API PES

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

.env.prod.example

@@ -3,10 +3,20 @@ EP_DATA_DIR=
 ALLOWED_HOSTS=
 DEBUG=
 LOG_LEVEL=
+MODEL_BUILDING_ENABLED=
+APPLICABILITY_DOMAIN_ENABLED=
 ENVIFORMER_PRESENT=
-FLAG_CELERY_PRESENT=
-SERVER_URL=
+ENVIFORMER_DEVICE=
 PLUGINS_ENABLED=
+SERVER_URL=
+SERVER_PATH=
+ADMIN_APPROVAL_REQUIRED=
+REGISTRATION_MANDATORY=
+LOG_DIR=
+# Celery
+FLAG_CELERY_PRESENT=
+CELERY_BROKER_URL=
+CELERY_RESULT_BACKEND=
 # DB
 POSTGRES_SERVICE_NAME=
 POSTGRES_DB=
@@ -16,5 +26,30 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-# MATOMO
-MATOMO_SITE_ID
+DEFAULT_FROM_EMAIL=
+SERVER_EMAIL=
+# SENTRY
+SENTRY_ENABLED=
+SENTRY_DSN=
+SENTRY_ENVIRONMENT=
+# MS ENTRA
+MS_ENTRA_ENABLED=
+MS_CLIENT_ID=
+MS_CLIENT_SECRET=
+MS_TENANT_ID=
+MS_REDIRECT_URI=
+MS_SCOPES=
+# Tenant
+TENANT=
+EPDB_PACKAGE_MODEL=
+# Captcha
+CAP_ENABLED=
+CAP_API_BASE=
+CAP_SITE_KEY=
+CAP_SECRET_KEY=
+# QUARKUS (JAVA)
+ENVIRULE_ENABLED=
+FINGERPRINT_URL=
+# Biotransformer
+BIOTRANSFORMER_ENABLED=
+BIOTRANSFORMER_URL=

Dockerfile

@@ -30,17 +30,21 @@ 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:1.0 .
+# docker build --ssh default -t envipath/envipy-bayer:1.0 .
 RUN --mount=type=ssh \
     uv sync --locked --extra ms-login --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
 COPY epauth epauth
 COPY epdb epdb
+COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper
@@ -71,6 +75,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxrender1 \
     libxext6 \
     libfontconfig1 \
+    nano \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django

bayer/admin.py

@@ -0,0 +1,19 @@
+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

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

bayer/epdb_hooks.py

@@ -0,0 +1,39 @@
+import logging
+
+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

@@ -0,0 +1,35 @@
+# 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

@@ -0,0 +1,22 @@
+# 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

@@ -0,0 +1,41 @@
+# 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

@@ -0,0 +1,236 @@
+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)}"
+        }

bayer/templates/actions/collections/new_pes.html

@@ -0,0 +1,9 @@
+{% 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

@@ -0,0 +1,8 @@
+<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

@@ -0,0 +1,175 @@
+{% 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

@@ -0,0 +1,174 @@
+{% 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

@@ -0,0 +1,174 @@
+{% 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

@@ -0,0 +1,19 @@
+{% 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">{{ compound_structure.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={{ compound_structure.pes_link|urlencode }}'/>
+      </div>
+    </div>
+  </div>
+{% endif %}

bayer/templates/objects/compound_viz.html

@@ -0,0 +1,19 @@
+{% 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">{{ compound.default_structure.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={{ compound.default_structure.pes_link|urlencode }}'/>
+      </div>
+    </div>
+  </div>
+{% endif %}

bayer/templates/objects/node_viz.html

@@ -0,0 +1,19 @@
+{% 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

@@ -0,0 +1,97 @@
+{% 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

@@ -0,0 +1,154 @@
+{% 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

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

bayer/urls.py

@@ -0,0 +1,19 @@
+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

@@ -0,0 +1,155 @@
+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():
+                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():
+                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)
+
+            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:
+        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

@@ -0,0 +1,183 @@
+import json
+import math
+from datetime import datetime
+from typing import List
+import enum
+import requests
+from django.conf import settings as s
+from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import register
+
+from bridge.contracts import Classifier  # noqa: I001
+from bridge.dto import (
+    BuildResult,
+    EnviPyDTO,
+    EvaluationResult,
+    RunResult,
+    TransformationProductPrediction,
+)  # noqa: I001
+
+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
+        retries = 0
+        while not started and retries < 5:
+            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
+
+            if res.status_code == 200:
+                started = True
+            elif res.status_code in [500, 502]:
+                retries += 1
+                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,
+            }
+
+            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
+
+            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
+
+        return result

bridge/contracts.py

@@ -254,7 +254,15 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-        return cls.Config(**(data or {}))
+
+        # remove empty strings a.k.a unset params to not overwrite defaults
+        cpy = {}
+        if data is not None:
+            for k, v in data.items():
+                if v != "":
+                    cpy[k] = v
+
+        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

docker-compose.dev.yml

@@ -1,26 +1,54 @@
 services:
   db:
     image: postgres:18
-    container_name: envipath-postgres
+    container_name: eppostgres
     environment:
-      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: envipath
+      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_DB: ${POSTGRES_DB}
     ports:
       - "5432:5432"
     volumes:
-      - postgres_data:/var/lib/postgresql
+      - ep_bayer_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: envipath-redis
+    container_name: epredis
     ports:
       - "6379:6379"
+    volumes:
+      - ep_bayer_redis_data:/data
+
+  biotransformer3:
+    image: envipath/biotransformer3:1.0
+    container_name: epbiotransformer3
+
+#  web:
+#    image: envipath/envipy-bayer:1.0
+#    container_name: epdjango
+#    ports:
+#      - "127.0.0.1:8000:8000"
+#    env_file:
+#      - .env
+#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
+#    volumes:
+#      - ep_bayer_data:/opt/enviPy/
+
+  celery_worker:
+    image: envipath/envipy-bayer:1.0
+    container_name: epcelery
+    env_file:
+      - .env.dev
+    command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
+    volumes:
+      - ep_bayer_data:/opt/enviPy/
 
