forked from enviPath/enviPy
adjusted migration
Initial bayer app Show Pack Classification Adjusted docker compose to bayer specifics Adjusted Dockerfile for Bayer Adding secret flags to group, add secret pools to packages Adjusted View for Package creation Prep configs, added Package Create Modal wip More on PES wip wip Wip minor PW interactions API PES wip Make Select Widget reflect required make required generallay available Update UI if pathway mode is set to build Added ais circle adjustments Initial Zoom, fix AD Creation wip
This commit is contained in:
Tim Lorsbach
@ -1,594 +0,0 @@
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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')),
|
||||
('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')),
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('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')),
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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='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(
|
||||
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')),
|
||||
('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
@ -1,128 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-08-25 18:07
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('contenttypes', '0002_remove_content_type_name'),
|
||||
('epdb', '0001_initial'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name='ExternalDatabase',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
|
||||
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
|
||||
('description', models.TextField(blank=True, verbose_name='Description')),
|
||||
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
|
||||
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
|
||||
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Database',
|
||||
'verbose_name_plural': 'External Databases',
|
||||
'db_table': 'epdb_external_database',
|
||||
'ordering': ['name'],
|
||||
},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='apitoken',
|
||||
options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
|
||||
),
|
||||
migrations.AlterModelOptions(
|
||||
name='edge',
|
||||
options={},
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name='edge',
|
||||
name='polymorphic_ctype',
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='apitoken',
|
||||
name='is_active',
|
||||
field=models.BooleanField(default=True, help_text='Whether this token is active'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='apitoken',
|
||||
name='modified',
|
||||
field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='functional_groups',
|
||||
field=models.JSONField(blank=True, default=dict, null=True),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='created',
|
||||
field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='expires_at',
|
||||
field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='hashed_key',
|
||||
field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='name',
|
||||
field=models.CharField(help_text='Descriptive name for this token', max_length=100),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='apitoken',
|
||||
name='user',
|
||||
field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='applicabilitydomain',
|
||||
name='num_neighbours',
|
||||
field=models.IntegerField(default=5),
|
||||
),
|
||||
migrations.AlterModelTable(
|
||||
name='apitoken',
|
||||
table='epdb_api_token',
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalIdentifier',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('object_id', models.IntegerField()),
|
||||
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
|
||||
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
|
||||
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
|
||||
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Identifier',
|
||||
'verbose_name_plural': 'External Identifiers',
|
||||
'db_table': 'epdb_external_identifier',
|
||||
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
|
||||
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
|
||||
},
|
||||
),
|
||||
]
|
||||
@ -1,228 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-08-26 17:05
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
def populate_url(apps, schema_editor):
|
||||
MODELS = [
|
||||
'User',
|
||||
'Group',
|
||||
'Package',
|
||||
'Compound',
|
||||
'CompoundStructure',
|
||||
'Pathway',
|
||||
'Edge',
|
||||
'Node',
|
||||
'Reaction',
|
||||
'SimpleAmbitRule',
|
||||
'SimpleRDKitRule',
|
||||
'ParallelRule',
|
||||
'SequentialRule',
|
||||
'Scenario',
|
||||
'Setting',
|
||||
'MLRelativeReasoning',
|
||||
'EnviFormer',
|
||||
'ApplicabilityDomain',
|
||||
]
|
||||
for model in MODELS:
|
||||
obj_cls = apps.get_model("epdb", model)
|
||||
for obj in obj_cls.objects.all():
|
||||
obj.url = assemble_url(obj)
|
||||
if obj.url is None:
|
||||
raise ValueError(f"Could not assemble url for {obj}")
|
||||
obj.save()
|
||||
|
||||
|
||||
def assemble_url(obj):
|
||||
from django.conf import settings as s
|
||||
match obj.__class__.__name__:
|
||||
case 'User':
|
||||
return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Group':
