[Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407

Dockerfile

@@ -36,13 +36,13 @@ RUN --mount=type=ssh \
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bayer bayer
-COPY bridge bridge
 COPY biotransformer biotransformer
+COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
+COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper

bayer/admin.py

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

bayer/apps.py

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

bayer/epdb_hooks.py

@@ -1,31 +0,0 @@
-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",
-)
-
-# PES Viz
-register_template(
-    "epdb.objects.compound.viz",
-    "objects/compound_viz.html",
-)
-
-register_template(
-    "epdb.objects.compound_structure.viz",
-    "objects/compound_structure_viz.html",
-)
-
-register_template(
-    "epdb.objects.node.viz",
-    "objects/node_viz.html",
-)

bayer/migrations/0001_initial.py

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

bayer/migrations/0002_initial.py

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

bayer/migrations/0003_package_data_pool.py

@@ -1,20 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-14 19:07
-
-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.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/migrations/0004_pescompound_pesstructure.py

@@ -1,35 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-15 20:03
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0003_package_data_pool'),
-        ('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')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.compoundstructure',),
-        ),
-    ]

bayer/migrations/0005_pesstructure_pes_link.py

@@ -1,19 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-16 08:43
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0004_pescompound_pesstructure'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='pesstructure',
-            name='pes_link',
-            field=models.URLField(default=None, verbose_name='PES Link'),
-            preserve_default=False,
-        ),
-    ]

bayer/models.py

@@ -1,168 +0,0 @@
-from typing import List
-import urllib.parse
-import nh3
-from django.conf import settings as s
-from django.db import models, transaction
-from django.db.models import QuerySet
-from django.urls import reverse
-
-from epdb.models import (
-    EnviPathModel,
-    Compound,
-    CompoundStructure,
-    ParallelRule,
-    SequentialRule,
-    SimpleAmbitRule,
-    SimpleRDKitRule,
-)
-
-
-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():
-            return PESStructure.objects.get(pes_link=pes_url, compound__package=package).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()
-
-        is_standardized = standardized_smiles == smiles
-
-        if not is_standardized:
-            _ = CompoundStructure.create(
-                c,
-                standardized_smiles,
-                name="Normalized structure of {}".format(name),
-                description="{} (in its normalized form)".format(description),
-                normalized_structure=True,
-            )
-
-        cs = CompoundStructure.create(
-            c, 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")
-
-    def d3_json(self):
-        return {
-            "is_pes": True,
-            "pes_link": self.pes_link,
-            # Will overwrite image from Node
-            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
-        }

bayer/templates/actions/collections/new_pes.html

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

bayer/templates/modals/collections/new_package_modal.html

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

bayer/templates/modals/collections/new_pes_modal.html

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

bayer/templates/objects/compound_structure_viz.html

@@ -1,12 +0,0 @@
-{% if compound_structure.pes_link %}
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/compound_viz.html

@@ -1,12 +0,0 @@
-{% if compound.default_structure.pes_link %}
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound.default_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/node_viz.html

@@ -1,12 +0,0 @@
-{% if node.default_node_label.pes_link %}
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ node.default_node_label.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/package.html

@@ -1,97 +0,0 @@
-{% extends "framework_modern.html" %}
-
-{% 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 }} - ({{ package.get_classification_level_display }})</h2>
-          <div id="actionsButton" class="dropdown dropdown-e nd hidden">
-            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
-              <svg
-                xmlns="http://www.w3.org/2000/svg"
-                width="16"
-                height="16"
-                viewBox="0 0 24 24"
-                fill="none"
-                stroke="currentColor"
-                stroke-width="2"
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                class="lucide lucide-wrench"
-              >
-                <path
-                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
-                />
-              </svg>
-              Actions
-            </div>
-            <ul
-              tabindex="-1"
-              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
-            >
-              {% block actions %}
-                {% include "actions/objects/package.html" %}
-              {% endblock %}
-            </ul>
-          </div>
-        </div>
-        <p class="mt-2">{{ package.description|safe }}</p>
-        <ul class="menu bg-base-200 rounded-box mt-4 w-full">
-          <li>
-            <a href="{{ package.url }}/pathway" class="hover:bg-base-300"
-              >Pathways ({{ package.pathways.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/rule" class="hover:bg-base-300"
-              >Rules ({{ package.rules.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/compound" class="hover:bg-base-300"
-              >Compounds ({{ package.compounds.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/reaction" class="hover:bg-base-300"
-              >Reactions ({{ package.reactions.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/model" class="hover:bg-base-300"
-              >Models ({{ package.models.count }})</a
-            >
-          </li>
-          <li>
-            <a href="{{ package.url }}/scenario" class="hover:bg-base-300"
-              >Scenarios ({{ package.scenarios.count }})</a
-            >
-          </li>
-        </ul>
-      </div>
-    </div>
-  </div>
-
-  <script>
-    // Show actions button if there are actions
-    document.addEventListener("DOMContentLoaded", function () {
-      const actionsButton = document.getElementById("actionsButton");
-      const actionsList = actionsButton?.querySelector("ul");
-      if (actionsList && actionsList.children.length > 0) {
-        actionsButton?.classList.remove("hidden");
-      }
-    });
-  </script>
-{% endblock content %}

