Merge pull request #76 from KeithKelleher/main

make endpoints consistent, and share endpoint generation code

Author: KeithKelleher

src/api_adapters/arango_api_adapter.py

@@ -257,7 +257,7 @@ def resolve_id(self, data_model: str, id: str, sortby: dict = {}) -> ResolveResu
 
         query = f"""
             FOR doc IN `{label}`
-                FILTER '{id}' IN doc.xref
+                FILTER '{id}' IN doc.xref OR doc.id == '{id}'
                 {self._get_sortby_clause(sortby)}
                 LIMIT 11
                 RETURN {self._get_document_cleanup_clause()}

src/api_adapters/strawberry_models/pharos_query_models.py

@@ -1,13 +1,11 @@
-from typing import Optional, List, Literal
+from typing import Optional, List, Literal, Dict
 
 import strawberry
 from strawberry import Info
 
-from src.api_adapters.strawberry_models.class_generators import make_linked_list_result_type, make_resolve_result_type, \
-    make_details_result_type, make_list_result_type
-from src.api_adapters.strawberry_models.input_types import FilterOption, ListFilterSettings, LinkedListFilterSettings, \
-    ListQueryContext
-from src.api_adapters.strawberry_models.shared_query_models import Provenance
+from src.api_adapters.strawberry_models.class_generators import make_linked_list_result_type
+from src.api_adapters.strawberry_models.input_types import FilterOption, ListFilterSettings, LinkedListFilterSettings
+from src.api_adapters.strawberry_models.shared_query_models import Provenance, generate_resolvers
 from src.interfaces.result_types import LinkedListQueryContext
 from src.interfaces.simple_enum import NodeLabel, RelationshipLabel
 from src.models.analyte import Synonym
@@ -297,20 +295,6 @@ def provenance(root) -> Provenance:
 
     evidence: List[GoEvidence]
 
-
-ProteinListResult = make_list_result_type("ProteinListResult", Protein)
-GeneListResult = make_list_result_type("GeneListResult", Gene)
-TranscriptListResult = make_list_result_type("TranscriptListResult", Transcript)
-LigandListResult = make_list_result_type("LigandListResult", Ligand)
-GoTermListResult = make_list_result_type("GoTermListResult", GoTerm)
-
-ResolveProteinResult = make_resolve_result_type("ResolveProteinResult", Protein)
-ResolveGeneResult = make_resolve_result_type("ResolveGeneResult", Gene)
-ResolveTranscriptResult = make_resolve_result_type("ResolveTranscriptResult", Transcript)
-ResolveLigandResult = make_resolve_result_type("ResolveLigandResult", Ligand)
-
-GoTermResult = make_details_result_type("GoTermResult", GoTerm)
-
 ProteinGeneQueryResult = make_linked_list_result_type("ProteinGeneQueryResult", "ProteinGeneDetails", GeneProteinRelationship, Gene)
 ProteinTranscriptQueryResult = make_linked_list_result_type("ProteinTranscriptQueryResult", "ProteinTranscriptDetails", TranscriptProteinRelationship, Transcript)
 ProteinGoTermQueryResult = make_linked_list_result_type("ProteinGoTermQueryResult", "ProteinGoTermDetails", ProteinGoTermRelationship, GoTerm)
@@ -328,86 +312,32 @@ def provenance(root) -> Provenance:
 
 LigandProteinQueryResult = make_linked_list_result_type("LigandProteinQueryResult", "LigandProteinDetails", ProteinLigandRelationship, Protein)
 