|
||||
return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Package':
|
||||
return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case 'Compound':
|
||||
return '{}/compound/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'CompoundStructure':
|
||||
return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
|
||||
case 'SimpleAmbitRule':
|
||||
return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'SimpleRDKitRule':
|
||||
return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'ParallelRule':
|
||||
return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'SequentialRule':
|
||||
return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
|
||||
case 'Reaction':
|
||||
return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Pathway':
|
||||
return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Node':
|
||||
return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
|
||||
case 'Edge':
|
||||
return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
|
||||
case 'MLRelativeReasoning':
|
||||
return '{}/model/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'EnviFormer':
|
||||
return '{}/model/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'ApplicabilityDomain':
|
||||
return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
|
||||
case 'Scenario':
|
||||
return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
|
||||
case 'Setting':
|
||||
return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
|
||||
case _:
|
||||
raise ValueError(f"Unknown model {obj.__class__.__name__}")
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compoundstructure',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='epmodel',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='group',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='package',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='reaction',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='scenario',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='setting',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=False, verbose_name='URL'),
|
||||
),
|
||||
|
||||
migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
|
||||
|
||||
migrations.AlterField(
|
||||
model_name='applicabilitydomain',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='compound',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='compoundstructure',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='edge',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='epmodel',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='group',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='node',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='package',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='pathway',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='reaction',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='rule',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='scenario',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='setting',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='user',
|
||||
name='url',
|
||||
field=models.TextField(null=True, unique=True, verbose_name='URL'),
|
||||
),
|
||||
]
|
||||
@ -1,55 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-09 09:21
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterModelOptions(
|
||||
name='mlrelativereasoning',
|
||||
options={},
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='RuleBasedRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
|
||||
('min_count', models.IntegerField(default=10)),
|
||||
('max_count', models.IntegerField(default=0)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.DeleteModel(
|
||||
name='RuleBaseRelativeReasoning',
|
||||
),
|
||||
]
|
||||
@ -1,18 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-11 06:21
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterField(
|
||||
model_name='group',
|
||||
name='group_member',
|
||||
field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
|
||||
),
|
||||
]
|
||||
@ -1,23 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-09-18 06:42
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0005_alter_group_group_member'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='mlrelativereasoning',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rulebasedrelativereasoning',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
@ -1,53 +0,0 @@
|
||||
# Generated by Django 5.2.1 on 2025-10-07 08:19
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AlterModelOptions(
|
||||
name='enviformer',
|
||||
options={},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='eval_results',
|
||||
field=models.JSONField(blank=True, default=dict, null=True),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='model_status',
|
||||
field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='multigen_eval',
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='enviformer',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
|
||||
),
|
||||
]
|
||||
@ -1,64 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-10-10 06:58
