[Fix] Simplify Depth adjustment (#386)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#386

Dockerfile

@@ -37,7 +37,6 @@ RUN --mount=type=ssh \
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
 COPY biotransformer biotransformer
-COPY bayer bayer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi

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_pescompound_pesstructure_package_data_pool.py

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

bayer/models.py

@@ -1,236 +0,0 @@
-from typing import List
-import urllib.parse
-import nh3
-from django.conf import settings as s
-from django.db import models, transaction
-from django.db.models import QuerySet
-from django.urls import reverse
-
-from epdb.models import (
-    EnviPathModel,
-    Compound,
-    CompoundStructure,
-    ParallelRule,
-    SequentialRule,
-    SimpleAmbitRule,
-    SimpleRDKitRule,
-)
-from utilities.chem import FormatConverter
-
-
-class Package(EnviPathModel):
-    reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
-    license = models.ForeignKey(
-        "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
-    )
-
-    class Classification(models.IntegerChoices):
-        INTERNAL = 0, "Internal"
-        RESTRICTED = 10 , "Restricted"
-        SECRET = 20, "Secret"
-
-    classification_level = models.IntegerField(
-        choices=Classification,
-        default=Classification.RESTRICTED,
-    )
-
-    data_pool = models.ForeignKey("epdb.Group", on_delete=models.SET_NULL, blank=True, null=True,
-                                  verbose_name="Data pool", default=None)
-
-    def delete(self, *args, **kwargs):
-        # explicitly handle related Rules
-        for r in self.rules.all():
-            r.delete()
-        super().delete(*args, **kwargs)
-
-    def __str__(self):
-        return f"{self.name} (pk={self.pk})"
-
-    @property
-    def compounds(self) -> QuerySet:
-        return self.compound_set.all()
-
-    @property
-    def rules(self) -> QuerySet:
-        return self.rule_set.all()
-
-    @property
-    def reactions(self) -> QuerySet:
-        return self.reaction_set.all()
-
-    @property
-    def pathways(self) -> QuerySet:
-        return self.pathway_set.all()
-
-    @property
-    def scenarios(self) -> QuerySet:
-        return self.scenario_set.all()
-
-    @property
-    def models(self) -> QuerySet:
-        return self.epmodel_set.all()
-
-    def _url(self):
-        return "{}/package/{}".format(s.SERVER_URL, self.uuid)
-
-    def get_applicable_rules(self) -> List["Rule"]:
-        """
-        Returns a ordered set of rules where the following applies:
-        1. All Composite will be added to result
-        2. All SimpleRules will be added if theres no CompositeRule present using the SimpleRule
-        Ordering is based on "url" field.
-        """
-        rules = []
-        rule_qs = self.rules
-
-        reflected_simple_rules = set()
-
-        for r in rule_qs:
-            if isinstance(r, ParallelRule) or isinstance(r, SequentialRule):
-                rules.append(r)
-                for sr in r.simple_rules.all():
-                    reflected_simple_rules.add(sr)
-
-        for r in rule_qs:
-            if isinstance(r, SimpleAmbitRule) or isinstance(r, SimpleRDKitRule):
-                if r not in reflected_simple_rules:
-                    rules.append(r)
-
-        rules = sorted(rules, key=lambda x: x.url)
-        return rules
-
-    class Meta:
-        db_table = "epdb_package"
-
-
-class PESCompound(Compound):
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
-    ) -> "Compound":
-
-        pes_url = pes_data["pes_url"]
-
-        # Check if we find a direct match for a given pes_link
-        if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
-            # Due to normalization we might end up in having multiple structures
-            # All of them point to the same compound -> pick any
-            return PESStructure.objects.filter(pes_link=pes_url, compound__package=package).first().compound
-
-        # Generate Compound
-        c = PESCompound()
-        c.package = package
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if name is None or name == "":
-            name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
-
-        c.name = name
-
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
-            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        c.save()
-
-        molfile = pes_data.get("representativeStructures", [{}])[0].get("ctab")
-
-        if molfile is None:
-            raise ValueError("PES data does not contain a valid mol file!")
-
-        smiles = FormatConverter.to_smiles(FormatConverter.from_molfile(molfile))
-
-        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
-
-        is_standardized = standardized_smiles == smiles
-
-        if not is_standardized:
-            _ = PESStructure.create(
-                c,
-                pes_url,
-                molfile,
-                standardized_smiles,
-                name="Normalized structure of {}".format(name),
-                description="{} (in its normalized form)".format(description),
-                normalized_structure=True,
-            )
-
-
-        cs = PESStructure.create(
-            c,
-            pes_url,
-            molfile,
-            smiles,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized
-        )
-
-        c.default_structure = cs
-        c.save()
-
-        return c
-
-
-class PESStructure(CompoundStructure):
-    pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-            compound: Compound,
-            pes_link: str,
-            mol_file: str,
-            smiles: str,
-            name: str = None,
-            description: str = None,
-            *args,
-            **kwargs
-    ):
-        if compound.pk is None:
-            raise ValueError("Unpersisted Compound! Persist compound first!")
-
-        cs = PESStructure()
-        # Clean for potential XSS
-        if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if description is not None:
-            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        cs.smiles = smiles
-        cs.mol_file = mol_file
-        cs.pes_link = pes_link
-        cs.compound = compound
-
-        if "normalized_structure" in kwargs:
-            cs.normalized_structure = kwargs["normalized_structure"]
-
-        cs.save()
-
-        return cs
-
-    @transaction.atomic
-    def add_structure(
-        self,
-        smiles: str,
-        name: str = None,
-        description: str = None,
-        default_structure: bool = False,
-        *args,
-        **kwargs,
-    ) -> "CompoundStructure":
-        raise ValueError("Not supported!")
-
-    def d3_json(self):
-        return {
-            "is_pes": True,
-            "pes_link": self.pes_link,
-            # Will overwrite image from Node
-            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
-        }