 volumes:
-  postgres_data:
+  ep_bayer_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_postgres_data:/var/lib/postgresql
+      - ep_bayer_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_redis_data:/data
+      - ep_bayer_redis_data:/data
 
   biotransformer3:
     image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
   web:
-    image: envipath/envipy:1.0
+    image: envipath/envipy-bayer: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_data:/opt/enviPy/
+      - ep_bayer_data:/opt/enviPy/
 
   celery_worker:
-    image: envipath/envipy:1.0
+    image: envipath/envipy-bayer:1.0
     container_name: epcelery
     env_file:
       - .env
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
-      - ep_data:/opt/enviPy/
+      - ep_bayer_data:/opt/enviPy/
 
 volumes:
-  ep_postgres_data:
-  ep_redis_data:
-  ep_data:
+  ep_bayer_postgres_data:
+  ep_bayer_redis_data:
+  ep_bayer_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")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -143,6 +143,12 @@ 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
@@ -191,11 +197,21 @@ ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") ==
 # SESAME_MAX_AGE = 300
 # # TODO set to "home"
 # LOGIN_REDIRECT_URL = "/"
+
+
+SERVER_HOST = os.environ.get("SERVER_URL", "http://localhost:8000")
+SERVER_PATH = os.environ.get("SERVER_PATH", "")
+
+SERVER_URL = SERVER_HOST
+if SERVER_PATH:
+    SERVER_URL = os.path.join(SERVER_HOST, SERVER_PATH)
+
+
 LOGIN_URL = "/login/"
+if SERVER_PATH:
+    LOGIN_URL = f"/{SERVER_PATH}/login/"
 
-SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
-
-CSRF_TRUSTED_ORIGINS = [SERVER_URL]
+CSRF_TRUSTED_ORIGINS = [SERVER_HOST]
 
 AMBIT_URL = "http://localhost:9001"
 DEFAULT_VALUES = {"description": "no description"}
@@ -229,6 +245,8 @@ PAGINATION_MAX_PER_PAGE_SIZE = int(
 STATIC_ROOT = STATIC_DIR
 
 STATIC_URL = "/static/"
+if SERVER_PATH:
+    STATIC_URL = f"/{SERVER_PATH}/static/"
 
 # Where the sources are stored...
 STATICFILES_DIRS = (BASE_DIR / "static",)
@@ -331,10 +349,11 @@ DEFAULT_MODEL_THRESHOLD = 0.25
 
 # Loading Plugins
 PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
-BASE_PLUGINS = [
-    "pepper.PEPPER",
-    "biotransformer.Biotransformer",
-]
+BASE_PLUGINS = os.environ.get("BASE_PLUGINS", None)
+if BASE_PLUGINS:
+    BASE_PLUGINS = BASE_PLUGINS.split(",")
+else:
+    BASE_PLUGINS = []
 
 CLASSIFIER_PLUGINS = {}
 PROPERTY_PLUGINS = {}
@@ -387,7 +406,6 @@ LOGIN_EXEMPT_URLS = [
     "/o/userinfo/",
     "/password_reset/",
     "/reset/",
-    "/microsoft/",
     "/terms",
     "/privacy",
     "/cookie-policy",
@@ -396,8 +414,13 @@ LOGIN_EXEMPT_URLS = [
     "/careers",
     "/cite",
     "/legal",
+    "/entra/",
+    "/auth/",
 ]
 
+if SERVER_PATH:
+    LOGIN_EXEMPT_URLS = [f"/{SERVER_PATH}{x}" for x in LOGIN_EXEMPT_URLS]
+
 # MS AD/Entra
 MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
 if MS_ENTRA_ENABLED:
@@ -424,5 +447,47 @@ CAP_SECRET_KEY = os.environ.get("CAP_SECRET_KEY", None)
 BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "True"
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
-    INSTALLED_APPS.append("biotransformer")
     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")

envipath/urls.py

@@ -21,19 +21,27 @@ from django.urls import include, path
 
 from .api import api_v1, api_legacy
 
+PATH_PREFIX = s.SERVER_PATH
+if PATH_PREFIX and not PATH_PREFIX.endswith("/"):
+    PATH_PREFIX += "/"
+
+
 urlpatterns = [
-    path("", include("epdb.urls")),
-    path("admin/", admin.site.urls),
-    path("api/v1/", api_v1.urls),
-    path("api/legacy/", api_legacy.urls),
-    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
+    path(f"{PATH_PREFIX}", include("epdb.urls")),
+    path(f"{PATH_PREFIX}admin/", admin.site.urls),
+    path(f"{PATH_PREFIX}api/v1/", api_v1.urls),
+    path(f"{PATH_PREFIX}api/legacy/", api_legacy.urls),
+    path(f"{PATH_PREFIX}o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
 
 if "migration" in s.INSTALLED_APPS:
-    urlpatterns.append(path("", include("migration.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("migration.urls")))
 
 if s.MS_ENTRA_ENABLED:
-    urlpatterns.append(path("", include("epauth.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
+
+if s.TENANT != "public":
+    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
 
 # Custom error handlers
 handler400 = "epdb.views.handler400"

epapi/v1/endpoints/groups.py

@@ -0,0 +1,23 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.logic import GroupManager
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import GroupOutSchema
+
+router = Router()
+
+
+@router.get("/groups/", response=EnhancedPageNumberPagination.Output[GroupOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_groups(request):
+    """
+    List all groups the user has access to.
+    """
+    user = request.user
+    return GroupManager.get_groups(user)

epapi/v1/endpoints/settings.py

@@ -15,9 +15,9 @@ router = Router()
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
 )
-def list_all_pathways(request):
+def list_all_settings(request):
     """
-    List all pathways from reviewed packages.
+    List all settings the user has access to.
     """
     user = request.user
     return SettingManager.get_all_settings(user)

epapi/v1/router.py

@@ -1,6 +1,7 @@
 from ninja import Router
 from ninja.security import SessionAuth
 
