Initial bayer app

bayer/admin.py

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+from django.contrib import admin
+
+# Register your models here.

bayer/apps.py

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+from django.apps import AppConfig
+
+
+class BayerConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'bayer'

bayer/migrations/0001_initial.py

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+# 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

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+# 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/models.py

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+from typing import List
+
+from django.conf import settings as s
+from django.db import models
+from django.db.models import QuerySet
+
+from epdb.models import (
+    EnviPathModel,
+    ParallelRule,
+    SequentialRule,
+    SimpleAmbitRule,
+    SimpleRDKitRule,
+)
+
+
+class Package(EnviPathModel):
+    reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
+    license = models.ForeignKey(
+        "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
+    )
+
+    class Classification(models.IntegerChoices):
+        INTERNAL = 0, "Internal"
+        RESTRICTED = 10 , "Restricted"
+        SECRET = 20, "Secret"
+
+    classification_level = models.IntegerField(
+        choices=Classification,
+        default=Classification.RESTRICTED,
+    )
+
+    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"

bayer/templates/objects/package.html

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+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+    {% include "modals/objects/edit_package_modal.html" %}
+    {% include "modals/objects/edit_package_permissions_modal.html" %}
+    {% include "modals/objects/publish_package_modal.html" %}
+    {% include "modals/objects/set_license_modal.html" %}
+    {% include "modals/objects/export_package_modal.html" %}
+    {% include "modals/objects/generic_delete_modal.html" %}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">{{ package.name }} FROM APP</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/tests.py

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+from django.test import TestCase
+
+# Create your tests here.

bayer/views.py

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+from django.shortcuts import render
+
+# Create your views here.