wip

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
       - id: trailing-whitespace
         exclude: epiuclid/schemas/
       - id: end-of-file-fixer
-        exclude: ^epiuclid/schemas/|^static/js/ketcher3/
+        exclude: epiuclid/schemas/
       - id: check-yaml
       - id: check-added-large-files
-        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/|^static/js/ketcher3/
+        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3

Dockerfile

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

bayer/admin.py

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

bayer/apps.py

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

bayer/epdb_hooks.py

@@ -0,0 +1,39 @@
+import logging
+
+from epdb.template_registry import register_template
+
+logger = logging.getLogger(__name__)
+
+# PES Create
+register_template(
+    "epdb.actions.collections.compound",
+    "actions/collections/new_pes.html",
+)
+register_template(
+    "modals.collections.compound",
+    "modals/collections/new_pes_modal.html",
+)
+register_template(
+    "epdb.actions.objects.pathway.add",
+    "actions/objects/pathway_add_pes.html",
+)
+register_template(
+    "epdb.modals.objects.pathway.add",
+    "modals/objects/add_pathway_pes_node_modal.html"
+)
+
+# PES Viz
+register_template(
+    "epdb.objects.compound.viz",
+    "objects/compound_viz.html",
+)
+
+register_template(
+    "epdb.objects.compound_structure.viz",
+    "objects/compound_structure_viz.html",
+)
+
+register_template(
+    "epdb.objects.node.viz",
+    "objects/node_viz.html",
+)

bayer/migrations/0001_initial.py

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

bayer/migrations/0002_initial.py

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

bayer/migrations/0003_pescompound_pesstructure_package_data_pool.py

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

bayer/models.py

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

bayer/templates/actions/collections/new_pes.html

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

bayer/templates/actions/objects/pathway_add_pes.html

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

bayer/templates/modals/collections/new_package_modal.html

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

bayer/templates/modals/collections/new_pes_modal.html

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

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

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

bayer/templates/objects/compound_structure_viz.html

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

bayer/templates/objects/compound_viz.html

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

bayer/templates/objects/node_viz.html

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

bayer/templates/objects/package.html

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

bayer/templates/static/login.html

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

bayer/tests.py

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

bayer/urls.py

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

bayer/views.py

@@ -0,0 +1,163 @@
+import base64
+
+import requests
+from django.conf import settings as s
+from django.core.exceptions import BadRequest
+from django.http import HttpResponse
+from django.shortcuts import redirect
+
+from bayer.models import PESCompound
+from epdb.logic import PackageManager
+from epdb.models import Pathway, Node
+from epdb.views import _anonymous_or_real
+from utilities.decorators import package_permission_required
+
+Package = s.GET_PACKAGE_MODEL()
+
+
+@package_permission_required()
+def create_pes(request, package_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+
+    if request.method == "POST":
+
+        if current_package.classification_level == Package.Classification.INTERNAL:
+            raise BadRequest("Cannot create PESs for internal packages.")
+
+        compound_name = request.POST.get('compound-name')
+        compound_description = request.POST.get('compound-description')
+        pes_link = request.POST.get('pes-link')
+
+        if pes_link:
+            try:
+                pes_data = fetch_pes(request, pes_link)
+            except ValueError as e:
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return BadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
+
+            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
+
+            return redirect(pes.url)
+        else:
+            return BadRequest("Please provide a PES link.")
+    else:
+        pass
+
+
+@package_permission_required()
+def create_pes_node(request, package_uuid, pathway_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+
+    if request.method == "POST":
+
+        if current_package.classification_level == Package.Classification.INTERNAL:
+            raise BadRequest("Cannot create PESs for internal packages.")
+
+        compound_name = request.POST.get('compound-name')
+        compound_description = request.POST.get('compound-description')
+        pes_link = request.POST.get('pes-link')
+
+        if pes_link:
+            try:
+                pes_data = fetch_pes(request, pes_link)
+            except ValueError as e:
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+
+                if current_package.classification_level != Package.Classification.SECRET:
+                    return BadRequest("Cannot create PESs for non-secret packages.")
+
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return BadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
+
+            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
+
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
+            if node_qs.exists():
+                return redirect(current_pathway.url)
+
+            n = Node()
+            n.stereo_removed = False
+            n.pathway = current_pathway
+            n.depth = 0
+
+            n.default_node_label = pes.default_structure
+            n.save()
+
+            n.node_labels.add(pes.default_structure)
+            n.save()
+
+            return redirect(current_pathway.url)
+
+        else:
+            return BadRequest("Please provide a PES link.")
+    else:
+        pass
+
+
+def fetch_pes(request, pes_url) -> dict:
+    from epauth.views import get_access_token_from_request
+    token = get_access_token_from_request(request)
+
+    if token:
+        for k, v in s.PES_API_MAPPING.items():
+            if pes_url.startswith(k):
+                pes_id = pes_url.split('/')[-1]
+
+                if pes_id == 'dummy':
+                    import json
+                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
+                    res_data["pes_url"] = pes_url
+                    return res_data
+                else:
+                    headers = {"Authorization": f"Bearer {token['access_token']}"}
+                    params = {"pes_reg_entity_corporate_id": pes_id}
+
+                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
+
+                    try:
+                        res.raise_for_status()
+                        pes_data = res.json()
+
+                        if len(pes_data) == 0:
+                            raise ValueError(f"PES with id {pes_id} not found")
+
+                        res_data = pes_data[0]
+                        res_data["pes_url"] = pes_url
+                        return res_data
+
+                    except requests.exceptions.HTTPError as e:
+                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+        else:
+            raise ValueError(f"Unknown URL {pes_url}")
+    else:
+        raise ValueError("Could not fetch access token from request.")
+
+
+def visualize_pes(request):
+    pes_link = request.GET.get('pesLink')
+
+    if pes_link:
+        pes_data = fetch_pes(request, pes_link)
+
+        representations = pes_data.get('representations')
+
+        for rep in representations:
+            if rep.get('type') == 'color':
+                image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
+                return HttpResponse(image_data, content_type="image/png")

