forked from enviPath/enviPy
Compare commits
8 Commits
dd0f7eaf05
...
develop
| Author | SHA1 | Date | |
|---|---|---|---|
| 1e43c298d2 | |||
| b39fc7eaf8 | |||
| a2fc9f72cb | |||
| 734b02767e | |||
| 9d70db2ca2 | |||
| fec26d0233 | |||
| 689f7998eb | |||
| 8498e59fa1 |
@ -36,13 +36,13 @@ RUN --mount=type=ssh \
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# Now copy source and do a final sync to install the project itself
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# Ensure .dockerignore is reasonable
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COPY bayer bayer
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COPY bridge bridge
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COPY biotransformer biotransformer
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COPY bridge bridge
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COPY envipath envipath
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COPY epapi epapi
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COPY epauth epauth
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COPY epdb epdb
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COPY epiuclid epiuclid
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COPY fixtures fixtures
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COPY migration migration
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COPY pepper pepper
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@ -1,3 +0,0 @@
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from django.contrib import admin
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# Register your models here.
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@ -1,6 +0,0 @@
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from django.apps import AppConfig
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class BayerConfig(AppConfig):
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default_auto_field = 'django.db.models.BigAutoField'
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name = 'bayer'
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@ -1,35 +0,0 @@
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# Generated by Django 5.2.7 on 2026-03-06 10:51
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import django.utils.timezone
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import model_utils.fields
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import uuid
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from django.db import migrations, models
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class Migration(migrations.Migration):
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initial = True
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dependencies = [
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]
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operations = [
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migrations.CreateModel(
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name='Package',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
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('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
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('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
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('name', models.TextField(default='no name', verbose_name='Name')),
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('description', models.TextField(default='no description', verbose_name='Descriptions')),
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('url', models.TextField(null=True, unique=True, verbose_name='URL')),
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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
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('classification_level', models.IntegerField(choices=[(0, 'Internal'), (10, 'Restricted'), (20, 'Secret')], default=10)),
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],
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options={
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'db_table': 'epdb_package',
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},
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),
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]
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@ -1,22 +0,0 @@
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# Generated by Django 5.2.7 on 2026-03-06 10:51
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import django.db.models.deletion
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from django.db import migrations, models
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class Migration(migrations.Migration):
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initial = True
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dependencies = [
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('bayer', '0001_initial'),
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('epdb', '0019_remove_scenario_additional_information_and_more'),
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]
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operations = [
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migrations.AddField(
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model_name='package',
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name='license',
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field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License'),
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),
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]
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@ -1,20 +0,0 @@
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# Generated by Django 6.0.3 on 2026-04-14 19:07
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import django.db.models.deletion
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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('bayer', '0002_initial'),
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('epdb', '0023_alter_compoundstructure_options_and_more'),
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]
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operations = [
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migrations.AddField(
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model_name='package',
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name='data_pool',
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field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
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),
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]
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@ -1,98 +0,0 @@
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from typing import List
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from django.conf import settings as s
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from django.db import models
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from django.db.models import QuerySet
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from epdb.models import (
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EnviPathModel,
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ParallelRule,
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SequentialRule,
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SimpleAmbitRule,
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SimpleRDKitRule,
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)
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class Package(EnviPathModel):
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reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
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license = models.ForeignKey(
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"epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
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)
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class Classification(models.IntegerChoices):
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INTERNAL = 0, "Internal"
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RESTRICTED = 10 , "Restricted"
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SECRET = 20, "Secret"
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classification_level = models.IntegerField(
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choices=Classification,
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default=Classification.RESTRICTED,
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)
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data_pool = models.ForeignKey("epdb.Group", on_delete=models.SET_NULL, blank=True, null=True,
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verbose_name="Data pool", default=None)
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def delete(self, *args, **kwargs):
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# explicitly handle related Rules
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for r in self.rules.all():
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r.delete()
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super().delete(*args, **kwargs)
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def __str__(self):
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return f"{self.name} (pk={self.pk})"
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@property
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def compounds(self) -> QuerySet:
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return self.compound_set.all()
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@property
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def rules(self) -> QuerySet:
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return self.rule_set.all()
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@property
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def reactions(self) -> QuerySet:
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return self.reaction_set.all()
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@property
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def pathways(self) -> QuerySet:
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return self.pathway_set.all()
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@property
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def scenarios(self) -> QuerySet:
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return self.scenario_set.all()
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@property
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def models(self) -> QuerySet:
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return self.epmodel_set.all()
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def _url(self):
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return "{}/package/{}".format(s.SERVER_URL, self.uuid)
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def get_applicable_rules(self) -> List["Rule"]:
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"""
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Returns a ordered set of rules where the following applies:
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1. All Composite will be added to result
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2. All SimpleRules will be added if theres no CompositeRule present using the SimpleRule
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Ordering is based on "url" field.
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"""
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rules = []
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rule_qs = self.rules
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reflected_simple_rules = set()
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for r in rule_qs:
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if isinstance(r, ParallelRule) or isinstance(r, SequentialRule):
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rules.append(r)
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for sr in r.simple_rules.all():
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reflected_simple_rules.add(sr)
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for r in rule_qs:
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if isinstance(r, SimpleAmbitRule) or isinstance(r, SimpleRDKitRule):
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if r not in reflected_simple_rules:
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rules.append(r)
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rules = sorted(rules, key=lambda x: x.url)
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return rules
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class Meta:
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db_table = "epdb_package"
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@ -1,181 +0,0 @@
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{% load static %}
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<dialog
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id="new_package_modal"
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class="modal"
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x-data="{
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isSubmitting: false,
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packageClassification: null,
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reset() {
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this.isSubmitting = false;
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this.selectedType = '';
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this.buildAppDomain = false;
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this.requiresRulePackages = false;
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this.requiresDataPackages = false;
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this.additional_parameters = null;
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},
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setFormData(data) {
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this.formData = data;
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},
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get isSecret() {
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return this.packageClassification === '20';
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},
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submit(formId) {
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const form = document.getElementById(formId);
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// Remove previously injected inputs
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form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
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// Add values from dynamic form into the html form
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if (this.formData) {
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Object.entries(this.formData).forEach(([key, value]) => {
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const input = document.createElement('input');
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input.type = 'hidden';
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input.name = key;
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input.value = value;
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input.classList.add('dynamic-param');
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form.appendChild(input);
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});
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}
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if (form && form.checkValidity()) {
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this.isSubmitting = true;
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form.submit();
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} else if (form) {
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form.reportValidity();
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}
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}
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}"
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@close="reset()"
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>
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<div class="modal-box max-w-3xl">
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<!-- Header -->
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<h3 class="text-lg font-bold">New Package</h3>
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<!-- Close button (X) -->
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<form method="dialog">
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<button
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class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
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:disabled="isSubmitting"
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>
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✕
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</button>
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</form>
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<!-- Body -->
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<div class="py-4">
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<form
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id="new_package_form"
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accept-charset="UTF-8"
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action=""
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method="post"
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>
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{% csrf_token %}
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<!-- Name -->
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<div class="form-control mb-3">
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<label class="label" for="package-name">
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<span class="label-text">Name</span>
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</label>
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<input
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id="package-name"
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class="input input-bordered w-full"
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name="package-name"
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placeholder="Name"
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required
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/>
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</div>
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<!-- Description -->
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<div class="form-control mb-3">
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<label class="label" for="package-description">
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<span class="label-text">Description</span>
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</label>
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<input
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id="package-description"
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type="text"
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class="input input-bordered w-full"
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placeholder="Description..."
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name="package-description"
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/>
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</div>
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<!-- Classification Level -->
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<div class="form-control mb-3">
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<label class="label" for="package-classification">
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<span class="label-text">Package Classification</span>
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</label>
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<select
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id="package-classification"
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name="package-classification"
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class="select select-bordered w-full"
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x-model="packageClassification"
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required
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>
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<option value="null" disabled selected>Select Classification</option>
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<option value="0">Internal</option>
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<option value="10">Restricted</option>
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<option value="20">Secret</option>
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</select>
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</div>
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<!-- Secret Groups -->
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<div class="form-control mb-3" x-show="isSecret" x-cloak>
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<label class="label" for="package-data-pool">
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<span class="label-text">Data Pool for SECRET Package</span>
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</label>
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<p>Only users with this role can be granted access to this package</p>
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<select
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id="package-data-pool"
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name="package-data-pool"
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class="select select-bordered w-full"
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>
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<option value="" disabled selected>Select Data Pool</option>
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{% for obj in meta.available_groups %}
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{% if obj.secret %}
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<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
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{% endif %}
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{% endfor %}
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</select>
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</div>
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</form>
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</div>
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<!-- Footer -->
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<div class="modal-action">
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<button
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type="button"
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class="btn"
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onclick="this.closest('dialog').close()"
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:disabled="isSubmitting"
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>
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Cancel
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</button>
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<button
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type="button"
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class="btn btn-primary"
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@click="submit('new_package_form')"
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:disabled="isSubmitting || !selectedType || loadingSchemas"
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>
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<span x-show="!isSubmitting">Submit</span>
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<span
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x-show="isSubmitting"
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class="loading loading-spinner loading-sm"
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></span>
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<span x-show="isSubmitting">Creating...</span>
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</button>
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</div>
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</div>
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<!-- Backdrop -->
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<form method="dialog" class="modal-backdrop">
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<button :disabled="isSubmitting">close</button>
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</form>
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</dialog>
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@ -1,97 +0,0 @@
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{% extends "framework_modern.html" %}
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{% block content %}
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{% block action_modals %}
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{% include "modals/objects/edit_package_modal.html" %}
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{% include "modals/objects/edit_package_permissions_modal.html" %}
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{% include "modals/objects/publish_package_modal.html" %}
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{% include "modals/objects/set_license_modal.html" %}
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{% include "modals/objects/export_package_modal.html" %}
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{% include "modals/objects/generic_delete_modal.html" %}
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{% endblock action_modals %}
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<div class="space-y-2 p-4">
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<!-- Header Section -->
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<div class="card bg-base-100">
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<div class="card-body">
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<div class="flex items-center justify-between">
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<h2 class="card-title text-2xl">{{ package.name }} - ({{ package.get_classification_level_display }})</h2>
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<div id="actionsButton" class="dropdown dropdown-e nd hidden">
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<div tabindex="0" role="button" class="btn btn-ghost btn-sm">
|
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<svg
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xmlns="http://www.w3.org/2000/svg"
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width="16"
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height="16"
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viewBox="0 0 24 24"
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fill="none"
|
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stroke="currentColor"
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stroke-width="2"
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stroke-linecap="round"
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stroke-linejoin="round"
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class="lucide lucide-wrench"
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>
|
||||
<path
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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"
|
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/>
|
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</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" %}
|
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{% endblock %}
|
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</ul>
|
||||
</div>
|
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</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 %}
