Merge pull request #118 from c3g/rearrange-schemas-validators

Rearrange schemas and validators
bento-platform · May 13, 2020 · 61dc5f8 · 61dc5f8
2 parents a41084c + 607a27b
commit 61dc5f8
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Showing 23 changed files with 878 additions and 287 deletions.
diff --git a/chord_metadata_service/experiments/api_views.py b/chord_metadata_service/experiments/api_views.py
@@ -1,7 +1,12 @@
 from rest_framework import viewsets
 from rest_framework.settings import api_settings
+from rest_framework.decorators import api_view, permission_classes
+from rest_framework.permissions import AllowAny
+from rest_framework.response import Response
+
 from .serializers import ExperimentSerializer
 from .models import Experiment
+from .schemas import EXPERIMENT_SCHEMA
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 
 
@@ -18,3 +23,14 @@ class ExperimentViewSet(viewsets.ModelViewSet):
     serializer_class = ExperimentSerializer
     pagination_class = LargeResultsSetPagination
     renderer_classes = tuple(api_settings.DEFAULT_RENDERER_CLASSES)
+
+
+@api_view(["GET"])
+@permission_classes([AllowAny])
+def get_experiment_schema(_request):
+    """
+    get:
+    Experiment schema
+    """
+    return Response(EXPERIMENT_SCHEMA)
+
diff --git a/chord_metadata_service/experiments/descriptions.py b/chord_metadata_service/experiments/descriptions.py
@@ -15,7 +15,7 @@
 
         "other_fields": "The other fields for the experiment",
 
-        "biosample": "Biosamples on which this experiment was done",
+        "biosample": "Biosample on which this experiment was done",
         "individual": "Donor on which this experiment was done",
 
         **EXTRA_PROPERTIES

diff --git a/chord_metadata_service/experiments/migrations/0005_auto_20200513_1401.py b/chord_metadata_service/experiments/migrations/0005_auto_20200513_1401.py
@@ -0,0 +1,36 @@
+# Generated by Django 2.2.12 on 2020-05-13 18:01
+
+import chord_metadata_service.restapi.validators
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0004_auto_20200401_1445'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='experiment',
+            name='biosample',
+            field=models.ForeignKey(blank=True, help_text='Biosample on which this experiment was done', null=True, on_delete=django.db.models.deletion.SET_NULL, to='phenopackets.Biosample'),
+        ),
+        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({'$id': 'chord_metadata_service:ontology_class_list_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'chord_metadata_service:ontology_class_schema', '$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'}, formats=None)]),
+        ),
+        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({'$id': 'chord_metadata_service:ontology_class_list_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'chord_metadata_service:ontology_class_schema', '$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'}, formats=None)]),
+        ),
+        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({'$id': 'chord_metadata_service:key_value_object_schema', '$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)]),
+        ),
+    ]
diff --git a/chord_metadata_service/experiments/models.py b/chord_metadata_service/experiments/models.py
@@ -38,22 +38,31 @@ 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, 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)
+    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(blank=True, null=True, validators=[ontology_list_validator], help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
-    molecule_ontology   = JSONField(blank=True, null=True, validators=[ontology_list_validator], 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'))
+    experiment_ontology = JSONField(blank=True, null=True, validators=[ontology_list_validator],
+                                    help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
+    molecule_ontology   = JSONField(blank=True, null=True, validators=[ontology_list_validator],
+                                    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(blank=True, null=True, validators=[key_value_validator], help_text=rec_help(d.EXPERIMENT, 'other_fields'))
+    other_fields = JSONField(blank=True, null=True, validators=[key_value_validator],
+                             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'))
+    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')
+            raise ValidationError('Either Biosample or Individual must be specified')
 
     def __str__(self):
         return str(self.id)
diff --git a/chord_metadata_service/experiments/schemas.py b/chord_metadata_service/experiments/schemas.py
@@ -0,0 +1,57 @@
+from .descriptions import EXPERIMENT
+from chord_metadata_service.restapi.description_utils import describe_schema
+from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS_LIST, KEY_VALUE_OBJECT
+
+
+EXPERIMENT_SCHEMA = describe_schema({
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "chord_metadata_service:experiment_schema",
+    "title": "Experiment schema",
+    "description": "Schema for describing an experiment.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "string"
+        },
+        "reference_registry_id": {
+            "type": "string"
+        },
+        "qc_flags": {
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        },
+        "experiment_type": {
+            "type": "string"
+        },
+        "experiment_ontology": ONTOLOGY_CLASS_LIST,
+        "molecule": {
+            "type": "string"
+        },
+        "molecule_ontology": ONTOLOGY_CLASS_LIST,
+        "library_strategy": {
+            "type": "string",
+            "enum": [
+                "DNase-Hypersensitivity",
+                "ATAC-seq",
+                "NOME-Seq",
+                "Bisulfite-Seq",
+                "MeDIP-Seq",
+                "MRE-Seq",
+                "ChIP-Seq",
+                "RNA-Seq",
+                "miRNA-Seq",
+                "WGS"
+            ]
+        },
+        "other_fields": KEY_VALUE_OBJECT,
+        "biosample": {
+            "type": "string"
+        },
+        "individual": {
+            "type": "string"
+        }
+    },
+    "required": ["id", "experiment_type", "library_strategy"]
+}, EXPERIMENT)
diff --git a/chord_metadata_service/mcode/api_views.py b/chord_metadata_service/mcode/api_views.py
@@ -1,5 +1,10 @@
 from rest_framework import viewsets
 from rest_framework.settings import api_settings
+from rest_framework.decorators import api_view, permission_classes
+from rest_framework.permissions import AllowAny
+from rest_framework.response import Response
+from .serializers import *
+from .schemas import MCODE_SCHEMA
 from .models import *
 from .serializers import *
 from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer
@@ -54,3 +59,13 @@ class MedicationStatementViewSet(McodeModelViewSet):
 class MCodePacketViewSet(McodeModelViewSet):
     queryset = MCodePacket.objects.all()
     serializer_class = MCodePacketSerializer
+
+
+@api_view(["GET"])
+@permission_classes([AllowAny])
+def get_mcode_schema(_request):
+    """
+    get:
+    Mcodepacket schema
+    """
+    return Response(MCODE_SCHEMA)