+from envipath import settings as s
 from .auth import BearerTokenAuth
 from .endpoints import (
     packages,
@@ -13,8 +14,8 @@ from .endpoints import (
     structure,
     additional_information,
     settings,
+    groups,
 )
-from envipath import settings as s
 
 # Main router with authentication
 router = Router(
@@ -35,6 +36,7 @@ router.add_router("", models.router)
 router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
+router.add_router("", groups.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -126,3 +126,10 @@ class SettingOutSchema(Schema):
     url: str = ""
     name: str
     description: str
+
+
+class GroupOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str

epauth/urls.py

@@ -3,6 +3,7 @@ from django.urls import path
 from . import views
 
 urlpatterns = [
-    path("microsoft/login/", views.microsoft_login, name="microsoft_login"),
-    path("microsoft/callback/", views.microsoft_callback, name="microsoft_callback"),
+    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

@@ -1,34 +1,51 @@
 import msal
 from django.conf import settings as s
-from django.contrib.auth import login
-from django.shortcuts import redirect
 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
+from epdb.logic import UserManager, GroupManager
+from epdb.models import Group
 
 
-def microsoft_login(request):
+def get_msal_app_with_cache(request):
+    """
+    Create MSAL app with session-based token cache.
+    """
+    cache = msal.SerializableTokenCache()
+
+    # Load cache from session if it exists
+    if request.session.get("msal_token_cache"):
+        cache.deserialize(request.session["msal_token_cache"])
+
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY
+        authority=s.MS_ENTRA_AUTHORITY,
+        token_cache=cache,
+    )
+
+    return msal_app, cache
+
+
+def entra_login(request):
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY,
     )
 
     flow = msal_app.initiate_auth_code_flow(
-        scopes=s.MS_ENTRA_SCOPES,
-        redirect_uri=s.MS_ENTRA_REDIRECT_URI
+        scopes=s.MS_ENTRA_SCOPES, redirect_uri=s.MS_ENTRA_REDIRECT_URI
     )
 
     request.session["msal_auth_flow"] = flow
     return redirect(flow["auth_uri"])
 
 
-def microsoft_callback(request):
-    msal_app = msal.ConfidentialClientApplication(
-        client_id=s.MS_ENTRA_CLIENT_ID,
-        client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY
-    )
+def entra_callback(request):
+    msal_app, cache = get_msal_app_with_cache(request)
 
     flow = request.session.pop("msal_auth_flow", None)
     if not flow:
@@ -37,30 +54,117 @@ def microsoft_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    if "access_token" in result:
-        # Optional: Fetch user info from Microsoft Graph
-        import requests
-        resp = requests.get(
-            "https://graph.microsoft.com/v1.0/me",
-            headers={"Authorization": f"Bearer {result['access_token']}"}
-        )
-        user_info = resp.json()
+    # Save the token cache to session
+    if cache.has_state_changed:
+        request.session["msal_token_cache"] = cache.serialize()
 
-        user_name = user_info["displayName"]
-        user_email = user_info["mail"]
-        user_oid = user_info["id"]
+    claims = result["id_token_claims"]
+
+    user_name = claims.get("name")
+    user_email = claims.get("emailaddress", claims.get("email"))
+    user_oid = claims.get("oid")
+
+    if not all([user_name, user_email, user_oid]):
+        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
 
     if User.objects.filter(uuid=user_oid).exists():
-            login(request, User.objects.get(uuid=user_oid))
+        u = User.objects.get(uuid=user_oid)
+
+        if u.username != user_name:
+            u.username = user_name
+            u.save()
+
     else:
         u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+
     login(request, u)
 
-        # TODO Group Sync
+    # EDIT START
 
-        return redirect("/")
+    # 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()
 
-    return redirect("/")  # Handle errors
+    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
+
+
+def get_access_token_from_request(request, scopes=None):
+    """
+    Get an access token from the request using MSAL token cache.
+    """
+
+    # Check if auth via Access Token
+    if request.headers.get("Authorization"):
+        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
+
+    if scopes is None:
+        scopes = s.MS_ENTRA_SCOPES
+
+    # Get user from request (must be authenticated)
+    if not request.user.is_authenticated:
+        return None
+
+    # Create MSAL app with persistent cache
+    msal_app, cache = get_msal_app_with_cache(request)
+
+    # Try to get accounts from cache
+    accounts = msal_app.get_accounts()
+
+    if not accounts:
+        return None
+
+    # Find the account that matches the current user
+    user_account = None
+    for account in accounts:
+        if account.get("local_account_id") == str(request.user.uuid):
+            user_account = account
+            break
+
+    # If no matching account found, use the first available account
+    if not user_account and accounts:
+        user_account = accounts[0]
+
+    if not user_account:
+        return None
+
+    # Try to acquire token silently from cache
+    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
+
+    # Save cache changes back to session
+    if cache.has_state_changed:
+        request.session["msal_token_cache"] = cache.serialize()
+
+    if result and "access_token" in result:
+        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/admin.py

@@ -1,5 +1,8 @@
+import logging
+
 from django.conf import settings as s
 from django.contrib import admin
+from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -29,6 +32,8 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
+logger = logging.getLogger(__name__)
+
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -45,6 +50,113 @@ class UserAdmin(admin.ModelAdmin):
         "date_joined",
     ]
 
