Merge pull request #129 from c3g/develop

Version 0.7.0

.readthedocs.yml

@@ -15,9 +15,7 @@ formats:
   - htmlzip
 
 # Optionally set the version of Python and requirements required to build your docs
-#python:
-#  version: 3.7
-#  install:
-#    - requirements: requirements.txt
-#    - requirements: docs/requirements.txt
-#    - method: pip
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt

.travis.yml

@@ -4,19 +4,19 @@ python:
   - "3.6"
   - "3.8"
 addons:
-  postgresql: "11"
+  postgresql: "12"
   apt:
     packages:
-      - postgresql-11
-      - postgresql-contrib-11
+      - postgresql-12
+      - postgresql-contrib-12
 before_install:
-  - sudo -u postgres psql -U postgres -p 5432 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
+  - sudo -u postgres psql -U postgres -p 5433 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
 install:
   - pip install -r requirements.txt
   - pip install .
 script:
-  - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5432
-  - python3 -m coverage run ./manage.py test
+  - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5433
+  - python3 -m tox
   - codecov
   - rm -rf chord_metadata_service
   - python3 -m coverage run ./manage.py test chord_metadata_service

MANIFEST.in

@@ -1,3 +1,4 @@
-include chord_metadata_service/chord/workflows/phenopackets_json.wdl
+include chord_metadata_service/chord/workflows/*.wdl
+include chord_metadata_service/chord/tests/*.json
 include chord_metadata_service/dats/*
 include chord_metadata_service/package.cfg

README.md

@@ -18,15 +18,24 @@ under the BSD 3-clause license.
 CHORD Metadata Service is a service to store epigenomic metadata.
 
 1. Patients service handles anonymized individual’s data (individual id, sex, age or date of birth)
-    * Data model: aggregated profile from GA4GH Phenopackets Individual and FHIR Patient
+    * Data model: aggregated profile from GA4GH Phenopackets Individual, FHIR Patient and mCODE Patient.
 
 2. Phenopackets service handles phenotypic and clinical data
     * Data model: [GA4GH Phenopackets schema](https://github.com/phenopackets/phenopacket-schema)
 
-3. CHORD service  handles metadata about dataset, has relation to phenopackets (one dataset can have many phenopackets)
+3. mCode service handles patient's oncology related data.
+    * Data model: [mCODE data elements](https://mcodeinitiative.org/)
+
+4. Experiments service handles experiment related data.
+    * Data model: derived from [IHEC Metadata Experiment](https://github.com/IHEC/ihec-ecosystems/blob/master/docs/metadata/2.0/Ihec_metadata_specification.md#experiments)
+
+5. Resources service handles metadata about ontologies used for data annotation.
+    * Data model: derived from Phenopackets Resource profile
+
+6. CHORD service  handles metadata about dataset, has relation to phenopackets (one dataset can have many phenopackets)
     * Data model: [DATS](https://github.com/datatagsuite)  + [GA4GH DUO](https://github.com/EBISPOT/DUO)
 
-4. Rest api service handles all generic functionality shared among other services
+7. Rest api service handles all generic functionality shared among other services
 
 
 ## REST API highlights
@@ -42,7 +51,6 @@ Phenopackets model is mapped to [FHIR](https://www.hl7.org/fhir/) using
 To retrieve data in fhir append `?format=fhir` .
 
 * Ingest endpoint: `/private/ingest`.
-Example of POST body is in `chord/views_ingest.py` (`METADATA_WORKFLOWS`).
 
 
 ## Install
@@ -131,22 +139,28 @@ out and tagged from the tagged major/minor release in `master`.
 
 Tests are located in tests directory in an individual app folder.
 
