Update UI if pathway mode is set to build

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

Dockerfile

@@ -6,18 +6,23 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    nodejs \
-    npm \
+    ca-certificates \
     && rm -rf /var/lib/apt/lists/*
 
-# Install pnpm
-RUN npm install -g pnpm
+# Install Node 22 + pnpm
+RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends nodejs \
+    && corepack enable \
+    && corepack prepare pnpm@latest --activate \
+    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -30,13 +35,15 @@ 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

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

bayer/templates/actions/collections/new_pes.html

@@ -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 +1,163 @@
+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():
+
+                if current_package.classification_level != Package.Classification.SECRET:
+                    return BadRequest("Cannot create PESs for non-secret packages.")
+
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return BadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
+
+            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
+
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
+            if node_qs.exists():
+                return redirect(current_pathway.url)
+
+            n = Node()
+            n.stereo_removed = False
+            n.pathway = current_pathway
+            n.depth = 0
+
+            n.default_node_label = pes.default_structure
+            n.save()
+
+            n.node_labels.add(pes.default_structure)
+            n.save()
+
+            return redirect(current_pathway.url)
+
+        else:
+            return BadRequest("Please provide a PES link.")
+    else:
+        pass
+
+
+def fetch_pes(request, pes_url) -> dict:
+    from epauth.views import get_access_token_from_request
+    token = get_access_token_from_request(request)
+
+    if token:
+        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

@@ -1,15 +1,15 @@
 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" ]
       interval: 5s
@@ -18,9 +18,37 @@ services:
 
   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
@@ -442,3 +448,48 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
+
+# PES
+PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
+if PES_API_MAPPING:
+    import json
+    PES_API_MAPPING = json.loads(PES_API_MAPPING)
+else:
+    PES_API_MAPPING = {}
+
+# Entra Groups
+ENTRA_GROUPS = os.environ.get("ENTRA_GROUPS", None)
+if ENTRA_GROUPS:
+    import json
+    ENTRA_GROUPS = json.loads(ENTRA_GROUPS)
+else:
+    ENTRA_GROUPS = {}
+
+ENTRA_SECRET_GROUPS = os.environ.get("ENTRA_SECRET_GROUPS", None)
+if ENTRA_SECRET_GROUPS:
+    import json
+    ENTRA_SECRET_GROUPS = json.loads(ENTRA_SECRET_GROUPS)
+else:
+    ENTRA_SECRET_GROUPS = {}
+
+# PES Data Pools vs Entra Mapping
+DATA_POOL_MAPPING = os.environ.get("DATA_POOL_MAPPING", None)
+if DATA_POOL_MAPPING:
+    import json
+    DATA_POOL_MAPPING = json.loads(DATA_POOL_MAPPING)
+else:
+    DATA_POOL_MAPPING = {}
+
+PROXIES = {}
+if os.environ.get("HTTP_PROXY"):
+    PROXIES["http"] = os.environ.get("HTTP_PROXY")
+    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
+
+# BB4g
+BB4G_URL = os.environ.get("BB4G_URL")
+BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
+BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
+BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
+BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
+
+os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

epapi/v1/endpoints/joblogs.py

@@ -0,0 +1,26 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.models import JobLog
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import JobLogOutSchema
+
+router = Router()
+
+
+@router.get("/joblog/", response=EnhancedPageNumberPagination.Output[JobLogOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_joblogs(request):
+    """
+    List all JobLogs from reviewed packages.
+    """
+    current_user = request.user
+
+    if current_user.is_superuser:
+        return JobLog.objects.all().order_by("-created")
+    else:
+        return JobLog.objects.filter(user=current_user).order_by("-created")

epapi/v1/router.py

@@ -15,6 +15,7 @@ from .endpoints import (
     additional_information,
     settings,
     groups,
+    joblogs,
 )
 
 # Main router with authentication
@@ -37,6 +38,7 @@ router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
 router.add_router("", groups.router)
+router.add_router("", joblogs.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -1,7 +1,10 @@
-from ninja import FilterSchema, FilterLookup, Schema
+from datetime import datetime
 from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
+from django.urls import reverse
+from ninja import Field, FilterSchema, FilterLookup, Schema
+
 