+    actions = ["send_welcome_mail", "send_affiliation_mail"]
+
+    @admin.action(description="Send welcome mail")
+    def send_welcome_mail(self, request, queryset):
+        from django.core.mail import EmailMultiAlternatives
+
+        tpl = """Hello {username},
+
+Your account has been successfully activated.
+
+To log in, please visit
+https://envipath.org/password_reset/
+and request a new password.
+
+If you have any questions or feedback, feel free to visit our community forum at
+https://community.envipath.org/.
+You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
+
+Best regards,
+
+The enviPath Team"""
+
+        users = []
+
+        for user in queryset:
+            if user.is_active:
+                logger.info(f"{user.username} already active - not sending mail again")
+                continue
+            try:
+                msg = EmailMultiAlternatives(
+                    "Your enviPath Account Is Now Active",
+                    tpl.format(username=user.username),
+                    "admin@envipath.org",
+                    [user.email],
+                    bcc=["admin@envipath.org"],
+                )
+
+                msg.send(fail_silently=False)
+
+                user.is_active = True
+                user.password = "ASDF"
+                user.save()
+
+                users.append(user)
+                logger.info(f"{user.username} -> {user.email} mail sent")
+            except Exception as e:
+                logger.info(f"Error sending mail to {user.username}: {e}")
+
+        self.message_user(
+            request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
+        )
+
+    @admin.action(description="Send affiliation mail")
+    def send_affiliation_mail(self, request, queryset):
+        from django.core.mail import EmailMultiAlternatives
+
+        tpl = """Dear {username},
+
+Thank you for your interest in enviPath!
+
+Please note that the public enviPath system is intended for non-commercial use only.
+We see that you registered using the email address {email}.
+If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
+
+If you would like us to update your account, simply reply to this email and let us know which address we should use.
+We will then change it in our system, and you will receive a password reset email at the new address.
+
+If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
+To book a meeting, please visit https://envipath.com/book
+
+If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
+
+Best regards,
+
+enviPath team"""
+
+        users = []
+
+        for user in queryset:
+            if user.is_active or user.contacted:
+                logger.info(
+                    f"{user.username} already active or already contacted - not sending mail again"
+                )
+                continue
+            try:
+                msg = EmailMultiAlternatives(
+                    "Regarding your enviPath registration",
+                    tpl.format(username=user.username, email=user.email),
+                    "admin@envipath.org",
+                    [user.email],
+                    bcc=["admin@envipath.org"],
+                )
+
+                msg.send(fail_silently=False)
+
+                user.contacted = True
+                user.save()
+
+                users.append(user)
+                logger.info(f"{user.username} -> {user.email} affiliation mail sent")
+            except Exception as e:
+                logger.info(f"Error sending mail to {user.username}: {e}")
+
+        self.message_user(
+            request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
+        )
+
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass

epdb/legacy_api.py

@@ -1,17 +1,20 @@
 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 SessionAuth
+from ninja.security import HttpBearer
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
-
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -46,6 +49,26 @@ 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):
@@ -59,7 +82,52 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-router = Router(auth=SessionAuth(csrf=False))
+def validate_token(token: str) -> dict:
+    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):
@@ -153,21 +221,6 @@ 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 #
@@ -767,6 +820,7 @@ class CreateCompound(Schema):
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
+    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -778,6 +832,25 @@ 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():
+                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
             )
@@ -1801,6 +1874,7 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
+    pesLink: str | None = None
 
 
 @router.post(
@@ -1812,14 +1886,43 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
+        if n.pesLink:
+            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():
+                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)
+
+            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)
             else:
                 node_depth = -1
 
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
-        return redirect(n.url)
+        return redirect(node.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -1929,13 +2032,16 @@ 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.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -1946,7 +2052,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -1967,9 +2074,12 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             description=e.edgeReason,
         )
 
+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

@@ -7,6 +7,7 @@ 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 (
@@ -264,8 +265,12 @@ class GroupManager(object):
         return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
-    def create_group(current_user, name, description):
+    def create_group(current_user, name, description, *args, **kwargs):
         g = Group()
+
+        if "uuid" in kwargs:
+            g.uuid = kwargs["uuid"]
+
         # Clean for potential XSS
         g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -341,52 +346,17 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        if (
-            UserPackagePermission.objects.filter(package=package, user=user).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package, group__in=GroupManager.get_groups(user)
+        return (
+            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
         )
-            or package.reviewed is True
-            or user.is_superuser
-        ):
-            return True
-
-        return False
 
     @staticmethod
     def writable(user, package):
-        if (
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.WRITE[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.WRITE[0],
-            ).exists()
-            or UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
+        return PackageManager.has_package_permission(user, package, "write")
 
     @staticmethod
     def administrable(user, package):
-        if (
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.ALL[0],
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
+        return PackageManager.has_package_permission(user, package, "all")
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -395,6 +365,14 @@ 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)
@@ -437,6 +415,7 @@ 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
@@ -446,6 +425,37 @@ 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...
@@ -470,7 +480,13 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
+
+        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -514,11 +530,13 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
 
-    @staticmethod
-    def get_packages():
-        return Package.objects.all()
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
+
+        return qs
 
     @staticmethod
     @transaction.atomic
@@ -623,6 +641,25 @@ 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()
 
@@ -708,7 +745,13 @@ 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()
@@ -716,6 +759,10 @@ class PackageManager(object):
                 struc.description = structure["description"]
                 struc.aliases = structure.get("aliases", [])
                 struc.smiles = structure["smiles"]
+
+                if structure.get("molfile"):
+                    struc.molfile = structure["molfile"]
+
                 struc.save()
 
                 for scen in structure["scenarios"]:
@@ -1018,52 +1065,9 @@ class PackageManager(object):
 