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-pes-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

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

bayer/templates/objects/compound_structure_viz.html

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

bayer/templates/objects/compound_viz.html

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

bayer/templates/objects/node_viz.html

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

bayer/templates/objects/package.html

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

bayer/templates/static/login.html

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

bayer/tests.py

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

bayer/urls.py

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

bayer/views.py

@@ -1,160 +0,0 @@
-import base64
-
-import requests
-from django.conf import settings as s
-from django.core.exceptions import BadRequest
-from django.http import HttpResponse
-from django.shortcuts import redirect
-
-from bayer.models import PESCompound
-from epdb.logic import PackageManager
-from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real
-from utilities.decorators import package_permission_required
-
-Package = s.GET_PACKAGE_MODEL()
-
-
-@package_permission_required()
-def create_pes(request, package_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                pes_data = fetch_pes(request, pes_link)
-            except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return BadRequest(
-                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
-
-            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
-
-            return redirect(pes.url)
-        else:
-            return BadRequest("Please provide a PES link.")
-    else:
-        pass
-
-
-@package_permission_required()
-def create_pes_node(request, package_uuid, pathway_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                pes_data = fetch_pes(request, pes_link)
-            except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return BadRequest(
-                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
-
-            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
-
-            n = Node()
-            n.stereo_removed = False
-            n.pathway = current_pathway
-            n.depth = 0
-
-            n.default_node_label = pes.default_structure
-            n.save()
-
-            n.node_labels.add(pes.default_structure)
-            n.save()
-
-            return redirect(current_pathway.url)
-
-        else:
-            return BadRequest("Please provide a PES link.")
-    else:
-        pass
-
-
-def fetch_pes(request, pes_url) -> dict:
-    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