-
-
-@strawberry.type
-class Query:
-    @strawberry.field()
-    def proteins(self, info: Info, filter: Optional[ListFilterSettings] = None) -> ProteinListResult:
-        api = info.context["api"]
-        context = ListQueryContext(
-            source_data_model="Protein",
-            filter = filter
-        )
-        result = api.get_list_obj(context)
-        return result
-
-    @strawberry.field()
-    def genes(self, info: Info, filter: Optional[ListFilterSettings] = None) -> GeneListResult:
-        api = info.context["api"]
-        context = ListQueryContext(
-            source_data_model="Gene",
-            filter = filter
-        )
-        result = api.get_list_obj(context)
-        return result
-
-    @strawberry.field()
-    def transcripts(self, info: Info, filter: Optional[ListFilterSettings] = None) -> TranscriptListResult:
-        api = info.context["api"]
-        context = ListQueryContext(
-            source_data_model="Transcript",
-            filter = filter
-        )
-        result = api.get_list_obj(context)
-        return result
-
-    @strawberry.field()
-    def ligands(self, info: Info, filter: Optional[ListFilterSettings] = None) -> LigandListResult:
-        api = info.context["api"]
-        context = ListQueryContext(
-            source_data_model="Ligand",
-            filter = filter
-        )
-        result = api.get_list_obj(context)
-        return result
-
-    @strawberry.field()
-    def go_terms(self, info: Info, filter: Optional[ListFilterSettings] = None) -> GoTermListResult:
-        api = info.context["api"]
-        context = ListQueryContext(
-            source_data_model="GoTerm",
-            filter = filter
-        )
-        result = api.get_list_obj(context)
-        return result
-
-    @strawberry.field()
-    def resolve_protein(self, info: Info, id: str) -> ResolveProteinResult:
-        api = info.context["api"]
-        result = api.resolve_id("Protein", id=id, sortby={"uniprot_reviewed": "desc", "uniprot_canonical": "desc", "mapping_ratio": "desc"})
-        return result
-
-    @strawberry.field()
-    def resolve_gene(self, info: Info, id: str) -> ResolveGeneResult:
-        api = info.context["api"]
-        result = api.resolve_id("Gene", id=id, sortby={"mapping_ratio": "desc"})
-        return result
-
-    @strawberry.field()
-    def resolve_transcript(self, info: Info, id: str) -> ResolveTranscriptResult:
-        api = info.context["api"]
-        result = api.resolve_id("Transcript", id=id, sortby={"mapping_ratio": "desc"})
-        return result
-
-    @strawberry.field()
-    def resolve_ligand(self, info: Info, id: str) -> ResolveLigandResult:
-        api = info.context["api"]
-        result = api.resolve_id("Ligand", id=id)
-        return result
-
-    @strawberry.field()
-    def go_term(self, info: Info, id: str) -> GoTermResult:
-        api = info.context["api"]
-        result = api.get_details("GoTerm", id=id)
-        return result
+ENDPOINTS: Dict[type, Dict[str, str]] = {
+    Protein: {
+        "list": "proteins",
+        "details": "resolve_protein",
+        "sortby": {"uniprot_reviewed": "desc", "uniprot_canonical": "desc", "mapping_ratio": "desc"}
+    },
+    Gene: {
+        "list": "genes",
+        "details": "resolve_gene",
+        "sortby": {"mapping_ratio": "desc"}
+    },
+    Transcript: {
+        "list": "transcripts",
+        "details": "resolve_transcript",
+        "sortby": {"mapping_ratio": "desc"}
+    },
+    Ligand: {
+        "list": "ligands",
+        "details": "resolve_ligand"
+    },
+    GoTerm: {
+        "list": "go_terms",
+        "details": "resolve_go_term"
+    }
+}
+
+resolvers = generate_resolvers(ENDPOINTS)
+
+Query = strawberry.type(type("Query", (), resolvers))

src/api_adapters/strawberry_models/pounce_query_models.py

@@ -1,12 +1,12 @@
-from typing import Optional, Union, List
+from typing import Optional, Union, List, Dict
 
 import strawberry
 from strawberry import Info
 
 from src.api_adapters.arango_api_adapter import ArangoAPIAdapter
 from src.api_adapters.strawberry_models.class_generators import make_linked_list_result_type
 from src.api_adapters.strawberry_models.input_types import LinkedListFilterSettings
-from src.api_adapters.strawberry_models.shared_query_models import Provenance, generate_list_resolver
+from src.api_adapters.strawberry_models.shared_query_models import Provenance, generate_resolvers
 from src.interfaces.result_types import LinkedListQueryContext
 from src.models.node import EquivalentId
 from src.models.pounce.data import (Biospecimen as BiospecimenBase, Sample as SampleBase,
@@ -468,22 +468,45 @@ class GeneDataResults:
 
 top_level_classes = [Biospecimen, Sample, Investigator, Protein, Project, ProjectType, Experiment, Gene, Metabolite]
 