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
+
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            in_count = defaultdict(lambda: 0)
-            out_count = defaultdict(lambda: 0)
-
-            for e in pw.edges:
-                # TODO check if this will remain
-                for react in e.start_nodes.all():
-                    out_count[str(react.uuid)] += 1
-
-                for prod in e.end_nodes.all():
-                    in_count[str(prod.uuid)] += 1
-
-            root_nodes = []
-            for n in pw.nodes:
-                num_parents = in_count[str(n.uuid)]
-                if num_parents == 0:
-                    # must be a root node or unconnected node
-                    if n.depth != 0:
-                        n.depth = 0
-                        n.save()
-
-                    # Only root node may have children
-                    if out_count[str(n.uuid)] > 0:
-                        root_nodes.append(n)
-
-            levels = [root_nodes]
-            seen = set()
-            # Do a bfs to determine depths starting with level 0 a.k.a. root nodes
-            for i, level_nodes in enumerate(levels):
-                new_level = []
-                for n in level_nodes:
-                    for e in n.out_edges.all():
-                        for prod in e.end_nodes.all():
-                            if str(prod.uuid) not in seen:
-                                old_depth = prod.depth
-                                if old_depth != i + 1:
-                                    prod.depth = i + 1
-                                    prod.save()
-
-                                new_level.append(prod)
-
-                    seen.add(str(n.uuid))
-
-                if new_level:
-                    levels.append(new_level)
-
+            pw.update_depths()
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack

epdb/migrations/0001_initial.py

@@ -1,594 +0,0 @@
-# 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

@@ -1,128 +0,0 @@
-# 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

@@ -1,228 +0,0 @@
-# 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

@@ -1,55 +0,0 @@
-# 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

@@ -1,18 +0,0 @@
-# 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

@@ -1,23 +0,0 @@
-# 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

@@ -1,53 +0,0 @@
-# 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

@@ -1,64 +0,0 @@
-# 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

@@ -1,66 +0,0 @@
-# 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

@@ -1,18 +0,0 @@
-# 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

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

@@ -1,22 +0,0 @@
-# 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

@@ -1,25 +0,0 @@
-# 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

@@ -1,17 +0,0 @@
-# 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

@@ -1,17 +0,0 @@
-# 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

@@ -1,179 +0,0 @@
-# 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

@@ -1,93 +0,0 @@
-# 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

@@ -1,132 +0,0 @@
-# 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

@@ -1,20 +1,741 @@
-# Generated by Django 5.2.7 on 2026-02-23 08:45
+# Generated by Django 5.2.7 on 2026-03-06 10:51
 
-from django.db import migrations
+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 = [
-        ("epdb", "0018_auto_20260220_1203"),
+        ('auth', '0012_alter_user_first_name_max_length'),
+        ('contenttypes', '0002_remove_content_type_name'),
+        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
-        migrations.RemoveField(
-            model_name="scenario",
-            name="additional_information",
+        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')),
+                ('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.RemoveField(
-            model_name="scenario",
-            name="parent",
+        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')),
+                ('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

@@ -0,0 +1,54 @@
+# Generated by Django 6.0.3 on 2026-04-21 11:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="compoundstructure",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="epmodel",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="parallelrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="rule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="sequentialrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simpleambitrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simplerdkitrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simplerule",
+            options={},
+        ),
+        migrations.AddField(
+            model_name="compoundstructure",
+            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/0024_user_contacted.py

@@ -0,0 +1,17 @@
+# Generated by Django 6.0.3 on 2026-04-21 19:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0023_alter_compoundstructure_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="user",
+            name="contacted",
+            field=models.BooleanField(blank=True, null=True),
+        ),
+    ]

epdb/migrations/0025_auto_20260511_2025.py

@@ -0,0 +1,56 @@
+# Generated by Django 6.0.3 on 2026-05-11 20:25
+
+from django.db import migrations
+from envipy_additional_information import HalfLife, HalfLifeModel, HalfLifeWS
+
+MAPPING = {
+    "": HalfLifeModel.OTHER,
+    "HS-SFO": HalfLifeModel.HS_SFO,
+    "FOMC": HalfLifeModel.FOMC,
+    "FOTC": HalfLifeModel.DFOP,
+    "FMOC": HalfLifeModel.FOMC,
+    "DFOP": HalfLifeModel.DFOP,
+    "SFO + SFO": HalfLifeModel.SFO_SFO,
+    "FOMC-SFO": HalfLifeModel.FOMC_SFO,
+    "first order kinetics": HalfLifeModel.SFO,
+    "SFO²": HalfLifeModel.SFO,
+    "HS": HalfLifeModel.HS,
+    "top down": HalfLifeModel.OTHER,
+    "SFO": HalfLifeModel.SFO,
+    "First Order": HalfLifeModel.SFO,
+    "SFO/SFO": HalfLifeModel.SFO_SFO,
+    "FOMC + SFO": HalfLifeModel.FOMC_SFO,
+    "true": HalfLifeModel.SFO,
+    "SFO-SFO": HalfLifeModel.SFO_SFO,
+    "DFOP-SFO": HalfLifeModel.DFOP_SFO,
+}
+
+
+def forward_func(apps, schema_editor):
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    hls = AdditionalInformation.objects.filter(type="HalfLife")
+
+    for hl in hls:
+        data = hl.data
+        data["model"] = MAPPING[data["model"]].value
+        hl.data = HalfLife(**data).model_dump(mode="json")
+        hl.save()
+
+    hlws = AdditionalInformation.objects.filter(type="HalfLifeWS")
+
+    for hl in hlws:
+        data = hl.data
+        data["model"] = MAPPING[data["model"]].value
+        hl.data = HalfLifeWS(**data).model_dump(mode="json")
+        hl.save()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0024_user_contacted"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/models.py

@@ -75,6 +75,7 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
+    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -203,6 +204,7 @@ 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"
     )
@@ -866,18 +868,25 @@ class Compound(
 
         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 CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
+        if qs.exists():
+            return qs.first().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 CompoundStructure.objects.filter(
-            smiles=standardized_smiles, compound__package=package
-        ).exists():
+        if qs.exists():
             # TODO should we add a structure?
-            return CompoundStructure.objects.get(
-                smiles=standardized_smiles, compound__package=package
-            ).compound
+            return qs.first().compound
 
         # Generate Compound
         c = Compound()
@@ -1112,6 +1121,7 @@ class CompoundStructure(
     canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
     inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
+    molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
@@ -1208,6 +1218,9 @@ class CompoundStructure(
 
         return dict(hls)
 
