forked from enviPath/enviPy
Make URL a Field instead a property (#63)
This PR adds a new Field to all existing Models. As its a data migrations the Migration is added. Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#63
This commit is contained in:
50
epdb/management/commands/localize_urls.py
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50
epdb/management/commands/localize_urls.py
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@ -0,0 +1,50 @@
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from django.apps import apps
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from django.core.management.base import BaseCommand
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from django.db.models import F, Value
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from django.db.models.functions import Replace
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class Command(BaseCommand):
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def add_arguments(self, parser):
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parser.add_argument(
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'--old',
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type=str,
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help='Old Host, most likely https://envipath.org/',
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required=True,
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)
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parser.add_argument(
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'--new',
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type=str,
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help='New Host, most likely http://localhost:8000/',
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required=True,
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)
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def handle(self, *args, **options):
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MODELS = [
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'User',
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'Group',
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'Package',
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'Compound',
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'CompoundStructure',
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'Pathway',
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'Edge',
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'Node',
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'Reaction',
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'SimpleAmbitRule',
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'SimpleRDKitRule',
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'ParallelRule',
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'SequentialRule',
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'Scenario',
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'Setting',
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'MLRelativeReasoning',
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'EnviFormer',
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'ApplicabilityDomain',
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]
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for model in MODELS:
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obj_cls = apps.get_model("epdb", model)
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print(f"Localizing urls for {model}")
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obj_cls.objects.update(
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url=Replace(F('url'), Value(options['old']), Value(options['new']))
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)
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594
epdb/migrations/0001_initial.py
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594
epdb/migrations/0001_initial.py
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@ -0,0 +1,594 @@
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# Generated by Django 5.2.1 on 2025-07-22 20:58
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import datetime
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import django.contrib.auth.models
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import django.contrib.auth.validators
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import django.contrib.postgres.fields
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import django.db.models.deletion
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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.conf import settings
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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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('auth', '0012_alter_user_first_name_max_length'),
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('contenttypes', '0002_remove_content_type_name'),
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]
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operations = [
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migrations.CreateModel(
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name='Compound',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
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],
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),
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migrations.CreateModel(
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name='EPModel',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('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')),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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),
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migrations.CreateModel(
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name='Permission',
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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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('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
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],
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),
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migrations.CreateModel(
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name='License',
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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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('link', models.URLField(verbose_name='link')),
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('image_link', models.URLField(verbose_name='Image link')),
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],
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),
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migrations.CreateModel(
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name='Rule',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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),
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migrations.CreateModel(
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name='User',
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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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('password', models.CharField(max_length=128, verbose_name='password')),
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('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
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('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
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('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')),
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('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
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('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
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('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
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('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')),
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('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
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('email', models.EmailField(max_length=254, unique=True)),