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="EnzymeLink",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
(
|
||||
"created",
|
||||
model_utils.fields.AutoCreatedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="created"
|
||||
),
|
||||
),
|
||||
(
|
||||
"modified",
|
||||
model_utils.fields.AutoLastModifiedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="modified"
|
||||
),
|
||||
),
|
||||
(
|
||||
"uuid",
|
||||
models.UUIDField(
|
||||
default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
|
||||
),
|
||||
),
|
||||
("name", models.TextField(default="no name", verbose_name="Name")),
|
||||
(
|
||||
"description",
|
||||
models.TextField(default="no description", verbose_name="Descriptions"),
|
||||
),
|
||||
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
|
||||
("kv", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("ec_number", models.TextField(verbose_name="EC Number")),
|
||||
("classification_level", models.IntegerField(verbose_name="Classification Level")),
|
||||
("linking_method", models.TextField(verbose_name="Linking Method")),
|
||||
("edge_evidence", models.ManyToManyField(to="epdb.edge")),
|
||||
("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
|
||||
(
|
||||
"rule",
|
||||
models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
),
|
||||
]
|
||||
@ -1,66 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-10-27 09:39
|
||||
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0008_enzymelink"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="JobLog",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
(
|
||||
"created",
|
||||
model_utils.fields.AutoCreatedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="created"
|
||||
),
|
||||
),
|
||||
(
|
||||
"modified",
|
||||
model_utils.fields.AutoLastModifiedField(
|
||||
default=django.utils.timezone.now, editable=False, verbose_name="modified"
|
||||
),
|
||||
),
|
||||
("task_id", models.UUIDField(unique=True)),
|
||||
("job_name", models.TextField()),
|
||||
(
|
||||
"status",
|
||||
models.CharField(
|
||||
choices=[
|
||||
("INITIAL", "Initial"),
|
||||
("SUCCESS", "Success"),
|
||||
("FAILURE", "Failure"),
|
||||
("REVOKED", "Revoked"),
|
||||
("IGNORED", "Ignored"),
|
||||
],
|
||||
default="INITIAL",
|
||||
max_length=20,
|
||||
),
|
||||
),
|
||||
("done_at", models.DateTimeField(blank=True, default=None, null=True)),
|
||||
("task_result", models.TextField(blank=True, default=None, null=True)),
|
||||
(
|
||||
"user",
|
||||
models.ForeignKey(
|
||||
on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
),
|
||||
]
|
||||
@ -1,18 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-11-11 14:11
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0009_joblog"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="license",
|
||||
name="cc_string",
|
||||
field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
|
||||
preserve_default=False,
|
||||
),
|
||||
]
|
||||
@ -1,59 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-11-11 14:13
|
||||
|
||||
import re
|
||||
|
||||
from django.contrib.postgres.aggregates import ArrayAgg
|
||||
from django.db import migrations
|
||||
from django.db.models import Min
|
||||
|
||||
|
||||
def set_cc(apps, schema_editor):
|
||||
License = apps.get_model("epdb", "License")
|
||||
|
||||
# For all existing licenses extract cc_string from link
|
||||
for license in License.objects.all():
|
||||
pattern = r"/licenses/([^/]+)/4\.0"
|
||||
match = re.search(pattern, license.link)
|
||||
if match:
|
||||
license.cc_string = match.group(1)
|
||||
license.save()
|
||||
else:
|
||||
raise ValueError(f"Could not find license for {license.link}")
|
||||
|
||||
# Ensure we have all licenses
|
||||
cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
|
||||
for cc_string in cc_strings:
|
||||
if not License.objects.filter(cc_string=cc_string).exists():
|
||||
new_license = License()
|
||||
new_license.cc_string = cc_string
|
||||
new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
|
||||
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
|
||||
new_license.save()
|
||||
|
||||
# As we might have existing Licenses representing the same License,
|
||||
# get min pk and all pks as a list
|
||||
license_lookup_qs = License.objects.values("cc_string").annotate(
|
||||
lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
|
||||
)
|
||||
|
||||
license_lookup = {
|
||||
row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
|
||||
}
|
||||
|
||||
Packages = apps.get_model("epdb", "Package")
|
||||
|
||||
for k, v in license_lookup.items():
|
||||
# Set min pk to all packages pointing to any of the duplicates
|
||||
Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
|
||||
# remove the min pk from "other" pks as we use them for deletion
|
||||
v[1].remove(v[0])
|
||||
# Delete redundant License objects
|
||||
License.objects.filter(pk__in=v[1]).delete()
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0010_license_cc_string"),
|
||||
]
|
||||
|
||||
operations = [migrations.RunPython(set_cc)]
|
||||
@ -1,22 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-02 13:09
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0011_auto_20251111_1413"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="node",