bayer/templates/static/login.html

@@ -1,149 +0,0 @@
-{% extends "static/login_base.html" %}
-
-{% 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 class="card bg-base-200 mb-6 ">
-    <div class="card-body">
-      <h3 class="card-title">Welcome to the new enviPath!</h3>
-    </div>
-  </div>
-  <!-- Tab Navigation -->
-  <div class="border-base-300 mb-6 border-b">
-    <div class="flex justify-start">
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-sso"
-        class="tab-radio"
-        checked
-      />
-      <label for="tab-sso" class="tab-label">SSO</label>
-
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-signin"
-        class="tab-radio"
-      />
-      <label for="tab-signin" class="tab-label">Local User</label>
-    </div>
-  </div>
-
-  <!-- SSO Tab -->
-  <div id="content-sso" class="tab-content active">
-      <button role="link" onclick="window.location.href='/entra/login'" name="sso" class="btn btn-primary w-full">
-        Login with Microsoft
-      </button>
-  </div>
-
-  <!-- Sign In Tab -->
-  <div id="content-signin" class="tab-content">
-    <form method="post" action="{% url 'login' %}" class="space-y-4">
-      {% csrf_token %}
-      <input type="hidden" name="login" value="true" />
-
-      <div class="form-control">
-        <label class="label" for="username">
-          <span class="label-text">Account</span>
-        </label>
-        <input
-          type="text"
-          id="username"
-          name="username"
-          placeholder="Username or Email"
-          class="input input-bordered w-full"
-          required
-          autocomplete="username"
-        />
-      </div>
-
-      <div class="form-control">
-        <label class="label" for="passwordinput">
-          <span class="label-text">Password</span>
-        </label>
-        <input
-          type="password"
-          id="passwordinput"
-          name="password"
-          placeholder="••••••••"
-          class="input input-bordered w-full"
-          required
-          autocomplete="current-password"
-        />
-      </div>
-
-      <div class="text-right">
-        <a href="{% url 'password_reset' %}" class="link link-primary text-sm"
-          >Forgot password?</a
-        >
-      </div>
-
-      <input type="hidden" name="next" value="{{ next }}" />
-
-      <button type="submit" name="signin" class="btn btn-primary w-full">
-        Sign In
-      </button>
-    </form>
-  </div>
-
-{% endblock %}
-
-{% block extra_scripts %}
-  <script>
-    // Tab switching functionality
-    document.querySelectorAll('input[name="auth-tab"]').forEach((radio) => {
-      radio.addEventListener("change", function () {
-        // Hide all content
-        document.querySelectorAll(".tab-content").forEach((content) => {
-          content.classList.remove("active");
-        });
-
-        // Show selected content
-        const contentId = "content-" + this.id.replace("tab-", "");
-        document.getElementById(contentId).classList.add("active");
-      });
-    });
-
-    // Check for hash in URL to auto-select tab
-    window.addEventListener("DOMContentLoaded", function () {
-      const hash = window.location.hash.substring(1); // Remove the # symbol
-      if (hash === "signup" || hash === "signin") {
-        const tabRadio = document.getElementById("tab-" + hash);
-        if (tabRadio) {
-          tabRadio.checked = true;
-          // Trigger change event to show correct content
-          tabRadio.dispatchEvent(new Event("change"));
-        }
-      }
-    });
-  </script>
-{% endblock %}

