Merge pull request #818 from populationgenomics/dev

Author: illusional

.github/workflows/test.yaml

@@ -72,7 +72,7 @@ jobs:
           echo "rc=$rc" >> $GITHUB_OUTPUT
 
       - name: "Upload coverage report"
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: ./coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}

api/graphql/schema.py

@@ -26,6 +26,7 @@
     AssayLayer,
     CohortLayer,
     FamilyLayer,
+    OurDnaDashboardLayer,
     SampleLayer,
     SequencingGroupLayer,
 )
@@ -53,6 +54,7 @@
 )
 from models.models.analysis_runner import AnalysisRunnerInternal
 from models.models.family import PedRowInternal
+from models.models.ourdna import OurDNADashboard, OurDNALostSample
 from models.models.project import ProjectId
 from models.models.sample import sample_id_transform_to_raw
 from models.utils.cohort_id_format import cohort_id_format, cohort_id_transform_to_raw
@@ -89,6 +91,28 @@ async def m(info: Info) -> list[str]:
 GraphQLAnalysisStatus = strawberry.enum(AnalysisStatus)
 
 
+@strawberry.experimental.pydantic.type(model=OurDNALostSample, all_fields=True)  # type: ignore
+class GraphQLOurDNALostSample:
+    """OurDNA Lost Sample GraphQL model to be used in OurDNA Dashboard"""
+
+    pass  # pylint: disable=unnecessary-pass
+
+
+@strawberry.experimental.pydantic.type(model=OurDNADashboard)  # type: ignore
+class GraphQLOurDNADashboard:
+    """OurDNA Dashboard model"""
+
+    collection_to_process_end_time: strawberry.scalars.JSON
+    collection_to_process_end_time_statistics: strawberry.scalars.JSON
+    collection_to_process_end_time_24h: strawberry.scalars.JSON
+    processing_times_by_site: strawberry.scalars.JSON
+    total_samples_by_collection_event_name: strawberry.scalars.JSON
+    samples_lost_after_collection: list[GraphQLOurDNALostSample]
+    samples_concentration_gt_1ug: strawberry.scalars.JSON
+    participants_consented_not_collected: list[int]
+    participants_signed_not_consented: list[int]
+
+
 # Create cohort GraphQL model
 @strawberry.type
 class GraphQLCohort:
@@ -244,6 +268,18 @@ async def analysis_runner(
         analysis_runners = await alayer.query(filter_)
         return [GraphQLAnalysisRunner.from_internal(ar) for ar in analysis_runners]
 
+    @strawberry.field
+    async def ourdna_dashboard(
+        self, info: Info, root: 'Project'
+    ) -> 'GraphQLOurDNADashboard':
+        connection = info.context['connection']
+        ourdna_layer = OurDnaDashboardLayer(connection)
+        if not root.id:
+            raise ValueError('Project must have an id')
+        ourdna_dashboard = await ourdna_layer.query(project_id=root.id)
+        # pylint: disable=no-member
+        return GraphQLOurDNADashboard.from_pydantic(ourdna_dashboard)
+
     @strawberry.field()
     async def pedigree(
         self,

db/python/layers/__init__.py

@@ -6,6 +6,7 @@
 from db.python.layers.billing import BillingLayer
 from db.python.layers.cohort import CohortLayer
 from db.python.layers.family import FamilyLayer
+from db.python.layers.ourdna.dashboard import OurDnaDashboardLayer
 from db.python.layers.participant import ParticipantLayer
 from db.python.layers.sample import SampleLayer
 from db.python.layers.search import SearchLayer