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('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
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('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')),
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('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')),
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],
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options={
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'verbose_name': 'user',
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'verbose_name_plural': 'users',
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'abstract': False,
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},
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managers=[
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('objects', django.contrib.auth.models.UserManager()),
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],
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),
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migrations.CreateModel(
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name='APIToken',
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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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('hashed_key', models.CharField(max_length=128, unique=True)),
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('created', models.DateTimeField(auto_now_add=True)),
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('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
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('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
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('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
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],
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),
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migrations.CreateModel(
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name='CompoundStructure',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
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('smiles', models.TextField(verbose_name='SMILES')),
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('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
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('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
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('normalized_structure', models.BooleanField(default=False)),
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('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
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],
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options={
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'abstract': False,
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},
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),
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migrations.AddField(
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model_name='compound',
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name='default_structure',
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field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
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),
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migrations.CreateModel(
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name='Edge',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
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('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
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('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')),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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),
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migrations.CreateModel(
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name='EnviFormer',
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fields=[
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('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')),
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('threshold', models.FloatField(default=0.5)),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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bases=('epdb.epmodel',),
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),
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migrations.CreateModel(
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name='PluginModel',
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fields=[
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('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')),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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bases=('epdb.epmodel',),
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),
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migrations.CreateModel(
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name='RuleBaseRelativeReasoning',
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fields=[
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('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')),
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],
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options={
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'abstract': False,
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'base_manager_name': 'objects',
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},
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bases=('epdb.epmodel',),
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),
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migrations.CreateModel(
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name='Group',
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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(verbose_name='Group name')),
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('public', models.BooleanField(default=False, verbose_name='Public Group')),
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('description', models.TextField(default='no description', verbose_name='Descriptions')),
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('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
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('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
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('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
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],
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options={
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'abstract': False,
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},
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),
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migrations.AddField(
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model_name='user',
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name='default_group',
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field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
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),
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migrations.CreateModel(
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name='Node',
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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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('kv', models.JSONField(blank=True, default=dict, null=True)),
|
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('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
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('depth', models.IntegerField(verbose_name='Node depth')),
|
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('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')),
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('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
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('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
|
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],
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options={
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'abstract': False,
|
||||
},
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),
