-                ('scenario_type', models.CharField(default='Not specified', max_length=256)),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='reaction',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compoundstructure',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.CreateModel(
-            name='Setting',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('public', models.BooleanField(default=False)),
-                ('global_default', models.BooleanField(default=False)),
-                ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
-                ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
-                ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
-                ('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
-                ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
-                ('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='setting',
-            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_setting',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
-        ),
-        migrations.CreateModel(
-            name='EnviFormer',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='MLRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='model',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='app_domain',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='data_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='eval_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='rule_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
-        ),
-        migrations.CreateModel(
-            name='RuleBasedRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('min_count', models.IntegerField(default=10)),
-                ('max_count', models.IntegerField(default=0)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='ExternalIdentifier',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('object_id', models.IntegerField()),
-                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
-                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
-                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
-                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
-            ],
-            options={
-                'verbose_name': 'External Identifier',
-                'verbose_name_plural': 'External Identifiers',
-                'db_table': 'epdb_external_identifier',
-                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
-                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
-            },
-        ),
-        migrations.CreateModel(
-            name='SimpleAmbitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('smirks', models.TextField(verbose_name='SMIRKS')),
-                ('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
-                ('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRDKitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SequentialRuleOrdering',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('order_index', models.IntegerField()),
-                ('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
-                ('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
-            ],
-        ),
-        migrations.AddField(
-            model_name='sequentialrule',
-            name='simple_rules',
-            field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
-        ),
-        migrations.CreateModel(
-            name='ParallelRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-                ('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.AlterUniqueTogether(
-            name='compound',
-            unique_together={('uuid', 'package')},
-        ),
-        migrations.CreateModel(
-            name='AdditionalInformation',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('type', models.TextField(verbose_name='Additional Information Type')),
-                ('data', models.JSONField(blank=True, default=dict, null=True)),
-                ('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
-                ('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
-            ],
-            options={
-                'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
-                'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
-            },
-        ),
-        migrations.CreateModel(
-            name='GroupPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
-            ],
-            options={
-                'unique_together': {('package', 'group')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('package', 'user')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserSettingPermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('setting', 'user')},
-            },
-            bases=('epdb.permission',),
         ),
     ]

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -46,9 +46,4 @@ class Migration(migrations.Migration):
             name="molfile",
             field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
         ),
-        migrations.AddField(
-            model_name="group",
-            name="secret",
-            field=models.BooleanField(default=False, verbose_name="Secret Group"),
-        ),
     ]

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/models.py

@@ -31,7 +31,10 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import InvalidSMILESException
+from epdb.exceptions import (
+    InvalidMolfileException,
+    InvalidSMILESException,
+)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -205,7 +208,6 @@ class Group(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name="Group name")
     owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name="Public Group", default=False)
-    secret = models.BooleanField(verbose_name="Secret Group", default=False)
     description = models.TextField(
         blank=False, null=False, verbose_name="Descriptions", default="no description"
     )
@@ -577,10 +579,6 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
-    def contains_pes(self):
-        from bayer.models import PESStructure
-        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
-            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #
@@ -794,6 +792,13 @@ class Compound(
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
+    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
+        for struct in self.structures.all():
+            if struct.smiles == smiles:
+                return struct
+
+        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
+
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -862,8 +867,24 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package",
+        smiles: str,
+        molfile: str | None = None,
+        name: str | None = None,
+        description: str | None = None,
+        *args,
+        **kwargs,
     ) -> "Compound":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles.strip() == "":
             raise InvalidSMILESException("SMILES is required")
 
@@ -873,50 +894,34 @@ class Compound(
         if parsed is None:
             raise InvalidSMILESException("Given SMILES is invalid")
 
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
-        subclasses = CompoundStructure.__subclasses__()
-
-        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
-
         # Check if we find a direct match for a given SMILES
-        if qs.exists():
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            found_structure = qs.first()
+            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
-            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)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
-        if qs.exists():
+        if CompoundStructure.objects.filter(
-            # TODO should we add a structure?
+            smiles=standardized_smiles, compound__package=package
-            found_structure = qs.first()
+        ).exists():
-            found_compound = found_structure.compound
+            found_c = CompoundStructure.objects.get(
+                smiles=standardized_smiles, compound__package=package
+            ).compound
 
-            if name:
+            # As a direct match wasn't found add a new structure
-                found_structure.add_alias(name)
+            # TODO return newly created structure
-                found_compound.add_alias(name)
+            _ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
 
-            return found_compound
+            return found_c
 
         # 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}"
 
@@ -940,7 +945,12 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+            c,
+            smiles,
+            molfile=molfile,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         c.default_structure = cs
@@ -953,11 +963,22 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
+        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -977,16 +998,28 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            smiles__in=smiles, compound__package=self.package
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-        ).exists():
+
-            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         cs = CompoundStructure.create(
-            self, smiles, name=name, description=description, normalized_structure=is_standardized
+            self,
+            smiles,
+            name=name,
+            molfile=molfile,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         if default_structure:
@@ -1167,17 +1200,33 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
+        compound: Compound,
+        smiles: str,
+        molfile: str = None,
+        name: str = None,
+        description: str = None,
+        *args,
+        **kwargs,
     ):
-        # Clean for potential XSS
+        # Molfile has precendence over SMILES
-        if name is not None:
+        if molfile is not None and molfile.strip() != "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
 
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound=compound)
 
-            if name:
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                found_cs.add_alias(name)
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
 
             return found_cs
 
@@ -1185,18 +1234,18 @@ class CompoundStructure(
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-
+        # Clean for potential XSS
         if name is not None:
-            cs.name = name
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.smiles = smiles
         cs.compound = compound
+        cs.smiles = smiles
 
         # Check if molfile is present and valid
-        if molfile is not None and FormatConverter.from_molfile(molfile) is not None:
+        if molfile is not None and molfile.strip() != "":
             cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
@@ -1415,9 +1464,6 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1429,17 +1475,14 @@ 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}"
 
@@ -1687,11 +1730,6 @@ class Reaction(
         rules: Union[Rule | List[Rule]] = None,
         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 = []
 
@@ -1746,19 +1784,14 @@ 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
 
-        if r is not None:
+        # Clean for potential XSS
-            r.name = name
+        if name is not None and name.strip() != "":
+            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1994,6 +2027,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
+                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -2003,6 +2037,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
+                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -2010,6 +2045,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
+                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -2020,6 +2056,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
+                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2229,11 +2266,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
-        depth: Optional[int] = -1,
+        description: str | None = None,
+        depth: int = -1,
     ):
-        return Node.create(self, smiles, depth, name=name, description=description)
+        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2329,17 +2367,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
-        if self.name == "no name":
+        if self.name is None or self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.default_node_label.name} (taken from underlying structure)"
+            if include_suffix:
-        )
+                return f"{self.default_node_label.name} (taken from underlying structure)"
+            else:
+                return self.default_node_label.name
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2369,6 +2409,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             ),
             "image_type": "svg",
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2391,28 +2432,43 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
+        description: str | None = None,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(pathway.package, smiles, name=name, description=description)
+        c = Compound.create(
+            pathway.package, smiles, molfile=molfile, name=name, description=description
+        )
 
-        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+        structure = c.get_structure_by_smiles(smiles)
-            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
+
+        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = c.default_structure
+        n.default_node_label = structure
         n.save()
 
-        n.node_labels.add(c.default_structure)
+        n.node_labels.add(structure)
         n.save()
 
         return n
@@ -2460,6 +2516,28 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
+    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())
+
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2481,6 +2559,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2595,17 +2674,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.edge_label.name} (taken from underlying reaction)"
+            if include_suffix:
-        )
+                return f"{self.edge_label.name} (taken from underlying reaction)"
+            else:
+                return self.edge_label.name
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):

epdb/views.py

@@ -19,7 +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 .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -389,9 +389,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
-            # EDIT START
-            "secret_groups": Group.objects.filter(secret=True),
-            # EDIT END
         },
     }
 
@@ -591,38 +588,10 @@ def packages(request):
                 "package-description", s.DEFAULT_VALUES["description"]
             )
 
