Make URL a Field instead a property (#63)

This PR adds a new Field to all existing Models.
As its a data migrations the Migration is added.

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#63
This commit is contained in:
2025-08-27 06:46:09 +12:00
parent 6a4c8d96c3
commit 13816ecaf3
7 changed files with 2063 additions and 47 deletions

View File

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

View File

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

View File

@ -0,0 +1,229 @@
# Generated by Django 5.2.1 on 2025-08-26 17:05
from django.db import migrations, models
def populate_url(apps, schema_editor):
MODELS = [
'User',
'Group',
'Package',
'Compound',
'CompoundStructure',
'Pathway',
'Edge',
'Node',
'Reaction',
'SimpleAmbitRule',
'SimpleRDKitRule',
'ParallelRule',
'SequentialRule',
'Scenario',
'Setting',
'MLRelativeReasoning',
'EnviFormer',
'ApplicabilityDomain',
]
for model in MODELS:
obj_cls = apps.get_model("epdb", model)
print(f"Populating url for {model}")
for obj in obj_cls.objects.all():
obj.url = assemble_url(obj)
if obj.url is None:
raise ValueError(f"Could not assemble url for {obj}")
obj.save()
def assemble_url(obj):
from django.conf import settings as s
match obj.__class__.__name__:
case 'User':
return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
case 'Group':
return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
case 'Package':
return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
case 'Compound':
return '{}/compound/{}'.format(obj.package.url, obj.uuid)
case 'CompoundStructure':
return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
case 'SimpleAmbitRule':
return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
case 'SimpleRDKitRule':
return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
case 'ParallelRule':
return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
case 'SequentialRule':
return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
case 'Reaction':
return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
case 'Pathway':
return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
case 'Node':
return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
case 'Edge':
return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
case 'MLRelativeReasoning':
return '{}/model/{}'.format(obj.package.url, obj.uuid)
case 'EnviFormer':
return '{}/model/{}'.format(obj.package.url, obj.uuid)
case 'ApplicabilityDomain':
return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
case 'Scenario':
return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
case 'Setting':
return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
case _:
raise ValueError(f"Unknown model {obj.__class__.__name__}")
class Migration(migrations.Migration):
dependencies = [
('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
]
operations = [
migrations.AddField(
model_name='applicabilitydomain',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='compound',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='compoundstructure',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='edge',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='epmodel',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='group',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='node',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='package',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='pathway',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='reaction',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='rule',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='scenario',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='setting',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='user',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
migrations.AlterField(
model_name='applicabilitydomain',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='compound',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='compoundstructure',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='edge',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='epmodel',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='group',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='node',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='package',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='pathway',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='reaction',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='rule',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='scenario',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='setting',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='user',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
]