 # Filter schema for query parameters
 class ReviewStatusFilter(FilterSchema):
@@ -133,3 +136,23 @@ class GroupOutSchema(Schema):
     url: str = ""
     name: str
     description: str
+
+
+class SimpleUserOutSchema(Schema):
+    uuid: UUID
+    url: str
+    name: str = Field(alias="username")
+
+
+class JobLogOutSchema(Schema):
+    user: SimpleUserOutSchema
+    id: UUID = Field(alias="task_id")
+    url: str
+    name: str = Field(alias="job_name")
+    created: datetime = Field(alias="created")
+    status: str = Field(alias="status")
+    done: Optional[datetime] = Field(None, alias="done_at")
+
+    @staticmethod
+    def resolve_url(obj):
+        return reverse("job detail", kwargs={"job_uuid": obj.task_id})

epauth/urls.py

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

epauth/views.py

@@ -2,9 +2,11 @@ import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.contrib.auth import login
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
-from epdb.logic import UserManager
+from epdb.logic import UserManager, GroupManager
+from epdb.models import Group
 
 
 def get_msal_app_with_cache(request):
@@ -80,6 +82,33 @@ def entra_callback(request):
 
     login(request, u)
 
+    # EDIT START
+
+    # Ensure groups exists in eP
+    for id, name in s.ENTRA_SECRET_GROUPS.items():
+        if not Group.objects.filter(uuid=id).exists():
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+                                          uuid=id)
+        else:
+            g = Group.objects.get(uuid=id)
+        # Ensure its secret
+        g.secret = True
+        g.save()
+
+    for id, name in s.ENTRA_GROUPS.items():
+        if not Group.objects.filter(uuid=id).exists():
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+                                          uuid=id)
+        else:
+            g = Group.objects.get(uuid=id)
+
+    for group_uuid in claims.get("groups", []):
+        if Group.objects.filter(uuid=group_uuid).exists():
+            g = Group.objects.get(uuid=group_uuid)
+            g.user_member.add(u)
+
+    # EDIT END
+
     return redirect(s.SERVER_URL)  # Handle errors
 
 
@@ -87,6 +116,11 @@ 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
 
@@ -128,3 +162,9 @@ def get_access_token_from_request(request, scopes=None):
         return result
 
     return None
+
+
+def get_token(request):
+    token = get_access_token_from_request(request)
+    msg = f"{token}"
+    return HttpResponse(msg, content_type='text/plain')

epdb/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 #
@@ -386,23 +439,50 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        users = User.objects.filter(
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.READ[0]
-            ).values_list("user", flat=True)
-        ).distinct()
+        readers = []
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
+            "group", flat=True
+        )
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        users = User.objects.filter(
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.WRITE[0]
-            ).values_list("user", flat=True)
-        ).distinct()
+        writers = []
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(
+            package=obj,
+            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
+        ).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(
+            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
+        ).values_list("group", flat=True)
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -767,6 +847,7 @@ 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 +859,25 @@ 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
             )
@@ -799,6 +899,27 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
+class CreateCompoundStructure(Schema):
+    smiles: str
+    name: str | None = None
+    description: str | None = None
+    inchi: str | None = None
+    molfile: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
+def create_package_compound_structure(
+    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
+):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+        c = Compound.objects.get(package=p, uuid=compound_uuid)
+        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
+        return redirect(cs.url)
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1325,6 +1446,7 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
+    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1468,6 +1590,7 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
+        if request.POST.get("adInfoTypes[]"):
             url_parser = EPDBURLParser(request.POST.get("attach_obj"))
             attach_obj = url_parser.get_object()
 
@@ -1491,6 +1614,33 @@ def create_package_additional_information(request, package_uuid):
                     content_object=attach_obj,
                 )
 