|
||||
name="stereo_removed",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="pathway",
|
||||
name="predicted",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
@ -1,25 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-14 11:30
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0012_node_stereo_removed_pathway_predicted"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="setting",
|
||||
name="expansion_schema",
|
||||
field=models.CharField(
|
||||
choices=[
|
||||
("BFS", "Breadth First Search"),
|
||||
("DFS", "Depth First Search"),
|
||||
("GREEDY", "Greedy"),
|
||||
],
|
||||
default="BFS",
|
||||
max_length=20,
|
||||
),
|
||||
),
|
||||
]
|
||||
@ -1,17 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2025-12-14 16:02
|
||||
|
||||
from django.db import migrations
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0013_setting_expansion_schema"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RenameField(
|
||||
model_name="setting",
|
||||
old_name="expansion_schema",
|
||||
new_name="expansion_scheme",
|
||||
),
|
||||
]
|
||||
@ -1,17 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2026-01-19 19:26
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name="user",
|
||||
name="is_reviewer",
|
||||
field=models.BooleanField(default=False),
|
||||
),
|
||||
]
|
||||
@ -1,179 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-12 09:38
|
||||
|
||||
import django.db.models.deletion
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0015_user_is_reviewer"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RemoveField(
|
||||
model_name="enviformer",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="model_status",
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="epmodel",
|
||||
name="model_status",
|
||||
field=models.CharField(
|
||||
choices=[
|
||||
("INITIAL", "Initial"),
|
||||
("INITIALIZING", "Model is initializing."),
|
||||
("BUILDING", "Model is building."),
|
||||
(
|
||||
"BUILT_NOT_EVALUATED",
|
||||
"Model is built and can be used for predictions, Model is not evaluated yet.",
|
||||
),
|
||||
("EVALUATING", "Model is evaluating"),
|
||||
("FINISHED", "Model has finished building and evaluation."),
|
||||
("ERROR", "Model has failed."),
|
||||
],
|
||||
default="INITIAL",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="enviformer",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="enviformer",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="mlrelativereasoning",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="eval_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name="rulebasedrelativereasoning",
|
||||
name="rule_packages",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name="PropertyPluginModel",
|
||||
fields=[
|
||||
(
|
||||
"epmodel_ptr",
|
||||
models.OneToOneField(
|
||||
auto_created=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
parent_link=True,
|
||||
primary_key=True,
|
||||
serialize=False,
|
||||
to="epdb.epmodel",
|
||||
),
|
||||
),
|
||||
("threshold", models.FloatField(default=0.5)),
|
||||
("eval_results", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("multigen_eval", models.BooleanField(default=False)),
|
||||
("plugin_identifier", models.CharField(max_length=255)),
|
||||
(
|
||||
"app_domain",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
default=None,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.SET_NULL,
|
||||
to="epdb.applicabilitydomain",
|
||||
),
|
||||
),
|
||||
(
|
||||
"data_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_data_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Data Packages",
|
||||
),
|
||||
),
|
||||
(
|
||||
"eval_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_eval_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Evaluation Packages",
|
||||
),
|
||||
),
|
||||
(
|
||||
"rule_packages",
|
||||
models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="%(app_label)s_%(class)s_rule_packages",
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Rule Packages",
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"abstract": False,
|
||||
},
|
||||
bases=("epdb.epmodel",),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="setting",
|
||||
name="property_models",
|
||||
field=models.ManyToManyField(
|
||||
blank=True,
|
||||
related_name="settings",
|
||||
to="epdb.propertypluginmodel",
|
||||
verbose_name="Setting Property Models",
|
||||
),
|
||||
),
|
||||
migrations.DeleteModel(
|
||||
name="PluginModel",
|
||||
),
|
||||
]
|
||||
@ -1,93 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-20 12:02
|
||||
|
||||
import django.db.models.deletion
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("contenttypes", "0002_remove_content_type_name"),
|
||||
("epdb", "0016_remove_enviformer_model_status_and_more"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.CreateModel(
|
||||
name="AdditionalInformation",
|
||||
fields=[
|
||||
(
|
||||
"id",
|
||||
models.BigAutoField(
|
||||
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
|
||||
),
|
||||
),
|
||||
("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
