switch graphql schema to use concrete types for filters

This works around an issue in strawberry graphql where using generic
input types on fields that may return many items causes severe
performance degredation.

api/graphql/filters.py

@@ -1,8 +1,10 @@
+import datetime
 from typing import Callable, Generic, TypeVar
 
 import strawberry
 
 from db.python.utils import GenericFilter, GenericMetaFilter
+from models.enums.analysis import AnalysisStatus
 
 T = TypeVar('T')
 Y = TypeVar('Y')
@@ -26,7 +28,7 @@ def all_values(self):
         """
         Get all values used anywhere in a filter, useful for getting values to map later
         """
-        v = []
+        v: list[T] = []
         if self.eq:
             v.append(self.eq)
         if self.in_:
@@ -80,6 +82,91 @@ def to_internal_filter_mapped(self, f: Callable[[T], Y]) -> GenericFilter[Y]:
         )
 
 
+GraphQLAnalysisStatus = strawberry.enum(AnalysisStatus)
+
+
+# The below concrete types are specified individually because there is a performance
+# issue in strawberry graphql where the usage of generics in input types causes major
+# slowdowns.
+# @see https://github.com/strawberry-graphql/strawberry/issues/3544
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterStr(GraphQLFilter[str]):
+    eq: str | None = None
+    in_: list[str] | None = None
+    nin: list[str] | None = None
+    gt: str | None = None
+    gte: str | None = None
+    lt: str | None = None
+    lte: str | None = None
+    contains: str | None = None
+    icontains: str | None = None
+
+
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterInt(GraphQLFilter[int]):
+    eq: int | None = None
+    in_: list[int] | None = None
+    nin: list[int] | None = None
+    gt: int | None = None
+    gte: int | None = None
+    lt: int | None = None
+    lte: int | None = None
+    contains: int | None = None
+    icontains: int | None = None
+
+
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterBool(GraphQLFilter[bool]):
+    eq: bool | None = None
+    in_: list[bool] | None = None
+    nin: list[bool] | None = None
+    gt: bool | None = None
+    gte: bool | None = None
+    lt: bool | None = None
+    lte: bool | None = None
+    contains: bool | None = None
+    icontains: bool | None = None
+
+
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterAnalysisStatus(GraphQLFilter[AnalysisStatus]):
+    eq: AnalysisStatus | None = None
+    in_: list[AnalysisStatus] | None = None
+    nin: list[AnalysisStatus] | None = None
+    gt: AnalysisStatus | None = None
+    gte: AnalysisStatus | None = None
+    lt: AnalysisStatus | None = None
+    lte: AnalysisStatus | None = None
+    contains: AnalysisStatus | None = None
+    icontains: AnalysisStatus | None = None
+
+
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterDatetime(GraphQLFilter[datetime.datetime]):
+    eq: datetime.datetime | None = None
+    in_: list[datetime.datetime] | None = None
+    nin: list[datetime.datetime] | None = None
+    gt: datetime.datetime | None = None
+    gte: datetime.datetime | None = None
+    lt: datetime.datetime | None = None
+    lte: datetime.datetime | None = None
+    contains: datetime.datetime | None = None
+    icontains: datetime.datetime | None = None
+
+
+@strawberry.input(description='Filter for GraphQL queries')
+class GraphQLFilterDate(GraphQLFilter[datetime.date]):
+    eq: datetime.date | None = None
+    in_: list[datetime.date] | None = None
+    nin: list[datetime.date] | None = None
+    gt: datetime.date | None = None
+    gte: datetime.date | None = None
+    lt: datetime.date | None = None
+    lte: datetime.date | None = None
+    contains: datetime.date | None = None
+    icontains: datetime.date | None = None
+
+
 GraphQLMetaFilter = strawberry.scalars.JSON
 
 

api/graphql/schema.py

@@ -14,7 +14,12 @@
 from strawberry.types import Info
 
 from api.graphql.filters import (
-    GraphQLFilter,
+    GraphQLFilterAnalysisStatus,
+    GraphQLFilterBool,
+    GraphQLFilterDate,
+    GraphQLFilterDatetime,
+    GraphQLFilterInt,
+    GraphQLFilterStr,
     GraphQLMetaFilter,
     graphql_meta_filter_to_internal_filter,
 )
@@ -89,8 +94,6 @@ async def m(info: Info) -> list[str]:
 
 GraphQLEnum = strawberry.type(type('GraphQLEnum', (object,), enum_methods))
 
