Merge pull request #140 from c3g/mcode-data-type

A few mcode fixes; update dependencies

chord_metadata_service/chord/ingest.py

@@ -183,7 +183,7 @@ def create_phenotypic_feature(pf):
         negated=pf.get("negated", False),
         severity=pf.get("severity"),
         modifier=pf.get("modifier", []),  # TODO: Validate ontology term in schema...
-        onset=pf.get("onset", None),
+        onset=pf.get("onset"),
         evidence=pf.get("evidence")  # TODO: Separate class?
     )
 

chord_metadata_service/chord/tests/test_api_search.py

@@ -27,17 +27,18 @@
     TEST_FHIR_SEARCH_QUERY,
 )
 from ..models import Project, Dataset, TableOwnership, Table
-from ..data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_PHENOPACKET, DATA_TYPES
+from ..data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_MCODEPACKET, DATA_TYPE_PHENOPACKET, DATA_TYPES
 
 
 class DataTypeTest(APITestCase):
     def test_data_type_list(self):
         r = self.client.get(reverse("data-type-list"))
         self.assertEqual(r.status_code, status.HTTP_200_OK)
         c = r.json()
-        self.assertEqual(len(c), 2)
-        ids = (c[0]["id"], c[1]["id"])
+        self.assertEqual(len(c), 3)
+        ids = (c[0]["id"], c[1]["id"], c[2]["id"])
         self.assertIn(DATA_TYPE_EXPERIMENT, ids)
+        self.assertIn(DATA_TYPE_MCODEPACKET, ids)
         self.assertIn(DATA_TYPE_PHENOPACKET, ids)
 
     def test_data_type_detail(self):

chord_metadata_service/chord/views_search.py

@@ -16,25 +16,26 @@
 from chord_lib.search import build_search_response, postgres
 from chord_metadata_service.experiments.models import Experiment
 from chord_metadata_service.experiments.serializers import ExperimentSerializer
+from chord_metadata_service.mcode.models import MCodePacket
 from chord_metadata_service.metadata.elastic import es
 from chord_metadata_service.metadata.settings import DEBUG, CHORD_SERVICE_ARTIFACT, CHORD_SERVICE_ID
 from chord_metadata_service.patients.models import Individual
 from chord_metadata_service.phenopackets.api_views import PHENOPACKET_PREFETCH
 from chord_metadata_service.phenopackets.models import Phenopacket
 from chord_metadata_service.phenopackets.serializers import PhenopacketSerializer
 
-from .data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_PHENOPACKET, DATA_TYPES
+from .data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_MCODEPACKET, DATA_TYPE_PHENOPACKET, DATA_TYPES
 from .models import Dataset, TableOwnership, Table
 from .permissions import ReadOnly, OverrideOrSuperUserOnly
 
 
 @api_view(["GET"])
 @permission_classes([AllowAny])
 def data_type_list(_request):
-    return Response([
-        {"id": DATA_TYPE_EXPERIMENT, "schema": DATA_TYPES[DATA_TYPE_EXPERIMENT]["schema"]},
-        {"id": DATA_TYPE_PHENOPACKET, "schema": DATA_TYPES[DATA_TYPE_PHENOPACKET]["schema"]},
-    ])
+    return Response(sorted(
+        ({"id": k, "schema": dt["schema"]} for k, dt in DATA_TYPES.items()),
+        key=lambda dt: dt["id"]
+    ))
 
 
 @api_view(["GET"])
@@ -151,6 +152,15 @@ def experiment_table_summary(table):
     })
 
 
+def mcodepacket_table_summary(table):
+    mcodepackets = MCodePacket.objects.filter(table=table)  # TODO
+
+    return Response({
+        "count": mcodepackets.count(),
+        "data_type_specific": {},  # TODO
+    })
+
+
 def phenopacket_table_summary(table):
     phenopackets = Phenopacket.objects.filter(table=table)  # TODO
 
@@ -220,6 +230,7 @@ def count_individual(ind):
 