|
||||
@ -1,3 +0,0 @@
|
||||
from django.test import TestCase
|
||||
|
||||
# Create your tests here.
|
||||
@ -1,3 +0,0 @@
|
||||
from django.shortcuts import render
|
||||
|
||||
# Create your views here.
|
||||
@ -1,54 +1,26 @@
|
||||
services:
|
||||
db:
|
||||
image: postgres:18
|
||||
container_name: eppostgres
|
||||
container_name: envipath-postgres
|
||||
environment:
|
||||
POSTGRES_USER: ${POSTGRES_USER}
|
||||
POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
|
||||
POSTGRES_DB: ${POSTGRES_DB}
|
||||
POSTGRES_USER: postgres
|
||||
POSTGRES_PASSWORD: postgres
|
||||
POSTGRES_DB: envipath
|
||||
ports:
|
||||
- "5432:5432"
|
||||
volumes:
|
||||
- ep_bayer_postgres_data:/var/lib/postgresql
|
||||
- postgres_data:/var/lib/postgresql
|
||||
healthcheck:
|
||||
test: [ "CMD-SHELL", "pg_isready -U postgres" ]
|
||||
test: ["CMD-SHELL", "pg_isready -U postgres"]
|
||||
interval: 5s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
|
||||
redis:
|
||||
image: redis:7-alpine
|
||||
container_name: epredis
|
||||
container_name: envipath-redis
|
||||
ports:
|
||||
- "6379:6379"
|
||||
volumes:
|
||||
- ep_bayer_redis_data:/data
|
||||
|
||||
biotransformer3:
|
||||
image: envipath/biotransformer3:1.0
|
||||
container_name: epbiotransformer3
|
||||
|
||||
# web:
|
||||
# image: envipath/envipy-bayer:1.0
|
||||
# container_name: epdjango
|
||||
# ports:
|
||||
# - "127.0.0.1:8000:8000"
|
||||
# env_file:
|
||||
# - .env
|
||||
# command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
|
||||
# volumes:
|
||||
# - ep_bayer_data:/opt/enviPy/
|
||||
|
||||
celery_worker:
|
||||
image: envipath/envipy-bayer:1.0
|
||||
container_name: epcelery
|
||||
env_file:
|
||||
- .env.dev
|
||||
command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
|
||||
volumes:
|
||||
- ep_bayer_data:/opt/enviPy/
|
||||
|
||||
volumes:
|
||||
ep_bayer_postgres_data:
|
||||
ep_bayer_redis_data:
|
||||
ep_bayer_data:
|
||||
postgres_data:
|
||||
|
||||
@ -7,7 +7,7 @@ services:
|
||||
POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
|
||||
POSTGRES_DB: ${POSTGRES_DB}
|
||||
volumes:
|
||||
- ep_bayer_postgres_data:/var/lib/postgresql
|
||||
- ep_postgres_data:/var/lib/postgresql
|
||||
healthcheck:
|
||||
test: [ "CMD-SHELL", "pg_isready -U postgres" ]
|
||||
interval: 5s
|
||||
@ -18,14 +18,14 @@ services:
|
||||
image: redis:7-alpine
|
||||
container_name: epredis
|
||||
volumes:
|
||||
- ep_bayer_redis_data:/data
|
||||
- ep_redis_data:/data
|
||||
|
||||
biotransformer3:
|
||||
image: envipath/biotransformer3:1.0
|
||||
container_name: epbiotransformer3
|
||||
|
||||
web:
|
||||
image: envipath/envipy-bayer:1.0
|
||||
image: envipath/envipy:1.0
|
||||
container_name: epdjango
|
||||
ports:
|
||||
- "127.0.0.1:8000:8000"
|
||||
@ -33,18 +33,18 @@ services:
|
||||
- .env
|
||||
command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
|
||||
volumes:
|
||||
- ep_bayer_data:/opt/enviPy/
|
||||
- ep_data:/opt/enviPy/
|
||||
|
||||
celery_worker:
|
||||
image: envipath/envipy-bayer:1.0
|
||||
image: envipath/envipy:1.0
|
||||
container_name: epcelery
|
||||
env_file:
|
||||
- .env
|
||||
command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
|
||||
volumes:
|
||||
- ep_bayer_data:/opt/enviPy/
|
||||
- ep_data:/opt/enviPy/
|
||||
|
||||
volumes:
|
||||
ep_bayer_postgres_data:
|
||||
ep_bayer_redis_data:
|
||||
ep_bayer_data:
|
||||
ep_postgres_data:
|
||||
ep_redis_data:
|
||||
ep_data:
|
||||
|
||||
@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
|
||||
For the full list of settings and their values, see
|
||||
https://docs.djangoproject.com/en/4.2/ref/settings/
|
||||
"""
|
||||
import json
|
||||
|
||||
import os
|
||||
from pathlib import Path
|
||||
|
||||
@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
|
||||
# Build paths inside the project like this: BASE_DIR / 'subdir'.
|
||||
BASE_DIR = Path(__file__).resolve().parent.parent
|
||||
|
||||
ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
|
||||
ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
|
||||
print(f"Loading env from {ENV_PATH}")
|
||||
load_dotenv(ENV_PATH, override=False)
|
||||
|
||||
@ -442,14 +442,3 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
|
||||
FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
|
||||
if BIOTRANSFORMER_ENABLED:
|
||||
BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
|
||||
|
||||
# PES
|
||||
PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
|
||||
if PES_API_MAPPING:
|
||||
import json
|
||||
PES_API_MAPPING = json.loads(PES_API_MAPPING)
|
||||
else:
|
||||
PES_API_MAPPING = {}
|
||||
|
||||
# AD Group Mapping
|
||||
|
||||
|
||||
@ -40,6 +40,9 @@ if "migration" in s.INSTALLED_APPS:
|
||||
if s.MS_ENTRA_ENABLED:
|
||||
urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
|
||||
|
||||
if s.TENANT != "public":
|
||||
urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
|
||||
|
||||
# Custom error handlers
|
||||
handler400 = "epdb.views.handler400"
|
||||
handler403 = "epdb.views.handler403"
|
||||
|
||||
@ -1,12 +1,32 @@
|
||||
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.shortcuts import redirect
|
||||
from django.contrib.auth import get_user_model
|
||||
|
||||
from epdb.logic import UserManager
|
||||
|
||||
|
||||
def get_msal_app_with_cache(request):
|
||||
"""
|
||||
Create MSAL app with session-based token cache.
|
||||
"""
|
||||
cache = msal.SerializableTokenCache()
|
||||
|
||||
# Load cache from session if it exists
|
||||
if request.session.get("msal_token_cache"):
|
||||
cache.deserialize(request.session["msal_token_cache"])
|
||||
|
||||
msal_app = msal.ConfidentialClientApplication(
|
||||
client_id=s.MS_ENTRA_CLIENT_ID,
|
||||
client_credential=s.MS_ENTRA_CLIENT_SECRET,
|
||||
authority=s.MS_ENTRA_AUTHORITY,
|
||||
token_cache=cache,
|
||||
)
|
||||
|
||||
return msal_app, cache
|
||||
|
||||
|
||||
def entra_login(request):
|
||||
msal_app = msal.ConfidentialClientApplication(
|
||||
client_id=s.MS_ENTRA_CLIENT_ID,
|
||||
@ -23,11 +43,7 @@ def entra_login(request):
|
||||
|
||||
|
||||
def entra_callback(request):
|
||||
msal_app = msal.ConfidentialClientApplication(
|
||||
client_id=s.MS_ENTRA_CLIENT_ID,
|
||||
client_credential=s.MS_ENTRA_CLIENT_SECRET,
|
||||
authority=s.MS_ENTRA_AUTHORITY,
|
||||
)
|
||||
msal_app, cache = get_msal_app_with_cache(request)
|
||||
|
||||
flow = request.session.pop("msal_auth_flow", None)
|
||||
if not flow:
|
||||
@ -36,11 +52,18 @@ def entra_callback(request):
|
||||
# Acquire token using the flow and callback request
|
||||
result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
|
||||
|
||||
# Save the token cache to session
|
||||
if cache.has_state_changed:
|
||||
request.session["msal_token_cache"] = cache.serialize()
|
||||
|
||||
claims = result["id_token_claims"]
|
||||
|
||||
user_name = claims["name"]
|
||||
user_email = claims["emailaddress"]
|
||||
user_oid = claims["oid"]
|
||||
user_name = claims.get("name")
|
||||
user_email = claims.get("emailaddress", claims.get("email"))
|
||||
user_oid = claims.get("oid")
|
||||
|
||||
if not all([user_name, user_email, user_oid]):
|
||||
raise ValueError("Missing required claims in ID token")
|
||||
|
||||
# Get implementing class
|
||||
User = get_user_model()
|
||||
@ -57,4 +80,51 @@ def entra_callback(request):
|
||||
|
||||
login(request, u)
|
||||
|
||||
return redirect("/") # Handle errors
|
||||
return redirect(s.SERVER_URL) # Handle errors
|
||||
|
||||
|
||||
def get_access_token_from_request(request, scopes=None):
|
||||
"""
|
||||
Get an access token from the request using MSAL token cache.
|
||||
"""
|
||||
if scopes is None:
|
||||
scopes = s.MS_ENTRA_SCOPES
|
||||
|
||||
# Get user from request (must be authenticated)
|
||||
if not request.user.is_authenticated:
|
||||
return None
|
||||
|
||||
# Create MSAL app with persistent cache
|
||||
msal_app, cache = get_msal_app_with_cache(request)
|
||||
|
||||
# Try to get accounts from cache
|
||||
accounts = msal_app.get_accounts()
|
||||
|
||||
if not accounts:
|
||||
return None
|
||||
|
||||
# Find the account that matches the current user
|
||||
user_account = None
|
||||
for account in accounts:
|
||||
if account.get("local_account_id") == str(request.user.uuid):
|
||||
user_account = account
|
||||
break
|
||||
|
||||
# If no matching account found, use the first available account
|
||||
if not user_account and accounts:
|
||||
user_account = accounts[0]
|
||||
|
||||
if not user_account:
|
||||
return None
|
||||
|
||||
# Try to acquire token silently from cache
|
||||
result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
|
||||
|
||||
# Save cache changes back to session
|
||||
if cache.has_state_changed:
|
||||
request.session["msal_token_cache"] = cache.serialize()
|
||||
|
||||
if result and "access_token" in result:
|
||||
return result
|
||||
|
||||
return None
|
||||
|
||||
112
epdb/admin.py
112
epdb/admin.py
@ -1,5 +1,8 @@
|
||||
import logging
|
||||
|
||||
from django.conf import settings as s
|
||||
from django.contrib import admin
|
||||
from django.contrib import messages
|
||||
|
||||
from .models import (
|
||||
AdditionalInformation,
|
||||
@ -29,6 +32,8 @@ from .models import (
|
||||
|
||||
Package = s.GET_PACKAGE_MODEL()
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
|
||||
class AdditionalInformationAdmin(admin.ModelAdmin):
|
||||
pass
|
||||
@ -45,6 +50,113 @@ class UserAdmin(admin.ModelAdmin):
|
||||
"date_joined",
|
||||
]
|
||||
|
||||
actions = ["send_welcome_mail", "send_affiliation_mail"]
|
||||
|
||||
@admin.action(description="Send welcome mail")
|
||||
def send_welcome_mail(self, request, queryset):
|
||||
from django.core.mail import EmailMultiAlternatives
|
||||
|
||||
tpl = """Hello {username},
|
||||
|
||||
Your account has been successfully activated.