bayer/tests.py

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

bayer/urls.py

@@ -1,14 +0,0 @@
-from django.urls import re_path
-
-from . import views as v
-
-UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
-
-urlpatterns = [
-    re_path(r"^depict_pes$", v.visualize_pes, name="depict_pes"),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/compound$",
-        v.create_pes,
-        name="create pes",
-    ),
-]

bayer/views.py

@@ -1,96 +0,0 @@
-import base64
-
-import requests
-from django.conf import settings as s
-from django.core.exceptions import BadRequest
-from django.http import HttpResponse
-from django.shortcuts import redirect
-
-from bayer.models import PESCompound
-from epdb.logic import PackageManager
-from epdb.views import _anonymous_or_real
-from utilities.decorators import package_permission_required
-
-
-@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":
-        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}")
-
-            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
-
-
-
-def fetch_pes(request, pes_url) -> dict:
-    proxies = {
-        "http": "http://10.185.190.100:8080",
-        "https": "http://10.185.190.100:8080",
-    }
-
-    from epauth.views import get_access_token_from_request
-    token = get_access_token_from_request(request)
-
-    if token or True:
-        for k, v in s.PES_API_MAPPING.items():
-            if pes_url.startswith(k):
-                pes_id = pes_url.split('/')[-1]
-
-                if pes_id == 'dummy' or True:
-                    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=proxies)
-
-                    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")

docker-compose.dev.yml

@@ -1,15 +1,15 @@
 services:
   db:
     image: postgres:18
-    container_name: eppostgres
+    container_name: envipath-postgres
     environment:
-      POSTGRES_USER: ${POSTGRES_USER}
-      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: envipath
     ports:
       - "5432:5432"
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - postgres_data:/var/lib/postgresql
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 5s
@@ -18,37 +18,9 @@ services:
 
   redis:
     image: redis:7-alpine
-    container_name: epredis
+    container_name: envipath-redis
     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:
-  ep_bayer_postgres_data:
-  ep_bayer_redis_data:
-  ep_bayer_data:
+  postgres_data:

docker-compose.yml

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

envipath/settings.py

@@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
-import json
+
 import os
 from pathlib import Path
 
@@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -442,35 +442,3 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
-
-# PES
-PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
-if PES_API_MAPPING:
-    import json
-    PES_API_MAPPING = json.loads(PES_API_MAPPING)
-else:
-    PES_API_MAPPING = {}
-
-# Entra Groups
-ENTRA_GROUPS = os.environ.get("ENTRA_GROUPS", None)
-if ENTRA_GROUPS:
-    import json
-    ENTRA_GROUPS = json.loads(ENTRA_GROUPS)
-else:
-    ENTRA_GROUPS = {}
-
-ENTRA_SECRET_GROUPS = os.environ.get("ENTRA_SECRET_GROUPS", None)
-if ENTRA_SECRET_GROUPS:
-    import json
-    ENTRA_SECRET_GROUPS = json.loads(ENTRA_SECRET_GROUPS)
-else:
-    ENTRA_SECRET_GROUPS = {}
-
-# PES Data Pools vs Entra Mapping
-DATA_POOL_MAPPING = os.environ.get("DATA_POOL_MAPPING", None)
-if DATA_POOL_MAPPING:
-    import json
-    DATA_POOL_MAPPING = json.loads(DATA_POOL_MAPPING)
-else:
-    DATA_POOL_MAPPING = {}
-

envipath/urls.py

@@ -41,9 +41,7 @@ if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
 if s.TENANT != "public":
-    urlpatterns.append(
-        path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls"))
-    )
+    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
 
 # Custom error handlers
 handler400 = "epdb.views.handler400"

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/views.py

@@ -4,8 +4,7 @@ from django.contrib.auth import get_user_model
 from django.contrib.auth import login
 from django.shortcuts import redirect
 
-from epdb.logic import UserManager, GroupManager
-from epdb.models import Group
+from epdb.logic import UserManager
 
 
 def get_msal_app_with_cache(request):
@@ -22,7 +21,7 @@ def get_msal_app_with_cache(request):
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
         authority=s.MS_ENTRA_AUTHORITY,
-        token_cache=cache
+        token_cache=cache,
     )
 
     return msal_app, cache
@@ -59,9 +58,12 @@ def entra_callback(request):
 
     claims = result["id_token_claims"]
 
