Merge pull request #105 from romgrk/experiments-add-relations

experiments: define biosamples & donor

chord_metadata_service/experiments/descriptions.py

@@ -15,6 +15,9 @@
 
         "other_fields": "The other fields for the experiment",
 
+        "biosample": "Biosamples on which this experiment was done",
+        "individual": "Donor on which this experiment was done",
+
         **EXTRA_PROPERTIES
     }
 }

chord_metadata_service/experiments/migrations/0003_auto_20200331_1841.py

@@ -0,0 +1,59 @@
+# Generated by Django 2.2.11 on 2020-03-31 18:41
+
+import chord_metadata_service.restapi.validators
+import django.contrib.postgres.fields
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('patients', '0004_auto_20200129_1537'),
+        ('phenopackets', '0004_auto_20200129_1537'),
+        ('experiments', '0002_auto_20200327_1728'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='experiment',
+            name='biosample',
+            field=models.ForeignKey(blank=True, help_text='Biosamples on which this experiment was done', null=True, on_delete=django.db.models.deletion.SET_NULL, to='phenopackets.Biosample'),
+        ),
+        migrations.AddField(
+            model_name='experiment',
+            name='individual',
+            field=models.ForeignKey(blank=True, help_text='Donor on which this experiment was done', null=True, on_delete=django.db.models.deletion.SET_NULL, to='patients.Individual'),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='experiment_ontology',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='(Ontology: OBI) links to experiment ontology information.', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'ONTOLOGY_CLASS_LIST', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'ONTOLOGY_CLASS', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'todo', 'properties': {'id': {'description': 'CURIE style identifier.', 'type': 'string'}, 'label': {'description': 'Human-readable class name.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'})]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='molecule',
+            field=models.CharField(blank=True, choices=[('total RNA', 'total RNA'), ('polyA RNA', 'polyA RNA'), ('cytoplasmic RNA', 'cytoplasmic RNA'), ('nuclear RNA', 'nuclear RNA'), ('small RNA', 'small RNA'), ('genomic DNA', 'genomic DNA'), ('protein', 'protein'), ('other', 'other')], help_text='(Controlled Vocabulary) The type of molecule that was extracted from the biological material. Include one of the following: total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, small RNA, genomic DNA, protein, or other.', max_length=20, null=True),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='molecule_ontology',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='(Ontology: SO) links to molecule ontology information.', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'ONTOLOGY_CLASS_LIST', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'ONTOLOGY_CLASS', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'todo', 'properties': {'id': {'description': 'CURIE style identifier.', 'type': 'string'}, 'label': {'description': 'Human-readable class name.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'})]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='other_fields',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='The other fields for the experiment', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'KEY_VALUE_OBJECT', '$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'})]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='qc_flags',
+            field=django.contrib.postgres.fields.ArrayField(base_field=models.CharField(help_text='Any quanlity control observations can be noted here. This field can be omitted if empty', max_length=100), blank=True, default=list, null=True, size=None),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='reference_registry_id',
+            field=models.CharField(blank=True, help_text='The IHEC EpiRR ID for this dataset, only for IHEC Reference Epigenome datasets. Otherwise leave empty.', max_length=30, null=True),
+        ),
+    ]

chord_metadata_service/experiments/models.py

@@ -1,12 +1,13 @@
 from django.db import models
 from django.db.models import CharField
-from django.core.validators import RegexValidator
 from django.core.exceptions import ValidationError
 from django.contrib.postgres.fields import JSONField, ArrayField
 from chord_metadata_service.restapi.models import IndexableMixin
 from chord_metadata_service.restapi.description_utils import rec_help
 from chord_metadata_service.restapi.validators import ontologyListValidator, keyValueValidator
 from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS_LIST, KEY_VALUE_OBJECT
+from chord_metadata_service.patients.models import Individual
+from chord_metadata_service.phenopackets.models import Biosample
 import chord_metadata_service.experiments.descriptions as d
 
 class Experiment(models.Model, IndexableMixin):
@@ -38,16 +39,22 @@ class Experiment(models.Model, IndexableMixin):
 
     id = CharField(primary_key=True, max_length=200, help_text=rec_help(d.EXPERIMENT, 'id'))
 