|
||||
|
||||
To log in, please visit
|
||||
https://envipath.org/password_reset/
|
||||
and request a new password.
|
||||
|
||||
If you have any questions or feedback, feel free to visit our community forum at
|
||||
https://community.envipath.org/.
|
||||
You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
|
||||
|
||||
Best regards,
|
||||
|
||||
The enviPath Team"""
|
||||
|
||||
users = []
|
||||
|
||||
for user in queryset:
|
||||
if user.is_active:
|
||||
logger.info(f"{user.username} already active - not sending mail again")
|
||||
continue
|
||||
try:
|
||||
msg = EmailMultiAlternatives(
|
||||
"Your enviPath Account Is Now Active",
|
||||
tpl.format(username=user.username),
|
||||
"admin@envipath.org",
|
||||
[user.email],
|
||||
bcc=["admin@envipath.org"],
|
||||
)
|
||||
|
||||
msg.send(fail_silently=False)
|
||||
|
||||
user.is_active = True
|
||||
user.password = "ASDF"
|
||||
user.save()
|
||||
|
||||
users.append(user)
|
||||
logger.info(f"{user.username} -> {user.email} mail sent")
|
||||
except Exception as e:
|
||||
logger.info(f"Error sending mail to {user.username}: {e}")
|
||||
|
||||
self.message_user(
|
||||
request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
|
||||
)
|
||||
|
||||
@admin.action(description="Send affiliation mail")
|
||||
def send_affiliation_mail(self, request, queryset):
|
||||
from django.core.mail import EmailMultiAlternatives
|
||||
|
||||
tpl = """Dear {username},
|
||||
|
||||
Thank you for your interest in enviPath!
|
||||
|
||||
Please note that the public enviPath system is intended for non-commercial use only.
|
||||
We see that you registered using the email address {email}.
|
||||
If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
|
||||
|
||||
If you would like us to update your account, simply reply to this email and let us know which address we should use.
|
||||
We will then change it in our system, and you will receive a password reset email at the new address.
|
||||
|
||||
If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
|
||||
To book a meeting, please visit https://envipath.com/book
|
||||
|
||||
If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
|
||||
|
||||
Best regards,
|
||||
|
||||
enviPath team"""
|
||||
|
||||
users = []
|
||||
|
||||
for user in queryset:
|
||||
if user.is_active or user.contacted:
|
||||
logger.info(
|
||||
f"{user.username} already active or already contacted - not sending mail again"
|
||||
)
|
||||
continue
|
||||
try:
|
||||
msg = EmailMultiAlternatives(
|
||||
"Regarding your enviPath registration",
|
||||
tpl.format(username=user.username, email=user.email),
|
||||
"admin@envipath.org",
|
||||
[user.email],
|
||||
bcc=["admin@envipath.org"],
|
||||
)
|
||||
|
||||
msg.send(fail_silently=False)
|
||||
|
||||
user.contacted = True
|
||||
user.save()
|
||||
|
||||
users.append(user)
|
||||
logger.info(f"{user.username} -> {user.email} affiliation mail sent")
|
||||
except Exception as e:
|
||||
logger.info(f"Error sending mail to {user.username}: {e}")
|
||||
|
||||
self.message_user(
|
||||
request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
|
||||
)
|
||||
|
||||
|
||||
class UserPackagePermissionAdmin(admin.ModelAdmin):
|
||||
pass
|
||||
|
||||
@ -1967,9 +1967,12 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
|
||||
description=e.edgeReason,
|
||||
)
|
||||
|
||||
# Update depths as sideeffect of above operation
|
||||
pw.update_depths()
|
||||
|
||||
return redirect(new_e.url)
|
||||
except ValueError:
|
||||
return 403, {"message": "Adding node failed!"}
|
||||
return 403, {"message": "Adding Edge failed!"}
|
||||
|
||||
|
||||
@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
|
||||
|
||||
110
epdb/logic.py
110
epdb/logic.py
@ -264,8 +264,12 @@ class GroupManager(object):
|
||||
return bool(re.findall(GroupManager.group_pattern, url))
|
||||
|
||||
@staticmethod
|
||||
def create_group(current_user, name, description):
|
||||
def create_group(current_user, name, description, *args, **kwargs):
|
||||
g = Group()
|
||||
|
||||
if "uuid" in kwargs:
|
||||
g.uuid = kwargs["uuid"]
|
||||
|
||||
# Clean for potential XSS
|
||||
g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
|
||||
@ -341,52 +345,17 @@ class PackageManager(object):
|
||||
|
||||
@staticmethod
|
||||
def readable(user, package):
|
||||
if (
|
||||
UserPackagePermission.objects.filter(package=package, user=user).exists()
|
||||
or GroupPackagePermission.objects.filter(
|
||||
package=package, group__in=GroupManager.get_groups(user)
|
||||
)
|
||||
or package.reviewed is True
|
||||
or user.is_superuser
|
||||
):
|
||||
return True
|
||||
|
||||
return False
|
||||
return (
|
||||
PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
|
||||
)
|
||||
|
||||
@staticmethod
|
||||
def writable(user, package):
|
||||
if (
|
||||
UserPackagePermission.objects.filter(
|
||||
package=package, user=user, permission=Permission.WRITE[0]
|
||||
).exists()
|
||||
or GroupPackagePermission.objects.filter(
|
||||
package=package,
|
||||
group__in=GroupManager.get_groups(user),
|
||||
permission=Permission.WRITE[0],
|
||||
).exists()
|
||||
or UserPackagePermission.objects.filter(
|
||||
package=package, user=user, permission=Permission.ALL[0]
|
||||
).exists()
|
||||
or user.is_superuser
|
||||
):
|
||||
return True
|
||||
return False
|
||||
return PackageManager.has_package_permission(user, package, "write")
|
||||
|
||||
@staticmethod
|
||||
def administrable(user, package):
|
||||
if (
|
||||
UserPackagePermission.objects.filter(
|
||||
package=package, user=user, permission=Permission.ALL[0]
|
||||
).exists()
|
||||
or GroupPackagePermission.objects.filter(
|
||||
package=package,
|
||||
group__in=GroupManager.get_groups(user),
|
||||
permission=Permission.ALL[0],
|
||||
).exists()
|
||||
or user.is_superuser
|
||||
):
|
||||
return True
|
||||
return False
|
||||
return PackageManager.has_package_permission(user, package, "all")
|
||||
|
||||
@staticmethod
|
||||
def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
|
||||
@ -470,7 +439,9 @@ class PackageManager(object):
|
||||
# remove package if user is owner and package is reviewed e.g. admin
|
||||
qs = qs.filter(reviewed=False)
|
||||
|
||||
return qs.distinct()
|
||||
qs = qs.distinct()
|
||||
|
||||
return qs
|
||||
|
||||
@staticmethod
|
||||
def get_all_writeable_packages(user):
|
||||
@ -514,7 +485,9 @@ class PackageManager(object):
|
||||
|
||||
qs = qs.filter(reviewed=False)
|
||||
|
||||
return qs.distinct()
|
||||
qs = qs.distinct()
|
||||
|
||||
return qs
|
||||
|
||||
@staticmethod
|
||||
def get_packages():
|
||||
@ -716,6 +689,10 @@ class PackageManager(object):
|
||||
struc.description = structure["description"]
|
||||
struc.aliases = structure.get("aliases", [])
|
||||
struc.smiles = structure["smiles"]
|
||||
|
||||
if structure.get("molfile"):
|
||||
struc.molfile = structure["molfile"]
|
||||
|
||||
struc.save()
|
||||
|
||||
for scen in structure["scenarios"]:
|
||||
@ -1018,52 +995,9 @@ class PackageManager(object):
|
||||
|
||||
print("Fixing Node depths...")