+    def d3_json(self):
+        return {}
+
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -2173,6 +2186,56 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
+    def update_depths(self):
+        # Collect number of in and out links per node
+        in_count = defaultdict(lambda: 0)
+        out_count = defaultdict(lambda: 0)
+
+        for e in self.edges:
+            for react in e.start_nodes.all():
+                out_count[str(react.uuid)] += 1
+
+            for prod in e.end_nodes.all():
+                in_count[str(prod.uuid)] += 1
+
+        depth_map = {}
+        depth_map[0] = list()
+
+        for n in self.nodes:
+            num_parents = in_count[str(n.uuid)]
+            if num_parents == 0:
+                # must be a root node or unconnected node
+                if n.depth != 0:
+                    n.depth = 0
+                    n.save()
+
+                # Only root node may have children
+                if out_count[str(n.uuid)] > 0:
+                    depth_map[0].append(n)
+
+        # At most depth len(nodes) is possible
+        for i in range(self.nodes.count()):
+            level_nodes = depth_map.get(i, [])
+
+            if len(level_nodes) == 0:
+                break
+
+            unique_next_level = set()
+            for n in level_nodes:
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            unique_next_level.add(p)
+
+            if len(unique_next_level) > 0:
+                depth_map[i + 1] = list(unique_next_level)
+
+        for depth, nodes in depth_map.items():
+            for n in nodes:
+                if n.depth != depth:
+                    n.depth = depth
+                    n.save()
+
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2214,7 +2277,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        return {
+        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        # by overwriting keys
+        structure_data = self.default_node_label.d3_json()
+
+        res = {
             "depth": self.depth,
             "stereo_removed": self.stereo_removed,
             "url": self.url,
@@ -2223,6 +2290,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
+            "image_type": "svg",
             "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@@ -2235,8 +2303,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
+            **structure_data,
         }
 
+        return res
+
     @staticmethod
     @transaction.atomic
     def create(

epdb/views.py

@@ -388,6 +388,9 @@ 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
         },
     }
 
@@ -556,7 +559,7 @@ def packages(request):
 
         # Context for paginated template
         context["entity_type"] = "package"
-        context["api_endpoint"] = "/api/v1/packages/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/packages/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "packages"
 
@@ -587,10 +590,38 @@ 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":
@@ -614,7 +645,7 @@ def compounds(request):
 
         # Context for paginated template
         context["entity_type"] = "compound"
-        context["api_endpoint"] = "/api/v1/compounds/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/compounds/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -643,7 +674,7 @@ def rules(request):
 
         # Context for paginated template
         context["entity_type"] = "rule"
-        context["api_endpoint"] = "/api/v1/rules/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/rules/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -671,7 +702,7 @@ def reactions(request):
 
         # Context for paginated template
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = "/api/v1/reactions/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/reactions/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -699,7 +730,7 @@ def pathways(request):
 
         # Context for paginated template
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = "/api/v1/pathways/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/pathways/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -729,7 +760,7 @@ def scenarios(request):
 
         # Context for paginated template
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = "/api/v1/scenarios/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/scenarios/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -789,7 +820,7 @@ def models(request):
 
         # Context for paginated template
         context["entity_type"] = "model"
-        context["api_endpoint"] = "/api/v1/models/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "models"
 
@@ -871,7 +902,7 @@ def package_models(request, package_uuid):
         context["object_type"] = "model"
         context["breadcrumbs"] = breadcrumbs(current_package, "model")
         context["entity_type"] = "model"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/model/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/model/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "models"
 
@@ -906,12 +937,14 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-            "EnviFormer": {
+        }
+
+        if s.ENVIFORMER_PRESENT:
+            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
             },
-        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1341,7 +1374,7 @@ def package_compounds(request, package_uuid):
         context["object_type"] = "compound"
         context["breadcrumbs"] = breadcrumbs(current_package, "compound")
         context["entity_type"] = "compound"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/compound/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -1494,7 +1527,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
         context["entity_type"] = "structure"
         context["page_title"] = f"{current_compound.get_name()} - Structures"
         context["api_endpoint"] = (
-            f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
+            f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
         )
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["compound"] = current_compound
@@ -1657,7 +1690,7 @@ def package_rules(request, package_uuid):
         context["object_type"] = "rule"
         context["breadcrumbs"] = breadcrumbs(current_package, "rule")
         context["entity_type"] = "rule"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/rule/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/rule/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -1865,7 +1898,7 @@ def package_reactions(request, package_uuid):
         context["object_type"] = "reaction"
         context["breadcrumbs"] = breadcrumbs(current_package, "reaction")
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/reaction/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/reaction/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -2015,7 +2048,7 @@ def package_pathways(request, package_uuid):
         context["object_type"] = "pathway"
         context["breadcrumbs"] = breadcrumbs(current_package, "pathway")
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/pathway/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/pathway/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -2506,6 +2539,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
+        # Update depths as sideeffect of above operation
+        current_pathway.update_depths()
+
         return redirect(current_pathway.url)
 
     else:
@@ -2591,7 +2627,7 @@ def package_scenarios(request, package_uuid):
         context["object_type"] = "scenario"
         context["breadcrumbs"] = breadcrumbs(current_package, "scenario")
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/scenario/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/scenario/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -2846,9 +2882,15 @@ def groups(request):
             {"Group": s.SERVER_URL + "/group"},
         ]
 
-        context["objects"] = Group.objects.all()
+        # Context for paginated template
+        context["entity_type"] = "group"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/groups/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "groups"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/groups_paginated.html", context)
 
-        return render(request, "collections/objects_list.html", context)
     elif request.method == "POST":
         group_name = request.POST.get("group-name")
         group_description = request.POST.get("group-description", s.DEFAULT_VALUES["description"])
@@ -2940,7 +2982,7 @@ def settings(request):
 