-            # EDIT START
-            data_pool = None
-            package_classification = request.POST.get("package-classification")
-            classification = Package.Classification(int(package_classification))
-            # For SECRET we'll need a data pool which will be an additional perm check later
-            if classification == Package.Classification.SECRET:
-                package_data_pool = request.POST.get("package-data-pool")
-
-                if package_data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool is required!")
-
-                data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
-
-                if data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
-
-                if not data_pool.secret:
-                    return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
-
             created_package = PackageManager.create_package(
                 current_user, package_name, package_description
             )
 
-            created_package.classification_level = classification
-
-            # Set previously determined data pool
-            if classification == Package.Classification.SECRET:
-                created_package.data_pool = data_pool
-
-            created_package.save()
-            # EDIT END
-
             return redirect(created_package.url)
 
     elif request.method == "OPTIONS":
@@ -1415,12 +1384,18 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
+        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
+
         try:
             c = Compound.create(
-                current_package, compound_smiles, compound_name, compound_description
+                current_package,
+                compound_smiles,
+                molfile=compound_molfile,
+                name=compound_name,
+                description=compound_description,
             )
-        except ValueError as e:
+        except (InvalidSMILESException, InvalidMolfileException) as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1546,11 +1521,15 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
+        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles, structure_name, structure_description
+                structure_smiles,
+                molfile=structure_molfile,
+                name=structure_name,
+                description=structure_description,
             )
         except ValueError:
             return error(
@@ -2121,12 +2100,14 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
+        is_predict_mode = pw_mode in {"predict", "incremental"}
+
         pw = Pathway.create(
             current_package,
-            stand_smiles,
+            stand_smiles if is_predict_mode else smiles,
             name=name,
             description=description,
-            predicted=pw_mode in {"predict", "incremental"},
+            predicted=is_predict_mode,
         )
 
         # set mode
@@ -2368,9 +2349,12 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
+        node_molfile = request.POST.get("node-molfile").strip()
 
         try:
-            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+            current_pathway.add_node(
+                node_smiles, molfile=node_molfile, name=node_name, description=node_description
+            )
         except InvalidSMILESException:
             return error(
                 request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
@@ -2482,7 +2466,26 @@ 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"])
 
@@ -3014,15 +3017,9 @@ def settings(request):
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         # min 2, max s.DEFAULT_MAX_NUMBER_OF_NODES
-        temp_max_nodes = request.POST.get("prediction-setting-max-nodes")
-        if temp_max_nodes is None or temp_max_nodes == "" or int(temp_max_nodes) == -1:
-            temp_max_nodes = s.DEFAULT_MAX_NUMBER_OF_NODES
-        else:
-            temp_max_nodes = int(request.POST.get("prediction-setting-max-nodes", 1))
-
         max_nodes = min(
             max(
-                temp_max_nodes,
+                int(request.POST.get("prediction-setting-max-nodes", 1)),
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -3043,7 +3040,6 @@ def settings(request):
 
             model_uuid = model_url.split("/")[-1]
             params["model"] = EPModel.objects.get(uuid=model_uuid)
-            # TODO Check if removed if request contains "" or not at all
             params["model_threshold"] = request.POST.get(
                 "model-based-prediction-setting-threshold", s.DEFAULT_MODEL_THRESHOLD
             )

static/css/input.css

@@ -39,3 +39,7 @@ select.select[multiple] {
   display: block;
   white-space: normal;
 }
+
+p a {
+  @apply underline;
+}

static/images/bayer-logo.svg

@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<svg version="1.1" id="Layer_2" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
-	 viewBox="0 0 76 76" style="enable-background:new 0 0 76 76;" xml:space="preserve">
-<style type="text/css">
-	.st0{fill:#10384F;}
-	.st1{fill:#89D329;}
-	.st2{fill:#00BCFF;}
-</style>
-<g id="Bayer_Cross_1_">
-	<path class="st0" d="M35.9,11.3h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9h-4.4V11.3z M35.9,15.5h4.5c0.6,0,1-0.4,1-1
-		c0-0.6-0.4-1-1-1h-4.5V15.5z M43,12.3c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2h-7.3V7.3l7.2,0c1.7,0,3.1,1.4,3.1,3.1
-		C43.7,11.1,43.4,11.8,43,12.3z M44.7,30.3H42l-0.8-1.8h-5.9l-0.8,1.8h-2.7L37,19.8h2.4L44.7,30.3z M38.2,22.5l-1.8,3.8H40
-		L38.2,22.5z M41.8,32.6h3l-5.3,6.8v3.7h-2.5v-3.7l-5.3-6.8h3l3.6,4.8L41.8,32.6z M55.7,32.6v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3
-		h-9.5V32.6H55.7z M63.4,39.1h-1.9v4h-2.5V32.6h6.4c1.8,0,3.2,1.5,3.2,3.3c0,1.5-1,2.7-2.3,3.1l3.1,4.1h-3L63.4,39.1z M65.2,34.8
-		h-3.6v2h3.6c0.6,0,1-0.5,1-1C66.2,35.3,65.7,34.8,65.2,34.8z M32.8,43.1h-2.7l-0.8-1.8h-5.9l-0.8,1.8h-2.7l5.3-10.5h2.4L32.8,43.1z
-		 M26.3,35.3l-1.8,3.8h3.7L26.3,35.3z M10.4,36.6h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9l-4.4,0V36.6z M10.4,40.8h4.5
-		c0.6,0,1-0.4,1-1c0-0.6-0.4-1-1-1h-4.5V40.8z M17.5,37.6c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2H7.9V32.6h7.2
-		c1.7,0,3.1,1.4,3.1,3.1C18.2,36.4,17.9,37.1,17.5,37.6z M43,45.3v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3h-9.5V45.3H43z M41.2,61.6
-		c0-0.6-0.4-1-1-1h-4.3v2h4.3C40.8,62.6,41.2,62.2,41.2,61.6z M33.4,68.9V58.4h7c1.8,0,3.2,1.5,3.2,3.3c0,1.4-0.8,2.5-2,3l3.2,4.2
-		h-3l-3-4h-2.9v4H33.4z"/>
-	<path class="st1" d="M76.1,35.6C74.9,15.8,58.4,0,38.2,0C18,0,1.5,15.8,0.3,35.6c0,0.8,0.1,1.6,0.2,2.4c0.8,6.6,3.3,12.7,7.1,17.8
-		c6.9,9.4,18,15.5,30.6,15.5c-17.6,0-32-13.7-33.2-30.9c-0.1-0.8-0.1-1.6-0.1-2.4c0-0.8,0-1.6,0.1-2.4C6.2,18.4,20.6,4.7,38.2,4.7
-		c12.6,0,23.7,6.1,30.6,15.5c3.8,5.1,6.3,11.2,7.1,17.8c0.1,0.8,0.2,1.6,0.2,2.3c0-0.8,0.1-1.6,0.1-2.4
-		C76.2,37.2,76.2,36.4,76.1,35.6"/>
-	<path class="st2" d="M0.3,40.4C1.5,60.2,18,76,38.2,76c20.2,0,36.7-15.8,37.9-35.6c0-0.8-0.1-1.6-0.2-2.4
-		c-0.8-6.6-3.3-12.7-7.1-17.8c-6.9-9.4-18-15.5-30.6-15.5c17.6,0,32,13.7,33.2,30.9c0.1,0.8,0.1,1.6,0.1,2.4c0,0.8,0,1.6-0.1,2.4
-		c-1.2,17.3-15.6,30.9-33.2,30.9c-12.6,0-23.7-6.1-30.6-15.5C3.8,50.7,1.3,44.6,0.5,38c-0.1-0.8-0.2-1.6-0.2-2.3
-		c0,0.8-0.1,1.6-0.1,2.4C0.2,38.8,0.2,39.6,0.3,40.4"/>
-</g>
-</svg>

static/js/alpine/pagination.js

@@ -5,6 +5,126 @@
  */
 
 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

@@ -1,13 +1,19 @@
 console.log("loaded pw.js")
 