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migrations.AddField(
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model_name='edge',
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name='end_nodes',
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field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
|
||||
),
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migrations.AddField(
|
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model_name='edge',
|
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name='start_nodes',
|
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field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
|
||||
),
|
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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')),
|
||||
('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 +1,229 @@
|
||||
# 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)
|
||||
print(f"Populating url for {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 '{}/user/{}'.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'),
|
||||
),
|
||||
]
|
||||
@ -37,9 +37,8 @@ logger = logging.getLogger(__name__)
|
||||
|
||||
class User(AbstractUser):
|
||||
email = models.EmailField(unique=True)
|
||||
|
||||
uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True,
|
||||
default=uuid4)
|
||||
uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
|
||||
url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
|
||||
default_package = models.ForeignKey('epdb.Package', verbose_name='Default Package', null=True,
|
||||
on_delete=models.SET_NULL)
|
||||
default_group = models.ForeignKey('Group', verbose_name='Default Group', null=True, blank=False,
|
||||
@ -50,8 +49,13 @@ class User(AbstractUser):
|
||||
USERNAME_FIELD = "email"
|
||||
REQUIRED_FIELDS = ['username']
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def save(self, *args, **kwargs):
|
||||
if not self.url:
|
||||
self.url = self._url()
|
||||
|
||||
super().save(*args, **kwargs)
|
||||
|
||||
def _url(self):
|
||||
return '{}/user/{}'.format(s.SERVER_URL, self.uuid)
|
||||
|
||||
def prediction_settings(self):
|
||||
@ -169,6 +173,7 @@ class APIToken(TimeStampedModel):
|
||||
|
||||
class Group(TimeStampedModel):
|
||||
uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
|
||||
url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
|
||||
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)
|
||||
@ -179,8 +184,13 @@ class Group(TimeStampedModel):
|
||||
def __str__(self):
|
||||
return f"{self.name} (pk={self.pk})"
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def save(self, *args, **kwargs):
|
||||
if not self.url:
|
||||
self.url = self._url()
|
||||
|
||||
super().save(*args, **kwargs)
|
||||
|
||||
def _url(self):
|
||||
return '{}/group/{}'.format(s.SERVER_URL, self.uuid)
|
||||
|
||||
|
||||
@ -476,11 +486,18 @@ class EnviPathModel(TimeStampedModel):
|
||||
name = models.TextField(blank=False, null=False, verbose_name='Name', default='no name')
|
||||
description = models.TextField(blank=False, null=False, verbose_name='Descriptions', default='no description')
|
||||
|
||||
url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
|
||||
|
||||
kv = JSONField(null=True, blank=True, default=dict)
|
||||
|
||||
@property
|
||||
def save(self, *args, **kwargs):
|
||||
if not self.url:
|
||||
self.url = self._url()
|
||||
|
||||
super().save(*args, **kwargs)
|
||||
|
||||
@abc.abstractmethod
|
||||
def url(self):
|
||||
def _url(self):
|
||||
pass
|
||||
|
||||
def simple_json(self, include_description=False):
|
||||
@ -585,8 +602,7 @@ class Package(EnviPathModel):
|
||||
def models(self):
|
||||
return EPModel.objects.filter(package=self)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/package/{}'.format(s.SERVER_URL, self.uuid)
|
||||
|
||||
def get_applicable_rules(self):
|
||||
@ -632,8 +648,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
|
||||
def normalized_structure(self):
|
||||
return CompoundStructure.objects.get(compound=self, normalized_structure=True)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/compound/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
@transaction.atomic
|
||||
@ -773,8 +788,7 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
|
||||
|
||||
super().save(*args, **kwargs)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/structure/{}'.format(self.compound.url, self.uuid)
|
||||
|
||||
@staticmethod
|
||||
@ -917,8 +931,7 @@ class SimpleAmbitRule(SimpleRule):
|
||||
r.save()
|
||||
return r
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/simple-ambit-rule/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
def apply(self, smiles):
|
||||
@ -953,8 +966,7 @@ class SimpleRDKitRule(SimpleRule):
|
||||
def apply(self, smiles):
|
||||
return FormatConverter.apply(smiles, self.reaction_smarts)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/simple-rdkit-rule/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
|
||||
@ -963,8 +975,7 @@ class SimpleRDKitRule(SimpleRule):
|
||||
class ParallelRule(Rule):
|
||||
simple_rules = models.ManyToManyField('epdb.SimpleRule', verbose_name='Simple rules')
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/parallel-rule/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
@property
|
||||
@ -1003,8 +1014,7 @@ class SequentialRule(Rule):
|
||||
simple_rules = models.ManyToManyField('epdb.SimpleRule', verbose_name='Simple rules',
|
||||
through='SequentialRuleOrdering')
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/sequential-rule/{}'.format(self.compound.url, self.uuid)
|
||||
|
||||
@property
|
||||
@ -1039,8 +1049,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
|
||||
|
||||
external_identifiers = GenericRelation('ExternalIdentifier')
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/reaction/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
@staticmethod
|
||||
@ -1167,8 +1176,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
|
||||
def edges(self):
|
||||
return Edge.objects.filter(pathway=self)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/pathway/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
# Mode
|
||||
@ -1386,8 +1394,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
|
||||
out_edges = models.ManyToManyField('epdb.Edge', verbose_name='Outgoing Edges')
|
||||
depth = models.IntegerField(verbose_name='Node depth', null=False, blank=False)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/node/{}'.format(self.pathway.url, self.uuid)
|
||||
|
||||
def d3_json(self):
|
||||
@ -1463,8 +1470,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
|
||||
start_nodes = models.ManyToManyField('epdb.Node', verbose_name='Start Nodes', related_name='edge_educts')
|
||||
end_nodes = models.ManyToManyField('epdb.Node', verbose_name='End Nodes', related_name='edge_products')
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/edge/{}'.format(self.pathway.url, self.uuid)
|
||||
|
||||
def d3_json(self):
|
||||
@ -1556,8 +1562,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
|
||||
class EPModel(PolymorphicModel, EnviPathModel):
|
||||
package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/model/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
|
||||
@ -2173,8 +2178,7 @@ class Scenario(EnviPathModel):
|
||||
|
||||
additional_information = models.JSONField(verbose_name='Additional Information')
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/scenario/{}'.format(self.package.url, self.uuid)
|
||||
|
||||
@staticmethod
|
||||
@ -2238,8 +2242,7 @@ class Setting(EnviPathModel):
|
||||
blank=True)
|
||||
model_threshold = models.FloatField(null=True, blank=True, verbose_name='Setting Model Threshold', default=0.25)
|
||||
|
||||
@property
|
||||
def url(self):
|
||||
def _url(self):
|
||||
return '{}/setting/{}'.format(s.SERVER_URL, self.uuid)
|
||||
|
||||
@cached_property
|
||||
|
||||
@ -439,16 +439,7 @@ def scenarios(request):
|
||||
if request.GET.get('all'):
|
||||
return JsonResponse({
|
||||
"objects": [
|
||||
{"name": s.name, "url": s.full_url, "reviewed": True}
|
||||
for s in reviewed_scenario_qs.annotate(
|
||||
full_url=Concat(
|
||||
Value(s.SERVER_URL + '/package/'),
|
||||
F("package__uuid"),
|
||||
Value("/scenario/"),
|
||||
F("uuid"),
|
||||
output_field=CharField(),
|
||||
)
|
||||
)
|
||||
{"name": s.name, "url": s.url, "reviewed": True} for s in reviewed_scenario_qs
|
||||
]
|
||||
})
|
||||
|
||||
|
||||
Reference in New Issue
Block a user