Merge pull request #102 from romgrk/experiments-api

Experiments API

chord_metadata_service/experiments/api_views.py

@@ -0,0 +1,20 @@
+from rest_framework import viewsets
+from rest_framework.settings import api_settings
+from .serializers import ExperimentSerializer
+from .models import Experiment
+from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
+
+
+class ExperimentViewSet(viewsets.ModelViewSet):
+    """
+    get:
+    Return a list of all existing experiments
+
+    post:
+    Create a new experiment
+    """
+
+    queryset = Experiment.objects.all().order_by("id")
+    serializer_class = ExperimentSerializer
+    pagination_class = LargeResultsSetPagination
+    renderer_classes = tuple(api_settings.DEFAULT_RENDERER_CLASSES)

chord_metadata_service/experiments/migrations/0002_auto_20200327_1728.py

@@ -0,0 +1,40 @@
+# Generated by Django 2.2.11 on 2020-03-27 17:28
+
+import chord_metadata_service.restapi.validators
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='experiment',
+            name='experiment_ontology',
+            field=django.contrib.postgres.fields.jsonb.JSONField(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(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(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(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='reference_registry_id',
+            field=models.CharField(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

@@ -5,13 +5,10 @@
 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 JsonSchemaValidator
+from chord_metadata_service.restapi.validators import ontologyListValidator, keyValueValidator
 from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS_LIST, KEY_VALUE_OBJECT
 import chord_metadata_service.experiments.descriptions as d
 
-ontologyListValidator = JsonSchemaValidator(ONTOLOGY_CLASS_LIST)
-keyValueValidator     = JsonSchemaValidator(KEY_VALUE_OBJECT)
-
 class Experiment(models.Model, IndexableMixin):
     """ Class to store Experiment information """
 
@@ -41,16 +38,16 @@ 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, blank=True, help_text=rec_help(d.EXPERIMENT, 'reference_registry_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)
-    experiment_type = CharField(max_length=30, null=False, blank=False, help_text=rec_help(d.EXPERIMENT, 'experiment_type'))
-    experiment_ontology = JSONField(null=True, blank=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
-    molecule_ontology = JSONField(null=True, blank=True, validators=[ontologyListValidator], help_text=rec_help(d.EXPERIMENT, 'molecule_ontology'))
-    molecule = CharField(choices=MOLECULE, max_length=20, null=True, blank=True, help_text=rec_help(d.EXPERIMENT, 'molecule'))
+    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'))
 
-    library_strategy = CharField(choices=LIBRARY_STRATEGY, max_length=25, null=False, blank=False, help_text=rec_help(d.EXPERIMENT, 'library_strategy'))
+    library_strategy = CharField(choices=LIBRARY_STRATEGY, max_length=25, help_text=rec_help(d.EXPERIMENT, 'library_strategy'))
 
-    other_fields = JSONField(blank=True, null=True, validators=[keyValueValidator], help_text=rec_help(d.EXPERIMENT, 'other_fields'))
+    other_fields = JSONField(null=True, validators=[keyValueValidator], help_text=rec_help(d.EXPERIMENT, 'other_fields'))
 
     def __str__(self):
         return str(self.id)

chord_metadata_service/experiments/serializers.py

@@ -0,0 +1,11 @@
+from rest_framework import serializers
+from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS, AGE_OR_AGE_RANGE
+from chord_metadata_service.restapi.validators import JsonSchemaValidator, ontologyListValidator, keyValueValidator
+from chord_metadata_service.restapi.serializers import GenericSerializer
+from .models import Experiment
+
+
+class ExperimentSerializer(GenericSerializer):
+    class Meta:
+        model = Experiment
+        fields = '__all__'

chord_metadata_service/restapi/urls.py

@@ -1,6 +1,7 @@
 from django.urls import path, include
 from rest_framework import routers
 from chord_metadata_service.chord import api_views as chord_views
+from chord_metadata_service.experiments import api_views as experiment_views
 from chord_metadata_service.patients import api_views as individual_views
 from chord_metadata_service.phenopackets import api_views as phenopacket_views
 
@@ -10,6 +11,9 @@
 
 router = routers.DefaultRouter(trailing_slash=False)
 
+# Experiments app urls
+router.register(r'experiments', experiment_views.ExperimentViewSet)
+
 # Patients app urls
 router.register(r'individuals', individual_views.IndividualViewSet)
 

chord_metadata_service/restapi/validators.py

@@ -1,5 +1,6 @@
 from rest_framework import serializers
 from jsonschema import Draft7Validator
+from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS, ONTOLOGY_CLASS_LIST, KEY_VALUE_OBJECT, AGE_OR_AGE_RANGE
 
 class JsonSchemaValidator(object):
     """ Custom class based validator to validate against Json schema for JSONField """
@@ -22,3 +23,8 @@ def deconstruct(self):
             [self.schema],
             {}
         )
+
+ontologyValidator      = JsonSchemaValidator(ONTOLOGY_CLASS)
+ontologyListValidator  = JsonSchemaValidator(ONTOLOGY_CLASS_LIST)
+keyValueValidator      = JsonSchemaValidator(KEY_VALUE_OBJECT)
+ageOrAgeRangeValidator = JsonSchemaValidator(AGE_OR_AGE_RANGE)