         # Context for paginated template
         context["entity_type"] = "setting"
-        context["api_endpoint"] = "/api/v1/settings/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/settings/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "settings"
         context["list_mode"] = "combined"

pepper/__init__.py

@@ -46,7 +46,7 @@ class PepperPrediction(PropertyPrediction):
 
         import matplotlib.patches as mpatches
         import numpy as np
-        from matplotlib import pyplot as plt
+        from matplotlib.figure import Figure
         from scipy import stats
 
         """
@@ -101,7 +101,8 @@ class PepperPrediction(PropertyPrediction):
         mask_red = x > vp
 
         # Plot
-        fig, ax = plt.subplots(figsize=(9, 5.5))
+        fig = Figure(figsize=(9, 5.5))
+        ax = fig.subplots()
         ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
 
         if np.any(mask_green):
@@ -146,13 +147,12 @@ class PepperPrediction(PropertyPrediction):
         ]
         ax.legend(handles=patches, frameon=True)
 
-        plt.tight_layout()
+        fig.tight_layout()
 
         # --- Export to SVG string ---
         buf = io.StringIO()
         fig.savefig(buf, format="svg", bbox_inches="tight")
         svg = buf.getvalue()
-        plt.close(fig)
         buf.close()
 
         return svg

pepper/impl/pepper.py

@@ -187,8 +187,9 @@ class Pepper:
         groups = [group for group in dataset.group_by("structure_id")]
 
         # Unless explicitly set compute everything serial
-        if os.environ.get("N_PEPPER_THREADS", 1) > 1:
-            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
+        n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
+        if n_threads > 1:
+            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

static/images/bayer-logo.svg

@@ -0,0 +1,30 @@
+<?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/pw.js

@@ -605,7 +605,36 @@ function draw(pathway, elem) {
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
         .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
+      .on("click", function(event, d) {
+          const wasHighlighted = d3.select(this).classed("highlighted");
 
+          d3.selectAll("line").classed("highlighted", false);
+
+          if (!wasHighlighted) {
+              const toHighlight = [];
+              toHighlight.push(d.el);
+
+              if (d.source.pseudo || d.target.pseudo) {
+                  if (d.target.pseudo) {
+                      d3.selectAll("line").each(e => {
+                          if (e !== undefined && e.source.id === d.target.id) {
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  } else {
+                      d3.selectAll("line").each(e => {
+                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  }
+              }
+
+              for (const e of toHighlight) {
+                  d3.select(e).classed("highlighted", true);
+              }
+          }
+      })
 
     // add element to links array
     link.each(function (d) {
@@ -624,7 +653,13 @@ function draw(pathway, elem) {
             .on("drag", dragged)
             .on("end", dragended))
         .on("click", function (event, d) {
+            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+
+            d3.selectAll('circle.highlighted').classed('highlighted', false);
+
+            if (!wasHighlighted) {
                 d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
+            }
         })
 
     // Kreise für die Knoten hinzufügen
@@ -637,6 +672,7 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
+        if (d.image_type === "svg") {
             // Parse the SVG string
             const parser = new DOMParser();
             const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@@ -646,19 +682,19 @@ function draw(pathway, elem) {
             const prefix = `node-${i}-`;
 
             // Rename all IDs and fix <use> references
-        svgElem.querySelectorAll('[id]').forEach(el => {
+            svgElem.querySelectorAll("[id]").forEach(el => {
                 const oldId = el.id;
                 const newId = prefix + oldId;
                 el.id = newId;
 
                 const XLINK_NS = "http://www.w3.org/1999/xlink";
                 // Update <use> elements that reference this old ID
-            const uses = Array.from(svgElem.querySelectorAll('use')).filter(
-                u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
+                const uses = Array.from(svgElem.querySelectorAll("use")).filter(
+                    u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
                 );
 
                 uses.forEach(u => {
-                u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
+                    u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
                 });
             });
 
@@ -675,6 +711,17 @@ function draw(pathway, elem) {
                 .attr("height", svgHeight * scale)
                 .attr("x", -svgWidth * scale / 2)
                 .attr("y", -svgHeight * scale / 2);
+        } else {
+            // We have a image type different than svg
+            // include it via img url
+            g.append("svg:image")
+                .attr("xlink:href", d.image)
+                .attr("width", 40)
+                .attr("height", 40)
+                .attr("x", -20)
+                .attr("y", -20);
+        }
+
     });
 
     // add element to nodes array

templates/actions/collections/group.html

@@ -1,8 +0,0 @@
-<li>
-  <a
-    role="button"
-    onclick="document.getElementById('new_group_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-plus"></span> New Group</a
-  >
-</li>

templates/actions/objects/pathway.html

@@ -1,3 +1,5 @@
+{% load envipytags %}
+
 {% if meta.can_edit %}
   <li>
     <a
@@ -15,7 +17,12 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+
+  {% for tpl in action_button_templates %}
+    {% include tpl %}
+  {% endfor %}
+  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
   <a
@@ -67,7 +74,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
   <li>
     <a
       class="button"
@@ -92,11 +99,16 @@
       <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
   <li>
     <a
       class="button"
-      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_node_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
     >
@@ -104,7 +116,12 @@
   <li>
     <a
       class="button"
-      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_edge_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
     >

templates/collections/compounds_paginated.html

@@ -5,7 +5,7 @@
 
 {% block action_button %}
   <div class="flex items-center gap-2">
-    {% if meta.can_edit %}
+    {% if meta.can_edit or not meta.url_contains_package %}
       <button
         type="button"
         class="btn btn-primary btn-sm"

templates/collections/groups_paginated.html

@@ -0,0 +1,21 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Groups{% endblock %}
+
+{% block action_button %}
+  <button
+    type="button"
+    class="btn btn-primary btn-sm"
+    onclick="document.getElementById('new_group_modal').showModal(); return false;"
+  >
+    New Group
+  </button>
+{% endblock action_button %}
+
+{% block action_modals %}
+  {% include "modals/collections/new_group_modal.html" %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>Users can team up in groups to share packages.</p>
+{% endblock description %}

templates/collections/models_paginated.html

@@ -3,7 +3,8 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
+  {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.enabled_features.MODEL_BUILDING %}
       <button
         type="button"
         class="btn btn-primary btn-sm"
@@ -12,6 +13,7 @@
         New Model
       </button>
     {% endif %}
+  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/packages_paginated.html