|
||||
total_pws = Pathway.objects.filter(package=pack).count()
|
||||
|
||||
for p, pw in enumerate(Pathway.objects.filter(package=pack)):
|
||||
in_count = defaultdict(lambda: 0)
|
||||
out_count = defaultdict(lambda: 0)
|
||||
|
||||
for e in pw.edges:
|
||||
# TODO check if this will remain
|
||||
for react in e.start_nodes.all():
|
||||
out_count[str(react.uuid)] += 1
|
||||
|
||||
for prod in e.end_nodes.all():
|
||||
in_count[str(prod.uuid)] += 1
|
||||
|
||||
root_nodes = []
|
||||
for n in pw.nodes:
|
||||
num_parents = in_count[str(n.uuid)]
|
||||
if num_parents == 0:
|
||||
# must be a root node or unconnected node
|
||||
if n.depth != 0:
|
||||
n.depth = 0
|
||||
n.save()
|
||||
|
||||
# Only root node may have children
|
||||
if out_count[str(n.uuid)] > 0:
|
||||
root_nodes.append(n)
|
||||
|
||||
levels = [root_nodes]
|
||||
seen = set()
|
||||
# Do a bfs to determine depths starting with level 0 a.k.a. root nodes
|
||||
for i, level_nodes in enumerate(levels):
|
||||
new_level = []
|
||||
for n in level_nodes:
|
||||
for e in n.out_edges.all():
|
||||
for prod in e.end_nodes.all():
|
||||
if str(prod.uuid) not in seen:
|
||||
old_depth = prod.depth
|
||||
if old_depth != i + 1:
|
||||
prod.depth = i + 1
|
||||
prod.save()
|
||||
|
||||
new_level.append(prod)
|
||||
|
||||
seen.add(str(n.uuid))
|
||||
|
||||
if new_level:
|
||||
levels.append(new_level)
|
||||
|
||||
pw.update_depths()
|
||||
print(f"{p + 1}/{total_pws} fixed.", end="\r")
|
||||
|
||||
return pack
|
||||
|
||||
594
epdb/migrations/0001_initial.py
Normal file
594
epdb/migrations/0001_initial.py
Normal file
@ -0,0 +1,594 @@
|
||||
# Generated by Django 5.2.1 on 2025-07-22 20:58
|
||||
|
||||
import datetime
|
||||
import django.contrib.auth.models
|
||||
import django.contrib.auth.validators
|
||||
import django.contrib.postgres.fields
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
initial = True
|
||||
|
||||
dependencies = [
|
||||
('auth', '0012_alter_user_first_name_max_length'),
|
||||
('contenttypes', '0002_remove_content_type_name'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name='Compound',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EPModel',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Permission',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='License',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('link', models.URLField(verbose_name='link')),
|
||||
('image_link', models.URLField(verbose_name='Image link')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Rule',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='User',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('password', models.CharField(max_length=128, verbose_name='password')),
|
||||
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
|
||||
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
|
||||
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
|
||||
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
|
||||
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
|
||||
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
|
||||
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
|
||||
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
|
||||
('email', models.EmailField(max_length=254, unique=True)),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
|
||||
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'user',
|
||||
'verbose_name_plural': 'users',
|
||||
'abstract': False,
|
||||
},
|
||||
managers=[
|
||||
('objects', django.contrib.auth.models.UserManager()),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='APIToken',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('hashed_key', models.CharField(max_length=128, unique=True)),
|
||||
('created', models.DateTimeField(auto_now_add=True)),
|
||||
('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
|
||||
('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='CompoundStructure',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('smiles', models.TextField(verbose_name='SMILES')),
|
||||
('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
|
||||
('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
|
||||
('normalized_structure', models.BooleanField(default=False)),
|
||||
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='default_structure',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Edge',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EnviFormer',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='PluginModel',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='RuleBaseRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Group',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(verbose_name='Group name')),
|
||||
('public', models.BooleanField(default=False, verbose_name='Public Group')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
|
||||
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
|
||||
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_group',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Node',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('depth', models.IntegerField(verbose_name='Node depth')),
|
||||
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
|
||||
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
|
||||
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='end_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='start_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Package',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
|
||||
('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='epmodel',
|
||||
name='package',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='package',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_package',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='package',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='polymorphic_ctype',
|
||||
field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Pathway',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Reaction',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
|
||||
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
|
||||
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
|
||||
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
|
||||
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='edge_label',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Scenario',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('scenario_date', models.CharField(default='No date', max_length=256)),
|
||||
('scenario_type', models.CharField(default='Not specified', max_length=256)),
|
||||
('additional_information', models.JSONField(verbose_name='Additional Information')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
|
||||
('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='reaction',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compoundstructure',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Setting',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('public', models.BooleanField(default=False)),
|
||||
('global_default', models.BooleanField(default=False)),
|
||||
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
|
||||
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
|
||||
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
|
||||
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='setting',
|
||||
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_setting',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='MLRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ApplicabilityDomain',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('num_neighbours', models.FloatField(default=5)),
|
||||
('reliability_threshold', models.FloatField(default=0.5)),
|
||||
('local_compatibilty_threshold', models.FloatField(default=0.5)),
|
||||
('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleAmbitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('smirks', models.TextField(verbose_name='SMIRKS')),
|
||||
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
|
||||
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRDKitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRuleOrdering',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('order_index', models.IntegerField()),
|
||||
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
|
||||
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
|
||||
],
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='sequentialrule',
|
||||
name='simple_rules',
|
||||
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ParallelRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.AlterUniqueTogether(
|
||||
name='compound',
|
||||
unique_together={('uuid', 'package')},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='GroupPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'group')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserSettingPermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('setting', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
]
|
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,128 @@
|
||||
# Generated by Django 5.2.1 on 2025-08-25 18:07
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('contenttypes', '0002_remove_content_type_name'),
|
||||
('epdb', '0001_initial'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name='ExternalDatabase',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
|
||||
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
|
||||
('description', models.TextField(blank=True, verbose_name='Description')),
|
||||
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
|
||||
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
|
||||
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Database',
|
||||
'verbose_name_plural': 'External Databases',
|
||||
'db_table': 'epdb_external_database',
|
||||
'ordering': ['name'],
|
||||
},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='apitoken',
|
||||
options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='edge',
|
||||
options={},
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name='edge',
|
||||
name='polymorphic_ctype',
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='apitoken',
|
||||
name='is_active',
|
||||
field=models.BooleanField(default=True, help_text='Whether this token is active'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='apitoken',
|
||||
name='modified',
|
||||
field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='functional_groups',
|
||||
field=models.JSONField(blank=True, default=dict, null=True),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='created',
|
||||
field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='expires_at',
|
||||
field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='hashed_key',
|
||||
field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='name',
|
||||
field=models.CharField(help_text='Descriptive name for this token', max_length=100),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='user',
|
||||
field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='applicabilitydomain',
|
||||
name='num_neighbours',
|
||||
field=models.IntegerField(default=5),
|
||||
),
|
||||
migrations.AlterModelTable(
|
||||
name='apitoken',
|
||||
table='epdb_api_token',
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalIdentifier',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('object_id', models.IntegerField()),
|
||||
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
|
||||
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
|
||||
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
|
||||
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Identifier',
|
||||
'verbose_name_plural': 'External Identifiers',
|
||||
'db_table': 'epdb_external_identifier',
|
||||
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
|
||||
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
|
||||
},
|
||||
),
|
||||
]
|
||||
@ -0,0 +1,228 @@
|
||||
# Generated by Django 5.2.1 on 2025-08-26 17:05
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
def populate_url(apps, schema_editor):
|
||||
MODELS = [
|
||||
'User',
|
||||
'Group',
|
||||
'Package',
|
||||
'Compound',
|
||||
'CompoundStructure',
|
||||
'Pathway',
|
||||
'Edge',
|
||||
'Node',
|
||||
'Reaction',
|
||||
'SimpleAmbitRule',
|
||||
'SimpleRDKitRule',
|
||||
'ParallelRule',
|
||||
'SequentialRule',
|
||||
'Scenario',
|
||||
'Setting',
|
||||
'MLRelativeReasoning',
|
||||
'EnviFormer',
|
||||
'ApplicabilityDomain',
|
||||
]
|
||||
for model in MODELS:
|
||||
obj_cls = apps.get_model("epdb", model)
|
||||
for obj in obj_cls.objects.all():
|
||||
obj.url = assemble_url(obj)
|
||||
if obj.url is None:
|
||||
raise ValueError(f"Could not assemble url for {obj}")
|
||||
obj.save()
|
||||
|
||||
|
||||
def assemble_url(obj):
|
||||
from django.conf import settings as s
|
||||
match obj.__class__.__name__:
|
||||
case 'User':
|
||||
return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Group':
|
||||
return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Package':
|
||||
return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Compound':
|
||||
return '{}/compound/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'CompoundStructure':
|
||||
return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
|
||||
case 'SimpleAmbitRule':
|
||||
return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'SimpleRDKitRule':
|
||||
return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'ParallelRule':
|
||||
return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'SequentialRule':
|
||||
return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
|
||||
case 'Reaction':
|
||||
return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Pathway':
|
||||
return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Node':
|
||||
return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
|
||||
case 'Edge':
|
||||
return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
|
||||
case 'MLRelativeReasoning':
|
||||
return '{}/model/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'EnviFormer':
|
||||
return '{}/model/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'ApplicabilityDomain':
|
||||
return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
|
||||
case 'Scenario':
|
||||
return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Setting':
|
||||
return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case _:
|
||||
raise ValueError(f"Unknown model {obj.__class__.__name__}")
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compoundstructure',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='epmodel',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='group',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='package',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='reaction',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='scenario',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='setting',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
|
||||
migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
|
||||
|
||||
migrations.AlterField(
|
||||
model_name='applicabilitydomain',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='compound',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='compoundstructure',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='edge',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='epmodel',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='group',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='node',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='package',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='pathway',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='reaction',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='rule',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='scenario',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='setting',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='user',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
]
|
||||
@ -0,0 +1,55 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-09 09:21
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterModelOptions(
|
||||
name='mlrelativereasoning',
|
||||
options={},
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='RuleBasedRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
|
||||
('min_count', models.IntegerField(default=10)),
|
||||
('max_count', models.IntegerField(default=0)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.DeleteModel(
|
||||
name='RuleBaseRelativeReasoning',
|
||||
),
|
||||
]
|
||||
18