-GraphQLAnalysisStatus = strawberry.enum(AnalysisStatus)
-
 
 @strawberry.experimental.pydantic.type(model=OurDNALostSample, all_fields=True)  # type: ignore
 class GraphQLOurDNALostSample:
@@ -250,11 +253,11 @@ async def analysis_runner(
         self,
         info: Info,
         root: 'Project',
-        ar_guid: GraphQLFilter[str] | None = None,
-        author: GraphQLFilter[str] | None = None,
-        repository: GraphQLFilter[str] | None = None,
-        access_level: GraphQLFilter[str] | None = None,
-        environment: GraphQLFilter[str] | None = None,
+        ar_guid: GraphQLFilterStr | None = None,
+        author: GraphQLFilterStr | None = None,
+        repository: GraphQLFilterStr | None = None,
+        access_level: GraphQLFilterStr | None = None,
+        environment: GraphQLFilterStr | None = None,
     ) -> list['GraphQLAnalysisRunner']:
         connection = info.context['connection']
         alayer = AnalysisRunnerLayer(connection)
@@ -314,8 +317,8 @@ async def families(
         self,
         info: Info,
         root: 'GraphQLProject',
-        id: GraphQLFilter[int] | None = None,
-        external_id: GraphQLFilter[str] | None = None,
+        id: GraphQLFilterInt | None = None,
+        external_id: GraphQLFilterStr | None = None,
     ) -> list['GraphQLFamily']:
         # don't need a data loader here as we're presuming we're not often running
         # the "families" method for many projects at once. If so, we might need to fix that
@@ -342,9 +345,9 @@ async def samples(
         self,
         info: Info,
         root: 'GraphQLProject',
-        type: GraphQLFilter[str] | None = None,
-        external_id: GraphQLFilter[str] | None = None,
-        id: GraphQLFilter[str] | None = None,
+        type: GraphQLFilterStr | None = None,
+        external_id: GraphQLFilterStr | None = None,
+        id: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
     ) -> list['GraphQLSample']:
         loader = info.context[LoaderKeys.SAMPLES_FOR_PROJECTS]
@@ -362,12 +365,12 @@ async def sequencing_groups(
         self,
         info: Info,
         root: 'GraphQLProject',
-        id: GraphQLFilter[str] | None = None,
-        external_id: GraphQLFilter[str] | None = None,
-        type: GraphQLFilter[str] | None = None,
-        technology: GraphQLFilter[str] | None = None,
-        platform: GraphQLFilter[str] | None = None,
-        active_only: GraphQLFilter[bool] | None = None,
+        id: GraphQLFilterStr | None = None,
+        external_id: GraphQLFilterStr | None = None,
+        type: GraphQLFilterStr | None = None,
+        technology: GraphQLFilterStr | None = None,
+        platform: GraphQLFilterStr | None = None,
+        active_only: GraphQLFilterBool | None = None,
     ) -> list['GraphQLSequencingGroup']:
         loader = info.context[LoaderKeys.SEQUENCING_GROUPS_FOR_PROJECTS]
         filter_ = SequencingGroupFilter(
@@ -394,12 +397,12 @@ async def analyses(
         self,
         info: Info,
         root: 'Project',
-        type: GraphQLFilter[str] | None = None,
-        status: GraphQLFilter[GraphQLAnalysisStatus] | None = None,
-        active: GraphQLFilter[bool] | None = None,
+        type: GraphQLFilterStr | None = None,
+        status: GraphQLFilterAnalysisStatus | None = None,
+        active: GraphQLFilterBool | None = None,
         meta: GraphQLMetaFilter | None = None,
-        timestamp_completed: GraphQLFilter[datetime.datetime] | None = None,
-        ids: GraphQLFilter[int] | None = None,
+        timestamp_completed: GraphQLFilterDatetime | None = None,
+        ids: GraphQLFilterInt | None = None,
     ) -> list['GraphQLAnalysis']:
         connection = info.context['connection']
         connection.project = root.id
@@ -429,11 +432,11 @@ async def cohorts(
         self,
         info: Info,
         root: 'Project',
-        id: GraphQLFilter[str] | None = None,
-        name: GraphQLFilter[str] | None = None,
-        author: GraphQLFilter[str] | None = None,
-        template_id: GraphQLFilter[str] | None = None,
-        timestamp: GraphQLFilter[datetime.datetime] | None = None,
+        id: GraphQLFilterStr | None = None,
+        name: GraphQLFilterStr | None = None,
+        author: GraphQLFilterStr | None = None,
+        template_id: GraphQLFilterStr | None = None,
+        timestamp: GraphQLFilterDatetime | None = None,
     ) -> list['GraphQLCohort']:
         connection = info.context['connection']
         connection.project = root.id
@@ -651,9 +654,9 @@ async def samples(
         self,
         info: Info,
         root: 'GraphQLParticipant',
-        type: GraphQLFilter[str] | None = None,
+        type: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
-        active: GraphQLFilter[bool] | None = None,
+        active: GraphQLFilterBool | None = None,
     ) -> list['GraphQLSample']:
         filter_ = SampleFilter(
             type=type.to_internal_filter() if type else None,
@@ -751,7 +754,7 @@ async def assays(
         self,
         info: Info,
         root: 'GraphQLSample',
-        type: GraphQLFilter[str] | None = None,
+        type: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
     ) -> list['GraphQLAssay']:
         loader_assays_for_sample_ids = info.context[LoaderKeys.ASSAYS_FOR_SAMPLES]
@@ -774,12 +777,12 @@ async def sequencing_groups(
         self,
         info: Info,
         root: 'GraphQLSample',
-        id: GraphQLFilter[str] | None = None,
-        type: GraphQLFilter[str] | None = None,
-        technology: GraphQLFilter[str] | None = None,
-        platform: GraphQLFilter[str] | None = None,
+        id: GraphQLFilterStr | None = None,
+        type: GraphQLFilterStr | None = None,
+        technology: GraphQLFilterStr | None = None,
+        platform: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
-        active_only: GraphQLFilter[bool] | None = None,
+        active_only: GraphQLFilterBool | None = None,
     ) -> list['GraphQLSequencingGroup']:
         loader = info.context[LoaderKeys.SEQUENCING_GROUPS_FOR_SAMPLES]
 