bb4g/__init__.py

@@ -0,0 +1,183 @@
+import json
+import math
+from datetime import datetime
+from typing import List
+import enum
+import requests
+from django.conf import settings as s
+from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import register
+
+from bridge.contracts import Classifier  # noqa: I001
+from bridge.dto import (
+    BuildResult,
+    EnviPyDTO,
+    EvaluationResult,
+    RunResult,
+    TransformationProductPrediction,
+)  # noqa: I001
+
+class SamplingAlgorithm(enum.Enum):
+    EXACT = "exact"
+
+
+@register("bb4gconfig")
+class BB4GConfig(EnviPyModel):
+    sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
+    cutoff: int = -5
+
+    class UI:
+        title = "BB4G Configuration"
+        sampling_algorithm = UIConfig(
+            widget=WidgetType.SELECT,
+            label="BB4G Sampling Algorithm",
+            order=1,
+            placeholder="If unset defaults to 'exact'"
+        )
+        cutoff = UIConfig(
+            widget=WidgetType.NUMBER,
+            label="BB4G Cutoff",
+            order=2,
+            placeholder="If unset defaults to -5"
+        )
+
+
+# Once stable these will be exposed by enviPy-plugins lib
+class BB4G(Classifier):
+    Config = BB4GConfig
+
+    def __init__(self, config: BB4GConfig | None = None):
+        super().__init__(config)
+        self.url = f"{s.BB4G_URL}"
+
+        self.token = self.acquire_token()
+        self.header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+    def acquire_token(self):
+        BB4G_TENANT_ID = s.BB4G_TENANT_ID
+        BB4G_CLIENT_ID = s.BB4G_CLIENT_ID
+        BB4G_CLIENT_SECRET = s.BB4G_CLIENT_SECRET
+        BB4G_SCOPE = s.BB4G_SCOPE
+
+        BB4G_TOKEN_URL = f"https://login.microsoftonline.com/{BB4G_TENANT_ID}/oauth2/v2.0/token"
+
+        payload = {
+            "client_id": BB4G_CLIENT_ID,
+            "client_secret": BB4G_CLIENT_SECRET,
+            "scope": BB4G_SCOPE,
+            "grant_type": "client_credentials"
+        }
+
+        # No Proxy required, URL is whitelisted
+        res = requests.post(BB4G_TOKEN_URL, data=payload)
+
+        res.raise_for_status()
+
+        return res.json()["access_token"]
+
+    def start(self):
+        header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+        started = False
+        retries = 0
+        while not started and retries < 5:
+            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
+
+            if res.status_code == 200:
+                started = True
+            elif res.status_code in [500, 502]:
+                retries += 1
+                import time
+                time.sleep(5)
+            else:
+                raise ValueError(f"Unexpected status code: {res.status_code}")
+
+    @classmethod
+    def requires_rule_packages(cls) -> bool:
+        return False
+
+    @classmethod
+    def requires_data_packages(cls) -> bool:
+        return False
+
+    @classmethod
+    def identifier(cls) -> str:
+        return "bb4g"
+
+    @classmethod
+    def name(cls) -> str:
+        return "BB4G Template Free Model"
+
+    @classmethod
+    def display(cls) -> str:
+        return "BB4G Template Free Model"
+
+    def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
+        return
+
+    def run(self, eP: EnviPyDTO, *args, **kwargs) -> RunResult:
+
+        # Ensure Service is running
+        self.start()
+
+        smiles = [c.smiles for c in eP.get_compounds()]
+        preds = self._post(smiles)
+
+        results = []
+
+        for substrate in preds.keys():
+            results.append(
+                TransformationProductPrediction(
+                    substrate=substrate,
+                    products=preds[substrate],
+                )
+            )
+
+        return RunResult(
+            producer=eP.get_context().url,
+            description=f"Generated at {datetime.now()}",
+            result=results,
+        )
+
+    def evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
+        pass
+
+    def build_and_evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
+        pass
+
+    def _post(self, smiles: List[str]) -> dict[str, dict[str, float]]:
+        header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+        result = {}
+
+        for smi in smiles:
+            data = {
+                "smiles": smi,
+                "sampling_alg": self.config.sampling_algorithm.value,
+                "cutoff": self.config.cutoff,
+            }
+
+            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
+
+            resp.raise_for_status()
+
+            for substrate, predictions in resp.json().items():
+                preds = {}
+
+                for pred in predictions:
+                    prod = pred["prediction"]
+                    prob = math.exp(pred["log_likelihood"])
+                    preds[prod] = prob
+
+                result[substrate] = preds
+
+        return result

bridge/contracts.py

@@ -261,6 +261,7 @@ class Classifier(Plugin):
             for k, v in data.items():
                 if v != "":
                     cpy[k] = v
+
         return cls.Config(**cpy)
 
     @classmethod

docker-compose.dev.yml

@@ -1,26 +1,54 @@
 services:
   db:
     image: postgres:18
-    container_name: envipath-postgres
+    container_name: eppostgres
     environment:
-      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: envipath
+      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_DB: ${POSTGRES_DB}
     ports:
       - "5432:5432"
     volumes:
-      - postgres_data:/var/lib/postgresql
+      - ep_bayer_postgres_data:/var/lib/postgresql
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready -U postgres"]
+      test: [ "CMD-SHELL", "pg_isready -U postgres" ]
       interval: 5s
       timeout: 5s
       retries: 5
 
   redis:
     image: redis:7-alpine
-    container_name: envipath-redis
+    container_name: epredis
     ports:
       - "6379:6379"
+    volumes:
+      - ep_bayer_redis_data:/data
+
+  biotransformer3:
+    image: envipath/biotransformer3:1.0
+    container_name: epbiotransformer3
+
+#  web:
+#    image: envipath/envipy-bayer:1.0
+#    container_name: epdjango
+#    ports:
+#      - "127.0.0.1:8000:8000"
+#    env_file:
+#      - .env
+#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
+#    volumes:
+#      - ep_bayer_data:/opt/enviPy/
+
+  celery_worker:
+    image: envipath/envipy-bayer:1.0
+    container_name: epcelery
+    env_file:
+      - .env.dev
+    command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
+    volumes:
+      - ep_bayer_data:/opt/enviPy/
 
 volumes:
-  postgres_data:
+  ep_bayer_postgres_data:
+  ep_bayer_redis_data:
+  ep_bayer_data:

docker-compose.yml

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

envipath/settings.py

@@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
-
+import json
 import os
 from pathlib import Path
 
@@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -143,6 +143,12 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
         "TEMPLATE": os.environ["TEMPLATE_DB"],
     }
 
+CACHES = {
+    "default": {
+        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
+        "LOCATION": "unique-snowflake",
+    }
+}
 
 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@@ -442,3 +448,48 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
+
+# PES
+PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
+if PES_API_MAPPING:
+    import json
+    PES_API_MAPPING = json.loads(PES_API_MAPPING)
+else:
+    PES_API_MAPPING = {}
+
+# Entra Groups
+ENTRA_GROUPS = os.environ.get("ENTRA_GROUPS", None)
+if ENTRA_GROUPS:
+    import json
+    ENTRA_GROUPS = json.loads(ENTRA_GROUPS)
+else:
+    ENTRA_GROUPS = {}
+
+ENTRA_SECRET_GROUPS = os.environ.get("ENTRA_SECRET_GROUPS", None)
+if ENTRA_SECRET_GROUPS:
+    import json
+    ENTRA_SECRET_GROUPS = json.loads(ENTRA_SECRET_GROUPS)
+else:
+    ENTRA_SECRET_GROUPS = {}
+
+# PES Data Pools vs Entra Mapping
+DATA_POOL_MAPPING = os.environ.get("DATA_POOL_MAPPING", None)
+if DATA_POOL_MAPPING:
+    import json
+    DATA_POOL_MAPPING = json.loads(DATA_POOL_MAPPING)
+else:
+    DATA_POOL_MAPPING = {}
+
+PROXIES = {}
+if os.environ.get("HTTP_PROXY"):
+    PROXIES["http"] = os.environ.get("HTTP_PROXY")
+    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
+
+# BB4g
+BB4G_URL = os.environ.get("BB4G_URL")
+BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
+BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
+BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
+BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
+
+os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