@@ -1,54 +1,26 @@
 services:
   db:
     image: postgres:18
-    container_name: eppostgres
+    container_name: envipath-postgres
     environment:
-      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_DB: envipath
     ports:
       - "5432:5432"
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - postgres_data:/var/lib/postgresql
     healthcheck:
-      test: [ "CMD-SHELL", "pg_isready -U postgres" ]
+      test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 5s
       timeout: 5s
       retries: 5
 
   redis:
     image: redis:7-alpine
-    container_name: epredis
+    container_name: envipath-redis
     ports:
       - "6379:6379"
-    volumes:
-      - ep_bayer_redis_data:/data
-
-  biotransformer3:
-    image: 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:
+  postgres_data:
-  ep_bayer_redis_data:
-  ep_bayer_data:

docker-compose.yml

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

envipath/settings.py

@@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
-import json
+
 import os
 from pathlib import Path
 
@@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -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 = {}
-

epauth/views.py

@@ -80,30 +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
 
 

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:
+router = Router(auth=SessionAuth(csrf=False))
-    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())
 
 
 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 #
@@ -1958,16 +1929,13 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
-        subclasses = CompoundStructure.__subclasses__()
-
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -1978,8 +1946,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -2000,6 +1967,9 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             description=e.edgeReason,
         )
 
+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
         return redirect(new_e.url)
     except ValueError:
         return 403, {"message": "Adding Edge failed!"}

epdb/logic.py

@@ -7,7 +7,6 @@ import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
-from django.db.models import QuerySet
 from pydantic import ValidationError
 
 from epdb.models import (
@@ -365,14 +364,6 @@ class PackageManager(object):
 
         groups = GroupManager.get_groups(user)
 
-        # EDIT START
-
-        if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
-                return False
-
-        # EDIT END
-
         perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
 
         valid_perms = perms.get(permission)
@@ -415,7 +406,6 @@ class PackageManager(object):
         try:
             p = Package.objects.get(uuid=package_id)
             if PackageManager.readable(user, p):
-                p = PackageManager.check_package_classification(user, p)
                 return p
             else:
                 # FIXME: use custom exception to be translatable to 403 in API
@@ -425,37 +415,6 @@ class PackageManager(object):
         except Package.DoesNotExist:
             raise ValueError("Package with ID {} does not exist!".format(package_id))
 
-    # EDIT START
-
-    @staticmethod
-    def check_package_classification(user, pack: Package):
-        if pack.classification_level == Package.Classification.SECRET:
-            if pack.data_pool.user_member.filter(id=user.id).exists():
-                return pack
-
-            raise ValueError("Package is secret and not accessible to user!")
-
-        else:
-            return pack
-
-
-    @staticmethod
-    def check_package_classifications(user, package_qs: QuerySet[Package]):
-        non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
-        secret = package_qs.filter(classification_level=Package.Classification.SECRET)
-
-        # TODO we should be able to do via the db
-        accessible_secret = []
-
-        for s_package in secret:
-            if s_package.data_pool.user_member.filter(id=user.id).exists():
-                accessible_secret.append(s_package.pk)
-
-        # Cannot combine a unique query with a non-unique query -> we have to call distinct
-        return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
-
-    # EDIT END
-
     @staticmethod
     def get_all_readable_packages(user, include_reviewed=False):
         # UserPermission only exists if at least read is granted...
@@ -482,10 +441,6 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
         return qs
 
     @staticmethod
@@ -532,12 +487,12 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
         return qs
 
+    @staticmethod
+    def get_packages():
+        return Package.objects.all()
+
     @staticmethod
     @transaction.atomic
     def create_package(current_user, name: str, description: str = None):
@@ -641,25 +596,6 @@ class PackageManager(object):
         else:
             pack.reviewed = False
 
-        # EDIT START
-        if data.get("classification"):
-            if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
-
-                if not "datapool" in data:
-                    raise ValueError("Missing datapool in package")
-
-                g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
-                pack.data_pool = g
-            else:
-                raise ValueError(f"Invalid classification {data['classification']}")
-
-        # EDIT END
-
         pack.description = data["description"]
         pack.save()
 