+        elif request.POST.get("ais"):
+            import json
+
+            parsed_ais = json.loads(request.POST.get("ais"))
+
+            for ai_type, ais in parsed_ais.items():
+                for ai in ais:
+                    attach_obj = None
+                    if ai.get("related"):
+                        url_parser = EPDBURLParser(ai.get("related").get("url"))
+                        attach_obj = url_parser.get_object()
+
+                        if not hasattr(attach_obj, "additional_information"):
+                            raise ValueError("Can't attach additional information to this object!")
+
+                        if not attach_obj.url.startswith(p.url):
+                            raise ValueError(
+                                "Additional Information can only be set to objects stored in the same package!"
+                            )
+
+                    AdditionalInformation.create(
+                        p,
+                        AdditionalInformation.from_dict(ai_type, ai),
+                        scenario=scenario,
+                        content_object=attach_obj,
+                    )
+
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
     except ValueError:
@@ -1540,6 +1690,7 @@ class PathwayNode(Schema):
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
     smiles: str = Field(None, alias="default_node_label.smiles")
+    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1693,6 +1844,29 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
+@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
+def update_pathway(request, package_uuid, pathway_uuid):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+
+        if request.POST.get("scenario"):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
+
+            pw.scenarios.add(scen)
+            pw.save()
+
+            return redirect(f"{pw.url}")
+
+        else:
+            return 400, {"message": "No scenario specified!"}
+
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
+        }
+
+
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1801,25 +1975,67 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
+    pesLink: str | None = None
 
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 403: Error},
+    response={200: str | Any, 400: Error, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
+        # TODO Code Dup from bayer.views
+
+        if n.pesLink:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, n.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+
+                if p.classification_level != Package.Classification.SECRET:
+                    return 400, "Cannot create PESs for non-secret packages."
+
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
+
+            c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
+
+            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
+            if node_qs.exists():
+                return redirect(pw.url)
+
+            node = Node()
+            node.stereo_removed = False
+            node.pathway = pw
+            node.depth = 0
+
+            node.default_node_label = c.default_structure
+            node.save()
+
+            node.node_labels.add(c.default_structure)
+            node.save()
+        else:
             if n.nodeDepth is not None and n.nodeDepth.strip() != "":
                 node_depth = int(n.nodeDepth)
             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 +2145,16 @@ 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 +2165,8 @@ 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,
                     )
@@ -1958,6 +2178,10 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
+        multi_step = False
+        if e.multistep and e.multistep.strip() == "true":
+            multi_step = True
+
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -1965,8 +2189,12 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
+            multi_step=multi_step,
         )
 
+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
         return redirect(new_e.url)
     except ValueError:
         return 403, {"message": "Adding Edge failed!"}

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 (
@@ -364,6 +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)
@@ -406,6 +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
@@ -415,6 +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...
@@ -441,6 +482,10 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
+
         return qs
 
     @staticmethod
@@ -487,11 +532,11 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        return qs
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
 
-    @staticmethod
-    def get_packages():
-        return Package.objects.all()
+        return qs
 
     @staticmethod
     @transaction.atomic
@@ -596,6 +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()
 
@@ -681,7 +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()
@@ -995,52 +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

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

epdb/migrations/0025_auto_20260511_2025.py

@@ -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/migrations/0026_auto_20260602_1718.py

@@ -0,0 +1,48 @@
+# Generated by Django 6.0.3 on 2026-06-02 17:18
+
+from django.db import migrations
+from envipy_additional_information import DOI
+
+
+def forward_func(apps, schema_editor):
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    refs = AdditionalInformation.objects.filter(type="Reference")
+
+    remaining = []
+
+    for ref in refs:
+        r = ref.data["reference"]
+        try:
+            # PubMed IDs are plain ints, try parsing
+            _ = int(r)
+            # Nothing to do
+        except ValueError:
+            DOMAINS = [
+                "http://dx.doi.org/",
+                "https://dx.doi.org/",
+                "http://doi.org/",
+                "https://doi.org/",
+            ]
+            for d in DOMAINS:
+                r = r.replace(d, "")
+
+            if r.startswith("10."):
+                ref.type = DOI.__name__
+                ref.data = {"doi": r}
+                ref.save()
+            else:
+                remaining.append(ref)
+
+    if len(remaining) > 0:
+        raise ValueError(f"Could not parse {len(remaining)} references")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0025_auto_20260511_2025"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/models.py