epapi/tests/v1/test_api_permissions.py

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

epapi/tests/v1/test_contract_get_entities.py

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

epauth/urls.py

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

epauth/views.py

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

epdb/exceptions.py

@@ -1,10 +0,0 @@
-class InvalidSMILESException(Exception):
-    pass
-
-
-class InvalidMolfileException(Exception):
-    pass
-
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -1,17 +1,20 @@
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
+import jwt
 import nh3
+import requests
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
+from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
+from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
-from ninja.security import SessionAuth
+from ninja.security import HttpBearer
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
-
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -46,6 +49,26 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
+def get_cached_jwks(tenant_id: str, force=False) -> Dict:
+    """Get JWKS using Django cache"""
+    cache_key = f"jwks_{tenant_id}"
+
+    jwks = cache.get(cache_key)
+
+    if jwks is None or force:
+        # Cache miss, fetch new keys
+        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
+        response = requests.get(jwks_uri)
+        response.raise_for_status()
+
+        jwks = response.json()
+
+        # Cache for 1 hour (3600 seconds)
+        cache.set(cache_key, jwks, 3600)
+
+    return jwks
+
+
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -59,7 +82,52 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-router = Router(auth=SessionAuth(csrf=False))
+def validate_token(token: str) -> dict:
+    TENANT_ID = s.MS_ENTRA_TENANT_ID
+    CLIENT_ID = s.MS_ENTRA_CLIENT_ID
+
+    jwks = get_cached_jwks(TENANT_ID)
+
+    header = jwt.get_unverified_header(token)
+
+    public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
+        next(k for k in jwks["keys"] if k["kid"] == header["kid"])
+    )
+
+    # Handle V1 and V2 tokens
+    try:
+        claims = jwt.decode(
+            token,
+            public_key,
+            algorithms=["RS256"],
+            audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
+            issuer=[
+                f"https://sts.windows.net/{TENANT_ID}/",
+                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
+            ]
+        )
+    except Exception as e:
+        raise ValueError(f"Token verification failed! - {e}")
+
+    return claims
+
+
+class MSBearerTokenAuth(HttpBearer):
+
+    def authenticate(self, request, token):
+        if token is None:
+            return None
+
+        claims = validate_token(token)
+
+        if not User.objects.filter(uuid=claims['oid']).exists():
+            return None
+
+        request.user = User.objects.get(uuid=claims['oid'])
+        return request.user
+
+
+router = Router(auth=MSBearerTokenAuth())
 
 
 class Error(Schema):
@@ -153,21 +221,6 @@ class SimpleModel(SimpleObject):
     identifier: str = "relative-reasoning"
 
 
-################
-# Login/Logout #
-################
-@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
-def login(request, loginusername: Form[str], loginpassword: Form[str]):
-    from django.contrib.auth import authenticate, login
-
-    email = User.objects.get(username=loginusername).email
-    user = authenticate(username=email, password=loginpassword)
-    if user:
-        login(request, user)
-        return user
-    else:
-        return 403, {"message": "Invalid username and/or password"}
-
 
 ########
 # User #
@@ -791,10 +844,10 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
-    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
+    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -805,14 +858,29 @@ def create_package_compound(
 ):
     try:
         p = get_package_for_write(request.user, package_uuid)
-        c = Compound.create(
-            p,
-            c.compoundSmiles,
-            molfile=c.compoundMolFile,
-            name=c.compoundName,
-            description=c.compoundDescription,
-            inchi=c.inchi,
-        )
+        # inchi is not used atm
+
+        if c.pesLink is not None:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, c.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
+
+            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
+        else:
+            c = Compound.create(
+                p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+            )
         return redirect(c.url)
     except ValueError as e:
         return 400, {"message": str(e)}
@@ -1615,13 +1683,13 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
-    idreact: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, str]] = []
-    smiles: str = Field(None, alias="smiles")
+    proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
+    smiles: str = Field(None, alias="default_node_label.smiles")
     pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
@@ -1635,10 +1703,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1890,34 +1972,68 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
-    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
+    pesLink: str | None = None
 
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 403: Error},
+    response={200: str | Any, 400: Error, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(float(n.nodeDepth))
-        else:
-            node_depth = -1
+        # TODO Code Dup from bayer.views
 
-        node = Node.create(
-            pw,
-            n.nodeAsSmiles,
-            node_depth,
-            molfile=n.nodeAsMolFile,
-            name=n.nodeName,
-            description=n.nodeReason,
-        )
+        if n.pesLink:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, n.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+
+                if p.classification_level != Package.Classification.SECRET:
+                    return 400, "Cannot create PESs for non-secret packages."
+
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
+
+            c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
+
+            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
+            if node_qs.exists():
+                return redirect(pw.url)
+
+            node = Node()
+            node.stereo_removed = False
+            node.pathway = pw
+            node.depth = 0
+
+            node.default_node_label = c.default_structure
+            node.save()
+
+            node.node_labels.add(c.default_structure)
+            node.save()
+        else:
+            if n.nodeDepth is not None and n.nodeDepth.strip() != "":
+                node_depth = int(n.nodeDepth)
+            else:
+                node_depth = -1
+
+            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
         return redirect(node.url)
     except ValueError:
@@ -2029,13 +2145,16 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
+        subclasses = CompoundStructure.__subclasses__()
+
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -2046,7 +2165,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -2268,26 +2388,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@router.post("/util", response={200: Any, 403: Error})
-def predict(request, np: Form[NonPersistent]):
-    try:
-        from epdb.logic import SPathway
-
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
-        spw.predict()
-        return spw.to_json()
-    except ValueError:
-        return 403, {
-            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -7,6 +7,7 @@ import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
+from django.db.models import QuerySet
 from pydantic import ValidationError
 
 from epdb.models import (
@@ -364,6 +365,14 @@ class PackageManager(object):
 
         groups = GroupManager.get_groups(user)
 
+        # EDIT START
+
+        if package.classification_level == Package.Classification.SECRET:
+            if package.data_pool not in groups:
+                return False
+
+        # EDIT END
+
         perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
 
         valid_perms = perms.get(permission)
@@ -406,6 +415,7 @@ class PackageManager(object):
         try:
             p = Package.objects.get(uuid=package_id)
             if PackageManager.readable(user, p):
+                p = PackageManager.check_package_classification(user, p)
                 return p
             else:
                 # FIXME: use custom exception to be translatable to 403 in API
@@ -415,6 +425,37 @@ class PackageManager(object):
         except Package.DoesNotExist:
             raise ValueError("Package with ID {} does not exist!".format(package_id))
 
+    # EDIT START
+
+    @staticmethod
+    def check_package_classification(user, pack: Package):
+        if pack.classification_level == Package.Classification.SECRET:
+            if pack.data_pool.user_member.filter(id=user.id).exists():
+                return pack
+
+            raise ValueError("Package is secret and not accessible to user!")
+
+        else:
+            return pack
+
+
+    @staticmethod
+    def check_package_classifications(user, package_qs: QuerySet[Package]):
+        non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
+        secret = package_qs.filter(classification_level=Package.Classification.SECRET)
+
+        # TODO we should be able to do via the db
+        accessible_secret = []
+
+        for s_package in secret:
+            if s_package.data_pool.user_member.filter(id=user.id).exists():
+                accessible_secret.append(s_package.pk)
+
+        # Cannot combine a unique query with a non-unique query -> we have to call distinct
+        return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
+
+    # EDIT END
+
     @staticmethod
     def get_all_readable_packages(user, include_reviewed=False):
         # UserPermission only exists if at least read is granted...
@@ -441,6 +482,10 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
+
         return qs
 
     @staticmethod
@@ -487,11 +532,11 @@ class PackageManager(object):
 
         qs = qs.distinct()
 
-        return qs
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
 
-    @staticmethod
-    def get_packages():
-        return Package.objects.all()
+        return qs
 
     @staticmethod
     @transaction.atomic
@@ -596,6 +641,25 @@ class PackageManager(object):
         else:
             pack.reviewed = False
 
+        # EDIT START
+        if data.get("classification"):
+            if data["classification"] == "INTERNAL":
+                pack.classification = Package.Classification.RESTRICTED
+            elif data["classification"] == "RESTRICTED":
+                pack.classification = Package.Classification.RESTRICTED
+            elif data["classification"] == "SECRET":
+                pack.classification = Package.Classification.SECRET
+
+                if not "datapool" in data:
+                    raise ValueError("Missing datapool in package")
+
+                g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
+                pack.data_pool = g
+            else:
+                raise ValueError(f"Invalid classification {data['classification']}")
+
+        # EDIT END
+
         pack.description = data["description"]
         pack.save()
 