@@ -745,13 +681,7 @@ class PackageManager(object):
             default_structure = None
 
             for structure in compound["structures"]:
-                if structure.get("pesLink"):
+                struc = CompoundStructure()
-                    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()
@@ -1065,52 +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)
+            pw.update_depths()
-            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)
-
             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
+from django.db import migrations
-import django.contrib.auth.validators
-import django.contrib.postgres.fields
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
-    initial = True
-
     dependencies = [
-        ('auth', '0012_alter_user_first_name_max_length'),
+        ("epdb", "0018_auto_20260220_1203"),
-        ('contenttypes', '0002_remove_content_type_name'),
-        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
-        migrations.CreateModel(
+        migrations.RemoveField(
-            name='ApplicabilityDomain',
+            model_name="scenario",
-            fields=[
+            name="additional_information",
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('num_neighbours', models.IntegerField(default=5)),
-                ('reliability_threshold', models.FloatField(default=0.5)),
-                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
-                ('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
-            ],
-            options={
-                'abstract': False,
-            },
         ),
-        migrations.CreateModel(
+        migrations.RemoveField(
-            name='Edge',
+            model_name="scenario",
-            fields=[
+            name="parent",
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='EPModel',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='ExternalDatabase',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
-                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
-                ('description', models.TextField(blank=True, verbose_name='Description')),
-                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
-                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
-                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
-            ],
-            options={
-                'verbose_name': 'External Database',
-                'verbose_name_plural': 'External Databases',
-                'db_table': 'epdb_external_database',
-                'ordering': ['name'],
-            },
-        ),
-        migrations.CreateModel(
-            name='Permission',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
-            ],
-        ),
-        migrations.CreateModel(
-            name='License',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('cc_string', models.TextField(verbose_name='CC string')),
-                ('link', models.URLField(verbose_name='link')),
-                ('image_link', models.URLField(verbose_name='Image link')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='Rule',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='User',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('password', models.CharField(max_length=128, verbose_name='password')),
-                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
-                ('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
-                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
-                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
-                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
-                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
-                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
-                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
-                ('email', models.EmailField(max_length=254, unique=True)),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('is_reviewer', models.BooleanField(default=False)),
-                ('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
-                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
-                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
-            ],
-            options={
-                'verbose_name': 'user',
-                'verbose_name_plural': 'users',
-                'abstract': False,
-            },
-            managers=[
-                ('objects', django.contrib.auth.models.UserManager()),
-            ],
-        ),
-        migrations.CreateModel(
-            name='APIToken',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
-                ('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
-                ('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
-                ('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
-                ('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
-            ],
-            options={
-                'verbose_name': 'API Token',
-                'verbose_name_plural': 'API Tokens',
-                'db_table': 'epdb_api_token',
-                'ordering': ['-created'],
-            },
-        ),
-        migrations.CreateModel(
-            name='Compound',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='CompoundStructure',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('smiles', models.TextField(verbose_name='SMILES')),
-                ('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
-                ('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
-                ('normalized_structure', models.BooleanField(default=False)),
-                ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='default_structure',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
-        ),
-        migrations.CreateModel(
-            name='PropertyPluginModel',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('plugin_identifier', models.CharField(max_length=255)),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='Group',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('name', models.TextField(verbose_name='Group name')),
-                ('public', models.BooleanField(default=False, verbose_name='Public Group')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
-                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
-                ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_group',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
-        ),
-        migrations.CreateModel(
-            name='JobLog',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('task_id', models.UUIDField(unique=True)),
-                ('job_name', models.TextField()),
-                ('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
-                ('done_at', models.DateTimeField(blank=True, default=None, null=True)),
-                ('task_result', models.TextField(blank=True, default=None, null=True)),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='Package',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
-                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
-            ],
-            options={