|
||||
("kv", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("type", models.TextField(verbose_name="Additional Information Type")),
|
||||
("data", models.JSONField(blank=True, default=dict, null=True)),
|
||||
("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
|
||||
(
|
||||
"content_type",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
to="contenttypes.contenttype",
|
||||
),
|
||||
),
|
||||
(
|
||||
"package",
|
||||
models.ForeignKey(
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
to=settings.EPDB_PACKAGE_MODEL,
|
||||
verbose_name="Package",
|
||||
),
|
||||
),
|
||||
(
|
||||
"scenario",
|
||||
models.ForeignKey(
|
||||
blank=True,
|
||||
null=True,
|
||||
on_delete=django.db.models.deletion.CASCADE,
|
||||
related_name="scenario_additional_information",
|
||||
to="epdb.scenario",
|
||||
),
|
||||
),
|
||||
],
|
||||
options={
|
||||
"indexes": [
|
||||
models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
|
||||
models.Index(
|
||||
fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
|
||||
),
|
||||
models.Index(
|
||||
fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
|
||||
),
|
||||
models.Index(
|
||||
fields=["scenario", "content_type", "object_id"],
|
||||
name="epdb_additi_scenari_ef2bf5_idx",
|
||||
),
|
||||
],
|
||||
"constraints": [
|
||||
models.CheckConstraint(
|
||||
condition=models.Q(
|
||||
models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
|
||||
models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
|
||||
_connector="OR",
|
||||
),
|
||||
name="ck_addinfo_gfk_pair",
|
||||
),
|
||||
models.CheckConstraint(
|
||||
condition=models.Q(
|
||||
("scenario__isnull", False),
|
||||
("content_type__isnull", False),
|
||||
_connector="OR",
|
||||
),
|
||||
name="ck_addinfo_not_both_null",
|
||||
),
|
||||
],
|
||||
},
|
||||
),
|
||||
]
|
||||
@ -1,132 +0,0 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-20 12:03
|
||||
|
||||
from django.db import migrations
|
||||
|
||||
|
||||
def get_additional_information(scenario):
|
||||
from envipy_additional_information import registry
|
||||
from envipy_additional_information.parsers import TypeOfAerationParser
|
||||
|
||||
for k, vals in scenario.additional_information.items():
|
||||
if k == "enzyme":
|
||||
continue
|
||||
|
||||
if k == "SpikeConentration":
|
||||
k = "SpikeConcentration"
|
||||
|
||||
if k == "AerationType":
|
||||
k = "TypeOfAeration"
|
||||
|
||||
for v in vals:
|
||||
# Per default additional fields are ignored
|
||||
MAPPING = {c.__name__: c for c in registry.list_models().values()}
|
||||
try:
|
||||
inst = MAPPING[k](**v)
|
||||
except Exception:
|
||||
if k == "TypeOfAeration":
|
||||
toa = TypeOfAerationParser()
|
||||
inst = toa.from_string(v["type"])
|
||||
|
||||
# Add uuid to uniquely identify objects for manipulation
|
||||
if "uuid" in v:
|
||||
inst.__dict__["uuid"] = v["uuid"]
|
||||
|
||||
yield inst
|
||||
|
||||
|
||||
def forward_func(apps, schema_editor):
|
||||
Scenario = apps.get_model("epdb", "Scenario")
|
||||
ContentType = apps.get_model("contenttypes", "ContentType")
|
||||
AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
|
||||
|
||||
bulk = []
|
||||
related = []
|
||||
ctype = {o.model: o for o in ContentType.objects.all()}
|
||||
parents = Scenario.objects.prefetch_related(
|
||||
"compound_set",
|
||||
"compoundstructure_set",
|
||||
"reaction_set",
|
||||
"rule_set",
|
||||
"pathway_set",
|
||||
"node_set",
|
||||
"edge_set",
|
||||
).filter(parent__isnull=True)
|
||||
|
||||
for i, scenario in enumerate(parents):
|
||||
print(f"{i + 1}/{len(parents)}", end="\r")
|
||||
if scenario.parent is not None:
|
||||
related.append(scenario.parent)
|
||||
continue
|
||||
|
||||
for ai in get_additional_information(scenario):
|
||||
bulk.append(
|
||||
AdditionalInformation(
|
||||
package=scenario.package,
|
||||
scenario=scenario,
|
||||
type=ai.__class__.__name__,
|
||||
data=ai.model_dump(mode="json"),
|
||||
)
|
||||
)
|
||||
|
||||
print("\n", len(bulk))
|
||||
|
||||
related = Scenario.objects.prefetch_related(
|
||||
"compound_set",
|
||||
"compoundstructure_set",
|
||||
"reaction_set",
|
||||
"rule_set",
|
||||
"pathway_set",
|
||||
"node_set",
|
||||
"edge_set",
|
||||
).filter(parent__isnull=False)
|
||||
|
||||
for i, scenario in enumerate(related):
|
||||
print(f"{i + 1}/{len(related)}", end="\r")
|
||||
parent = scenario.parent
|
||||
# Check to which objects this scenario is attached to
|
||||
for ai in get_additional_information(scenario):
|
||||
rel_objs = [
|
||||
"compound",
|
||||
"compoundstructure",
|
||||
"reaction",
|
||||
"rule",
|
||||
"pathway",
|
||||
"node",
|
||||
"edge",
|
||||
]
|
||||
for rel_obj in rel_objs:
|
||||
for o in getattr(scenario, f"{rel_obj}_set").all():
|
||||
bulk.append(
|
||||
AdditionalInformation(
|
||||
package=scenario.package,
|
||||
scenario=parent,
|
||||
type=ai.__class__.__name__,
|
||||
data=ai.model_dump(mode="json"),
|
||||
content_type=ctype[rel_obj],
|
||||
object_id=o.pk,
|
||||
)
|
||||
)
|
||||
|
||||
print("Start creating additional information objects...")
|
||||
AdditionalInformation.objects.bulk_create(bulk)
|
||||
print("Done!")