-function findPaths(source_idx, target_idx, links) {
+function findPaths(source_idx, links) {
     const resultLinks = new Set();
     const visited = new Set();
     // Helper function for depth-first search
     function dfs(current) {
-        if (current === target_idx) {
+
+        if (visited.has(current)) {
             return;
         }
+
+        if (links.filter(link => link.target.id === current).length === 0) {
+            return;
+        }
+
         visited.add(current);
         links.forEach(link => {
             if (
@@ -23,7 +29,7 @@ function findPaths(source_idx, target_idx, links) {
     }
     // Start DFS
     dfs(source_idx);
-    return Array.from(resultLinks); // Convert Set to Array for result
+    return Array.from(resultLinks);
 }
 
 function predictFromNode(url) {
@@ -61,6 +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);
 
@@ -148,6 +157,11 @@ function draw(pathway, elem) {
         });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
+
+        linkText
+         .attr("x", d => (d.source.x + d.target.x) / 2)
+         .attr("y", d => (d.source.y + d.target.y) / 2);
+
     }
 
     function dragstarted(event, d) {
@@ -250,7 +264,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 1000;
+    var popupWaitBeforeShow = 750;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -482,7 +496,7 @@ function draw(pathway, elem) {
         if (n.stereo_removed) {
             popupContent += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span>";
         }
-        popupContent += "<a href='" + n.url + "'>" + n.name + "</a><br>";
+        popupContent += "<a href='" + n.url + "'>" + n.plain_name + "</a><br>";
         popupContent += "Depth " + n.depth + "<br>"
 
         if (appDomainViewEnabled) {
@@ -522,6 +536,21 @@ function draw(pathway, elem) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of n.scenarios) {
                 popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
+                for (var prop in n.proposed) {
+                    if (n.proposed[prop].scenarioId === s.url) {
+                        if("proposed" in n.proposed[prop]){
+                            popupContent += "This compound is a proposed intermediate" + "<br>";
+                        }
+                        if("Confidence" in n.proposed[prop]){
+                            popupContent += "Confidence: " + n.proposed[prop]["Confidence"] + "<br>";
+                        }
+                        if("Transformation product importance" in n.proposed[prop]){
+                            popupContent += "Transformation product importance: " + n.proposed[prop]["Transformation product importance"] + "<br>";
+                        }
+                    }
+                }
+                popupContent += "<br>";
+
             }
         }
 
@@ -534,7 +563,7 @@ function draw(pathway, elem) {
     }
 
     function edge_popup(e) {
-        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br><br>";
+        popupContent = "<a href='" + e.url + "'>" + e.plain_name + "</a><br><br>";
 
         if (e.reaction.rules) {
             for (var rule of e.reaction.rules) {
@@ -585,7 +614,7 @@ function draw(pathway, elem) {
 
     // Add background rectangle FIRST to enable pan/zoom on empty space
     // This must be inserted before zoomable group so it's behind everything
-    svg.insert("rect", "#zoomable")
+    const rect = svg.insert("rect", "#zoomable")
         .attr("x", 0)
         .attr("y", 0)
         .attr("width", width)
@@ -594,6 +623,30 @@ function draw(pathway, elem) {
         .attr("pointer-events", "all")
         .style("cursor", "grab");
 
+    // Click on empty SVG space (not on a node or link)
+    rect.on("click", function(event) {
+        // Only treat it as a background click if the direct target is the rect itself
+        // (clicks on nodes/links bubble up but originate from different elements)
+        const target = event.target;
+        const isNode = target.closest && (
+            target.closest("circle") !== null ||
+            target.closest("image") !== null ||
+            target.closest(".node") !== null
+        );
+        const isLink = target.closest && (
+            target.closest("path.link") !== null ||
+            target.closest("path.link_no_arrow") !== null
+        );
+        if (!isNode && !isLink) {
+            // console.log("Clicked outside a node or link");
+            // Clear all highlights
+            d3.selectAll("circle").classed("highlighted", false);
+            d3.selectAll("path").classed("highlighted", false);
+            d3.selectAll("path").classed("inedge", false);
+            d3.selectAll("path").classed("outedge", false);
+        }
+    });
+
     // Zoom Funktion aktivieren
     const zoom = d3.zoom()
         .scaleExtent([0.5, 5])
@@ -640,18 +693,28 @@ function draw(pathway, elem) {
         .force("center", d3.forceCenter(width / 2, height / 4))
         .on("tick", ticked);
 
-    // Kanten zeichnen
+    // Draw Edges
-    const link = zoomable.append("g")
+    const linkGroup = zoomable.append("g")
-        .selectAll("path")
+      .selectAll("g")
       .data(links)
-        .enter().append("path")
+      .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");
@@ -682,6 +745,32 @@ function draw(pathway, elem) {
           }
         });
 
+    function reaction_name(d) {
+        const to_pseudo = d?.to_pseudo || false;
+
+        if (to_pseudo) {
+            return "";
+        }
+
+        var suffix = "";
+        if ("reaction_probability" in d && d["reaction_probability"] !== null) {
+            suffix = " (p= " + d["reaction_probability"].toFixed(2) + ")"
+        }
+        return d.plain_name + suffix;
+    }
+
+    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 => reaction_name(d))
+      .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) {
         d.el = this;  // attach the DOM element to the data object
@@ -689,7 +778,7 @@ function draw(pathway, elem) {
 
     pop_add(link, "Reaction", edge_popup);
 
-    // Knoten zeichnen
+    // Draw Nodes
     const node = zoomable.append("g")
         .selectAll("g")
         .data(nodes)
@@ -707,7 +796,7 @@ function draw(pathway, elem) {
 
           if (!wasHighlighted) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            const inEdges = findPaths(d.id, 3, links);
+            const inEdges = findPaths(d.id, links);
             const outEdges = []
             // Colorize out edges green
             for (const l of links) {
@@ -805,14 +894,14 @@ 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/components/navbar.html

@@ -35,7 +35,6 @@
             <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
           </svg>
         </a>
-        <img src="{% static 'images/bayer-logo.svg' %}" width="40">
       </div>
 
       {% if not public_mode %}
@@ -89,23 +88,12 @@
                   >Scenario</a
                 >
               </li>
-                <hr/>
-              <li>
-                <a href="{{ meta.server_url }}/group" id="scenarioLink"
-                  >Group</a
-                >
-              </li>
             </ul>
           </div>
         </div>
       {% endif %}
 
       <div class="navbar-end">
-        {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}
-          <img src="{% static 'images/restricted_mid.png' %}" width="200">
-        {% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
-          <img src="{% static 'images/secret_mid.png' %}" width="120">
-        {% endif %}
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">
             <div

templates/modals/objects/add_pathway_edge_modal.html

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

templates/objects/edge.html

@@ -82,9 +82,6 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ edge.edge_label.as_svg|safe }}</div>
       </div>
-      {% if edge.edge_label.contains_pes %}
-        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-      {% endif %}
     </div>
 
     <!-- Reaction Description -->

templates/objects/node.html

@@ -55,6 +55,14 @@
       </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

@@ -21,12 +21,13 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
-      /* marker-end: url(#arrow); */
+      stroke-width: 1.5px;
     }
 
     .link_no_arrow {
       stroke: #999;
       stroke-opacity: 0.6;
+      stroke-width: 1.5px;
     }
 