epdb/migrations/0005_alter_group_group_member.py
Normal file
18
epdb/migrations/0005_alter_group_group_member.py
Normal file
@ -0,0 +1,18 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-11 06:21
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterField(
|
||||
model_name='group',
|
||||
name='group_member',
|
||||
field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
|
||||
),
|
||||
]
|
||||
@ -0,0 +1,23 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-18 06:42
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0005_alter_group_group_member'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rulebasedrelativereasoning',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
@ -0,0 +1,53 @@
|
||||
# Generated by Django 5.2.1 on 2025-10-07 08:19
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterModelOptions(
|
||||
name='enviformer',
|
||||
options={},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='eval_results',
|
||||
field=models.JSONField(blank=True, default=dict, null=True),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='model_status',
|
||||
field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
|
||||
),
|
||||
]
|
||||
64
epdb/migrations/0008_enzymelink.py
Normal file
64
epdb/migrations/0008_enzymelink.py
Normal file
@ -0,0 +1,64 @@
|
||||
# Generated by Django 5.2.7 on 2025-10-10 06:58
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="EnzymeLink",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
(
|
||||
"created",
|
||||
model_utils.fields.AutoCreatedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="created"
|
||||
),
|
||||
),
|
||||
(
|
||||
"modified",
|
||||
model_utils.fields.AutoLastModifiedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="modified"
|
||||
),
|
||||
),
|
||||
(
|
||||
"uuid",
|
||||
models.UUIDField(
|
||||
default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
|
||||
),
|
||||
),
|
||||
("name", models.TextField(default="no name", verbose_name="Name")),
|
||||
(
|
||||
"description",
|
||||
models.TextField(default="no description", verbose_name="Descriptions"),
|
||||
),
|
||||
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
|
||||
("kv", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("ec_number", models.TextField(verbose_name="EC Number")),
|
||||
("classification_level", models.IntegerField(verbose_name="Classification Level")),
|
||||
("linking_method", models.TextField(verbose_name="Linking Method")),
|
||||
("edge_evidence", models.ManyToManyField(to="epdb.edge")),
|
||||
("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
|
||||
(
|
||||
"rule",
|
||||
models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
),
|
||||
]
|
||||
66
epdb/migrations/0009_joblog.py
Normal file
66
epdb/migrations/0009_joblog.py
Normal file
@ -0,0 +1,66 @@
|
||||
# Generated by Django 5.2.7 on 2025-10-27 09:39
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0008_enzymelink"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="JobLog",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
(
|
||||
"created",
|
||||
model_utils.fields.AutoCreatedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="created"
|
||||
),
|
||||
),
|
||||
(
|
||||
"modified",
|
||||
model_utils.fields.AutoLastModifiedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="modified"
|
||||
),
|
||||
),
|
||||
("task_id", models.UUIDField(unique=True)),
|
||||
("job_name", models.TextField()),
|
||||
(
|
||||
"status",
|
||||
models.CharField(
|
||||
choices=[
|
||||
("INITIAL", "Initial"),
|
||||
("SUCCESS", "Success"),
|
||||
("FAILURE", "Failure"),
|
||||
("REVOKED", "Revoked"),
|
||||
("IGNORED", "Ignored"),
|
||||
],
|
||||
default="INITIAL",
|
||||
max_length=20,
|
||||
),
|
||||
),
|
||||
("done_at", models.DateTimeField(blank=True, default=None, null=True)),
|
||||
("task_result", models.TextField(blank=True, default=None, null=True)),
|
||||
(
|
||||
"user",
|
||||
models.ForeignKey(
|
||||
on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
),
|
||||
]
|
||||
18
epdb/migrations/0010_license_cc_string.py
Normal file
18
epdb/migrations/0010_license_cc_string.py
Normal file
@ -0,0 +1,18 @@
|
||||
# Generated by Django 5.2.7 on 2025-11-11 14:11
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0009_joblog"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="license",
|
||||
name="cc_string",
|
||||
field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
|
||||
preserve_default=False,
|
||||
),
|
||||
]
|
||||
59
epdb/migrations/0011_auto_20251111_1413.py
Normal file
59
epdb/migrations/0011_auto_20251111_1413.py
Normal file
@ -0,0 +1,59 @@
|
||||
# Generated by Django 5.2.7 on 2025-11-11 14:13
|
||||
|
||||
import re
|
||||
|
||||
from django.contrib.postgres.aggregates import ArrayAgg
|
||||
from django.db import migrations
|
||||
from django.db.models import Min
|
||||
|
||||
|
||||
def set_cc(apps, schema_editor):
|
||||
License = apps.get_model("epdb", "License")
|
||||
|
||||
# For all existing licenses extract cc_string from link
|
||||
for license in License.objects.all():
|
||||
pattern = r"/licenses/([^/]+)/4\.0"
|
||||
match = re.search(pattern, license.link)
|
||||
if match:
|
||||
license.cc_string = match.group(1)
|
||||
license.save()
|
||||
else:
|
||||
raise ValueError(f"Could not find license for {license.link}")
|
||||
|
||||
# Ensure we have all licenses
|
||||
cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
|
||||
for cc_string in cc_strings:
|
||||
if not License.objects.filter(cc_string=cc_string).exists():
|
||||
new_license = License()
|
||||
new_license.cc_string = cc_string
|
||||
new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
|
||||
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
|
||||
new_license.save()
|
||||
|
||||
# As we might have existing Licenses representing the same License,
|
||||
# get min pk and all pks as a list
|
||||
license_lookup_qs = License.objects.values("cc_string").annotate(
|
||||
lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
|
||||
)
|
||||
|
||||
license_lookup = {
|
||||
row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
|
||||
}
|
||||
|
||||
Packages = apps.get_model("epdb", "Package")
|
||||
|
||||
for k, v in license_lookup.items():
|
||||
# Set min pk to all packages pointing to any of the duplicates
|
||||
Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
|
||||
# remove the min pk from "other" pks as we use them for deletion
|
||||
v[1].remove(v[0])
|
||||
# Delete redundant License objects
|
||||
License.objects.filter(pk__in=v[1]).delete()
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0010_license_cc_string"),
|
||||
]
|
||||
|
||||
operations = [migrations.RunPython(set_cc)]
|
||||
@ -0,0 +1,22 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-02 13:09
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0011_auto_20251111_1413"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="node",
|
||||
name="stereo_removed",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="pathway",
|
||||
name="predicted",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
25
epdb/migrations/0013_setting_expansion_schema.py
Normal file
25
epdb/migrations/0013_setting_expansion_schema.py
Normal file
@ -0,0 +1,25 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-14 11:30
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0012_node_stereo_removed_pathway_predicted"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="setting",
|
||||
name="expansion_schema",
|
||||
field=models.CharField(
|
||||
choices=[
|
||||
("BFS", "Breadth First Search"),
|
||||
("DFS", "Depth First Search"),
|
||||
("GREEDY", "Greedy"),
|
||||
],
|
||||
default="BFS",
|
||||
max_length=20,
|
||||
),
|
||||
),
|
||||
]
|
||||
@ -0,0 +1,17 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-14 16:02
|
||||
|
||||
from django.db import migrations
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0013_setting_expansion_schema"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RenameField(
|
||||
model_name="setting",
|
||||
old_name="expansion_schema",
|
||||
new_name="expansion_scheme",
|
||||
),
|
||||
]
|
||||
17
epdb/migrations/0015_user_is_reviewer.py
Normal file
17
epdb/migrations/0015_user_is_reviewer.py
Normal file
@ -0,0 +1,17 @@
|
||||
# Generated by Django 5.2.7 on 2026-01-19 19:26
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="user",
|
||||
name="is_reviewer",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
179
epdb/migrations/0016_remove_enviformer_model_status_and_more.py
Normal file
179
epdb/migrations/0016_remove_enviformer_model_status_and_more.py
Normal file
@ -0,0 +1,179 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-12 09:38
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0015_user_is_reviewer"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RemoveField(
|
||||
model_name="enviformer",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="epmodel",
|
||||
name="model_status",
|
||||
field=models.CharField(
|
||||
choices=[
|
||||
("INITIAL", "Initial"),
|
||||
("INITIALIZING", "Model is initializing."),
|
||||
("BUILDING", "Model is building."),
|
||||
(
|
||||
"BUILT_NOT_EVALUATED",
|
||||
"Model is built and can be used for predictions, Model is not evaluated yet.",
|
||||
),
|
||||
("EVALUATING", "Model is evaluating"),
|
||||
("FINISHED", "Model has finished building and evaluation."),
|
||||
("ERROR", "Model has failed."),
|
||||
],
|
||||
default="INITIAL",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="enviformer",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="enviformer",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name="PropertyPluginModel",
|
||||
fields=[
|
||||
(
|
||||
"epmodel_ptr",
|
||||
models.OneToOneField(
|
||||
auto_created=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
parent_link=True,
|
||||
primary_key=True,
|
||||
serialize=False,
|
||||
to="epdb.epmodel",
|
||||
),
|
||||
),
|
||||
("threshold", models.FloatField(default=0.5)),
|
||||
("eval_results", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("multigen_eval", models.BooleanField(default=False)),
|
||||
("plugin_identifier", models.CharField(max_length=255)),
|
||||
(
|
||||
"app_domain",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
default=None,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.SET_NULL,
|
||||
to="epdb.applicabilitydomain",
|
||||
),
|
||||
),
|
||||
(
|
||||
"data_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_data_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Data Packages",
|
||||
),
|
||||
),
|
||||
(
|
||||
"eval_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
(
|
||||
"rule_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
bases=("epdb.epmodel",),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="setting",
|
||||
name="property_models",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="settings",
|
||||
to="epdb.propertypluginmodel",
|
||||
verbose_name="Setting Property Models",
|
||||
),
|
||||
),
|
||||
migrations.DeleteModel(
|
||||
name="PluginModel",
|
||||
),
|
||||
]
|
||||
93
epdb/migrations/0017_additionalinformation.py
Normal file
93
epdb/migrations/0017_additionalinformation.py
Normal file
@ -0,0 +1,93 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-20 12:02
|
||||
|
||||
import django.db.models.deletion
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("contenttypes", "0002_remove_content_type_name"),
|
||||
("epdb", "0016_remove_enviformer_model_status_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="AdditionalInformation",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
|
||||
("kv", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("type", models.TextField(verbose_name="Additional Information Type")),
|
||||
("data", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
|
||||
(
|
||||
"content_type",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
to="contenttypes.contenttype",
|
||||
),
|
||||
),
|
||||
(
|
||||
"package",
|
||||
models.ForeignKey(
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Package",
|
||||
),
|
||||
),
|
||||
(
|
||||
"scenario",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
related_name="scenario_additional_information",
|
||||
to="epdb.scenario",
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"indexes": [
|
||||
models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
|
||||
models.Index(
|
||||
fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
|
||||
),
|
||||
models.Index(
|
||||
fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
|
||||
),
|
||||
models.Index(
|
||||
fields=["scenario", "content_type", "object_id"],
|
||||
name="epdb_additi_scenari_ef2bf5_idx",
|
||||
),
|
||||
],
|
||||
"constraints": [
|
||||
models.CheckConstraint(
|
||||
condition=models.Q(
|
||||
models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
|
||||
models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
|
||||
_connector="OR",
|
||||
),
|
||||
name="ck_addinfo_gfk_pair",
|
||||
),
|
||||
models.CheckConstraint(
|
||||
condition=models.Q(
|
||||
("scenario__isnull", False),
|
||||
("content_type__isnull", False),
|
||||
_connector="OR",
|
||||
),
|
||||
name="ck_addinfo_not_both_null",
|
||||
),
|
||||
],
|
||||
},
|
||||
),
|
||||
]
|
||||
132
epdb/migrations/0018_auto_20260220_1203.py
Normal file
132
epdb/migrations/0018_auto_20260220_1203.py
Normal file
@ -0,0 +1,132 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-20 12:03
|
||||
|
||||
from django.db import migrations
|
||||
|
||||
|
||||
def get_additional_information(scenario):
|
||||
from envipy_additional_information import registry
|
||||
from envipy_additional_information.parsers import TypeOfAerationParser
|
||||
|
||||
for k, vals in scenario.additional_information.items():
|
||||
if k == "enzyme":
|
||||
continue
|
||||
|
||||
if k == "SpikeConentration":
|
||||
k = "SpikeConcentration"
|
||||
|
||||
if k == "AerationType":
|
||||
k = "TypeOfAeration"
|
||||
|
||||
for v in vals:
|
||||
# Per default additional fields are ignored
|
||||
MAPPING = {c.__name__: c for c in registry.list_models().values()}
|
||||
try:
|
||||
inst = MAPPING[k](**v)
|
||||
except Exception:
|
||||
if k == "TypeOfAeration":
|
||||
toa = TypeOfAerationParser()
|
||||
inst = toa.from_string(v["type"])
|
||||
|
||||
# Add uuid to uniquely identify objects for manipulation
|
||||
if "uuid" in v:
|
||||
inst.__dict__["uuid"] = v["uuid"]
|
||||
|
||||
yield inst
|
||||
|
||||
|
||||
def forward_func(apps, schema_editor):
|
||||
Scenario = apps.get_model("epdb", "Scenario")
|
||||
ContentType = apps.get_model("contenttypes", "ContentType")
|
||||
AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
|
||||
|
||||
bulk = []
|
||||
related = []
|
||||
ctype = {o.model: o for o in ContentType.objects.all()}
|
||||
parents = Scenario.objects.prefetch_related(
|
||||
"compound_set",
|
||||
"compoundstructure_set",
|
||||
"reaction_set",
|
||||
"rule_set",
|
||||
"pathway_set",
|
||||
"node_set",
|
||||
"edge_set",
|
||||
).filter(parent__isnull=True)
|
||||
|
||||
for i, scenario in enumerate(parents):
|
||||
print(f"{i + 1}/{len(parents)}", end="\r")
|
||||
if scenario.parent is not None:
|
||||
related.append(scenario.parent)
|
||||
continue
|
||||
|
||||
for ai in get_additional_information(scenario):
|
||||
bulk.append(
|
||||
AdditionalInformation(
|
||||
package=scenario.package,
|
||||
scenario=scenario,
|
||||
type=ai.__class__.__name__,
|
||||
data=ai.model_dump(mode="json"),
|
||||
)
|
||||
)
|
||||
|
||||
print("\n", len(bulk))
|
||||
|
||||
related = Scenario.objects.prefetch_related(
|
||||
"compound_set",
|
||||
"compoundstructure_set",
|
||||
"reaction_set",
|
||||
"rule_set",
|
||||
"pathway_set",
|
||||
"node_set",
|
||||
"edge_set",
|
||||
).filter(parent__isnull=False)
|
||||
|
||||
for i, scenario in enumerate(related):
|
||||
print(f"{i + 1}/{len(related)}", end="\r")
|
||||
parent = scenario.parent
|
||||
# Check to which objects this scenario is attached to
|
||||
for ai in get_additional_information(scenario):
|
||||
rel_objs = [
|
||||
"compound",
|
||||
"compoundstructure",
|
||||
"reaction",
|
||||
"rule",
|
||||
"pathway",
|
||||
"node",
|
||||
"edge",
|
||||
]
|
||||
for rel_obj in rel_objs:
|
||||
for o in getattr(scenario, f"{rel_obj}_set").all():
|
||||
bulk.append(
|
||||
AdditionalInformation(
|
||||
package=scenario.package,
|
||||
scenario=parent,
|
||||
type=ai.__class__.__name__,
|
||||
data=ai.model_dump(mode="json"),
|
||||
content_type=ctype[rel_obj],
|
||||
object_id=o.pk,
|
||||
)
|
||||
)
|
||||
|
||||
print("Start creating additional information objects...")