|
||||
print(len(bulk))
|
||||
|
||||
Scenario.objects.filter(parent__isnull=False).delete()
|
||||
# Call ai save to fix urls
|
||||
ais = AdditionalInformation.objects.all()
|
||||
total = ais.count()
|
||||
|
||||
for i, ai in enumerate(ais):
|
||||
print(f"{i + 1}/{total}", end="\r")
|
||||
ai.save()
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
dependencies = [
|
||||
("epdb", "0017_additionalinformation"),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
|
||||
]
|
||||
@ -1,20 +1,741 @@
|
||||
# Generated by Django 5.2.7 on 2026-02-23 08:45
|
||||
# Generated by Django 5.2.7 on 2026-03-06 10:51
|
||||
|
||||
from django.db import migrations
|
||||
import django.contrib.auth.models
|
||||
import django.contrib.auth.validators
|
||||
import django.contrib.postgres.fields
|
||||
import django.db.models.deletion
|
||||
import django.utils.timezone
|
||||
import model_utils.fields
|
||||
import uuid
|
||||
from django.conf import settings
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
initial = True
|
||||
|
||||
dependencies = [
|
||||
("epdb", "0018_auto_20260220_1203"),
|
||||
('auth', '0012_alter_user_first_name_max_length'),
|
||||
('contenttypes', '0002_remove_content_type_name'),
|
||||
migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.RemoveField(
|
||||
model_name="scenario",
|
||||
name="additional_information",
|
||||
migrations.CreateModel(
|
||||
name='ApplicabilityDomain',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('num_neighbours', models.IntegerField(default=5)),
|
||||
('reliability_threshold', models.FloatField(default=0.5)),
|
||||
('local_compatibilty_threshold', models.FloatField(default=0.5)),
|
||||
('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.RemoveField(
|
||||
model_name="scenario",
|
||||
name="parent",
|
||||
migrations.CreateModel(
|
||||
name='Edge',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EPModel',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalDatabase',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
|
||||
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
|
||||
('description', models.TextField(blank=True, verbose_name='Description')),
|
||||
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
|
||||
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
|
||||
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Database',
|
||||
'verbose_name_plural': 'External Databases',
|
||||
'db_table': 'epdb_external_database',
|
||||
'ordering': ['name'],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Permission',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='License',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('cc_string', models.TextField(verbose_name='CC string')),
|
||||
('link', models.URLField(verbose_name='link')),
|
||||
('image_link', models.URLField(verbose_name='Image link')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Rule',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='User',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('password', models.CharField(max_length=128, verbose_name='password')),
|
||||
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
|
||||
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
|
||||
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
|
||||
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
|
||||
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
|
||||
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
|
||||
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
|
||||
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
|
||||
('email', models.EmailField(max_length=254, unique=True)),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('is_reviewer', models.BooleanField(default=False)),
|
||||
('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
|
||||
('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
|
||||
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'user',
|
||||
'verbose_name_plural': 'users',
|
||||
'abstract': False,
|
||||
},
|
||||
managers=[
|
||||
('objects', django.contrib.auth.models.UserManager()),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='APIToken',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
|
||||
('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
|
||||
('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
|
||||
('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
|
||||
('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'API Token',
|
||||
'verbose_name_plural': 'API Tokens',
|
||||
'db_table': 'epdb_api_token',
|
||||
'ordering': ['-created'],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Compound',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='CompoundStructure',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('smiles', models.TextField(verbose_name='SMILES')),
|
||||
('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
|
||||
('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
|
||||
('normalized_structure', models.BooleanField(default=False)),
|
||||
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='default_structure',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='PropertyPluginModel',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('plugin_identifier', models.CharField(max_length=255)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Group',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('name', models.TextField(verbose_name='Group name')),
|
||||
('public', models.BooleanField(default=False, verbose_name='Public Group')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
|
||||
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
|
||||
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_group',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='JobLog',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('task_id', models.UUIDField(unique=True)),
|
||||
('job_name', models.TextField()),
|
||||
('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
|
||||
('done_at', models.DateTimeField(blank=True, default=None, null=True)),
|
||||
('task_result', models.TextField(blank=True, default=None, null=True)),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Package',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
|
||||
('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
|
||||
],
|
||||
options={
|
||||
'swappable': 'EPDB_PACKAGE_MODEL',
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Node',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('depth', models.IntegerField(verbose_name='Node depth')),
|
||||
('stereo_removed', models.BooleanField(default=False)),
|
||||
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
|
||||
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
|
||||
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='end_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='start_nodes',
|
||||
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Pathway',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('predicted', models.BooleanField(default=False)),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='pathway',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Reaction',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
|
||||
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
|
||||
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
|
||||