-    reference_registry_id = CharField(max_length=30, null=True, help_text=rec_help(d.EXPERIMENT, 'reference_registry_id'))
-    qc_flags = ArrayField(CharField(max_length=100, help_text=rec_help(d.EXPERIMENT, 'qc_flags')), null=True, default=list)
+    reference_registry_id = CharField(max_length=30, blank=True, null=True, help_text=rec_help(d.EXPERIMENT, 'reference_registry_id'))
+    qc_flags = ArrayField(CharField(max_length=100, help_text=rec_help(d.EXPERIMENT, 'qc_flags')), null=True, blank=True, default=list)
     experiment_type = CharField(max_length=30, help_text=rec_help(d.EXPERIMENT, 'experiment_type'))
-    experiment_ontology = JSONField(null=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
-    molecule_ontology = JSONField(null=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'molecule_ontology'))
-    molecule = CharField(choices=MOLECULE, max_length=20, null=True, help_text=rec_help(d.EXPERIMENT, 'molecule'))
-
+    experiment_ontology = JSONField(blank=True, null=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
+    molecule_ontology   = JSONField(blank=True, null=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'molecule_ontology'))
+    molecule = CharField(choices=MOLECULE, max_length=20, blank=True, null=True, help_text=rec_help(d.EXPERIMENT, 'molecule'))
     library_strategy = CharField(choices=LIBRARY_STRATEGY, max_length=25, help_text=rec_help(d.EXPERIMENT, 'library_strategy'))
 
-    other_fields = JSONField(null=True, validators=[keyValueValidator], help_text=rec_help(d.EXPERIMENT, 'other_fields'))
+    other_fields = JSONField(blank=True, null=True, validators=[keyValueValidator], help_text=rec_help(d.EXPERIMENT, 'other_fields'))
+
+    biosample  = models.ForeignKey(Biosample,  on_delete=models.SET_NULL, blank=True, null=True, help_text=rec_help(d.EXPERIMENT, 'biosample'))
+    individual = models.ForeignKey(Individual, on_delete=models.SET_NULL, blank=True, null=True, help_text=rec_help(d.EXPERIMENT, 'individual'))
+
+    def clean(self):
+        if not (self.biosample or self.individual):
+            raise ValidationError('Either Biosamples or Individual must be specified')
 
     def __str__(self):
         return str(self.id)

chord_metadata_service/experiments/tests/test_models.py

@@ -1,15 +1,18 @@
 from django.test import TestCase
+from django.core.exceptions import ValidationError
 from rest_framework import serializers
+from chord_metadata_service.patients.models import Individual
 from ..models import Experiment
 
 
 class ExperimentTest(TestCase):
     """ Test module for Experiment model """
 
     def setUp(self):
+        Individual.objects.create(id='patient:1', sex='FEMALE', age={"age": "P25Y3M2D"})
         Experiment.objects.create(
             id='experiment:1',
-            reference_registry_id='',
+            reference_registry_id='some_id',
             qc_flags=['flag 1', 'flag 2'],
             experiment_type='Chromatin Accessibility',
             experiment_ontology=[{"id": "ontology:1", "label": "Ontology term 1"}],
@@ -25,23 +28,38 @@ def create(self, **kwargs):
         e.save()
 
     def test_validation(self):
+        individual_one = Individual.objects.get(id='patient:1')
+
+        # Invalid experiment_ontology
         self.assertRaises(serializers.ValidationError, self.create,
                 id='experiment:2',
                 library_strategy='Bisulfite-Seq',
                 experiment_type='Chromatin Accessibility',
                 experiment_ontology=["invalid_value"],
+                individual=individual_one
         )
 
+        # Invalid molecule_ontology
         self.assertRaises(serializers.ValidationError, self.create,
                 id='experiment:2',
                 library_strategy='Bisulfite-Seq',
                 experiment_type='Chromatin Accessibility',
                 molecule_ontology=[{"id": "some_id"}],
+                individual=individual_one
         )
 
+        # Invalid value in other_fields
         self.assertRaises(serializers.ValidationError, self.create,
                 id='experiment:2',
                 library_strategy='Bisulfite-Seq',
                 experiment_type='Chromatin Accessibility',
-                other_fields={"some_field": "value", "invalid_value": 42}
+                other_fields={"some_field": "value", "invalid_value": 42},
+                individual=individual_one
+        )
+
+        # Missing individual or biosamples
+        self.assertRaises(ValidationError, self.create,
+                id='experiment:2',
+                library_strategy='Bisulfite-Seq',
+                experiment_type='Chromatin Accessibility'
         )