-                'swappable': 'EPDB_PACKAGE_MODEL',
-            },
-        ),
-        migrations.CreateModel(
-            name='Node',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('depth', models.IntegerField(verbose_name='Node depth')),
-                ('stereo_removed', models.BooleanField(default=False)),
-                ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
-                ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
-                ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='end_nodes',
-            field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='start_nodes',
-            field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
-        ),
-        migrations.CreateModel(
-            name='SequentialRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.CreateModel(
-            name='Pathway',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('predicted', models.BooleanField(default=False)),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.CreateModel(
-            name='Reaction',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
-                ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
-                ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
-                ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='EnzymeLink',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('ec_number', models.TextField(verbose_name='EC Number')),
-                ('classification_level', models.IntegerField(verbose_name='Classification Level')),
-                ('linking_method', models.TextField(verbose_name='Linking Method')),
-                ('edge_evidence', models.ManyToManyField(to='epdb.edge')),
-                ('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
-                ('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='edge_label',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
-        ),
-        migrations.CreateModel(
-            name='Scenario',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('scenario_date', models.CharField(default='No date', max_length=256)),
-                ('scenario_type', models.CharField(default='Not specified', max_length=256)),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='reaction',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compoundstructure',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.CreateModel(
-            name='Setting',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('public', models.BooleanField(default=False)),
-                ('global_default', models.BooleanField(default=False)),
-                ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
-                ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
-                ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
-                ('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
-                ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
-                ('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='setting',
-            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_setting',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
-        ),
-        migrations.CreateModel(
-            name='EnviFormer',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='MLRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='model',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='app_domain',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='data_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='eval_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
-        ),
-        migrations.AddField(
-            model_name='propertypluginmodel',
-            name='rule_packages',
-            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
-        ),
-        migrations.CreateModel(
-            name='RuleBasedRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('multigen_eval', models.BooleanField(default=False)),
-                ('min_count', models.IntegerField(default=10)),
-                ('max_count', models.IntegerField(default=0)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='ExternalIdentifier',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('object_id', models.IntegerField()),
-                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
-                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
-                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
-                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
-            ],
-            options={
-                'verbose_name': 'External Identifier',
-                'verbose_name_plural': 'External Identifiers',
-                'db_table': 'epdb_external_identifier',
-                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
-                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
-            },
-        ),
-        migrations.CreateModel(
-            name='SimpleAmbitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('smirks', models.TextField(verbose_name='SMIRKS')),
-                ('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
-                ('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRDKitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SequentialRuleOrdering',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('order_index', models.IntegerField()),
-                ('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
-                ('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
-            ],
-        ),
-        migrations.AddField(
-            model_name='sequentialrule',
-            name='simple_rules',
-            field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
-        ),
-        migrations.CreateModel(
-            name='ParallelRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-                ('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.AlterUniqueTogether(
-            name='compound',
-            unique_together={('uuid', 'package')},
-        ),
-        migrations.CreateModel(
-            name='AdditionalInformation',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('type', models.TextField(verbose_name='Additional Information Type')),
-                ('data', models.JSONField(blank=True, default=dict, null=True)),
-                ('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
-                ('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
-                ('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
-            ],
-            options={
-                'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
-                'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
-            },
-        ),
-        migrations.CreateModel(
-            name='GroupPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
-            ],
-            options={
-                'unique_together': {('package', 'group')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('package', 'user')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserSettingPermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('setting', 'user')},
-            },
-            bases=('epdb.permission',),
         ),
     ]