     .node image {
@@ -177,6 +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">
@@ -495,6 +542,10 @@
   {{ 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
@@ -530,6 +581,58 @@
         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.plain_name)
+                  .attr("text-anchor", "middle")
+                  .attr("y", -20)
+                  .style("font-size", "4px");
+              }
+            });
+          } else {
+            // Change back to eye icon
+            icon.innerHTML =
+              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
+            nodes.forEach((x) => {
+              d3.select(x.el).select("text").remove();
+            });
+          }
+        });
+      }
+      const reactionNamesBtn = document.getElementById(
+        "reaction-names-toggle-button",
+      );
+      if (reactionNamesBtn) {
+        reactionNamesBtn.addEventListener("click", function () {
+          reactionNamesViewEnabled = !reactionNamesViewEnabled;
+          const icon = document.getElementById("reaction-names-icon");
+          if (reactionNamesViewEnabled) {
+            // Change to eye-off icon
+            icon.innerHTML =
+              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
+            d3.selectAll(".link-label").style("display", null);
+          } else {
+            // Change back to eye icon
+            icon.innerHTML =
+              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
+            d3.selectAll(".link-label").style("display", "none");
+          }
+        });
+      }
+
       // App domain toggle
       const appDomainBtn = document.getElementById("app-domain-toggle-button");
       if (appDomainBtn) {

templates/objects/reaction.html

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

tests/test_compound_model.py

@@ -1,7 +1,7 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
+from epdb.exceptions import InvalidSMILESException, InvalidMolfileException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -19,6 +19,10 @@ class CompoundTest(TestCase):
         cls.user = User.objects.get(username="anonymous")
         cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
+        # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
+        cls.VALID_MOLFILE = """\n  Mrv2211 01012500002D\n\n 12 12  0  0  0  0            999 V2000\n    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.8875    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n    0.0000   -3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n    1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\n  2  7  1  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n  5 10  1  0  0  0  0\n 10 11  1  0  0  0  0\n 10 12  2  0  0  0  0\nM  CHG  2  10   1  11  -1\nM  END\n"""
+        cls.INVALID_MOLFILE = "this is not a valid molfile"
+
     def test_smoke(self):
         c = Compound.create(
             self.package,
@@ -190,3 +194,153 @@ class CompoundTest(TestCase):
 
         c1.set_default_structure(c2)
         self.assertNotEqual(default_structure, c2)
+
+    def test_create_structure_from_molfile(self):
+        c = Compound.create(
+            self.package,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Compound",
+            description="Created from molfile",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="Structure from molfile",
+        )
+
+        # The SMILES must have been derived from the molfile, not the placeholder
+        self.assertNotEqual(cs.smiles, "PLACEHOLDER")
+        self.assertIsNotNone(cs.smiles)
+        self.assertTrue(len(cs.smiles) > 0)
+
+    def test_create_structure_from_molfile_stores_molfile(self):
+        c = Compound.create(
+            self.package,
+            smiles="c1c(C(=O)O)ccc([N+]([O-])=O)c1",
+            name="Molfile Store Test",
+            description="No Desc",
+        )
+
+        cs = c.default_structure
+
+        # O=C(O)C1=CC=C([N+](=O)[O-])C=C1 will be overwritten with
+        # c1c(C(=O)O)ccc([N+]([O-])=O)c1 and molfile will be set
+        # on the existing structure
+        _ = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile=self.VALID_MOLFILE,
+            name="Structure with Molfile",
+            description="No Desc",
+        )
+
+        # Fetch fresh from DB to confirm persistence
+        cs_db = CompoundStructure.objects.get(pk=cs.pk)
+        self.assertIsNotNone(cs_db.molfile)
+        self.assertNotEqual(cs_db.molfile.strip(), "")
+
+    def test_create_structure_from_invalid_molfile_raises(self):
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Invalid Molfile Test",
+            description="No Desc",
+        )
+
+        with self.assertRaises(InvalidMolfileException):
+            CompoundStructure.create(
+                compound=c,
+                smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+                molfile=self.INVALID_MOLFILE,
+                name="Bad Structure",
+                description="No Desc",
+            )
+
+    def test_molfile_takes_precedence_over_smiles(self):
+        """When both molfile and smiles are supplied, molfile must win."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Precedence Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="C",  # intentionally wrong / different SMILES
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Wins",
+            description="No Desc",
+        )
+
+        # SMILES should be derived from molfile, not the supplied "C"
+        self.assertNotEqual(cs.smiles, "C")
+
+    def test_empty_molfile_falls_back_to_smiles(self):
+        """An empty or whitespace-only molfile should be ignored and SMILES used instead."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Empty Molfile Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile="   ",  # whitespace only – should be ignored
+            name="Fallback to SMILES",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
+
+    def test_none_molfile_falls_back_to_smiles(self):
+        """None as molfile should be ignored and SMILES used instead."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="None Molfile Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile=None,
+            name="Fallback None Molfile",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
+
+    def test_molfile_deduplication(self):
+        """Creating a structure twice from the same molfile should return the existing object."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Molfile Dedup Test",
+            description="No Desc",
+        )
+
+        cs1 = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="No Desc",
+        )
+
+        cs2 = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs1.pk, cs2.pk)

tests/views/test_compound_views.py

@@ -11,6 +11,9 @@ from epdb.models import Compound, Scenario, ExternalDatabase
 class CompoundViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
+    # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
+    VALID_MOLFILE = """\n  Mrv2211 01012500002D\n\n 12 12  0  0  0  0            999 V2000\n    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.8875    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n    0.0000   -3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n    1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\n  2  7  1  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n  5 10  1  0  0  0  0\n 10 11  1  0  0  0  0\n 10 12  2  0  0  0  0\nM  CHG  2  10   1  11  -1\nM  END\n"""
+
     @classmethod
     def setUpClass(cls):
         super(CompoundViewTest, cls).setUpClass()
@@ -396,3 +399,108 @@ class CompoundViewTest(TestCase):
 
         c = Compound.objects.get(url=compound_url)
         self.assertEqual(len(c.aliases), 0)
+
+    def test_create_compound_via_molfile(self):
+        """POSTing a valid molfile without a SMILES should create a compound successfully."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Created from molfile",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        self.assertEqual(c.name, "4-Nitrobenzoic acid")
+        self.assertEqual(c.description, "Created from molfile")
+        # SMILES should have been extracted from molfile, so it must be non-empty
+        self.assertIsNotNone(c.default_structure.smiles)
+        self.assertNotEqual(c.default_structure.smiles.strip(), "")
+
+    def test_create_compound_molfile_takes_precedence_over_smiles(self):
+        """When both molfile and SMILES are submitted, the molfile should win."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile precedence test",
+                "compound-smiles": "C",  # intentionally wrong/different
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        # The resulting SMILES must NOT be the dummy "C" supplied via compound-smiles
+        self.assertNotEqual(c.default_structure.smiles, "C")
+
+    def test_create_compound_via_invalid_molfile_returns_error(self):
+        """POSTing an invalid molfile should not create a compound and should return an error response."""
+        initial_count = self.user1_default_package.compounds.count()
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Bad Molfile Compound",
+                "compound-description": "Should fail",
+                "compound-molfile": "this is not a molfile at all",
+            },
+        )
+
+        # The view should signal an error (non-2xx or a redirect to an error page, not 302 to a new compound)
+        self.assertNotEqual(response.status_code, 302)
+        # No new compound should have been created
+        self.assertEqual(self.user1_default_package.compounds.count(), initial_count)
+
+    def test_create_compound_via_empty_molfile_falls_back_to_smiles(self):
+        """Submitting an empty molfile with a valid SMILES should fall back to SMILES."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Fallback SMILES Compound",
+                "compound-description": "Empty molfile fallback",
+                "compound-smiles": "C(CCl)Cl",
+                "compound-molfile": "   ",  # whitespace only
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
+
+    def test_create_compound_via_molfile_deduplication(self):
+        """Submitting the same molfile twice should return the existing compound."""
+        response1 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response1.status_code, 302)
+        compound_url_1 = response1.url
+
+        response2 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response2.status_code, 302)
+        self.assertEqual(response2.url, compound_url_1)
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)

tests/views/test_package_views.py

@@ -72,8 +72,10 @@ class PackageViewTest(TestCase):
 
     def test_import_package(self):
         file = SimpleUploadedFile(
-            "Fixture_Package.json",
+            "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json",
-            open(s.FIXTURE_DIRS[0] / "Fixture_Package.json", "rb").read(),
+            open(
+                s.FIXTURE_DIRS[0] / "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json", "rb"
+            ).read(),
             content_type="application/json",
         )
 
@@ -86,10 +88,11 @@ class PackageViewTest(TestCase):
 
         p = Package.objects.get(url=package_url)
 