 SUMMARY_HANDLERS: Dict[str, Callable[[Any], Response]] = {
     DATA_TYPE_EXPERIMENT: experiment_table_summary,
+    DATA_TYPE_MCODEPACKET: mcodepacket_table_summary,
     DATA_TYPE_PHENOPACKET: phenopacket_table_summary,
 }
 

requirements.txt

@@ -2,30 +2,30 @@ alabaster==0.7.12
 appdirs==1.4.4
 attrs==19.3.0
 Babel==2.8.0
-certifi==2020.4.5.2
+certifi==2020.6.20
 chardet==3.0.4
 chord-lib==0.9.0
 codecov==2.1.7
 colorama==0.4.3
 coreapi==2.3.3
 coreschema==0.0.4
-coverage==5.1
-distlib==0.3.0
-Django==2.2.13
-django-filter==2.2.0
+coverage==5.2
+distlib==0.3.1
+Django==2.2.14
+django-filter==2.3.0
 django-nose==1.4.6
 django-rest-swagger==2.2.0
 djangorestframework==3.11.0
-djangorestframework-camel-case==1.1.2
+djangorestframework-camel-case==1.2.0
 docutils==0.16
-elasticsearch==7.6.0
+elasticsearch==7.8.0
 entrypoints==0.3
 fhirclient==3.2.0
 filelock==3.0.12
 flake8==3.8.3
-idna==2.9
+idna==2.10
 imagesize==1.2.0
-importlib-metadata==1.6.0
+importlib-metadata==1.7.0
 isodate==0.6.0
 itypes==1.2.0
 Jinja2==2.11.2
@@ -39,7 +39,7 @@ openapi-codec==1.3.2
 packaging==20.4
 pluggy==0.13.1
 psycopg2-binary==2.8.5
-py==1.8.2
+py==1.9.0
 pycodestyle==2.6.0
 pyflakes==2.2.0
 Pygments==2.6.1
@@ -48,8 +48,8 @@ pyrsistent==0.16.0
 python-dateutil==2.8.1
 pytz==2020.1
 PyYAML==5.3.1
-rdflib==4.2.2
-rdflib-jsonld==0.4.0
+rdflib==5.0.0
+rdflib-jsonld==0.5.0
 redis==3.5.3
 requests==2.24.0
 rfc3987==1.3.8
@@ -67,10 +67,10 @@ sphinxcontrib-serializinghtml==1.1.4
 sqlparse==0.3.1
 strict-rfc3339==0.7
 toml==0.10.1
-tox==3.15.2
+tox==3.16.1
 uritemplate==3.0.1
 urllib3==1.25.9
-virtualenv==20.0.23
+virtualenv==20.0.25
 Werkzeug==1.0.1
 wincertstore==0.2
 zipp==3.1.0

setup.py

@@ -17,13 +17,13 @@
     python_requires=">=3.6",
     install_requires=[
         "chord_lib[django]==0.9.0",
-        "Django>=2.2.13,<3.0",
-        "django-filter>=2.2,<3.0",
+        "Django>=2.2.14,<3.0",
+        "django-filter>=2.3,<3.0",
         "django-nose>=1.4,<2.0",
         "djangorestframework>=3.11,<3.12",
-        "djangorestframework-camel-case>=1.1,<2.0",
+        "djangorestframework-camel-case>=1.2.0,<2.0",
         "django-rest-swagger==2.2.0",
-        "elasticsearch==7.1.0",
+        "elasticsearch==7.8.0",
         "fhirclient>=3.2,<4.0",
         "jsonschema>=3.2,<4.0",
         "psycopg2-binary>=2.8,<3.0",
@@ -32,7 +32,7 @@
         "strict-rfc3339==0.7",
         "rdflib==4.2.2",
         "rdflib-jsonld==0.4.0",
-        "requests>=2.23,<3.0",
+        "requests>=2.24.0,<3.0",
         "rfc3987==1.3.8",
         "uritemplate>=3.0,<4.0",
     ],