@@ -3,7 +3,6 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
     <div class="flex items-center gap-2">
       <button
         type="button"
@@ -71,7 +70,6 @@
         </ul>
       </div>
     </div>
-  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/pathways_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Pathways{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <div class="flex items-center gap-2">
       <a
         class="btn btn-primary btn-sm"

templates/collections/reactions_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/rules_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Rules{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/scenarios_paginated.html

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

templates/collections/structures_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/components/navbar.html

@@ -35,6 +35,7 @@
             <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 %}
@@ -88,12 +89,23 @@
                   >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/collections/new_prediction_setting_modal.html

@@ -203,11 +203,11 @@
               id="model-based-prediction-setting-threshold"
               name="model-based-prediction-setting-threshold"
               class="input input-bordered w-full"
-              placeholder="0.25"
+              value="0.25"
               type="number"
               min="0"
               max="1"
-              step="0.05"
+              step="any"
             />
           </div>
 

templates/modals/objects/delete_pathway_edge_modal.html

@@ -4,6 +4,25 @@
   id="delete_pathway_edge_modal"
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const links = d3.selectAll('line.highlighted');
+  console.log(links);
+   if (!links.empty()) {
+        const el = links.node();
+        const selectElement = document.getElementById('delete_pathway_edge_edges');
+        console.log(el);
+        console.log(el.__data__);
+        for (let option of selectElement.options) {
+            if (option.value === el.__data__.url) {
+                option.selected = true;
+                break;
+            }
+        }
+
+        selectElement.dispatchEvent(new Event('change'));
+
+   }
+  "
   @close="reset()"
 >
   <div class="modal-box">

templates/modals/objects/delete_pathway_node_modal.html

@@ -4,6 +4,22 @@
   id="delete_pathway_node_modal"
   class="modal"
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const el = d3.select('circle.highlighted').node();
+
+   if (el !== null) {
+    const selectElement = document.getElementById('delete_pathway_node_nodes');
+
+    for (let option of selectElement.options) {
+        if (option.value === el.__data__.url) {
+            option.selected = true;
+            break;
+        }
+    }
+
+    selectElement.dispatchEvent(new Event('change'));
+   }
+  "
   @close="reset()"
 >
   <div class="modal-box">

templates/objects/compound.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -82,6 +83,12 @@
       <div class="collapse-content">{{ compound.description }}</div>
     </div>
 
+    <!-- Extension Slot for Viz -->
+    {% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/compound_structure.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -50,6 +51,12 @@
       </div>
     </div>
 
+    <!-- Extension Slot for Viz -->
+    {% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/node.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -54,6 +55,12 @@
       </div>
     </div>
 
+    {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
+
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/pathway.html

@@ -1,5 +1,7 @@
 {% extends "framework_modern.html" %}
 {% load static %}
+{% load envipytags %}
+
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -76,6 +78,10 @@
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
+    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
+    {% for tpl in add_templates %}
+      {% include tpl %}
+    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}
@@ -100,12 +106,12 @@
     </div>
 
     <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse">
+    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
       </div>
-      <div class="collapse-content">
+      <div class="collapse-content ">
         <div class="bg-base-100 mb-2 rounded-lg p-2">
           <div class="navbar bg-base-100 rounded-lg">
             <div class="flex-1">
@@ -134,7 +140,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>

utilities/chem.py

@@ -88,6 +88,10 @@ class FormatConverter(object):
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
 
+    @staticmethod
+    def from_molfile(molfile: str):
+        return Chem.MolFromMolBlock(molfile)
+
     @staticmethod
     def to_smiles(mol, canonical=False):
         return Chem.MolToSmiles(mol, canonical=canonical)
@@ -171,12 +175,17 @@ class FormatConverter(object):
             try:
                 Chem.Kekulize(mol)
             except Exception:
-                mc = Chem.Mol(mol.ToBinary())
+                mol = Chem.Mol(mol.ToBinary())
 
-        if not mc.GetNumConformers():
-            Chem.rdDepictor.Compute2DCoords(mc)
+        if not mol.GetNumConformers():
+            Chem.rdDepictor.Compute2DCoords(mol)
 
-        pass
+        drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
+        opts = drawer.drawOptions()
+        opts.clearBackground = False
+        drawer.DrawMolecule(mol)
+        drawer.FinishDrawing()
+        return drawer.GetDrawingText()
 
     @staticmethod
     def normalize(smiles):

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS
+from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -473,17 +473,12 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            first_order = get_parameter_or_empty_string(request, "firstOrder")
+            # first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if first_order != "":
-                if model != "":
-                    raise ValueError("not both, model and firstOrder can be set!")
-                if first_order == "true":
-                    model = "SFO"
-                else:
-                    logger.info("firstOrder is set to false which is not meaningful")
+            if model:
+                model = HalfLifeModel(model.upper())
 
             return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
 
@@ -508,6 +503,10 @@ def build_additional_information_from_request(request, type_):
             comment_ws = get_parameter_or_empty_string(request, "comment_ws")
             source_ws = get_parameter_or_empty_string(request, "source_ws")
             model_ws = get_parameter_or_empty_string(request, "model_ws")
+
+            if model_ws:
+                model_ws = HalfLifeModel(model_ws.upper())
+
             fit_ws = get_parameter_or_empty_string(request, "fit_ws")
 
             dt50_total = IntervalParser.from_string(hl_ws_total)

uv.lock

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.3"
+version = "3.13.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
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+sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
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