-        self.assertEqual(p.pathways.count(), 22)
+        self.assertEqual(p.pathways.count(), 219)
-        self.assertEqual(p.rules.count(), 45)
+        self.assertEqual(p.rules.count(), 498)
-        self.assertEqual(p.compounds.count(), 223)
+        self.assertEqual(p.compounds.count(), 1399)
-        self.assertEqual(p.reactions.count(), 212)
+        self.assertEqual(p.reactions.count(), 1480)
+        self.assertEqual(p.scenarios.count(), 1914)
 
         upp = UserPackagePermission.objects.get(package=p, user=self.user1)
         self.assertEqual(upp.permission, Permission.ALL[0])

utilities/misc.py

@@ -9,32 +9,24 @@ from datetime import datetime
 from typing import Any, Dict, List, Optional, TYPE_CHECKING
 
 from django.conf import settings as s
-from django.db import transaction
 from ninja import Schema
-from pydantic import HttpUrl
+from pydantic import HttpUrl, ValidationError
 
+from epdb.exceptions import PackageImportException
 from epdb.models import (
     AdditionalInformation,
     Compound,
     CompoundStructure,
     Edge,
-    EnviFormer,
-    EPModel,
-    ExternalDatabase,
-    ExternalIdentifier,
     License,
-    MLRelativeReasoning,
     Node,
     ParallelRule,
     Pathway,
     Reaction,
     Rule,
-    RuleBasedRelativeReasoning,
     Scenario,
     Setting,
     SimpleAmbitRule,
-    SimpleRDKitRule,
-    SimpleRule,
 )
 from utilities.chem import FormatConverter
 
@@ -88,6 +80,9 @@ class RefPathwayExportSchema(RefExportSchema): ...
 class RefScenarioExportSchema(RefExportSchema): ...
 
 
+class RefEnzymeExportSchema(RefExportSchema): ...
+
+
 ############
 # Compound #
 ############
@@ -128,7 +123,28 @@ class ReactionExportSchema(RefReactionExportSchema):
 #########
 # Rules #
 #########
-class RuleExportSchema(RefRuleExportSchema):
+class EnzymeExportSchema(RefEnzymeExportSchema):
+    ec_number: str
+    classification_level: int
+    linking_method: str
+    reaction_evidence: List[RefReactionExportSchema]
+    edge_evidence: List[RefEdgeExportSchema]
+
+
+class EnzymeRuleExportSchema(RefRuleExportSchema):
+    enzymes: List[EnzymeExportSchema] | None = None
+
+    @staticmethod
+    def resolve_enzymes(obj):
+        if isinstance(obj, dict):
+            res = []
+            for e in obj.get("enzymes", []):
+                res.append(EnzymeExportSchema.model_validate(e))
+            return res
+        return obj.enzymelink_set.all()
+
+
+class RuleExportSchema(EnzymeRuleExportSchema):
     name: str
     description: str
     aliases: List[str]
@@ -138,7 +154,7 @@ class RuleExportSchema(RefRuleExportSchema):
     scenarios: List[RefScenarioExportSchema]
 
 
-class ParallelRuleExportSchema(RefRuleExportSchema):
+class ParallelRuleExportSchema(EnzymeRuleExportSchema):
     name: str
     description: str
     aliases: List[str]
@@ -210,7 +226,7 @@ class PackageExportSchema(Schema):
     description: str
     uuid: str
     reviewed: bool
-    license: LicenseExportSchema | None
+    license: LicenseExportSchema | None = None
     compounds: List[CompoundExportSchema]
     reactions: List[ReactionExportSchema]
     simple_rules: List[RuleExportSchema]
@@ -224,6 +240,15 @@ class PackageExportSchema(Schema):
         value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
         return str(value)
 
+    @staticmethod
+    def resolve_compounds(obj):
+        res = []
+        if isinstance(obj, dict):
+            for c in obj.get("compounds", []):
+                res.append(CompoundExportSchema.model_validate(c))
+            return res
+        return obj.compounds.all()
+
     @staticmethod
     def resolve_simple_rules(obj):
         if isinstance(obj, dict):
@@ -277,51 +302,239 @@ class PackageExporter:
 
 
 class PackageImporter:
-    """
+    def __init__(self, package: Dict[str, Any], preserve_uuids: bool = False):
-    Imports package data from JSON export.
-    Handles object creation, relationship mapping, and dependency resolution.
-    """
-
-    def __init__(
-        self,
-        package: Dict[str, Any],
-        preserve_uuids: bool = False,
-        add_import_timestamp=True,
-        trust_reviewed=False,
-    ):
-        """
-        Initialize the importer.
-
-        Args:
-            preserve_uuids: If True, preserve original UUIDs. If False, generate new ones.
-        """
         self.preserve_uuids = preserve_uuids
-        self.add_import_timestamp = add_import_timestamp
-        self.trust_reviewed = trust_reviewed
-        self.uuid_mapping = {}
-        self.object_cache = {}
         self._raw_package = package
-
+        self._cache = {}
-    def _get_or_generate_uuid(self, original_uuid: str) -> str:
-        """Get mapped UUID or generate new one if not preserving UUIDs."""
-        if self.preserve_uuids:
-            return original_uuid
-
-        if original_uuid not in self.uuid_mapping:
-            self.uuid_mapping[original_uuid] = str(uuid.uuid4())
-
-        return self.uuid_mapping[original_uuid]
-
-    def _cache_object(self, model_name: str, uuid_str: str, obj):
-        """Cache a created object for later reference."""
-        self.object_cache[(model_name, uuid_str)] = obj
-
-    def _get_cached_object(self, model_name: str, uuid_str: str):
-        """Get a cached object by model name and UUID."""
-        return self.object_cache.get((model_name, uuid_str))
 
