migrations

chord_metadata_service/chord/migrations/0006_v4_0_0.py

@@ -5,8 +5,6 @@
 
 class Migration(migrations.Migration):
 
-    replaces = [('chord', '0006_remove_tableownership_dataset'), ('chord', '0007_delete_table_delete_tableownership')]
-
     dependencies = [
         ('phenopackets', '0005_v4_0_0'),
         ('chord', '0005_v3_0_0'),

chord_metadata_service/chord/views_search.py

@@ -37,7 +37,7 @@
 from chord_metadata_service.patients.models import Individual
 
 from chord_metadata_service.phenopackets.api_views import PHENOPACKET_SELECT_REL, PHENOPACKET_PREFETCH
-from chord_metadata_service.phenopackets.models import Phenopacket, Biosample, Variant
+from chord_metadata_service.phenopackets.models import Phenopacket, Biosample
 from chord_metadata_service.phenopackets.serializers import PhenopacketSerializer
 
 from .data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_MCODEPACKET, DATA_TYPE_PHENOPACKET, DATA_TYPES

chord_metadata_service/experiments/migrations/0008_alter_experiment_experiment_ontology_and_more.py

@@ -0,0 +1,39 @@
+# Generated by Django 4.2.5 on 2023-09-11 20:17
+
+import chord_metadata_service.restapi.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0007_v4_0_0'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='experiment',
+            name='experiment_ontology',
+            field=models.JSONField(blank=True, default=list, help_text='Links to experiment ontology information (e.g. via the OBI ontology.).', validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'file:///chord_metadata_service/restapi/ontology_class_list', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'file:///chord_metadata_service/restapi/ontology_class', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'An ontology term.', 'help': 'An ontology term.', 'properties': {'id': {'$id': 'file:///chord_metadata_service/restapi/ontology_class/id', 'description': 'A CURIE-style identifier for an ontology term.', 'help': 'A CURIE-style identifier for an ontology term.', 'type': 'string'}, 'label': {'$id': 'file:///chord_metadata_service/restapi/ontology_class/label', 'description': 'A human readable class name for an ontology term.', 'help': 'A human readable class name for an ontology term.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='extra_properties',
+            field=models.JSONField(blank=True, default=dict, help_text='Extra properties that are not supported by current schema.', validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'file:///chord_metadata_service/restapi/key_value_object', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'The schema represents a key-value object.', 'patternProperties': {'^.*$': {'type': 'string'}}, 'title': 'Key-value object', 'type': 'object'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='molecule_ontology',
+            field=models.JSONField(blank=True, default=list, help_text='Links to molecule ontology information (e.g. via the SO ontology.).', validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'file:///chord_metadata_service/restapi/ontology_class_list', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'file:///chord_metadata_service/restapi/ontology_class', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'An ontology term.', 'help': 'An ontology term.', 'properties': {'id': {'$id': 'file:///chord_metadata_service/restapi/ontology_class/id', 'description': 'A CURIE-style identifier for an ontology term.', 'help': 'A CURIE-style identifier for an ontology term.', 'type': 'string'}, 'label': {'$id': 'file:///chord_metadata_service/restapi/ontology_class/label', 'description': 'A human readable class name for an ontology term.', 'help': 'A human readable class name for an ontology term.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='experimentresult',
+            name='extra_properties',
+            field=models.JSONField(blank=True, default=dict, help_text='Extra properties that are not supported by current schema.', validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'file:///chord_metadata_service/restapi/key_value_object', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'The schema represents a key-value object.', 'patternProperties': {'^.*$': {'type': 'string'}}, 'title': 'Key-value object', 'type': 'object'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='instrument',
+            name='extra_properties',
+            field=models.JSONField(blank=True, default=dict, help_text='Extra properties that are not supported by current schema.', validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'file:///chord_metadata_service/restapi/key_value_object', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'The schema represents a key-value object.', 'patternProperties': {'^.*$': {'type': 'string'}}, 'title': 'Key-value object', 'type': 'object'}, formats=None)]),
+        ),
+    ]