@@ -847,11 +850,11 @@ async def analyses(
         self,
         info: Info,
         root: 'GraphQLSequencingGroup',
-        status: GraphQLFilter[GraphQLAnalysisStatus] | None = None,
-        type: GraphQLFilter[str] | None = None,
+        status: GraphQLFilterAnalysisStatus | None = None,
+        type: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
-        active: GraphQLFilter[bool] | None = None,
-        project: GraphQLFilter[str] | None = None,
+        active: GraphQLFilterBool | None = None,
+        project: GraphQLFilterStr | None = None,
     ) -> list[GraphQLAnalysis]:
         connection = info.context['connection']
         loader = info.context[LoaderKeys.ANALYSES_FOR_SEQUENCING_GROUPS]
@@ -997,8 +1000,8 @@ def enum(self, info: Info) -> GraphQLEnum:  # type: ignore
     async def cohort_templates(
         self,
         info: Info,
-        id: GraphQLFilter[str] | None = None,
-        project: GraphQLFilter[str] | None = None,
+        id: GraphQLFilterStr | None = None,
+        project: GraphQLFilterStr | None = None,
     ) -> list[GraphQLCohortTemplate]:
         connection = info.context['connection']
         cohort_layer = CohortLayer(connection)
@@ -1046,11 +1049,11 @@ async def cohort_templates(
     async def cohorts(
         self,
         info: Info,
-        id: GraphQLFilter[str] | None = None,
-        project: GraphQLFilter[str] | None = None,
-        name: GraphQLFilter[str] | None = None,
-        author: GraphQLFilter[str] | None = None,
-        template_id: GraphQLFilter[str] | None = None,
+        id: GraphQLFilterStr | None = None,
+        project: GraphQLFilterStr | None = None,
+        name: GraphQLFilterStr | None = None,
+        author: GraphQLFilterStr | None = None,
+        template_id: GraphQLFilterStr | None = None,
     ) -> list[GraphQLCohort]:
         connection = info.context['connection']
         cohort_layer = CohortLayer(connection)
@@ -1098,13 +1101,13 @@ async def project(self, info: Info, name: str) -> GraphQLProject:
     async def sample(
         self,
         info: Info,
-        id: GraphQLFilter[str] | None = None,
-        project: GraphQLFilter[str] | None = None,
-        type: GraphQLFilter[str] | None = None,
+        id: GraphQLFilterStr | None = None,
+        project: GraphQLFilterStr | None = None,
+        type: GraphQLFilterStr | None = None,
         meta: GraphQLMetaFilter | None = None,
-        external_id: GraphQLFilter[str] | None = None,
-        participant_id: GraphQLFilter[int] | None = None,
-        active: GraphQLFilter[bool] | None = None,
+        external_id: GraphQLFilterStr | None = None,
+        participant_id: GraphQLFilterInt | None = None,
+        active: GraphQLFilterBool | None = None,
     ) -> list[GraphQLSample]:
         connection = info.context['connection']
         ptable = ProjectPermissionsTable(connection)
@@ -1148,14 +1151,14 @@ async def sample(
     async def sequencing_groups(
         self,
         info: Info,
-        id: GraphQLFilter[str] | None = None,
-        project: GraphQLFilter[str] | None = None,
-        sample_id: GraphQLFilter[str] | None = None,
-        type: GraphQLFilter[str] | None = None,
-        technology: GraphQLFilter[str] | None = None,
-        platform: GraphQLFilter[str] | None = None,
-        active_only: GraphQLFilter[bool] | None = None,
-        created_on: GraphQLFilter[datetime.date] | None = None,
+        id: GraphQLFilterStr | None = None,
+        project: GraphQLFilterStr | None = None,
+        sample_id: GraphQLFilterStr | None = None,
+        type: GraphQLFilterStr | None = None,
+        technology: GraphQLFilterStr | None = None,
+        platform: GraphQLFilterStr | None = None,
+        active_only: GraphQLFilterBool | None = None,
+        created_on: GraphQLFilterDate | None = None,
         assay_meta: GraphQLMetaFilter | None = None,
         has_cram: bool | None = None,
         has_gvcf: bool | None = None,
@@ -1254,7 +1257,9 @@ async def analysis_runner(
 
 
 schema = strawberry.Schema(
-    query=Query, mutation=None, extensions=[QueryDepthLimiter(max_depth=10)]
+    query=Query,
+    mutation=None,
+    extensions=[QueryDepthLimiter(max_depth=10)],
 )
 MetamistGraphQLRouter: GraphQLRouter = GraphQLRouter(
     schema, graphiql=True, context_getter=get_context