@@ -681,7 +745,13 @@ class PackageManager(object):
             default_structure = None
 
             for structure in compound["structures"]:
-                struc = CompoundStructure()
+                if structure.get("pesLink"):
+                    from bayer.models import PESStructure
+                    struc = PESStructure()
+                    struc.pes_link = structure["pesLink"]
+                else:
+                    struc = CompoundStructure()
+
                 # struc.object_url = Command.get_id(structure, keep_ids)
                 struc.compound = comp
                 struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@@ -1008,8 +1078,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1826,12 +1898,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

@@ -99,15 +99,11 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner, all_envipath_user_group):
-        p = PackageManager.import_legacy_package(
+    def import_package(self, data, owner):
+        return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
-        PackageManager.grant_read(owner, p, all_envipath_user_group)
-
-        return p
-
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -202,7 +198,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin, g)
+            imported_package = self.import_package(package_data, admin)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0001_initial.py

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

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

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

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

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

epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py

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

epdb/migrations/0005_alter_group_group_member.py

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

epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py

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

epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py

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

epdb/migrations/0008_enzymelink.py

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

epdb/migrations/0009_joblog.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/migrations/0012_node_stereo_removed_pathway_predicted.py

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

epdb/migrations/0013_setting_expansion_schema.py

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

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

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

epdb/migrations/0015_user_is_reviewer.py

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

epdb/migrations/0016_remove_enviformer_model_status_and_more.py

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

epdb/migrations/0017_additionalinformation.py

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

epdb/migrations/0018_auto_20260220_1203.py

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

epdb/migrations/0019_remove_scenario_additional_information_and_more.py

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

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

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

epdb/migrations/0027_alter_compound_aliases_and_more.py

@@ -1,150 +0,0 @@
-# Generated by Django 6.0.3 on 2026-07-01 20:59
-
-import django.contrib.postgres.fields
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0026_auto_20260602_1718"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="compound",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="default_structure",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                related_name="compound_default_structure",
-                to="epdb.compoundstructure",
-                verbose_name="Default Structure",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="edge_label",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                to="epdb.reaction",
-                verbose_name="Edge label",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="medline_references",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(),
-                blank=True,
-                null=True,
-                verbose_name="Medline References",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="rules",
-            field=models.ManyToManyField(
-                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-    ]

epdb/models.py

@@ -31,10 +31,6 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import (
-    InvalidMolfileException,
-    InvalidSMILESException,
-)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -208,6 +204,7 @@ class Group(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name="Group name")
     owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name="Public Group", default=False)
+    secret = models.BooleanField(verbose_name="Secret Group", default=False)
     description = models.TextField(
         blank=False, null=False, verbose_name="Descriptions", default="no description"
     )
@@ -635,7 +632,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -658,9 +655,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -786,19 +781,12 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.SET_NULL,
+        on_delete=models.CASCADE,
         null=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
-    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
-        for struct in self.structures.all():
-            if struct.smiles == smiles:
-                return struct
-
-        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
-
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -867,73 +855,47 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
-        smiles: str,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
-        *args,
-        **kwargs,
+        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles.strip() == "":
-            raise InvalidSMILESException("SMILES is required")
+            raise ValueError("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise InvalidSMILESException("Given SMILES is invalid")
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            raise ValueError("Given SMILES is invalid")
 
         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():
-            found_structure = qs.first()
-            found_compound = found_structure.compound
+            return qs.first().compound
 
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
 
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
+        if subclasses:
+            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
         if qs.exists():
-            found_structure = qs.first()
-            found_compound = found_structure.compound
-
-            # We've only found the standardized one, create the very structure
-            _ = found_compound.add_structure(
-                smiles, molfile=molfile, name=name, description=description
-            )
-
-            if name:
-                found_compound.add_alias(name)
-
-            return found_compound
+            # TODO should we add a structure?
+            return qs.first().compound
 
         # Generate Compound
         c = Compound()
         c.package = package
 
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -957,12 +919,7 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c,
-            smiles,
-            molfile=molfile,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized,
+            c, smiles, name=name, description=description, normalized_structure=is_standardized
         )
 
         c.default_structure = cs
@@ -975,22 +932,11 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
-        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -1010,28 +956,16 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
-            return found_cs
+        if CompoundStructure.objects.filter(
+            smiles__in=smiles, compound__package=self.package
+        ).exists():
+            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
 
         cs = CompoundStructure.create(
-            self,
-            smiles,
-            name=name,
-            molfile=molfile,
-            description=description,
-            normalized_structure=is_standardized,
+            self, smiles, name=name, description=description, normalized_structure=is_standardized
         )
 
         if default_structure:
@@ -1212,42 +1146,10 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound,
-        smiles: str,
-        molfile: str = None,
-        name: str = None,
-        description: str = None,
-        *args,
-        **kwargs,
+        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
-        # Clean for potential XSS
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
-
-            if name:
-                found_cs.add_alias(name)
-
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
-            return found_cs
+            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
@@ -1255,18 +1157,13 @@ class CompoundStructure(
         cs = CompoundStructure()
         # Clean for potential XSS
         if name is not None:
-            cs.name = name
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
+        if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.compound = compound
         cs.smiles = smiles
-
-        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
-        if molfile is not None:
-            cs.molfile = molfile
+        cs.compound = compound
 
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
@@ -1285,8 +1182,6 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
-        if self.molfile is not None and self.molfile.strip() != "":
-            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1484,9 +1379,6 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1498,17 +1390,14 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-
-            found_rule = query.first()
-
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
+            return query.first()
 
         r = SimpleAmbitRule()
         r.package = package
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1641,9 +1530,6 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         # Deduplication check
         query = ParallelRule.objects.annotate(
             srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@@ -1655,19 +1541,15 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(
-                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
-                )
-
-            found_rule = existing_rule_qs.first()
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
+                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+            return existing_rule_qs.first()
 
         r = ParallelRule()
         r.package = package
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1736,15 +1618,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1761,12 +1638,8 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = False,
+        multi_step: bool = True,
     ):
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         _educts = []
         _products = []
 
@@ -1821,21 +1694,14 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-
-            found_reaction = existing_reaction_qs.first()
-
-            if name:
-                found_reaction.add_alias(name)
-
-            return found_reaction
+            return existing_reaction_qs.first()
 
         r = Reaction()
         r.package = package
 
-        if name is None or name == "":
-            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
-
-        r.name = name
+        # Clean for potential XSS
+        if name is not None and name.strip() != "":
+            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -2071,7 +1937,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
-                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -2081,7 +1946,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
-                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -2089,7 +1953,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
-                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -2100,7 +1963,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
-                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2310,12 +2172,11 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
-        depth: int = -1,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
+        depth: Optional[int] = 0,
     ):
-        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
+        return Node.create(self, smiles, depth, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2344,25 +2205,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         depth_map[0] = list()
         processed = set()
 
-        data_driven_root_nodes = (
-            self.node_set.all()
-            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
-            .filter(prod_cnt=0, educt_cnt__gt=0)
-            .distinct()
-        )
-
-        # Eval QuerySet
-        root_nodes_by_depth = list(self.root_nodes)
-
-        data_driven_root_nodes.update(depth=0)
-        root_nodes = [n for n in data_driven_root_nodes]
-
-        for n in root_nodes_by_depth:
-            if n not in root_nodes:
-                if len(n.edge_products.all()) == 0:
-                    root_nodes.append(n)
-
-        for n in root_nodes:
+        for n in self.root_nodes:
             depth_map[0].append(n)
 