-    user_name = claims["name"]
-    user_email = claims.get("emailaddress", claims["email"])
-    user_oid = claims["oid"]
+    user_name = claims.get("name")
+    user_email = claims.get("emailaddress", claims.get("email"))
+    user_oid = claims.get("oid")
+
+    if not all([user_name, user_email, user_oid]):
+        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
@@ -78,32 +80,6 @@ def entra_callback(request):
 
     login(request, u)
 
-    # EDIT START
-    # Ensure groups exists in eP
-    for id, name in s.ENTRA_SECRET_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-        # Ensure its secret
-        g.secret = True
-        g.save()
-
-    for id, name in s.ENTRA_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-
-    for group_uuid in claims.get("groups", []):
-        if Group.objects.filter(uuid=group_uuid).exists():
-            g = Group.objects.get(uuid=group_uuid)
-            g.user_member.add(u)
-
-    # EDIT END
-
     return redirect(s.SERVER_URL)  # Handle errors
 
 
@@ -142,10 +118,7 @@ def get_access_token_from_request(request, scopes=None):
         return None
 
     # Try to acquire token silently from cache
-    result = msal_app.acquire_token_silent(
-        scopes=scopes,
-        account=user_account
-    )
+    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
 
     # Save cache changes back to session
     if cache.has_state_changed:

epdb/admin.py

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

epdb/legacy_api.py

@@ -1,22 +1,17 @@
-import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
-import jwt
-import requests
-
 import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
 from ninja import Field, Form, Query, Router, Schema
-from ninja.errors import HttpError
-from ninja.security import HttpBearer
 from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
+
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -64,46 +59,7 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-def validate_token(token: str) -> dict:
-    TENANT_ID = s.MS_ENTRA_TENANT_ID
-    CLIENT_ID = s.MS_ENTRA_CLIENT_ID
-
-    # Fetch Microsoft's public keys
-    jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
-    jwks = requests.get(jwks_uri).json()
-
-    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"])
-    )
-
-    claims = jwt.decode(
-        token,
-        public_key,
-        algorithms=["RS256"],
-        audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-        issuer=f"https://sts.windows.net/{TENANT_ID}/",
-    )
-    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())
+router = Router(auth=SessionAuth(csrf=False))
 
 
 class Error(Schema):
@@ -197,6 +153,21 @@ class SimpleModel(SimpleObject):
     identifier: str = "relative-reasoning"
 
 
+################
+# Login/Logout #
+################
+@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
+def login(request, loginusername: Form[str], loginpassword: Form[str]):
+    from django.contrib.auth import authenticate, login
+
+    email = User.objects.get(username=loginusername).email
+    user = authenticate(username=email, password=loginpassword)
+    if user:
+        login(request, user)
+        return user
+    else:
+        return 403, {"message": "Invalid username and/or password"}
+
 
 ########
 # User #
@@ -415,23 +386,50 @@ 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):
@@ -828,6 +826,27 @@ 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}"
 )
@@ -1354,6 +1373,7 @@ 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"
@@ -1497,6 +1517,7 @@ 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()
 
@@ -1520,6 +1541,33 @@ 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:
@@ -1569,6 +1617,7 @@ 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):
@@ -1722,6 +1771,29 @@ 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:
@@ -1842,7 +1914,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(n.nodeDepth)
+            node_depth = int(float(n.nodeDepth))
         else:
             node_depth = -1
 
@@ -1987,6 +2059,10 @@ 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,
@@ -1994,11 +2070,15 @@ 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 node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

@@ -345,52 +345,17 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        if (
-            UserPackagePermission.objects.filter(package=package, user=user).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package, group__in=GroupManager.get_groups(user)
+        return (
+            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
         )
-            or package.reviewed is True
-            or user.is_superuser
-        ):
-            return True
-
-        return False
 
     @staticmethod
     def writable(user, package):
-        if (
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.WRITE[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.WRITE[0],
-            ).exists()
-            or UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
+        return PackageManager.has_package_permission(user, package, "write")
 