-Run all tests for the whole project:
+Run all tests and linting checks for the whole project:
 
+```bash
+tox
 ```
+
+Run all tests for the whole project:
+
+```bash
 python manage.py test
 ```
 
 Run tests for an individual app, e.g.:
 
-```
+```bash
 python manage.py test chord_metadata_service.phenopackets.tests.test_api
 ```
 
-Create coverage html report:
+Test and create `coverage` HTML report:
 
-```
-coverage run manage.py test
+```bash
+tox
 coverage html
 ```
 

chord_metadata_service/chord/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import *
+from .models import Project, Dataset, TableOwnership, Table
 
 
 @admin.register(Project)
@@ -16,3 +16,8 @@ class DatasetAdmin(admin.ModelAdmin):
 @admin.register(TableOwnership)
 class TableOwnershipAdmin(admin.ModelAdmin):
     pass
+
+
+@admin.register(Table)
+class TableAdmin(admin.ModelAdmin):
+    pass

chord_metadata_service/chord/api_views.py

@@ -4,12 +4,12 @@
 
 from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, JSONLDDatasetRenderer, RDFDatasetRenderer
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
-from .models import *
+from .models import Project, Dataset, TableOwnership, Table
 from .permissions import OverrideOrSuperUserOnly
-from .serializers import *
+from .serializers import ProjectSerializer, DatasetSerializer, TableOwnershipSerializer, TableSerializer
 
 
-__all__ = ["ProjectViewSet", "DatasetViewSet", "TableOwnershipViewSet"]
+__all__ = ["ProjectViewSet", "DatasetViewSet", "TableOwnershipViewSet", "TableViewSet"]
 
 
 class ReadOnly(BasePermission):
@@ -61,8 +61,23 @@ class TableOwnershipViewSet(CHORDPublicModelViewSet):
 
     post:
     Create a new relationship between a dataset (and optionally a specific biosample) and a table
-    in another service
+    in a data service
     """
 
     queryset = TableOwnership.objects.all().order_by("table_id")
     serializer_class = TableOwnershipSerializer
+
+
+class TableViewSet(CHORDPublicModelViewSet):
+    """
+    get:
+    Return a list of tables
+
+    post:
+    Create a new table
+    """
+
+    # TODO: Create TableOwnership if needed - here or model?
+
+    queryset = Table.objects.all().prefetch_related("ownership_record").order_by("ownership_record_id")
+    serializer_class = TableSerializer

chord_metadata_service/chord/apps.py

@@ -2,4 +2,4 @@
 
 
 class ChordConfig(AppConfig):
-    name = 'chord'
+    name = 'chord_metadata_service.chord'

chord_metadata_service/chord/data_types.py

@@ -0,0 +1,35 @@
+from chord_metadata_service.experiments.search_schemas import EXPERIMENT_SEARCH_SCHEMA
+from chord_metadata_service.phenopackets.search_schemas import PHENOPACKET_SEARCH_SCHEMA
+from chord_metadata_service.mcode.schemas import MCODE_SCHEMA
+
+__all__ = [
+    "DATA_TYPE_EXPERIMENT",
+    "DATA_TYPE_PHENOPACKET",
+    "DATA_TYPE_MCODEPACKET",
+    "DATA_TYPES",
+]
+
+DATA_TYPE_EXPERIMENT = "experiment"
+DATA_TYPE_PHENOPACKET = "phenopacket"
+DATA_TYPE_MCODEPACKET = "mcodepacket"
+
+DATA_TYPES = {
+    DATA_TYPE_EXPERIMENT: {
+        "schema": EXPERIMENT_SEARCH_SCHEMA,
+        "metadata_schema": {
+            "type": "object",  # TODO
+        },
+    },
+    DATA_TYPE_PHENOPACKET: {
+        "schema": PHENOPACKET_SEARCH_SCHEMA,
+        "metadata_schema": {
+            "type": "object",  # TODO
+        }
+    },
+    DATA_TYPE_MCODEPACKET: {
+        "schema": MCODE_SCHEMA,
+        "metadata_schema": {
+            "type": "object",  # TODO
+        }
+    }
+}