         # At most depth len(nodes) is possible
@@ -2411,19 +2254,17 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
-        if self.name is None or self.name == "no name":
+        if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
-            return self.name
-        else:
-            if include_suffix:
-                return f"{self.default_node_label.name} (taken from underlying structure)"
-            else:
-                return self.default_node_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.default_node_label.name} (taken from underlying structure)"
+        )
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2444,16 +2285,10 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
-                if self.default_node_label.molfile is not None
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
+                self.default_node_label.smiles, width=40, height=40
             ),
             "image_type": "svg",
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2464,7 +2299,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.get_proposed_info(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2477,60 +2311,40 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(
-            pathway.package, smiles, molfile=molfile, name=name, description=description
-        )
+        c = Compound.create(pathway.package, smiles, name=name, description=description)
 
-        structure = c.get_structure_by_smiles(smiles)
-
-        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
-            return Node.objects.get(pathway=pathway, default_node_label=structure)
+        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = structure
+        n.default_node_label = c.default_structure
         n.save()
 
-        n.node_labels.add(structure)
+        n.node_labels.add(c.default_structure)
         n.save()
 
         return n
 
     @property
     def as_svg(self):
-        if (
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
-            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.type == "OECD301FTimeSeries":
-                return ai.get().model_dump(mode="json")
+            if ai.__class__.__name__ == "OECD301FTimeSeries":
+                return ai.model_dump(mode="json")
 
         return None
 
@@ -2561,35 +2375,13 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_proposed_info(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
-            scenario__isnull=False,
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
-
-            if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
-                    ai.get().importance.value
-                )
-
-        return list(collected.values())
-
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2604,7 +2396,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2719,19 +2510,17 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
-            return self.name
-        else:
-            if include_suffix:
-                return f"{self.edge_label.name} (taken from underlying reaction)"
-            else:
-                return self.edge_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.edge_label.name} (taken from underlying reaction)"
+        )
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):

epdb/views.py

@@ -19,7 +19,6 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -389,6 +388,9 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
+            # EDIT START
+            "secret_groups": Group.objects.filter(secret=True),
+            # EDIT END
         },
     }
 
@@ -588,10 +590,38 @@ def packages(request):
                 "package-description", s.DEFAULT_VALUES["description"]
             )
 
+            # EDIT START
+            data_pool = None
+            package_classification = request.POST.get("package-classification")
+            classification = Package.Classification(int(package_classification))
+            # For SECRET we'll need a data pool which will be an additional perm check later
+            if classification == Package.Classification.SECRET:
+                package_data_pool = request.POST.get("package-data-pool")
+
+                if package_data_pool is None:
+                    return error(request, "Invalid data pool.", "Data Pool is required!")
+
+                data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
+
+                if data_pool is None:
+                    return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
+
+                if not data_pool.secret:
+                    return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
+
             created_package = PackageManager.create_package(
                 current_user, package_name, package_description
             )
 
+            created_package.classification_level = classification
+
+            # Set previously determined data pool
+            if classification == Package.Classification.SECRET:
+                created_package.data_pool = data_pool
+
+            created_package.save()
+            # EDIT END
+
             return redirect(created_package.url)
 
     elif request.method == "OPTIONS":
@@ -755,11 +785,6 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -772,14 +797,12 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
-
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
+            "EnviFormer": {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
+        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -787,9 +810,6 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
-                    "additional_parameters": v.Config.__name__.lower()
-                    if v.Config.__name__ != ""
-                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -798,6 +818,12 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
+        # Context for paginated template
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -912,12 +938,13 @@ def package_models(request, package_uuid):
                 "requires_data_packages": True,
             },
         }
+
         if s.ENVIFORMER_PRESENT:
             context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1093,11 +1120,6 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
-                        res["pred"] = sorted(
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
-
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1201,7 +1223,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -1384,18 +1408,12 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
-        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
-
         try:
             c = Compound.create(
-                current_package,
-                compound_smiles,
-                molfile=compound_molfile,
-                name=compound_name,
-                description=compound_description,
+                current_package, compound_smiles, compound_name, compound_description
             )
-        except (InvalidSMILESException, InvalidMolfileException) as e:
+        except ValueError as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1521,15 +1539,11 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
-        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles,
-                molfile=structure_molfile,
-                name=structure_name,
-                description=structure_description,
+                structure_smiles, structure_name, structure_description
             )
         except ValueError:
             return error(
@@ -1917,9 +1931,9 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reaction_smiles = request.POST.get("reaction-smiles")
-        educts = reaction_smiles.split(">>")[0].split(".")
-        products = reaction_smiles.split(">>")[1].split(".")
+        reactions_smirks = request.POST.get("reaction-smirks")
+        educts = reactions_smirks.split(">>")[0].split(".")
+        products = reactions_smirks.split(">>")[1].split(".")
 
         r = Reaction.create(
             current_package,
@@ -2100,14 +2114,12 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
-        is_predict_mode = pw_mode in {"predict", "incremental"}
-
         pw = Pathway.create(
             current_package,
-            stand_smiles if is_predict_mode else smiles,
+            stand_smiles,
             name=name,
             description=description,
-            predicted=is_predict_mode,
+            predicted=pw_mode in {"predict", "incremental"},
         )
 
         # set mode
@@ -2348,17 +2360,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
 
-        node_smiles = request.POST.get("node-smiles")
-        node_molfile = request.POST.get("node-molfile")
-
-        try:
-            current_pathway.add_node(
-                node_smiles, molfile=node_molfile, name=node_name, description=node_description
-            )
-        except InvalidSMILESException:
-            return error(
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
+        node_smiles = request.POST.get("node-smiles").strip()
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
 
         return redirect(current_pathway.url)
 
@@ -2466,26 +2469,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.name = new_node_name
-
-            if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(
-                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
-                ).strip()
-                current_node.description = new_node_description
-
-            current_node.save()
-
-            return redirect(current_node.url)
-
-        return error(request, "Node update failed!", "No changes were made to the node")
-
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 

migration/views.py

@@ -65,25 +65,6 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
-    accepted_diffs = [
-        "bt0055-3469.1",
-        "bt0056-2685",
-        "bt0193-4263",
-        "bt0231-1871.1",
-        "bt0242-3803",
-        "bt0254-4224.1",
-        "bt0254-4224.2",
-        "bt0291-1129",
-        "bt0337-3543",
-        "bt0391-4285",
-        "bt0402-3576",
-        "bt0404-3928",
-        "bt0416-4269",
-        "bt0432-4254",
-        "bt0337-4117",
-        "bt0322-3393",
-    ]
-
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -128,11 +109,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res or r.name in accepted_diffs,
+                        "status": res,
                     }
                 )
 
-                if res or r.name in accepted_diffs:
+                if res:
                     success += 1
                 else:
                     error += 1
@@ -154,16 +135,7 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
-            if r["name"] in accepted_diffs:
-                r["status"] = True
 
-        migration_status["results"] = sorted(
-            migration_status["results"], key=lambda x: (x["status"], x["name"])
-        )
-
-        num_success = sum([int(x["status"]) for x in migration_status["results"]])
-        migration_status["success"] = num_success
-        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

static/css/input.css

@@ -34,12 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-select.select[multiple] {
-  display: block;
-  white-space: normal;
-}
-
-p a {
-  @apply underline;
-}

static/images/bayer-logo.svg

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

static/js/alpine/components/widgets.js

@@ -59,9 +59,6 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
-    get isRequired() {
-      return (this.schema.required || []).indexOf(this.fieldName) > -1
-    }
   });
 
   // Text widget

static/js/alpine/pagination.js

@@ -5,126 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    })
-  );
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/ketcher2/DEVNOTES.md