|
||||
AdditionalInformation.objects.bulk_create(bulk)
|
||||
print("Done!")
|
||||
print(len(bulk))
|
||||
|
||||
Scenario.objects.filter(parent__isnull=False).delete()
|
||||
# Call ai save to fix urls
|
||||
ais = AdditionalInformation.objects.all()
|
||||
total = ais.count()
|
||||
|
||||
for i, ai in enumerate(ais):
|
||||
print(f"{i + 1}/{total}", end="\r")
|
||||
ai.save()
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0017_additionalinformation"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
|
||||
]
|
||||
@ -1,741 +1,20 @@
|
||||
# Generated by Django 5.2.7 on 2026-03-06 10:51
|
||||
# Generated by Django 5.2.7 on 2026-02-23 08:45
|
||||
|
||||
import django.contrib.auth.models
|
||||
import django.contrib.auth.validators
|
||||
import django.contrib.postgres.fields
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
from django.db import migrations
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
initial = True
|
||||
|
||||
dependencies = [
|
||||
('auth', '0012_alter_user_first_name_max_length'),
|
||||
('contenttypes', '0002_remove_content_type_name'),
|
||||
migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
|
||||
("epdb", "0018_auto_20260220_1203"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name='ApplicabilityDomain',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('num_neighbours', models.IntegerField(default=5)),
|
||||
('reliability_threshold', models.FloatField(default=0.5)),
|
||||
('local_compatibilty_threshold', models.FloatField(default=0.5)),
|
||||
('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
migrations.RemoveField(
|
||||
model_name="scenario",
|
||||
name="additional_information",
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Edge',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EPModel',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalDatabase',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
|
||||
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
|
||||
('description', models.TextField(blank=True, verbose_name='Description')),
|
||||
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
|
||||
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
|
||||
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Database',
|
||||
'verbose_name_plural': 'External Databases',
|
||||
'db_table': 'epdb_external_database',
|
||||
'ordering': ['name'],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Permission',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='License',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('cc_string', models.TextField(verbose_name='CC string')),
|
||||
('link', models.URLField(verbose_name='link')),
|
||||
('image_link', models.URLField(verbose_name='Image link')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Rule',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='User',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('password', models.CharField(max_length=128, verbose_name='password')),
|
||||
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
|
||||
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
|
||||
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
|
||||
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
|
||||
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
|
||||
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
|
||||
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
|
||||
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
|
||||
('email', models.EmailField(max_length=254, unique=True)),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('is_reviewer', models.BooleanField(default=False)),
|
||||
('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
|
||||
('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
|
||||
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'user',
|
||||
'verbose_name_plural': 'users',
|
||||
'abstract': False,
|
||||
},
|
||||
managers=[
|
||||
('objects', django.contrib.auth.models.UserManager()),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='APIToken',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
|
||||
('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
|
||||
('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
|
||||
('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
|
||||
('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'API Token',
|
||||
'verbose_name_plural': 'API Tokens',
|
||||
'db_table': 'epdb_api_token',
|
||||
'ordering': ['-created'],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Compound',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='CompoundStructure',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('smiles', models.TextField(verbose_name='SMILES')),
|
||||
('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
|
||||
('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
|
||||
('normalized_structure', models.BooleanField(default=False)),
|
||||
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='default_structure',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='PropertyPluginModel',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('plugin_identifier', models.CharField(max_length=255)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Group',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('name', models.TextField(verbose_name='Group name')),
|
||||
('public', models.BooleanField(default=False, verbose_name='Public Group')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
|
||||
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
|
||||
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_group',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='JobLog',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('task_id', models.UUIDField(unique=True)),
|
||||
('job_name', models.TextField()),
|
||||
('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
|
||||
('done_at', models.DateTimeField(blank=True, default=None, null=True)),
|
||||
('task_result', models.TextField(blank=True, default=None, null=True)),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Package',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
|
||||
('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
|
||||
],
|
||||
options={
|
||||
'swappable': 'EPDB_PACKAGE_MODEL',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Node',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('depth', models.IntegerField(verbose_name='Node depth')),
|
||||
('stereo_removed', models.BooleanField(default=False)),
|
||||
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
|
||||
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
|
||||
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='end_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='start_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Pathway',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('predicted', models.BooleanField(default=False)),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Reaction',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
|
||||
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
|
||||
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
|
||||
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EnzymeLink',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('ec_number', models.TextField(verbose_name='EC Number')),
|
||||
('classification_level', models.IntegerField(verbose_name='Classification Level')),
|
||||
('linking_method', models.TextField(verbose_name='Linking Method')),
|
||||
('edge_evidence', models.ManyToManyField(to='epdb.edge')),
|
||||
('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
|
||||
('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='edge_label',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Scenario',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('scenario_date', models.CharField(default='No date', max_length=256)),
|
||||
('scenario_type', models.CharField(default='Not specified', max_length=256)),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='reaction',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compoundstructure',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Setting',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('public', models.BooleanField(default=False)),
|
||||
('global_default', models.BooleanField(default=False)),
|
||||
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
|
||||
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
|
||||
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
|
||||
('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
|
||||
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
|
||||
('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='setting',
|
||||
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_setting',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EnviFormer',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='MLRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='model',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='RuleBasedRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('min_count', models.IntegerField(default=10)),
|
||||
('max_count', models.IntegerField(default=0)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalIdentifier',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('object_id', models.IntegerField()),
|
||||
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
|
||||
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
|
||||
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
|
||||
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Identifier',
|
||||
'verbose_name_plural': 'External Identifiers',
|
||||
'db_table': 'epdb_external_identifier',
|
||||
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
|
||||
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleAmbitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('smirks', models.TextField(verbose_name='SMIRKS')),
|
||||
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
|
||||