     @staticmethod
     def administrable(user, package):
-        if (
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.ALL[0],
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
+        return PackageManager.has_package_permission(user, package, "all")
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -474,7 +439,9 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -518,7 +485,9 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_packages():
@@ -627,25 +596,6 @@ class PackageManager(object):
         else:
             pack.reviewed = False
 
-        # EDIT START
-        if data.get("classification"):
-            if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
-
-                if not "datapool" in data:
-                    raise ValueError("Missing datapool in package")
-
-                g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
-                pack.data_pool = g
-            else:
-                raise ValueError(f"Invalid classification {data['classification']}")
-
-        # EDIT END
-
         pack.description = data["description"]
         pack.save()
 
@@ -731,13 +681,7 @@ class PackageManager(object):
             default_structure = None
 
             for structure in compound["structures"]:
-                if structure.get("pesLink"):
-                    from bayer.models import PESStructure
-                    struc = PESStructure()
-                    struc.pes_link = structure["pesLink"]
-                else:
                 struc = CompoundStructure()
-
                 # struc.object_url = Command.get_id(structure, keep_ids)
                 struc.compound = comp
                 struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@@ -1051,52 +995,9 @@ 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

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

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

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

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

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

epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py

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

epdb/migrations/0005_alter_group_group_member.py

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

epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py

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

epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py

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

epdb/migrations/0008_enzymelink.py

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

epdb/migrations/0009_joblog.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/migrations/0012_node_stereo_removed_pathway_predicted.py

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

epdb/migrations/0013_setting_expansion_schema.py

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

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

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

epdb/migrations/0015_user_is_reviewer.py

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

epdb/migrations/0016_remove_enviformer_model_status_and_more.py

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

epdb/migrations/0017_additionalinformation.py

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

epdb/migrations/0018_auto_20260220_1203.py

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

epdb/migrations/0019_remove_scenario_additional_information_and_more.py

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

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -1,50 +1,49 @@
-# Generated by Django 6.0.3 on 2026-04-14 19:07
+# Generated by Django 6.0.3 on 2026-04-21 11:43
 
 from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
-        ('epdb', '0022_alter_classifierpluginmodel_data_packages_and_more'),
+        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
     ]
 
     operations = [
         migrations.AlterModelOptions(
-            name='compoundstructure',
+            name="compoundstructure",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='epmodel',
+            name="epmodel",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='parallelrule',
+            name="parallelrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='rule',
+            name="rule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='sequentialrule',
+            name="sequentialrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simpleambitrule',
+            name="simpleambitrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simplerdkitrule',
+            name="simplerdkitrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simplerule',
+            name="simplerule",
             options={},
         ),
         migrations.AddField(
-            model_name='group',
-            name='secret',
-            field=models.BooleanField(default=False, verbose_name='Secret Group'),
+            model_name="compoundstructure",
+            name="molfile",
+            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
         ),
     ]

epdb/migrations/0024_user_contacted.py

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

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/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

@@ -75,6 +75,7 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
+    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -203,7 +204,6 @@ class Group(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name="Group name")
     owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name="Public Group", default=False)
-    secret = models.BooleanField(verbose_name="Secret Group", default=False)
     description = models.TextField(
         blank=False, null=False, verbose_name="Descriptions", default="no description"
     )
@@ -1695,7 +1695,7 @@ 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 +1773,7 @@ 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 +1886,9 @@ 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 +2181,50 @@ 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(
@@ -2219,7 +2266,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        extra_structure_data = self.default_node_label.d3_json()
+        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        # by overwriting keys
+        structure_data = self.default_node_label.d3_json()
 
         res = {
             "depth": self.depth,
@@ -2230,7 +2279,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
-
+            "image_type": "svg",
             "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@@ -2243,9 +2292,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
+            **structure_data,
         }
 
-        res.update(**extra_structure_data)
         return res
 
     @staticmethod
@@ -2403,6 +2452,8 @@ 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
@@ -2432,7 +2483,7 @@ 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
@@ -4440,18 +4491,22 @@ 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

@@ -388,9 +388,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
-            # EDIT START
-            "secret_groups": Group.objects.filter(secret=True),
-            # EDIT END
         },
     }
 
@@ -590,38 +587,10 @@ def packages(request):
                 "package-description", s.DEFAULT_VALUES["description"]
             )
 