     def do_import(self) -> Package:
-        return self._import_package_from_json(self._raw_package)
+        return self._import_package_from_json()
+
+    def _import_compounds(
+        self,
+        package: Package,
+        compounds: List[CompoundExportSchema],
+    ):
+        for c in compounds:
+            new_c = Compound()
+            new_c.uuid = str(uuid.uuid4()) if not self.preserve_uuids else c.uuid
+            new_c.package = package
+            new_c.name = c.name
+            new_c.description = c.description
+            new_c.aliases = c.aliases
+            new_c.save()
+
+            self._cache[c.uuid] = new_c
+
+            for cs in c.structures:
+                new_cs = CompoundStructure()
+                new_cs.uuid = str(uuid.uuid4()) if not self.preserve_uuids else cs.uuid
+                new_cs.compound = new_c
+                new_cs.name = cs.name
+                new_cs.description = cs.description
+                new_cs.aliases = cs.aliases
+                new_cs.smiles = cs.smiles
+                new_cs.molfile = cs.molfile
+
+                new_cs.normalized_structure = cs.normalized_structure
+                new_cs.save()
+
+                self._cache[cs.uuid] = new_cs
+
+            # Now we can assigne the default_structure to the compound
+            new_c.default_structure = self._cache[c.default_structure.uuid]
+            new_c.save()
+
+    def _import_simple_rules(self, package: Package, rules: List[RuleExportSchema]):
+        for r in rules:
+            new_r = SimpleAmbitRule()
+            new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
+            new_r.package = package
+            new_r.name = r.name
+            new_r.description = r.description
+            new_r.aliases = r.aliases
+            new_r.smirks = r.smirks
+            new_r.reactant_filter_smarts = r.reactant_filter_smarts
+            new_r.product_filter_smarts = r.product_filter_smarts
+            new_r.save()
+
+            self._cache[r.uuid] = new_r
+
+    def _import_composite_rules(self, package: Package, rules: List[ParallelRuleExportSchema]):
+        for r in rules:
+            new_r = ParallelRule()
+            new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
+            new_r.package = package
+            new_r.name = r.name
+            new_r.description = r.description
+            new_r.aliases = r.aliases
+            new_r.save()
+
+            for sr in r.simple_rules:
+                new_r.simple_rules.add(self._cache[sr.uuid])
+
+            self._cache[r.uuid] = new_r
+
+    def _import_reactions(
+        self,
+        package: Package,
+        reactions: List[ReactionExportSchema],
+    ):
+        for r in reactions:
+            new_r = Reaction()
+            new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
+            new_r.package = package
+            new_r.name = r.name
+            new_r.description = r.description
+            new_r.aliases = r.aliases
+            new_r.multi_step = r.multi_step
+            new_r.medline_references = r.medline_references
+            new_r.save()
+
+            for educt in r.educts:
+                new_r.educts.add(self._cache[educt.uuid])
+
+            for product in r.products:
+                new_r.products.add(self._cache[product.uuid])
+
+            for rule in r.rules:
+                new_r.rules.add(self._cache[rule.uuid])
+
+            self._cache[r.uuid] = new_r
+
+    def _import_pathways(self, package: Package, pathways: List[PathwayExportSchema]):
+        for pw in pathways:
+            new_pw = Pathway()
+            new_pw.uuid = str(uuid.uuid4()) if not self.preserve_uuids else pw.uuid
+            new_pw.package = package
+            new_pw.name = pw.name
+            new_pw.description = pw.description
+            new_pw.aliases = pw.aliases
+            new_pw.predicted = pw.predicted
+            new_pw.save()
+
+            self._cache[pw.uuid] = new_pw
+
+            for n in pw.nodes:
+                new_n = Node()
+                new_n.uuid = str(uuid.uuid4()) if not self.preserve_uuids else n.uuid
+                new_n.pathway = new_pw
+                new_n.name = n.name
+                new_n.description = n.description
+                new_n.aliases = n.aliases
+                new_n.default_node_label = self._cache[n.default_node_label.uuid]
+                new_n.depth = n.depth
+                new_n.stereo_removed = n.stereo_removed
+                new_n.save()
+
+                for nl in n.node_labels:
+                    new_n.node_labels.add(self._cache[nl.uuid])
+
+                self._cache[n.uuid] = new_n
+
+            for e in pw.edges:
+                new_e = Edge()
+                new_e.uuid = str(uuid.uuid4()) if not self.preserve_uuids else e.uuid
+                new_e.pathway = new_pw
+                new_e.name = e.name
+                new_e.description = e.description
+                new_e.aliases = e.aliases
+                new_e.edge_label = self._cache[e.edge_label.uuid]
+                new_e.save()
+
+                for sn in e.start_nodes:
+                    new_e.start_nodes.add(self._cache[sn.uuid])
+
+                for en in e.end_nodes:
+                    new_e.end_nodes.add(self._cache[en.uuid])
+
+                self._cache[e.uuid] = new_e
+
+    def _import_scenarios(self, package: Package, scenarios: List[ScenarioExportSchema]):
+        for scen in scenarios:
+            new_s = Scenario()
+            new_s.uuid = str(uuid.uuid4()) if not self.preserve_uuids else scen.uuid
+            new_s.package = package
+            new_s.name = scen.name
+            new_s.description = scen.description
+            new_s.scenario_date = scen.scenario_date
+            new_s.scenario_type = scen.scenario_type
+            new_s.save()
+
+            self._cache[scen.uuid] = new_s
+
+    def _import_additional_information(
+        self, package: Package, additional_information: List[AdditionalInformationExportSchema]
+    ):
+        for ai in additional_information:
+            new_ai = AdditionalInformation()
+            new_ai.uuid = str(uuid.uuid4()) if not self.preserve_uuids else ai.uuid
+            new_ai.package = package
+            new_ai.type = ai.type
+            new_ai.data = ai.data
+
+            if ai.scenario:
+                new_ai.scenario = self._cache[ai.scenario.uuid]
+
+            if ai.attach_object:
+                new_ai.content_object = self._cache[ai.attach_object.uuid]
+
+            new_ai.save()
+
+            self._cache[ai.uuid] = new_ai
+
+    def _link_scenarios_after_import(self, data: PackageExportSchema):
+        collections = [
+            data.compounds,
+            data.simple_rules,
+            data.composite_rules,
+            data.reactions,
+            data.pathways,
+            [n for pw in data.pathways for n in pw.nodes],
+            [e for pw in data.pathways for e in pw.edges],
+        ]
+
+        for coll in collections:
+            for elem in coll:
+                elem_obj = self._cache[elem.uuid]
+                for scen in elem.scenarios:
+                    elem_obj.scenarios.add(self._cache[scen.uuid])
+
+    def _import_package_from_json(
+        self,
+    ) -> Package:
+        try:
+            parsed = PackageExportSchema.model_validate(self._raw_package)
+        except ValidationError as e:
+            logger.error(f"Error validating package data: {e}")
+            raise PackageImportException("Deserialization failed")
+
+        package_uuid = str(uuid.uuid4())
+        if self.preserve_uuids:
+            package_uuid = parsed.uuid
+
+        package_license = License.objects.get(link=parsed.license.link) if parsed.license else None
+
+        package = Package()
+        package.uuid = package_uuid
+        package.name = f"{parsed.name} - Imported at {datetime.now()}"
+        package.description = parsed.description
+        package.reviewed = False
+        package.license = package_license
+
+        package.save()
+
+        # Import Elements
+        self._import_compounds(package, parsed.compounds)
+        self._import_simple_rules(package, parsed.simple_rules)
+        self._import_composite_rules(package, parsed.composite_rules)
+        self._import_reactions(package, parsed.reactions)
+        self._import_pathways(package, parsed.pathways)
+        self._import_scenarios(package, parsed.scenarios)
+        self._import_additional_information(package, parsed.additional_information)
+        self._link_scenarios_after_import(parsed)
+
+        return package
 
     @staticmethod
     def sign(data: Dict[str, Any], key: str) -> Dict[str, Any]:
@@ -339,510 +552,6 @@ class PackageImporter:
         expected = hmac.new(key.encode(), json_str.encode(), hashlib.sha256).digest()
         return hmac.compare_digest(signature, expected)
 