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

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

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/models.py

@@ -204,7 +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"
     )
@@ -868,25 +867,18 @@ class Compound(
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
-        subclasses = CompoundStructure.__subclasses__()
-
-        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
-
         # Check if we find a direct match for a given SMILES
-        if qs.exists():
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            return qs.first().compound
+            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
-
-
-        qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
-        if qs.exists():
+        if CompoundStructure.objects.filter(
+            smiles=standardized_smiles, compound__package=package
+        ).exists():
             # TODO should we add a structure?
-            return qs.first().compound
+            return CompoundStructure.objects.get(
+                smiles=standardized_smiles, compound__package=package
+            ).compound
 
         # Generate Compound
         c = Compound()
@@ -2186,6 +2178,56 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
+    def update_depths(self):
+        # Collect number of in and out links per node
+        in_count = defaultdict(lambda: 0)
+        out_count = defaultdict(lambda: 0)
+
+        for e in self.edges:
+            for react in e.start_nodes.all():
+                out_count[str(react.uuid)] += 1
+
+            for prod in e.end_nodes.all():
+                in_count[str(prod.uuid)] += 1
+
+        depth_map = {}
+        depth_map[0] = list()
+
+        for n in self.nodes:
+            num_parents = in_count[str(n.uuid)]
+            if num_parents == 0:
+                # must be a root node or unconnected node
+                if n.depth != 0:
+                    n.depth = 0
+                    n.save()
+
+                # Only root node may have children
+                if out_count[str(n.uuid)] > 0:
+                    depth_map[0].append(n)
+
+        # At most depth len(nodes) is possible
+        for i in range(self.nodes.count()):
+            level_nodes = depth_map.get(i, [])
+
+            if len(level_nodes) == 0:
+                break
+
+            unique_next_level = set()
+            for n in level_nodes:
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            unique_next_level.add(p)
+
+            if len(unique_next_level) > 0:
+                depth_map[i + 1] = list(unique_next_level)
+
+        for depth, nodes in depth_map.items():
+            for n in nodes:
+                if n.depth != depth:
+                    n.depth = depth
+                    n.save()
+
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(

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:

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:
+        n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
-            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
+        if n_threads > 1:
+            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

static/images/bayer-logo.svg

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

templates/actions/objects/pathway.html

@@ -9,14 +9,6 @@
       <i class="glyphicon glyphicon-plus"></i> Add Compound</a
     >
   </li>
-  <li>
-    <a
-      class="button"
-      onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Add PES</a
-    >
-  </li>
   <li>
     <a
       class="button"

templates/components/navbar.html

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

templates/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

@@ -77,7 +77,6 @@
 
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
-    {% include "modals/objects/add_pathway_pes_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 %}

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS
+from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -473,17 +473,12 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            first_order = get_parameter_or_empty_string(request, "firstOrder")
+            # first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if first_order != "":
+            if model:
-                if model != "":
+                model = HalfLifeModel(model.upper())
-                    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")
 
             return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
 
@@ -508,6 +503,10 @@ def build_additional_information_from_request(request, type_):
             comment_ws = get_parameter_or_empty_string(request, "comment_ws")
             source_ws = get_parameter_or_empty_string(request, "source_ws")
             model_ws = get_parameter_or_empty_string(request, "model_ws")
+
+            if model_ws:
+                model_ws = HalfLifeModel(model_ws.upper())
+
             fit_ws = get_parameter_or_empty_string(request, "fit_ws")
 
             dt50_total = IntervalParser.from_string(hl_ws_total)

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#0a608c85c73a6ef5c38afea87d2b57fb43f01a70" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#676dae1c5678539beac637b87e49b9dadfdfd85a" }
 dependencies = [
     { name = "pydantic" },
 ]
@@ -2763,9 +2763,9 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform != 'linux' and sys_platform != 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54", upload-time = "2025-10-01T23:35:50Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58", upload-time = "2025-10-01T23:35:52Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390", upload-time = "2025-10-01T23:35:55Z" },
 ]
 
 [[package]]
@@ -2785,19 +2785,19 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5", upload-time = "2025-10-01T23:33:41Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d", upload-time = "2025-10-01T23:33:45Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e", upload-time = "2025-10-01T23:33:48Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d", upload-time = "2025-10-01T23:33:52Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434", upload-time = "2025-10-01T23:34:10Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d" },
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 ]
 
 [[package]]