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
|
||||
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EnzymeLink',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('ec_number', models.TextField(verbose_name='EC Number')),
|
||||
('classification_level', models.IntegerField(verbose_name='Classification Level')),
|
||||
('linking_method', models.TextField(verbose_name='Linking Method')),
|
||||
('edge_evidence', models.ManyToManyField(to='epdb.edge')),
|
||||
('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
|
||||
('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='edge_label',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Scenario',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('scenario_date', models.CharField(default='No date', max_length=256)),
|
||||
('scenario_type', models.CharField(default='Not specified', max_length=256)),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='rule',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='reaction',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='node',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='edge',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compoundstructure',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='compound',
|
||||
name='scenarios',
|
||||
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='Setting',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
|
||||
('name', models.TextField(default='no name', verbose_name='Name')),
|
||||
('description', models.TextField(default='no description', verbose_name='Descriptions')),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('public', models.BooleanField(default=False)),
|
||||
('global_default', models.BooleanField(default=False)),
|
||||
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
|
||||
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
|
||||
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
|
||||
('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
|
||||
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
|
||||
('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='pathway',
|
||||
name='setting',
|
||||
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='user',
|
||||
name='default_setting',
|
||||
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='EnviFormer',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='MLRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='applicabilitydomain',
|
||||
name='model',
|
||||
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='app_domain',
|
||||
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='data_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='eval_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='propertypluginmodel',
|
||||
name='rule_packages',
|
||||
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='RuleBasedRelativeReasoning',
|
||||
fields=[
|
||||
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
|
||||
('threshold', models.FloatField(default=0.5)),
|
||||
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('multigen_eval', models.BooleanField(default=False)),
|
||||
('min_count', models.IntegerField(default=10)),
|
||||
('max_count', models.IntegerField(default=0)),
|
||||
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
|
||||
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
|
||||
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
|
||||
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
},
|
||||
bases=('epdb.epmodel',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ExternalIdentifier',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
|
||||
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('object_id', models.IntegerField()),
|
||||
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
|
||||
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
|
||||
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
|
||||
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'External Identifier',
|
||||
'verbose_name_plural': 'External Identifiers',
|
||||
'db_table': 'epdb_external_identifier',
|
||||
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
|
||||
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleAmbitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('smirks', models.TextField(verbose_name='SMIRKS')),
|
||||
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
|
||||
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SimpleRDKitRule',
|
||||
fields=[
|
||||
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
|
||||
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.simplerule',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='SequentialRuleOrdering',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('order_index', models.IntegerField()),
|
||||
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
|
||||
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
|
||||
],
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name='sequentialrule',
|
||||
name='simple_rules',
|
||||
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='ParallelRule',
|
||||
fields=[
|
||||
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
|
||||
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
|
||||
],
|
||||
options={
|
||||
'abstract': False,
|
||||
'base_manager_name': 'objects',
|
||||
},
|
||||
bases=('epdb.rule',),
|
||||
),
|
||||
migrations.AlterUniqueTogether(
|
||||
name='compound',
|
||||
unique_together={('uuid', 'package')},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='AdditionalInformation',
|
||||
fields=[
|
||||
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
|
||||
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
|
||||
('kv', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('type', models.TextField(verbose_name='Additional Information Type')),
|
||||
('data', models.JSONField(blank=True, default=dict, null=True)),
|
||||
('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
|
||||
('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
|
||||
('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
|
||||
],
|
||||
options={
|
||||
'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
|
||||
'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
|
||||
},
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='GroupPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'group')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserPackagePermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('package', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
migrations.CreateModel(
|
||||
name='UserSettingPermission',
|
||||
fields=[
|
||||
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
|
||||
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
|
||||
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
|
||||
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
|
||||
],
|
||||
options={
|
||||
'unique_together': {('setting', 'user')},
|
||||
},
|
||||
bases=('epdb.permission',),
|
||||
),
|
||||
]
|
||||
|
||||
@ -46,4 +46,9 @@ class Migration(migrations.Migration):
|
||||
name="molfile",
|
||||
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
|
||||
),
|
||||
migrations.AddField(
|
||||
model_name="group",
|
||||
name="secret",
|
||||
field=models.BooleanField(default=False, verbose_name="Secret Group"),
|
||||
),
|
||||
]
|
||||
|
||||
Reference in New Issue
Block a user