@@ -0,0 +1,57 @@
+## Prerequisites
+
+   Stable [Node.js](https://nodejs.org) version
+
+## Build instructions
+
+    npm install
+    npm start
+
+For production build:
+
+    npm run build
+   
+You could also build only the style with command
+
+    npm run style
+
+## Indigo Service
+
+Ketcher uses Indigo Service for server operations.
+You can use `--api-path` parameter to start with it:
+
+    npm start -- --api-path=<server-url>
+For production build:
+
+    npm run build -- --api-path=<server-url>
+
+You can find the instruction for service installation
+[here](http://lifescience.opensource.epam.com/indigo/service/index.html).
+
+## Tests instructions
+
+You can start tests for input/output `.mol`-files and render.
+
+    npm test
+
+Tests are started for all structures in `test/fixtures` directory.
+
+To start the tests separately:
+
+    npm run test-io
+    npm run test-render
+
+#### Parameters
+
+You can use following parameters to start the tests:
+ - `--fixtures` - for the choice of a specific directory with molecules
+ - `--headless` - for start of the browser in headless mode
+
+```
+npm run test-render -- --fixtures=fixtures/super --headless
+```
+
+If you have added new structures for testing to the `test/fixtures` directory 
+you have to generate `svg` from them for correct render-test with:
+
+    npm run generate-svg    

static/js/ketcher2/LICENSE

@@ -0,0 +1,184 @@
+                               Apache License
+                         Version 2.0, January 2004
+                      http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
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+    the terms of any separate license agreement you may have executed
+    with Licensor regarding such Contributions.
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+ 6. Trademarks. This License does not grant permission to use the trade
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+ See the License for the specific language governing permissions and
+ limitations under the License.

static/js/ketcher2/LICENSE-history

@@ -0,0 +1,5 @@
+ Ketcher version 1 was released under GNU Affero General Public License v3.0
+ Ketcher version 2 was re-licensed under Apache License, Version 2.
+
+ Current version is distributed by the terms of the Apache License, Version 2.
+ which is included in the file LICENSE, found at the root of the Ketcher source tree.

static/js/ketcher2/NOTICE

@@ -0,0 +1,19 @@
+ Ketcher
+ Copyright (C) 2017 EPAM Systems
+ This product includes software developed at EPAM Systems, Inc.
+
+ In addition, this product contains dependencies on files licensed under:
+
+ The FreeBSD Documentation License https://www.freebsd.org/copyright/freebsd-doc-license.html
+ The MIT License https://opensource.org/licenses/MIT
+ X11 License http://www.xfree86.org/3.3.6/COPYRIGHT2.html
+ Academic Free License https://opensource.org/licenses/AFL-3.0
+ Apache License, Version 1.0 http://www.apache.org/licenses/LICENSE-1.0
+ Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0
+ The 2-Clause BSD License https://opensource.org/licenses/BSD-2-Clause
+ The 3-Clause BSD License https://opensource.org/licenses/BSD-3-Clause
+ ISC License (ISC) https://opensource.org/licenses/ISC
+ GNU Lesser General Public License version 2.1 https://opensource.org/licenses/LGPL-2.1
+ The Mozilla Public License https://opensource.org/licenses/MPL-1.0
+ Public Domain https://wiki.creativecommons.org/wiki/Public_domain
+ Unlicense http://unlicense.org/

static/js/ketcher2/README.md

@@ -0,0 +1,35 @@
+# EPAM Ketcher projects
+Copyright (c) 2017 EPAM Systems, Inc
+
+Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.
+
+## KEY FEATURES
+* Fast 2D structure representation that satisfies common chemical drawing standards
+* 3D structure visualization
+* Draw and edit structures using major tools: Atom Tool, Bond Tool, and Template Tool
+* Template library (including custom and user's templates)
+* Add atom and bond basic properties and query features, add aliases and Generic groups
+* Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
+* Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) and Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout) 
+* Aromatize/De-aromatize Tool
+* Calculate CIP Descriptors Tool
+* Structure Check Tool
+* MW and Structure Parameters Calculate Tool 
+* Stereochemistry support during editing, loading, and saving chemical structures
+* Storing history of actions, with the ability to rollback to previous state
+* Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
+* Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group) 
+* Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping) 
+* Flip/Rotate Tool
+* Zoom in/out, hotkeys, cut/copy/paste
+* OCR - ability to recognize structures at pictures (image files) and reproduce them
+* Copy and paste between different chemical editors
+* Settings support (Rendering, Displaying, Debugging)
+* Use of SVG to achieve best quality in-browser chemical structure rendering
+* Languages: JavaScript with third-party libraries
+
+## Build instructions
+Please read [DEVNOTES.md](DEVNOTES.md) for details.
+
+## License
+Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.