-            # EDIT START
-            data_pool = None
-            package_classification = request.POST.get("package-classification")
-            classification = Package.Classification(int(package_classification))
-            # For SECRET we'll need a data pool which will be an additional perm check later
-            if classification == Package.Classification.SECRET:
-                package_data_pool = request.POST.get("package-data-pool")
-
-                if package_data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool is required!")
-
-                data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
-
-                if data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
-
-                if not data_pool.secret:
-                    return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
-
             created_package = PackageManager.create_package(
                 current_user, package_name, package_description
             )
 
-            created_package.classification_level = classification
-
-            # Set previously determined data pool
-            if classification == Package.Classification.SECRET:
-                created_package.data_pool = data_pool
-
-            created_package.save()
-            # EDIT END
-
             return redirect(created_package.url)
 
     elif request.method == "OPTIONS":
@@ -2537,6 +2506,9 @@ 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:
@@ -3108,12 +3080,21 @@ 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")

pepper/__init__.py

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

pepper/impl/pepper.py

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

static/js/alpine/components/widgets.js

@@ -293,6 +293,34 @@ 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));
+            // }
         }
     });
 
@@ -637,14 +637,7 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
-        if (d.is_pes) {
-            g.append("svg:image")
-              .attr("xlink:href", d.image)
-              .attr("width", 40)
-              .attr("height", 40)
-              .attr("x", -20)
-              .attr("y", -20);
-        } else {
+        if (d.image_type === "svg") {
             // Parse the SVG string
             const parser = new DOMParser();
             const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@@ -683,6 +676,15 @@ function draw(pathway, elem) {
                 .attr("height", svgHeight * scale)
                 .attr("x", -svgWidth * scale / 2)
                 .attr("y", -svgHeight * scale / 2);
+        } else {
+            // We have a image type different than svg
+            // include it via img url
+            g.append("svg:image")
+                .attr("xlink:href", d.image)
+                .attr("width", 40)
+                .attr("height", 40)
+                .attr("x", -20)
+                .attr("y", -20);
         }
 
     });

templates/actions/objects/pathway.html

@@ -1,3 +1,5 @@
+{% load envipytags %}
+
 {% if meta.can_edit %}
   <li>
     <a
@@ -15,6 +17,11 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
+  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+
+  {% for tpl in action_button_templates %}
+    {% include tpl %}
+  {% endfor %}
   <li role="separator" class="divider"></li>
 {% endif %}
 <li>

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/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/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/components/navbar.html

@@ -88,12 +88,6 @@
                   >Scenario</a
                 >
               </li>
-                <hr/>
-              <li>
-                <a href="{{ meta.server_url }}/group" id="scenarioLink"
-                  >Group</a
-                >
-              </li>
             </ul>
           </div>
         </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/objects/compound.html

@@ -83,8 +83,8 @@
       <div class="collapse-content">{{ compound.description }}</div>
     </div>
 
+    <!-- Extension Slot for Viz -->
     {% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
-
     {% for tpl in viz_templates %}
       {% include tpl %}
     {% endfor %}

templates/objects/compound_structure.html

@@ -51,8 +51,8 @@
       </div>
     </div>
 
+    <!-- Extension Slot for Viz -->
     {% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
-
     {% for tpl in viz_templates %}
       {% include tpl %}
     {% endfor %}

templates/objects/node.html

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

templates/objects/pathway.html

@@ -1,5 +1,7 @@
 {% extends "framework_modern.html" %}
 {% load static %}
+{% load envipytags %}
+
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -76,6 +78,10 @@
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
+    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
+    {% for tpl in add_templates %}
+      {% include tpl %}
+    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}

utilities/chem.py

@@ -88,6 +88,10 @@ class FormatConverter(object):
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
 
+    @staticmethod
+    def from_molfile(molfile: str):
+        return Chem.MolFromMolBlock(molfile)
+
     @staticmethod
     def to_smiles(mol, canonical=False):
         return Chem.MolToSmiles(mol, canonical=canonical)
@@ -178,11 +182,9 @@ class FormatConverter(object):
 
         drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
         opts = drawer.drawOptions()
-
         opts.clearBackground = False
         drawer.DrawMolecule(mol)
         drawer.FinishDrawing()
-
         return drawer.GetDrawingText()
 
     @staticmethod

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

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.3"
+version = "3.13.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
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 ]
 
 [[package]]