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRDKitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRuleOrdering',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('order_index', models.IntegerField()),
|
||||
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
|
||||
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
|
||||
],
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='sequentialrule',
|
||||
name='simple_rules',
|
||||
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ParallelRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.AlterUniqueTogether(
|
||||
name='compound',
|
||||
unique_together={('uuid', 'package')},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='AdditionalInformation',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('type', models.TextField(verbose_name='Additional Information Type')),
|
||||
('data', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
|
||||
('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
|
||||
],
|
||||
options={
|
||||
'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
|
||||
'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='GroupPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'group')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserSettingPermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('setting', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
migrations.RemoveField(
|
||||
model_name="scenario",
|
||||
name="parent",
|
||||
),
|
||||
]
|
||||
|
||||
@ -1,50 +1,49 @@
|
||||
# Generated by Django 6.0.3 on 2026-04-14 19:07
|
||||
# Generated by Django 6.0.3 on 2026-04-21 11:43
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0022_alter_classifierpluginmodel_data_packages_and_more'),
|
||||
("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterModelOptions(
|
||||
name='compoundstructure',
|
||||
name="compoundstructure",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='epmodel',
|
||||
name="epmodel",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='parallelrule',
|
||||
name="parallelrule",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='rule',
|
||||
name="rule",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='sequentialrule',
|
||||
name="sequentialrule",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='simpleambitrule',
|
||||
name="simpleambitrule",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='simplerdkitrule',
|
||||
name="simplerdkitrule",
|
||||
options={},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='simplerule',
|
||||
name="simplerule",
|
||||
options={},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='group',
|
||||
name='secret',
|
||||
field=models.BooleanField(default=False, verbose_name='Secret Group'),
|
||||
model_name="compoundstructure",
|
||||
name="molfile",
|
||||
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
|
||||
),
|
||||
]
|
||||
|
||||
17
epdb/migrations/0024_user_contacted.py
Normal file
17
epdb/migrations/0024_user_contacted.py
Normal file
@ -0,0 +1,17 @@
|
||||
# Generated by Django 6.0.3 on 2026-04-21 19:56
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0023_alter_compoundstructure_options_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="user",
|
||||
name="contacted",
|
||||
field=models.BooleanField(blank=True, null=True),
|
||||
),
|
||||
]
|
||||
56
epdb/migrations/0025_auto_20260511_2025.py
Normal file
56
epdb/migrations/0025_auto_20260511_2025.py
Normal file
@ -0,0 +1,56 @@
|
||||
# Generated by Django 6.0.3 on 2026-05-11 20:25
|
||||
|
||||
from django.db import migrations
|
||||
from envipy_additional_information import HalfLife, HalfLifeModel, HalfLifeWS
|
||||
|
||||
MAPPING = {
|
||||
"": HalfLifeModel.OTHER,
|
||||
"HS-SFO": HalfLifeModel.HS_SFO,
|
||||
"FOMC": HalfLifeModel.FOMC,
|
||||
"FOTC": HalfLifeModel.DFOP,
|
||||
"FMOC": HalfLifeModel.FOMC,
|
||||
"DFOP": HalfLifeModel.DFOP,
|
||||
"SFO + SFO": HalfLifeModel.SFO_SFO,
|
||||
"FOMC-SFO": HalfLifeModel.FOMC_SFO,
|
||||
"first order kinetics": HalfLifeModel.SFO,
|
||||
"SFO²": HalfLifeModel.SFO,
|
||||
"HS": HalfLifeModel.HS,
|
||||
"top down": HalfLifeModel.OTHER,
|
||||
"SFO": HalfLifeModel.SFO,
|
||||
"First Order": HalfLifeModel.SFO,
|
||||
"SFO/SFO": HalfLifeModel.SFO_SFO,
|
||||
"FOMC + SFO": HalfLifeModel.FOMC_SFO,
|
||||
"true": HalfLifeModel.SFO,
|
||||
"SFO-SFO": HalfLifeModel.SFO_SFO,
|
||||
"DFOP-SFO": HalfLifeModel.DFOP_SFO,
|
||||
}
|
||||
|
||||
|
||||
def forward_func(apps, schema_editor):
|
||||
AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
|
||||
|
||||
hls = AdditionalInformation.objects.filter(type="HalfLife")
|
||||
|
||||
for hl in hls:
|
||||
data = hl.data
|
||||
data["model"] = MAPPING[data["model"]].value
|
||||
hl.data = HalfLife(**data).model_dump(mode="json")
|
||||
hl.save()
|
||||
|
||||
hlws = AdditionalInformation.objects.filter(type="HalfLifeWS")
|
||||
|
||||
for hl in hlws:
|
||||
data = hl.data
|
||||
data["model"] = MAPPING[data["model"]].value
|
||||
hl.data = HalfLifeWS(**data).model_dump(mode="json")
|
||||
hl.save()
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0024_user_contacted"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
|
||||
]
|
||||
@ -75,6 +75,7 @@ class User(AbstractUser):
|
||||
blank=False,
|
||||
)
|
||||
is_reviewer = models.BooleanField(default=False)
|
||||
contacted = models.BooleanField(null=True, blank=True)
|
||||
|
||||
USERNAME_FIELD = "email"
|
||||
REQUIRED_FIELDS = ["username"]
|
||||
@ -203,7 +204,6 @@ class Group(TimeStampedModel):
|
||||
name = models.TextField(blank=False, null=False, verbose_name="Group name")
|
||||
owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
|
||||
public = models.BooleanField(verbose_name="Public Group", default=False)
|
||||
secret = models.BooleanField(verbose_name="Secret Group", default=False)
|
||||
description = models.TextField(
|
||||
blank=False, null=False, verbose_name="Descriptions", default="no description"
|
||||
)
|
||||
@ -1113,6 +1113,7 @@ class CompoundStructure(
|
||||
canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
|
||||
inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
|
||||
normalized_structure = models.BooleanField(null=False, blank=False, default=False)
|
||||
molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
|
||||
|
||||
external_identifiers = GenericRelation("ExternalIdentifier")
|
||||
|
||||
@ -1209,6 +1210,9 @@ class CompoundStructure(
|
||||
|
||||
return dict(hls)
|
||||
|
||||
def d3_json(self):
|
||||
return {}
|
||||
|
||||
|
||||
class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
|
||||
rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
|
||||
@ -2174,6 +2178,56 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
|
||||
):
|
||||
return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
|
||||
|
||||
def update_depths(self):
|
||||
# Collect number of in and out links per node
|
||||
in_count = defaultdict(lambda: 0)
|
||||
out_count = defaultdict(lambda: 0)
|
||||
|
||||
for e in self.edges:
|
||||
for react in e.start_nodes.all():
|
||||
out_count[str(react.uuid)] += 1
|
||||
|
||||
for prod in e.end_nodes.all():
|
||||
in_count[str(prod.uuid)] += 1
|
||||
|
||||
depth_map = {}
|
||||
depth_map[0] = list()
|
||||
|
||||
for n in self.nodes:
|
||||
num_parents = in_count[str(n.uuid)]
|
||||
if num_parents == 0:
|
||||
# must be a root node or unconnected node
|
||||
if n.depth != 0:
|
||||
n.depth = 0
|
||||
n.save()
|
||||
|
||||
# Only root node may have children
|
||||
if out_count[str(n.uuid)] > 0:
|
||||
depth_map[0].append(n)
|
||||
|
||||
# At most depth len(nodes) is possible
|
||||
for i in range(self.nodes.count()):
|
||||
level_nodes = depth_map.get(i, [])
|
||||
|
||||
if len(level_nodes) == 0:
|
||||
break
|
||||
|
||||
unique_next_level = set()
|
||||
for n in level_nodes:
|
||||
for e in self.edges:
|
||||
if n in e.start_nodes.all():
|
||||
for p in e.end_nodes.all():
|
||||
unique_next_level.add(p)
|
||||
|
||||
if len(unique_next_level) > 0:
|
||||
depth_map[i + 1] = list(unique_next_level)
|
||||
|
||||
for depth, nodes in depth_map.items():
|
||||
for n in nodes:
|
||||
if n.depth != depth:
|
||||
n.depth = depth
|
||||
n.save()
|
||||
|
||||
|
||||
class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
|
||||
pathway = models.ForeignKey(
|
||||
@ -2215,7 +2269,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
|
||||
if isinstance(ai.get(), PropertyPrediction):
|
||||
predicted_properties[ai.get().__class__.__name__].append(ai.data)
|
||||
|
||||
return {
|
||||
# If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
|
||||
# by overwriting keys
|
||||
structure_data = self.default_node_label.d3_json()
|
||||
|
||||
res = {
|
||||
"depth": self.depth,
|
||||
"stereo_removed": self.stereo_removed,
|
||||
"url": self.url,
|
||||
@ -2224,6 +2282,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
|
||||
"image_svg": IndigoUtils.mol_to_svg(
|
||||
self.default_node_label.smiles, width=40, height=40
|
||||
),
|
||||
"image_type": "svg",
|
||||
"name": self.get_name(),
|
||||
"smiles": self.default_node_label.smiles,
|
||||
"scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
|
||||
@ -2236,8 +2295,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
|
||||
"predicted_properties": predicted_properties,
|
||||
"is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
|
||||
"timeseries": self.get_timeseries_data(),
|
||||
**structure_data,
|
||||
}
|
||||
|
||||
return res
|
||||
|
||||
@staticmethod
|
||||
@transaction.atomic
|
||||
def create(
|
||||
|
||||
@ -587,38 +587,10 @@ def packages(request):
|
||||
"package-description", s.DEFAULT_VALUES["description"]
|
||||
)
|
||||
|
||||
# EDIT START
|
||||
data_pool = None
|
||||
package_classification = request.POST.get("package-classification")
|
||||
classification = Package.Classification(int(package_classification))
|
||||
# For SECRET we'll need a data pool which will be an additional perm check later
|
||||
if classification == Package.Classification.SECRET:
|
||||
package_data_pool = request.POST.get("package-data-pool")
|
||||
|
||||
if package_data_pool is None:
|
||||
return error(request, "Invalid data pool.", "Data Pool is required!")