@@ -204,6 +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"
     )
@@ -867,18 +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()
@@ -1695,7 +1703,7 @@ class Reaction(
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and name.strip() != "":
+        if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1773,7 +1781,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
 
     @property
     def as_svg(self):
@@ -1886,6 +1894,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
+        for i in queue:
+            processed.add(i)
+
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2178,6 +2189,50 @@ 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()
+        processed = set()
+
+        for n in self.root_nodes:
+            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:
+                processed.add(n)
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            if p not in processed:
+                                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 and depth != 0:
+                    n.depth = depth
+                    n.save()
+
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2405,6 +2460,8 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
+        *args,
+        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2434,7 +2491,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=False,
+            multi_step=kwargs.get("multi_step", False),
         )
 
         e.edge_label = r
@@ -4442,18 +4499,22 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    def get(self) -> "EnviPyModel":
+    @staticmethod
+    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[self.type](**self.data)
+            inst = MAPPING[ai_type](**ai_data)
         except Exception as e:
-            print(f"Error loading {self.type}: {e}")
+            print(f"Error loading {ai_type}: {e}")
             raise e
 
-        inst.__dict__["uuid"] = str(self.uuid)
+        return inst
 
+    def get(self) -> "EnviPyModel":
+        inst = AdditionalInformation.from_dict(self.type, self.data)
+        inst.__dict__["uuid"] = str(self.uuid)
         return inst
 
     def __str__(self) -> str:

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
         },
     }
 
@@ -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":
@@ -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():
@@ -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:
@@ -3077,12 +3113,21 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        if current_user.is_superuser:
-            context["jobs"] = JobLog.objects.all().order_by("-created")
-        else:
-            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+        # if current_user.is_superuser:
+        #     context["jobs"] = JobLog.objects.all().order_by("-created")
+        # else:
+        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        return render(request, "collections/joblog.html", context)
+        # Context for paginated template
+        context["entity_type"] = "joblog"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "joblog"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/joblog_paginated.html", context)
+
+        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

package.json

@@ -21,5 +21,11 @@
     "django",
     "tailwindcss",
     "daisyui"
+  ],
+  "pnpm": {
+    "onlyBuiltDependencies": [
+      "@parcel/watcher",
+      "@tailwindcss/oxide"
     ]
   }
+}

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")
             )

pnpm-workspace.yaml

@@ -1,3 +1,5 @@
+allowBuilds:
+  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
   - '@tailwindcss/oxide'

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/alpine/components/widgets.js

@@ -59,6 +59,9 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
+    get isRequired() {
+      return (this.schema.required || []).indexOf(this.fieldName) > -1
+    }
   });
 
   // Text widget
@@ -293,6 +296,34 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
+    // PubMed link widget
+  Alpine.data(
+    "doiWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get doiUrl() {
+        return this.value
+          ? `https://dx.doi.org/${this.value}`
+          : null;
+      },
+    }),
+  );
+
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/pw.js

@@ -463,7 +463,7 @@ function draw(pathway, elem) {
                     // TODO needs to be generic once we store it as AddInf
                     for (var s of n.predicted_properties["PepperPrediction"]) {
                         if (s["mean"] != null) {
-                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + "<br>"
+                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + " days<br>"
                         }
                     }
                 }
@@ -581,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if (p.depth >= n.depth) {
-                // keep the .5 steps for pseudo nodes
-                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            }
+            // if (p.depth >= n.depth) {
+            //     // keep the .5 steps for pseudo nodes
+            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+            // }
         }
     });
 
@@ -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

templates/actions/objects/pathway.html

@@ -22,7 +22,7 @@
   {% for tpl in action_button_templates %}
     {% include tpl %}
   {% endfor %}
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
   <a
@@ -74,7 +74,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
   <li>
     <a
       class="button"
@@ -99,11 +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
     >
@@ -111,7 +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/_joblog_paginated_list_partial.html