-    @transaction.atomic
-    def _import_package_from_json(self, package_data: Dict[str, Any]) -> Package:
-        """
-        Import a complete package from JSON data.
-
-        Args:
-            package_data: Dictionary containing the package export data
-
-        Returns:
-            The created Package instance
-        """
-        print(f"Starting import of package: {package_data['name']}")
-
-        # Create the main package
-        package = self._create_package(package_data)
-
-        # Import in dependency order
-        self._import_compounds(package, package_data.get("compounds", []))
-        self._import_structures(package, package_data.get("structures", []))
-        self._import_rules(package, package_data.get("rules", {}))
-        self._import_reactions(package, package_data.get("reactions", []))
-        self._import_pathways(package, package_data.get("pathways", []))
-        self._import_nodes(package, package_data.get("nodes", []))
-        self._import_edges(package, package_data.get("edges", []))
-        self._import_scenarios(package, package_data.get("scenarios", []))
-
-        if package_data.get("models"):
-            self._import_models(package, package_data["models"])
-
-        # Set default structures for compounds (after all structures are created)
-        self._set_default_structures(package_data.get("compounds", []))
-
-        print(f"Package import completed: {package.name}")
-        return package
-
-    def _create_package(self, package_data: Dict[str, Any]) -> Package:
-        """Create the main package object."""
-        package_uuid = self._get_or_generate_uuid(package_data["uuid"])
-
-        # Handle license
-        license_obj = None
-        if package_data.get("license"):
-            license_data = package_data["license"]
-            license_obj, _ = License.objects.get_or_create(
-                name=license_data["name"],
-                defaults={
-                    "cc_string": license_data.get("cc_string", ""),
-                    "link": license_data.get("link", ""),
-                    "image_link": license_data.get("image_link", ""),
-                },
-            )
-
-        new_name = package_data.get("name")
-        if self.add_import_timestamp:
-            new_name = f"{new_name} - Imported at {datetime.now()}"
-
-        new_reviewed = False
-        if self.trust_reviewed:
-            new_reviewed = package_data.get("reviewed", False)
-
-        package = Package.objects.create(
-            uuid=package_uuid,
-            name=new_name,
-            description=package_data["description"],
-            kv=package_data.get("kv", {}),
-            reviewed=new_reviewed,
-            license=license_obj,
-        )
-
-        self._cache_object("Package", package_data["uuid"], package)
-        print(f"Created package: {package.name}")
-        return package
-
-    def _import_compounds(self, package: Package, compounds_data: List[Dict[str, Any]]):
-        """Import compounds."""
-        print(f"Importing {len(compounds_data)} compounds...")
-
-        for compound_data in compounds_data:
-            compound_uuid = self._get_or_generate_uuid(compound_data["uuid"])
-
-            compound = Compound.objects.create(
-                uuid=compound_uuid,
-                package=package,
-                name=compound_data["name"],
-                description=compound_data["description"],
-                kv=compound_data.get("kv", {}),
-                # default_structure will be set later
-            )
-
-            # Set aliases if present
-            if compound_data.get("aliases"):
-                compound.aliases = compound_data["aliases"]
-                compound.save()
-
-            self._cache_object("Compound", compound_data["uuid"], compound)
-
-            # Handle external identifiers
-            self._create_external_identifiers(
-                compound, compound_data.get("external_identifiers", [])
-            )
-
-    def _import_structures(self, package: Package, structures_data: List[Dict[str, Any]]):
-        """Import compound structures."""
-        print(f"Importing {len(structures_data)} compound structures...")
-
-        for structure_data in structures_data:
-            structure_uuid = self._get_or_generate_uuid(structure_data["uuid"])
-            compound_uuid = structure_data["compound"]["uuid"]
-            compound = self._get_cached_object("Compound", compound_uuid)
-
-            if not compound:
-                print(f"Warning: Compound with UUID {compound_uuid} not found for structure")
-                continue
-
-            structure = CompoundStructure.objects.create(
-                uuid=structure_uuid,
-                compound=compound,
-                name=structure_data["name"],
-                description=structure_data["description"],
-                kv=structure_data.get("kv", {}),
-                smiles=structure_data["smiles"],
-                canonical_smiles=structure_data["canonical_smiles"],
-                inchikey=structure_data["inchikey"],
-                normalized_structure=structure_data.get("normalized_structure", False),
-            )
-
-            # Set aliases if present
-            if structure_data.get("aliases"):
-                structure.aliases = structure_data["aliases"]
-                structure.save()
-
-            self._cache_object("CompoundStructure", structure_data["uuid"], structure)
-
-            # Handle external identifiers
-            self._create_external_identifiers(
-                structure, structure_data.get("external_identifiers", [])
-            )
-
-    def _import_rules(self, package: Package, rules_data: Dict[str, Any]):
-        """Import all types of rules."""
-        print("Importing rules...")
-
-        # Import simple rules first
-        simple_rules_data = rules_data.get("simple_rules", [])
-        print(f"Importing {len(simple_rules_data)} simple rules...")
-
-        for rule_data in simple_rules_data:
-            self._create_simple_rule(package, rule_data)
-
-        # Import parallel rules
-        parallel_rules_data = rules_data.get("parallel_rules", [])
-        print(f"Importing {len(parallel_rules_data)} parallel rules...")
-
-        for rule_data in parallel_rules_data:
-            self._create_parallel_rule(package, rule_data)
-
-    def _create_simple_rule(self, package: Package, rule_data: Dict[str, Any]):
-        """Create a simple rule (SimpleAmbitRule or SimpleRDKitRule)."""
-        rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
-        rule_type = rule_data.get("rule_type", "SimpleRule")
-
-        common_fields = {
-            "uuid": rule_uuid,
-            "package": package,
-            "name": rule_data["name"],
-            "description": rule_data["description"],
-            "kv": rule_data.get("kv", {}),
-        }
-
-        if rule_type == "SimpleAmbitRule":
-            rule = SimpleAmbitRule.objects.create(
-                **common_fields,
-                smirks=rule_data.get("smirks", ""),
-                reactant_filter_smarts=rule_data.get("reactant_filter_smarts", ""),
-                product_filter_smarts=rule_data.get("product_filter_smarts", ""),
-            )
-        elif rule_type == "SimpleRDKitRule":
-            rule = SimpleRDKitRule.objects.create(
-                **common_fields, reaction_smarts=rule_data.get("reaction_smarts", "")
-            )
-        else:
-            rule = SimpleRule.objects.create(**common_fields)
-
-        # Set aliases if present
-        if rule_data.get("aliases"):
-            rule.aliases = rule_data["aliases"]
-            rule.save()
-
-        self._cache_object("SimpleRule", rule_data["uuid"], rule)
-        return rule
-
-    def _create_parallel_rule(self, package: Package, rule_data: Dict[str, Any]):
-        """Create a parallel rule."""
-        rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
-
-        rule = ParallelRule.objects.create(
-            uuid=rule_uuid,
-            package=package,
-            name=rule_data["name"],
-            description=rule_data["description"],
-            kv=rule_data.get("kv", {}),
-        )
-
-        # Set aliases if present
-        if rule_data.get("aliases"):
-            rule.aliases = rule_data["aliases"]
-            rule.save()
-
-        # Add simple rules
-        for simple_rule_ref in rule_data.get("simple_rules", []):
-            simple_rule = self._get_cached_object("SimpleRule", simple_rule_ref["uuid"])
-            if simple_rule:
-                rule.simple_rules.add(simple_rule)
-
-        self._cache_object("ParallelRule", rule_data["uuid"], rule)
-        return rule
-
-    def _import_reactions(self, package: Package, reactions_data: List[Dict[str, Any]]):
-        """Import reactions."""
-        print(f"Importing {len(reactions_data)} reactions...")
-
-        for reaction_data in reactions_data:
-            reaction_uuid = self._get_or_generate_uuid(reaction_data["uuid"])
-
-            reaction = Reaction.objects.create(
-                uuid=reaction_uuid,
-                package=package,
-                name=reaction_data["name"],
-                description=reaction_data["description"],
-                kv=reaction_data.get("kv", {}),
-                multi_step=reaction_data.get("multi_step", False),
-                medline_references=reaction_data.get("medline_references", []),
-            )
-
-            # Set aliases if present
-            if reaction_data.get("aliases"):
-                reaction.aliases = reaction_data["aliases"]
-                reaction.save()
-
-            # Add educts and products
-            for educt_ref in reaction_data.get("educts", []):
-                compound = self._get_cached_object("CompoundStructure", educt_ref["uuid"])
-                if compound:
-                    reaction.educts.add(compound)
-
-            for product_ref in reaction_data.get("products", []):
-                compound = self._get_cached_object("CompoundStructure", product_ref["uuid"])
-                if compound:
-                    reaction.products.add(compound)
-
-            # Add rules
-            for rule_ref in reaction_data.get("rules", []):
-                # Try to find rule in different caches
-                rule = self._get_cached_object(
-                    "SimpleRule", rule_ref["uuid"]
-                ) or self._get_cached_object("ParallelRule", rule_ref["uuid"])
-                if rule:
-                    reaction.rules.add(rule)
-
-            self._cache_object("Reaction", reaction_data["uuid"], reaction)
-