static/js/ketcher2/doc/help.md

@@ -0,0 +1,570 @@
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions.
+
+# Ketcher Overview
+
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions. Ketcher operates in two modes, the Server mode with most
+functions available and the client mode with limited functions
+available.
+
+**Ketcher** consists of the following elements:
+
+ ![](main.png "Main window")
+
+**Note** : Depending on the screen size, some tools on the _Tool
+palette_ can be displayed in expanded or collapsed forms.
+
+Using the _Tool palette_, you can
+
+  * draw and edit a molecule or reaction by clicking on and dragging
+  atoms, bonds, and other elements provided with the buttons on the
+  _Atoms_ toolbar and _Tool palette_;
+
+  * delete any element of the drawing (atom or bond) by clicking on it
+  with the Erase tool;
+
+  * delete the entire molecule or its fragment by a lasso,
+  rectangular, or fragment selection with the Erase tool;
+
+  * draw special structures (see the following sections);
+
+  * select the entire molecule or its fragment in one of the following
+  ways (click on the button to see the list of available options):
+
+    * in the expanded form
+
+      ![](expanded.png "Expanded tool")
+
+    * in the collapsed form
+
+      ![](collapsed.png "Collapsed tool")
+
+To select one atom or bond, click Lasso or Rectangle Selection tool,
+and then click the atom or bond.
+
+To select the entire structure:
+
+  * Select the Fragment Selection tool and then click the object.
+
+  * Select the Lasso or Rectangle Selection tool, and then drag the
+  mouse to select the object.
+
+  * `Ctrl-click` with the Lasso or Rectangle Selection tool.
+
+To select multiple atoms, bonds, structures, or other objects, do one
+of the following:
+
+  * `Shift-click` with the Lasso or Rectangle Selection tool selects
+  some (connected or not) atoms/bonds.
+
+  * With the Lasso or Rectangle Selection tool click and drag the
+  mouse around the atoms, bonds, or structures that you want to
+  select.
+
+**Note** : `Ctrl+Shift-click` with the Lasso or Rectangle Selection tool
+selects several structures.
+
+You can use the buttons of the _Main_ toolbar:
+
+
+ ![](toolbar.png "Tolbar")
+
+  * **Clear Canvas** (1) button to start drawing a new molecule; this
+  command clears the drawing area;
+
+  * **Open…** (2) and **Save As…** (3) buttons to import a molecule
+  from a molecular file or save it to a supported molecular file
+  format;
+
+  * **Undo** / **Redo** (4), **Cut** (5), **Copy** (6), **Paste** (7),
+  **Zoom In** / **Out** (8), and **Scaling** (9) buttons to perform
+  the corresponding actions;
+
+  * **Layout** button (10) to change the position of the structure to
+  work with it with the most convenience;
+
+  * **Clean Up** button (11) to improve the appearance of the
+  structure by assigning them uniform bond lengths and angles.
+
+  * **Aromatize** / **Dearomatize** buttons (12) to mark aromatic
+  structures (to convert a structure to the Aromatic or Kekule
+  presentation);
+
+  * **Calculate CIP** button (13) to determine R/S and E/Z
+  configurations;
+
+  * **Check Structure** button (14) to check the following properties
+  of the structure:
+
+    ![](check.png "Structure Ckeck")
+
+  * **Calculated Values** button (15) to display some properties of
+  the structure:
+
+    ![](analyse.png "Calculated Values")
+
+  * **Recognize Molecule** button (16) to recognize a structure in the
+  image file and load it to the canvas;
+
+  * **3D Viewer** button (17) to open the structure in the
+  three-dimensional Viewer;
+
+  * **Settings** button (18) to make some settings for molecular
+    files:
+    
+    ![](settings.png "Settings")
+
+  * **Help** button (19) to view Help;
+    
+  * **About** button (20) to display version and copyright information
+  of the program.
+
+**Note** : **Layout,** **Clean Up,** **Aromatize** / **Dearomatize,**
+**Calculate CIP,** **Check Structure,** **Calculated Values,**
+**Recognize Molecule** and **3D View** buttons are active only in the
+Server mode.
+
+# 3D Viewer
+
+The structure appears in a modal window after clicking on the **3D
+Viewer** button:
+
+ ![](miew.png "3D Viewer")
+
+You can perform the following actions:
+
+  * Rotate the structure holding the left mouse button;
+
+  * Zoom In/Out the structure;
+
+Ketcher Settings allow to change the appearance of the structure and background coloring.
+
+"Lines" drawing method, "Bright" atom name coloring
+method and "Light" background coloring are default.
+
+# Drawing Atoms
+
+To draw/edit atoms you can:
+
+  * select an atom in the Atoms toolbar and click inside the drawing
+  area;
+
+  * if the desired atom is absent in the toolbar, click on
+  the ![](periodic-table.png) button to invoke the Periodic Table and
+  click on the desired atom (available options: _Single_ – selection
+  of a single atom, _List_ – choose an atom from the list of selected
+  options (To allow one atom from a list of atoms of your choice at
+  that position), _Not List_ - exclude any atom on your list at that
+  position).
+
+    ![](periodic-dialog.png "Periodic Table")
+
+  * add an atom to the existing molecule by selecting an atom in the
+  _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
+  the cursor; the atom will be added with a single bond; vacant
+  valences will be filled with the corresponding number of hydrogen
+  atoms;
+
+  * change an atom by selecting an atom in the _Atoms_ toolbar and
+  clicking on the atom to be changed; in the case a wrong valence thus
+  appears the atom will be underlined in red;
+
+  * change an atom by clicking on an existing atom with the
+  _Selection_ tool and waiting for a couple of seconds for the text
+  box to appear; type another atom symbol in the text box:
+
+    ![](inline-edit.png "Change Atom")
+
+  * change the charge of an atom by selecting the Charge Plus or
+  Charge Minus tool and clicking consecutively on an atom to
+  increase/decrease its charge
+
+    ![](charge.png "Ions")
+
+  * change an atom or its properties by double-clicking on the atom to
+  invoke the Atom Properties dialog (the dialog also provides atom
+  query features):
+
+    ![](atom-dialog.png "Atom Properties")
+
+  * click on the Periodic Table button, open the Extended table and
+  select a corresponding Generic group or Special Node:
+
+    ![](periodic-dialog-ext.png "Generic Groups")
+
+# Drawing Bonds
+
+To draw/edit bonds you can:
+
+  * Click an arrow on the Bond tool ![](bond.png) in the Tools palette
+  to open the drop-down list with the following bond types:
+
+    ![](bonds.png)
+
+    For the full screen format, the Bond tool from the Tools palette
+    splits into three: _Single Bond,__Single Up Bond,_ and _Any
+    Bond_,which include the corresponding bond types:
+
+    ![](bond-types.png)
+
+  * select a bond type from the drop down list and click inside the
+  drawing area; a bond of the selected type will be drawn;
+
+  * click on an atom in the molecule; a bond of the selected type will
+  be added to the atom at the angle of 120 degrees;
+
+  * add a bond to the existing molecule by clicking on an atom in the
+  molecule and dragging the cursor; in this case you can set the angle
+  manually;
+
+  * change the bond type by clicking on it;
+
+  * use the Chain Tool ![](chain.png) to draw consecutive single
+  bonds;
+
+  * change a bond or its properties by double-clicking on the bond to
+  invoke the Bond Properties dialog:
+
+    ![](bond-dialog.png "Bond Properties")
+
+  * clicking on a drawn stereo bond changes its direction.
+
+  * clicking with the Single Bond tool or Chain tool switches the bond type
+  cyclically: Single-Double-Triple-Single.
+
+# Drawing R-Groups
+
+Use the _R-Group_ toolbox ![](rgroup.png) to draw R-groups in Markush
+structures:
+
+ ![](rgroup-types.png)
+
+Selecting the _R-Group_ _Label_ Tool and clicking on an atom in the
+structure invokes the dialog to select the R-Group label for a current
+atom position in the structure:
+
+ ![](rgroup-dialog.png)
+
+Selecting the R-Group label and clicking **OK** converts the structure
+into a Markush structure with the selected R-Group label:
+
+ ![](rgroup-example1.png)
+
+**Note** : You can choose several R-Group labels simultaneously:
+
+ ![](rgroup-example2.png)
+
+Particular chemical fragments that may be substituted for a given
+R-Group form a set of R-Group members. R-Group members can be any
+structural fragment, including functional groups and single atoms or
+atom lists.
+
+To create a set of R-Group members:
+
+  1. Draw a structure to become an R-Group member.
+
+  2. Select the structure using the _R-Group Fragment Tool_ to invoke
+     the R-Group dialog; in this dialog select the label of the
+     R-Group to assign the fragment to.
+
+  3. Click on **OK** to convert the structure into an R-Group member.
+
+An R-Group attachment point is the atom in an R-Group member fragment
+that attaches the fragment to the initial Markush structure.
+
+Selecting the _Attachment Point Tool_ and clicking on an atom in the
+R-Group fragment converts this atom into an attachment point. If the
+R-Group contains more than one attachment point, you can specify one
+of them as primary and the other as secondary. You can select between