@@ -0,0 +1,102 @@
+{# Partial for paginated list content - expects to be inside a remotePaginatedList Alpine.js context #}
+{# Variables: empty_text (string), show_review_badge (bool), always_show_badge (bool) #}
+{% load envipytags %}
+{# Loading state #}
+<div
+  x-show="isLoading"
+  class="mx-auto flex h-32 w-32 items-center justify-center"
+>
+  {% include "components/loading-spinner.html" %}
+</div>
+
+{# Error state #}
+<div
+  x-show="!isLoading && error"
+  class="alert alert-error/50 text-sm"
+  x-text="error"
+></div>
+
+{# Content #}
+<template x-if="!isLoading && !error">
+  <div>
+    {# Empty state #}
+    <div
+      x-show="totalItems === 0"
+      class="text-base-content/70 py-8 text-center"
+    >
+      <p>No {{ empty_text|default:"items" }} found.</p>
+    </div>
+
+    {# Items list #}
+    <ul class="menu bg-base-100 rounded-box w-full" x-show="totalItems > 0">
+      <table class="table-zebra table">
+        <thead>
+          <tr>
+            <th>User</th>
+
+            <th>ID</th>
+            <th>Name</th>
+            <th>Status</th>
+            <th>Queued At</th>
+            <th>Done At</th>
+          </tr>
+        </thead>
+        <tbody>
+          <template x-for="obj in paginatedItems" :key="obj.url">
+            <tr>
+              <td>
+                <a :href="obj.user.url"><span x-text="obj.user.name"></span></a>
+              </td>
+
+              <td>
+                <a :href="obj.url"><span x-text="obj.id"></span></a>
+              </td>
+              <td><span x-text="obj.name"></span></td>
+              <td><span x-text="obj.status"></span></td>
+              <td><span x-text="obj.created"></span></td>
+              <td><span x-text="obj.done"></span></td>
+            </tr>
+          </template>
+        </tbody>
+      </table>
+    </ul>
+
+    {# Pagination controls #}
+    <div
+      x-show="totalPages > 1"
+      class="mt-4 flex items-center justify-between px-2"
+    >
+      <span class="text-base-content/70 text-sm">
+        Showing <span x-text="showingStart"></span>-<span
+          x-text="showingEnd"
+        ></span>
+        of <span x-text="totalItems"></span>
+      </span>
+      <div class="join">
+        <button
+          class="join-item btn btn-sm"
+          :disabled="currentPage === 1"
+          @click="prevPage()"
+        >
+          «
+        </button>
+        <template x-for="item in pageNumbers" :key="item.key">
+          <button
+            class="join-item btn btn-sm"
+            :class="{ 'btn-active': item.page === currentPage }"
+            :disabled="item.isEllipsis"
+            @click="!item.isEllipsis && goToPage(item.page)"
+            x-text="item.page"
+          ></button>
+        </template>
+        <button
+          class="join-item btn btn-sm"
+          :disabled="currentPage === totalPages"
+          @click="nextPage()"
+        >
+          »
+        </button>
+      </div>
+    </div>
+  </div>
+</template>

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/joblog_paginated.html

@@ -0,0 +1,13 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Jobs{% endblock %}
+
+{% block action_button %}
+{% endblock action_button %}
+
+{% block action_modals %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>List of Jobs submitted.</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/paginated_base.html

@@ -37,7 +37,11 @@
             perPage: {{ per_page|default:50 }}
           })"
       >
+        {% if entity_type == 'joblog' %}
+          {% include "collections/_joblog_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
+        {% else %}
           {% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
+        {% endif %}
       </div>
     {% else %}
       {# ===== TABBED MODE: Reviewed/Unreviewed tabs (default) ===== #}

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/components/schema_form.html