|
||||
|
||||
data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
|
||||
|
||||
if data_pool is None:
|
||||
return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
|
||||
|
||||
if not data_pool.secret:
|
||||
return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
|
||||
|
||||
created_package = PackageManager.create_package(
|
||||
current_user, package_name, package_description
|
||||
)
|
||||
|
||||
created_package.classification_level = classification
|
||||
|
||||
# Set previously determined data pool
|
||||
if classification == Package.Classification.SECRET:
|
||||
created_package.data_pool = data_pool
|
||||
|
||||
created_package.save()
|
||||
# EDIT END
|
||||
|
||||
return redirect(created_package.url)
|
||||
|
||||
elif request.method == "OPTIONS":
|
||||
@ -2534,6 +2506,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
|
||||
substrate_nodes, product_nodes, name=edge_name, description=edge_description
|
||||
)
|
||||
|
||||
# Update depths as sideeffect of above operation
|
||||
current_pathway.update_depths()
|
||||
|
||||
return redirect(current_pathway.url)
|
||||
|
||||
else:
|
||||
|
||||
@ -46,7 +46,7 @@ class PepperPrediction(PropertyPrediction):
|
||||
|
||||
import matplotlib.patches as mpatches
|
||||
import numpy as np
|
||||
from matplotlib import pyplot as plt
|
||||
from matplotlib.figure import Figure
|
||||
from scipy import stats
|
||||
|
||||
"""
|
||||
@ -101,7 +101,8 @@ class PepperPrediction(PropertyPrediction):
|
||||
mask_red = x > vp
|
||||
|
||||
# Plot
|
||||
fig, ax = plt.subplots(figsize=(9, 5.5))
|
||||
fig = Figure(figsize=(9, 5.5))
|
||||
ax = fig.subplots()
|
||||
ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
|
||||
|
||||
if np.any(mask_green):
|
||||
@ -146,13 +147,12 @@ class PepperPrediction(PropertyPrediction):
|
||||
]
|
||||
ax.legend(handles=patches, frameon=True)
|
||||
|
||||
plt.tight_layout()
|
||||
fig.tight_layout()
|
||||
|
||||
# --- Export to SVG string ---
|
||||
buf = io.StringIO()
|
||||
fig.savefig(buf, format="svg", bbox_inches="tight")
|
||||
svg = buf.getvalue()
|
||||
plt.close(fig)
|
||||
buf.close()
|
||||
|
||||
return svg
|
||||
|
||||
@ -187,8 +187,9 @@ class Pepper:
|
||||
groups = [group for group in dataset.group_by("structure_id")]
|
||||
|
||||
# Unless explicitly set compute everything serial
|
||||
if os.environ.get("N_PEPPER_THREADS", 1) > 1:
|
||||
results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
|
||||
n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
|
||||
if n_threads > 1:
|
||||
results = Parallel(n_jobs=n_threads)(
|
||||
delayed(compute_bayes_per_group)(group[1])
|
||||
for group in dataset.group_by("structure_id")
|
||||
)
|
||||
|
||||
@ -637,44 +637,56 @@ function draw(pathway, elem) {
|
||||
node.filter(d => !d.pseudo).each(function (d, i) {
|
||||
const g = d3.select(this);
|
||||
|
||||
// Parse the SVG string
|
||||
const parser = new DOMParser();
|
||||
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
|
||||
const svgElem = svgDoc.documentElement;
|
||||
if (d.image_type === "svg") {
|
||||
// Parse the SVG string
|
||||
const parser = new DOMParser();
|
||||
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
|
||||
const svgElem = svgDoc.documentElement;
|
||||
|
||||
// Create a unique prefix per node
|
||||
const prefix = `node-${i}-`;
|
||||
// Create a unique prefix per node
|
||||
const prefix = `node-${i}-`;
|
||||
|
||||
// Rename all IDs and fix <use> references
|
||||
svgElem.querySelectorAll('[id]').forEach(el => {
|
||||
const oldId = el.id;
|
||||
const newId = prefix + oldId;
|
||||
el.id = newId;
|
||||
// Rename all IDs and fix <use> references
|
||||
svgElem.querySelectorAll("[id]").forEach(el => {
|
||||
const oldId = el.id;
|
||||
const newId = prefix + oldId;
|
||||
el.id = newId;
|
||||
|
||||
const XLINK_NS = "http://www.w3.org/1999/xlink";
|
||||
// Update <use> elements that reference this old ID
|
||||
const uses = Array.from(svgElem.querySelectorAll('use')).filter(
|
||||
u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
|
||||
);
|
||||
const XLINK_NS = "http://www.w3.org/1999/xlink";
|
||||
// Update <use> elements that reference this old ID
|
||||
const uses = Array.from(svgElem.querySelectorAll("use")).filter(
|
||||
u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
|
||||
);
|
||||
|
||||
uses.forEach(u => {
|
||||
u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
|
||||
uses.forEach(u => {
|
||||
u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
|
||||
});
|
||||
});
|
||||
});
|
||||
|
||||
g.node().appendChild(svgElem);
|
||||
g.node().appendChild(svgElem);
|
||||
|
||||
const vb = svgElem.viewBox.baseVal;
|
||||
const svgWidth = vb.width || 40;
|
||||
const svgHeight = vb.height || 40;
|
||||
const vb = svgElem.viewBox.baseVal;
|
||||
const svgWidth = vb.width || 40;
|
||||
const svgHeight = vb.height || 40;
|
||||
|
||||
const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
|
||||
const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
|
||||
|
||||
g.select("svg")
|
||||
.attr("width", svgWidth * scale)
|
||||
.attr("height", svgHeight * scale)
|
||||
.attr("x", -svgWidth * scale / 2)
|
||||
.attr("y", -svgHeight * scale / 2);
|
||||
} else {
|
||||
// We have a image type different than svg
|
||||
// include it via img url
|
||||
g.append("svg:image")
|
||||
.attr("xlink:href", d.image)
|
||||
.attr("width", 40)
|
||||
.attr("height", 40)
|
||||
.attr("x", -20)
|
||||
.attr("y", -20);
|
||||
}
|
||||
|
||||
g.select("svg")
|
||||
.attr("width", svgWidth * scale)
|
||||
.attr("height", svgHeight * scale)
|
||||
.attr("x", -svgWidth * scale / 2)
|
||||
.attr("y", -svgHeight * scale / 2);
|
||||
});
|
||||
|
||||
// add element to nodes array
|
||||
|
||||
@ -1,3 +1,5 @@
|
||||
{% load envipytags %}
|
||||
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
@ -15,6 +17,11 @@
|
||||
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a
|
||||
>
|
||||
</li>
|
||||
{% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
|
||||
|
||||
{% for tpl in action_button_templates %}
|
||||
{% include tpl %}
|
||||
{% endfor %}
|
||||
<li role="separator" class="divider"></li>
|
||||
{% endif %}
|
||||
<li>
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
{% extends "framework_modern.html" %}
|
||||
{% load envipytags %}
|
||||
|
||||
{% block content %}
|
||||
|
||||
@ -82,6 +83,12 @@
|
||||
<div class="collapse-content">{{ compound.description }}</div>
|
||||
</div>
|
||||
|
||||
<!-- Extension Slot for Viz -->
|
||||
{% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
|
||||
{% for tpl in viz_templates %}
|
||||
{% include tpl %}
|
||||
{% endfor %}
|
||||
|
||||
<!-- Image Representation -->
|
||||
<div class="collapse-arrow bg-base-200 collapse">
|
||||
<input type="checkbox" checked />
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
{% extends "framework_modern.html" %}
|
||||
{% load envipytags %}
|
||||
|
||||
{% block content %}
|
||||
|
||||
@ -50,6 +51,12 @@
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<!-- Extension Slot for Viz -->
|
||||
{% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
|
||||
{% for tpl in viz_templates %}
|
||||
{% include tpl %}
|
||||
{% endfor %}
|
||||
|
||||
<!-- Image Representation -->
|
||||
<div class="collapse-arrow bg-base-200 collapse">
|
||||
<input type="checkbox" checked />
|
||||
|
||||
@ -1,5 +1,7 @@
|
||||
{% extends "framework_modern.html" %}
|
||||
{% load static %}
|
||||
{% load envipytags %}
|
||||
|
||||
{% block content %}
|
||||
<script src="https://d3js.org/d3.v7.min.js"></script>
|
||||
<style>
|
||||
@ -76,6 +78,10 @@
|
||||
{% block action_modals %}
|
||||
{% include "modals/objects/add_pathway_node_modal.html" %}
|
||||
{% include "modals/objects/add_pathway_edge_modal.html" %}
|
||||
{% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
|
||||
{% for tpl in add_templates %}
|
||||
{% include tpl %}
|
||||
{% endfor %}
|
||||
{% include "modals/objects/download_pathway_csv_modal.html" %}
|
||||
{% include "modals/objects/download_pathway_image_modal.html" %}
|
||||
{% include "modals/objects/identify_missing_rules_modal.html" %}
|
||||
|
||||
@ -88,6 +88,10 @@ class FormatConverter(object):
|
||||
def from_smiles(smiles):
|
||||
return Chem.MolFromSmiles(smiles)
|
||||
|
||||
@staticmethod
|
||||
def from_molfile(molfile: str):
|
||||
return Chem.MolFromMolBlock(molfile)
|
||||
|
||||
@staticmethod
|
||||
def to_smiles(mol, canonical=False):
|
||||
return Chem.MolToSmiles(mol, canonical=canonical)
|
||||
@ -171,12 +175,17 @@ class FormatConverter(object):
|
||||
try:
|
||||
Chem.Kekulize(mol)
|
||||
except Exception:
|
||||
mc = Chem.Mol(mol.ToBinary())
|
||||
mol = Chem.Mol(mol.ToBinary())
|
||||
|
||||
if not mc.GetNumConformers():
|
||||
Chem.rdDepictor.Compute2DCoords(mc)
|
||||
if not mol.GetNumConformers():
|
||||
Chem.rdDepictor.Compute2DCoords(mol)
|
||||
|
||||
pass
|
||||
drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
|
||||
opts = drawer.drawOptions()
|
||||
opts.clearBackground = False
|
||||
drawer.DrawMolecule(mol)
|
||||
drawer.FinishDrawing()
|
||||
return drawer.GetDrawingText()
|
||||
|
||||
@staticmethod
|
||||
def normalize(smiles):
|
||||
|
||||
@ -64,7 +64,7 @@
|
||||
|
||||
import logging
|
||||
|
||||
from envipy_additional_information import HalfLife, HalfLifeWS
|
||||
from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
|
||||
from envipy_additional_information.information import Interval
|
||||
from envipy_additional_information.parsers import (
|
||||
AcidityParser,
|
||||
@ -473,17 +473,12 @@ def build_additional_information_from_request(request, type_):
|
||||
|
||||
comment = get_parameter_or_empty_string(request, "comment")
|
||||
source = get_parameter_or_empty_string(request, "source")
|
||||
first_order = get_parameter_or_empty_string(request, "firstOrder")
|
||||
# first_order = get_parameter_or_empty_string(request, "firstOrder")
|
||||
model = get_parameter_or_empty_string(request, "model")
|
||||
fit = get_parameter_or_empty_string(request, "fit")
|
||||
|
||||
if first_order != "":
|
||||
if model != "":
|
||||
raise ValueError("not both, model and firstOrder can be set!")
|
||||
if first_order == "true":
|
||||
model = "SFO"
|
||||
else:
|
||||
logger.info("firstOrder is set to false which is not meaningful")
|
||||
if model:
|
||||
model = HalfLifeModel(model.upper())
|
||||
|
||||
return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
|
||||
|
||||
@ -508,6 +503,10 @@ def build_additional_information_from_request(request, type_):
|
||||
comment_ws = get_parameter_or_empty_string(request, "comment_ws")
|
||||
source_ws = get_parameter_or_empty_string(request, "source_ws")
|
||||
model_ws = get_parameter_or_empty_string(request, "model_ws")
|
||||
|
||||
if model_ws:
|
||||
model_ws = HalfLifeModel(model_ws.upper())
|
||||
|
||||
fit_ws = get_parameter_or_empty_string(request, "fit_ws")
|
||||
|
||||
dt50_total = IntervalParser.from_string(hl_ws_total)
|
||||
|
||||
180
uv.lock
generated
180
uv.lock
generated
@ -17,7 +17,7 @@ wheels = [
|
||||
|
||||
[[package]]
|
||||
name = "aiohttp"
|
||||
version = "3.13.3"
|
||||
version = "3.13.5"
|
||||
source = { registry = "https://pypi.org/simple" }
|
||||
dependencies = [
|
||||
{ name = "aiohappyeyeballs" },
|
||||
@ -28,76 +28,76 @@ dependencies = [
|
||||
{ name = "propcache" },
|
||||
{ name = "yarl" },
|
||||
]
|
||||
sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
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||||
sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
|
||||
wheels = [
|
||||
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||||
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Reference in New Issue
Block a user