-            # Handle external identifiers
-            self._create_external_identifiers(
-                reaction, reaction_data.get("external_identifiers", [])
-            )
-
-    def _import_pathways(self, package: Package, pathways_data: List[Dict[str, Any]]):
-        """Import pathways."""
-        print(f"Importing {len(pathways_data)} pathways...")
-
-        for pathway_data in pathways_data:
-            pathway_uuid = self._get_or_generate_uuid(pathway_data["uuid"])
-
-            pathway = Pathway.objects.create(
-                uuid=pathway_uuid,
-                package=package,
-                name=pathway_data["name"],
-                description=pathway_data["description"],
-                kv=pathway_data.get("kv", {}),
-                # setting will be handled separately if needed
-            )
-
-            # Set aliases if present
-            if pathway_data.get("aliases"):
-                pathway.aliases = pathway_data["aliases"]
-                pathway.save()
-
-            self._cache_object("Pathway", pathway_data["uuid"], pathway)
-
-    def _import_nodes(self, package: Package, nodes_data: List[Dict[str, Any]]):
-        """Import pathway nodes."""
-        print(f"Importing {len(nodes_data)} nodes...")
-
-        for node_data in nodes_data:
-            node_uuid = self._get_or_generate_uuid(node_data["uuid"])
-            pathway_uuid = node_data["pathway"]["uuid"]
-            pathway = self._get_cached_object("Pathway", pathway_uuid)
-
-            if not pathway:
-                print(f"Warning: Pathway with UUID {pathway_uuid} not found for node")
-                continue
-
-            # For now, we'll set default_node_label to None and handle it later
-            # as it requires compound structures to be fully imported
-            node = Node.objects.create(
-                uuid=node_uuid,
-                pathway=pathway,
-                name=node_data["name"],
-                description=node_data["description"],
-                kv=node_data.get("kv", {}),
-                depth=node_data.get("depth", 0),
-                default_node_label=self._get_cached_object(
-                    "CompoundStructure", node_data["default_node_label"]["uuid"]
-                ),
-            )
-
-            # Set aliases if present
-            if node_data.get("aliases"):
-                node.aliases = node_data["aliases"]
-                node.save()
-
-            self._cache_object("Node", node_data["uuid"], node)
-            # Store node_data for later processing of relationships
-            node._import_data = node_data
-
-    def _import_edges(self, package: Package, edges_data: List[Dict[str, Any]]):
-        """Import pathway edges."""
-        print(f"Importing {len(edges_data)} edges...")
-
-        for edge_data in edges_data:
-            edge_uuid = self._get_or_generate_uuid(edge_data["uuid"])
-            pathway_uuid = edge_data["pathway"]["uuid"]
-            pathway = self._get_cached_object("Pathway", pathway_uuid)
-
-            if not pathway:
-                print(f"Warning: Pathway with UUID {pathway_uuid} not found for edge")
-                continue
-
-            # For now, we'll set edge_label to None and handle it later
-            edge = Edge.objects.create(
-                uuid=edge_uuid,
-                pathway=pathway,
-                name=edge_data["name"],
-                description=edge_data["description"],
-                kv=edge_data.get("kv", {}),
-                edge_label=self._get_cached_object("Reaction", edge_data["edge_label"]["uuid"]),
-            )
-
-            # Set aliases if present
-            if edge_data.get("aliases"):
-                edge.aliases = edge_data["aliases"]
-                edge.save()
-
-            # Add start and end nodes
-            for start_node_ref in edge_data.get("start_nodes", []):
-                node = self._get_cached_object("Node", start_node_ref["uuid"])
-                if node:
-                    edge.start_nodes.add(node)
-
-            for end_node_ref in edge_data.get("end_nodes", []):
-                node = self._get_cached_object("Node", end_node_ref["uuid"])
-                if node:
-                    edge.end_nodes.add(node)
-
-            self._cache_object("Edge", edge_data["uuid"], edge)
-
-    def _import_scenarios(self, package: Package, scenarios_data: List[Dict[str, Any]]):
-        """Import scenarios."""
-        print(f"Importing {len(scenarios_data)} scenarios...")
-
-        # First pass: create scenarios without parent relationships
-        for scenario_data in scenarios_data:
-            scenario_uuid = self._get_or_generate_uuid(scenario_data["uuid"])
-
-            scenario_date = None
-            if scenario_data.get("scenario_date"):
-                scenario_date = scenario_data["scenario_date"]
-
-            scenario = Scenario.objects.create(
-                uuid=scenario_uuid,
-                package=package,
-                name=scenario_data["name"],
-                description=scenario_data["description"],
-                kv=scenario_data.get("kv", {}),
-                scenario_date=scenario_date,
-                scenario_type=scenario_data.get("scenario_type"),
-                additional_information=scenario_data.get("additional_information", {}),
-            )
-
-            self._cache_object("Scenario", scenario_data["uuid"], scenario)
-            # Store scenario_data for later processing of parent relationships
-            scenario._import_data = scenario_data
-
-        # Second pass: set parent relationships
-        for scenario_data in scenarios_data:
-            if scenario_data.get("parent"):
-                scenario = self._get_cached_object("Scenario", scenario_data["uuid"])
-                parent = self._get_cached_object("Scenario", scenario_data["parent"]["uuid"])
-                if scenario and parent:
-                    scenario.parent = parent
-                    scenario.save()
-
-    def _import_models(self, package: Package, models_data: List[Dict[str, Any]]):
-        """Import EPModels."""
-        print(f"Importing {len(models_data)} models...")
-
-        for model_data in models_data:
-            model_uuid = self._get_or_generate_uuid(model_data["uuid"])
-            model_type = model_data.get("model_type", "EPModel")
-
-            common_fields = {
-                "uuid": model_uuid,
-                "package": package,
-                "name": model_data["name"],
-                "description": model_data["description"],
-                "kv": model_data.get("kv", {}),
-            }
-
-            # Add PackageBasedModel fields if present
-            if "threshold" in model_data:
-                common_fields.update(
-                    {
-                        "threshold": model_data.get("threshold"),
-                        "eval_results": model_data.get("eval_results", {}),
-                        "model_status": model_data.get("model_status", "INITIAL"),
-                    }
-                )
-
-            # Create the appropriate model type
-            if model_type == "RuleBasedRelativeReasoning":
-                model = RuleBasedRelativeReasoning.objects.create(
-                    **common_fields,
-                    min_count=model_data.get("min_count", 1),
-                    max_count=model_data.get("max_count", 10),
-                )
-            elif model_type == "MLRelativeReasoning":
-                model = MLRelativeReasoning.objects.create(**common_fields)
-            elif model_type == "EnviFormer":
-                model = EnviFormer.objects.create(**common_fields)
-            else:
-                model = EPModel.objects.create(**common_fields)
-
-            # Set aliases if present
-            if model_data.get("aliases"):
-                model.aliases = model_data["aliases"]
-                model.save()
-
-            # Add package relationships for PackageBasedModel
-            if hasattr(model, "rule_packages"):
-                for pkg_ref in model_data.get("rule_packages", []):
-                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
-                    if pkg:
-                        model.rule_packages.add(pkg)
-
-                for pkg_ref in model_data.get("data_packages", []):
-                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
-                    if pkg:
-                        model.data_packages.add(pkg)
-
-                for pkg_ref in model_data.get("eval_packages", []):
-                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
-                    if pkg:
-                        model.eval_packages.add(pkg)
-
-            self._cache_object("EPModel", model_data["uuid"], model)
-
-    def _set_default_structures(self, compounds_data: List[Dict[str, Any]]):
-        """Set default structures for compounds after all structures are created."""
-        print("Setting default structures for compounds...")
-
-        for compound_data in compounds_data:
-            if compound_data.get("default_structure"):
-                compound = self._get_cached_object("Compound", compound_data["uuid"])
-                structure = self._get_cached_object(
-                    "CompoundStructure", compound_data["default_structure"]["uuid"]
-                )
-                if compound and structure:
-                    compound.default_structure = structure
-                    compound.save()
-
-    def _create_external_identifiers(self, obj, identifiers_data: List[Dict[str, Any]]):
-        """Create external identifiers for an object."""
-        for identifier_data in identifiers_data:
-            # Get or create the external database
-            db_data = identifier_data["database"]
-            database, _ = ExternalDatabase.objects.get_or_create(
-                name=db_data["name"],
-                defaults={
-                    "base_url": db_data.get("base_url", ""),
-                    "full_name": db_data.get("name", ""),
-                    "description": "",
-                    "is_active": True,
-                },
-            )
-
-            # Create the external identifier
-            ExternalIdentifier.objects.create(
-                content_object=obj,
-                database=database,
-                identifier_value=identifier_data["identifier_value"],
-                url=identifier_data.get("url", ""),
-                is_primary=identifier_data.get("is_primary", False),
-            )
-
 
 class PathwayUtils:
     def __init__(self, pathway: "Pathway"):

uv.lock

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