@@ -123,6 +123,17 @@
             </div>
           </template>
 
+          <!-- DOI link widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'doi-link'"
+          >
+            <div
+              x-data="doiWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/doi_link_widget.html" %}
+            </div>
+          </template>
+
           <!-- Compound link widget -->
           <template
             x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"

templates/components/widgets/doi_link_widget.html

@@ -0,0 +1,69 @@
+{# DOI link widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: display as link -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value && doiUrl">
+            <a
+              :href="doiUrl"
+              class="link link-primary"
+              target="_blank"
+              x-text="value"
+            ></a>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="text"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          placeholder="DOI e.g. 10.1016/j.jhazmat.2016.08.036"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/select_widget.html

@@ -44,6 +44,7 @@
           :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
           x-model="value"
           :multiple="multiple"
+          :required="isRequired"
         >
           <option value="" :selected="!value">Select...</option>
 

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/group.html

@@ -56,7 +56,7 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a href="{{ um.url }}" class="hover:bg-base-300"
+                <a href="{% if not user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
                   >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >

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

@@ -106,7 +106,7 @@
     </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
@@ -140,7 +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>

templates/predict_pathway.html

@@ -105,7 +105,7 @@
         ></iframe>
       </div>
 
-      <label class="select mb-8 w-full">
+      <label class="select mb-8 w-full" id="prediction-setting-label">
         <span class="label">Predictor</span>
         <select id="prediction-setting" name="prediction-setting">
           <option disabled>Select a Setting</option>
@@ -148,6 +148,22 @@
   </div>
   {# prettier-ignore-start #}
   <script>
+    // Hide predictor selection and update button text if mode is "build"
+    function radioChange(event) {
+      if (event.target.value === "build") {
+        document.getElementById("prediction-setting-label").hidden = true;
+        document.getElementById("predict-submit-button").innerText = "Build";
+      } else {
+        document.getElementById("prediction-setting-label").hidden = false;
+        document.getElementById("predict-submit-button").innerText = "Predict";
+      }
+    }
+
+    const radioButtons = document.querySelectorAll('input[name="predict"]');
+    radioButtons.forEach(radio => {
+      radio.addEventListener('change', radioChange);
+    });
+
     // Helper function to safely get Ketcher instance from iframe
     function getKetcherInstance(iframeId) {
       const ketcherFrame = document.getElementById(iframeId);

templates/static/login_base.html

@@ -110,8 +110,6 @@
           <div
             class="text-base-content/50 flex items-center justify-center space-x-6 text-sm"
           >
-            <a href="/legal" class="link link-hover">Legal</a>
-            <span class="text-base-content/30">•</span>
             <a href="/terms" class="link link-hover">Terms of Use</a>
             <span class="text-base-content/30">•</span>
             <a href="/privacy" class="link link-hover">Privacy Policy</a>

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,
@@ -125,6 +125,7 @@ from envipy_additional_information.parsers import (
     LiquidMatrixSourceParser,
     OxygenUptakeRateParser,
     InitiatingOrganismParser,
+    PFASConfidenceParser,
 )
 
 logger = logging.getLogger(__name__)
@@ -141,7 +142,7 @@ def get_parameter(request, paramname):
     res = request.POST.get(paramname)
     if res is not None and res.strip() != "":
         return res
-    return ValueError("Not all parameters are set!")
+    raise ValueError("Not all parameters are set!")
 
 
 def get_parameter_or_empty_string(request, paramname):
@@ -473,17 +474,12 @@ 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 +504,10 @@ 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)
@@ -674,7 +674,8 @@ def build_additional_information_from_request(request, type_):
         elif type_ == "studywst":
             # study_wst_cond = get_parameter(request, "studywstcond")
             raise ValueError("studywstcond is not yet implemented")
-
+        elif type_ == "pfasconfidence":
+            return PFASConfidenceParser.from_string(get_parameter(request, "level"))
         else:
             raise ValueError(f"No corresponding AdditionalInformation for {type_} found!")
 

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#0a608c85c73a6ef5c38afea87d2b57fb43f01a70" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
 dependencies = [
     { name = "pydantic" },
 ]
@@ -2763,9 +2763,9 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform != 'linux' and sys_platform != 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58" },
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 [[package]]
@@ -2785,19 +2785,19 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
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 ]
 
 [[package]]