+either the primary or secondary attachment point using the dialog that
+appears after clicking on the atom:
+
+ ![](attpoints-dialog.png)
+
+If there are two attachment points on an R-Group member, there must be
+two corresponding attachments (bonds) to the R-Group atom that has the
+same R-Group label. Clicking on **OK** in the above dialog creates the
+attachment point.
+
+Schematically, the entire process of the R-Group member creation can
+be presented as:
+
+ ![](rgroup-example3.png)
+
+ ![](rgroup-example4.png)
+
+# R-Group Logic
+
+**Ketcher** enables one to add logic when using R-Groups. To access
+the R-Group logic:
+
+  1. Create an R-Group member fragment as described above.
+
+  2. Move the cursor over the entire fragment for the green frame to
+     appear, then click inside the fragment. The following dialog
+     appears:
+
+     ![](rlogic-dialog.png)
+
+  3. Specify **Occurrence** to define how many of an R-Group
+     occurs. If an R-Group atom appears several times in the initial
+     structure, you will specify **Occurrence**">n", n
+     being the number of occurrences; if it appears once, you see
+     "R1 > 0".
+
+  4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
+     clear the checkbox.
+
+  5. Specify the logical **Condition**. Use the R-Group condition **If
+     R(i) Then** to specify whether the presence of an R-Group is
+     dependent on the presence of another R-Group.
+
+
+# Marking S-Groups
+
+To mark S-Groups, use the _S-Group tool_ ![](sgroup.png) and the
+following dialog that appears after selecting a fragment with this
+tool:
+
+ ![](sgroup-dialog.png "S-Group Dialog")
+
+Available S-Group types:
+
+_Generic_
+
+Generic is a pair of brackets without any labels.
+
+_Multiple group_
+
+A Multiple group indicates a number of replications of a fragment or a part of a
+structure in contracted form.
+
+_SRU Polymer_
+
+The Structural Repeating Unit (SRU) brackets enclose the structural
+repeating of a polymer. You have three available patterns:
+head-to-tail (the default), head-to-head, and either/unknown.
+
+_Superatom_
+
+An abbreviated structure (abbreviation) is all or part of a structure
+(molecule or reaction component) that has been abbreviated to a text
+label. Structures that you abbreviate keep their chemical
+significance, but their underlying structure is hidden. The current
+version can't display contracted structures but correctly
+saves/reads them into/from files.
+
+# Data S-Groups
+
+The _Data S-Groups Tool_ ![](sdata.png) is a separate tool for
+comfortable use with the accustomed set of descriptors (like Attached
+Data in **Marvin** Editor).
+
+You can attach data to an atom, a fragment, a single bond, or a
+group. The defined set of _Names_ and _Values_ is introduced for each
+type of selected elements:
+
+ ![](sdata-dialog.png)
+
+  * Select the appropriate S-Group Field Name.
+
+  * Select or type the appropriate Field Value.
+
+  * Labels can be specified as Absolute, Relative or Attached.
+
+# Changing Structure Display
+
+Use the _Flip/Rotate_ tool ![](transform.png) to change the structure
+display:
+
+ ![](transform-types.png)
+
+For the full screen format, the _Flip/Rotate_ tool is split into
+separate buttons:
+
+ ![](rotate.png)
+
+_Rotate Tool_
+
+This tool allows rotating objects.
+  * If some objects are selected, the tool rotates the selected objects.
+  * If no objects are selected, or all objects are selected, the tool rotates the whole canvas
+  * The default rotation step is 15 degrees. 
+  * Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
+
+Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
+Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
+
+_Flip Tool_
+
+This tool flips the objects horizontally or vertically.
+  * If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
+  * If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
+  * If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
+  * If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
+
+# Drawing Reactions
+
+To draw/edit reactions you can
+
+  * draw reagents and products as described above;
+  * use options of the _Reaction Arrow Tool_ ![](reaction.png) to draw an
+  arrow and pluses in the reaction equation and map same atoms in
+  reagents and products.
+
+    ![](reaction-types.png)
+
+**Note** : Reaction Auto-Mapping Tool is available only in the Server
+mode.
+
+# Templates toolbar
+
+You can add templates (rings or other predefined structures) to the
+structure using the _Templates_ toolbar together with the _Custom
+Templates_ button located at the bottom:
+
+ ![](template.png)
+
+To add a ring to the molecule, select a ring from the toolbar and
+click inside the drawing area, or click on an atom or a bond in the
+molecule.
+
+Rules of using templates:
+
+  * Selecting a template and clicking on an atom in the existing
+  structure adds the template to the structure connected with a single
+  bond:
+
+    ![](template-example1.png)
+
+  * Selecting a template and dragging the cursor from an atom in the
+  existing structure adds the template directly to this atom resulting
+  in the fused structure:
+
+    ![](template-example2.png)
+
+  * Dragging the cursor from an atom in the existing structure results
+  in the single bond attachment if the cursor is dragged to more than
+  the bond length; otherwise the fused structure is drawn.
+  * Selecting a template and clicking on a bond in the existing
+  structure created a bond-to-bond fused structure:
+
+    ![](template-example3.png)
+
+  * The bond in the initial structure is replaced with the bond in the
+  template.
+
+  * This procedure doesn't change the length of the bond in the
+  initial structure.
+
+  * Dragging the cursor relative to the initial bond applies the
+  template at the corresponding side of the bond.
+
+**Note** : The added template will be fused by the default attachment
+atom or bond preset in the program.
+
+**Note** : User is able to define the attachment atom and bond by clicking
+the Edit button for template structure.
+
+
+The _Custom Templates_ button ![](template-lib.png)invokes the scrolling
+list of templates available in the program; both built-in and created
+by user:
+
+ ![](template-dialog.png)
+
+
+To create a user template:
+* draw a structure.
+* click the Save as button.
+* click the Save to Templates button.
+* enter a name and define the attachment atom and bond.
+
+# Working with Files
+
+Ketcher supports the following molecular formats that can be entered
+either manually or from files:
+
+  * MDL Molfile or RXN file;
+
+  * Daylight SMILES (Server mode only);
+
+  * Daylight SMARTS (Server mode only);
+
+  * InChi string (Server mode only);
+
+  * CML file (Server mode only).
+
+You can use the **Open…** and **Save As…** buttons of the _Main_
+toolbar to import a molecule from a molecular file or save it to a
+supported molecular file format. The _Open Structure_ dialog enables
+one to either browse for a file (Server mode) or manually input, e.g.,
+the Molfile ctable for the molecule to be imported:
+
+ ![](open.png)
+
+The _Save Structure_ dialog enables one to save the molecular file:
+
+ ![](save.png)
+
+**Note** : In the standalone version only mol/rxn are supported for
+Open and mol/rxn/SMILES for Save.
+
+
+# Hotkeys
+
+You can use keyboard hotkeys (including Numeric keypad) for some
+features/commands of the Editor. To display the hotkeys just place the
+cursor over a toolbar button. If a hotkey is available for the button,
+it will appear in brackets after the description of the button.
+
+| Key | Action |
+| --- | --- |
+| `Esc` | Switching between the Lasso/Rectangle/Fragment Selection tools |
+| `Del` | Delete the selected objects |
+| `0` | Draw Any bond. |
+| `1` | Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types. |
+| `2` | Double / Double Cis/Trans bond |
+| `3` | Draw a triple bond. |
+| `4` | Draw an aromatic bond. |
+| `5` | Charge Plus/Charge Minus |
+| `A` | Draw any atom |
+| `H` | Draw a hydrogen |
+| `C` | Draw a carbon |
+| `N` | Draw a nitrogen |
+| `O` | Draw an oxygen |
+| `S` | Draw a sulfur |
+| `F` | Draw a fluorine |
+| `P` | Draw a phosphorus |
+| `I` | Draw an iodine |
+| `T` | Basic templates. Consecutive pressing switches between different templates |
+| `Shift+t` | Open template library |
+| `Alt+r` | Rotate tool |
+| `Alt+v` | Flip vertically |
+| `Alt+h` | Flip horizontally |
+| `Ctrl+g` | S-Group tool / Data S-Group tool |
+| `Ctrl+d` | Align and select all S-Group data
+| `Ctrl+r` | Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool |
+| `Ctrl+Shift+r`  | R-Group Fragment Tool |
+| `Ctrl+Del` | Clear canvas |
+| `Ctrl+o` | Open |
+| `Ctrl+s` | Save As |
+| `Ctrl+z` | Undo |
+| `Ctrl+Shift+z` | Redo |
+| `Ctrl+x` | Cut selected objects |
+| `Ctrl+c` | Copy selected objects |
+| `Ctrl+v` | Paste selected objects |
+| `+` | Zoom In |
+| `-` | Zoom Out |
+| `Ctrl+l` | Layout |
+| `Ctrl+Shift+l` | Clean Up |
+| `Ctrl+p` | Calculate CIP |
+| `?` | Help |
+
+**Note** : Please, use `Ctrl+V` to paste the selected object in
+Google Chrome and Mozilla Firefox browsers.
+
+**Note 2** : Probably, you have forbidden access to the local storage.
+If you are using IE10 or IE11 and didn't forbid access to local storage 
+intentionally, you can pay attention here: https://stackoverflow.com/a/20848924