-
-LIST_RESOLVERS = {
-    "projects": Project,
-    "experiments": Experiment,
-    "investigators": Investigator,
-    "biospecimens": Biospecimen,
-    "samples": Sample,
-    "proteins": Protein,
-    "project_types": ProjectType,
-    "metabolite": Metabolite,
-    "genes": Gene
+ENDPOINTS: Dict[type, Dict[str, str]] = {
+    Project: {
+        "list": "projects",
+        "details": "resolve_project"
+    },
+    Experiment: {
+        "list": "experiments",
+        "details": "resolve_experiment"
+    },
+    Investigator: {
+        "list": "investigators",
+        "details": "resolve_investigator"
+    },
+    Biospecimen: {
+        "list": "biospecimens",
+        "details": "resolve_biospecimen"
+    },
+    Sample: {
+        "list": "samples",
+        "details": "resolve_sample"
+    },
+    Protein: {
+        "list": "proteins",
+        "details": "resolve_protein"
+    },
+    ProjectType: {
+        "list": "project_types",
+        "details": "resolve_project_type"
+    },
+    Metabolite: {
+        "list": "metabolites",
+        "details": "resolve_metabolite"
+    },
+    Gene: {
+        "list": "genes",
+        "details": "resolve_gene"
+    }
 }
 
-query_fields = {
-    name: generate_list_resolver(model_name)
-    for name, model_name in LIST_RESOLVERS.items()
-}
+resolvers = generate_resolvers(ENDPOINTS)
 
-Query = strawberry.type(type("Query", (), query_fields))
+Query = strawberry.type(type("Query", (), resolvers))

src/api_adapters/strawberry_models/shared_query_models.py

@@ -1,10 +1,10 @@
 from datetime import date, datetime
-from typing import Optional, List, Type
+from typing import Optional, List, Type, Dict
 
 import strawberry
 from strawberry import Info
 
-from src.api_adapters.strawberry_models.class_generators import make_list_result_type
+from src.api_adapters.strawberry_models.class_generators import make_list_result_type, make_resolve_result_type
 from src.api_adapters.strawberry_models.input_types import ListFilterSettings, ListQueryContext
 
 from src.shared.record_merger import FieldConflictBehavior
@@ -78,6 +78,16 @@ def parse_to_date(iso_format_str: str) -> Optional[date]:
     return date.fromisoformat(iso_format_str)
 
 
+def generate_details_resolver(source_data_model: Type, sortby = {}):
+    class_name = source_data_model.__name__
+    return_type = make_resolve_result_type(f"{class_name}ResolveResult", source_data_model)
+    @strawberry.field()
+    def resolver(self, info: Info, id: str) -> return_type:
+        api = info.context["api"]
+        return api.resolve_id(class_name, id=id, sortby=sortby)
+    return resolver
+
+
 def generate_list_resolver(source_data_model: Type):
     class_name = source_data_model.__name__
     return_type = make_list_result_type(f"{class_name}ListResult", source_data_model)
@@ -87,3 +97,22 @@ def resolver(self, info: Info, filter: Optional[ListFilterSettings] = None) -> r
         context = ListQueryContext(source_data_model=class_name, filter=filter)
         return api.get_list_obj(context)
     return resolver
+
+
+def generate_resolvers(ENDPOINTS: Dict[type, Dict[str, str]]):
+    global resolvers
+    list_resolvers = {
+        info["list"]: generate_list_resolver(model_cls)
+        for model_cls, info in ENDPOINTS.items()
+        if "list" in info
+    }
+    details_resolvers = {
+        info["details"]: generate_details_resolver(model_cls)
+        for model_cls, info in ENDPOINTS.items()
+        if "details" in info
+    }
+    resolvers = {
+        **list_resolvers,
+        **details_resolvers
+    }
+    return resolvers

src/use_cases/api/host_graphql_api.py

@@ -4,11 +4,11 @@
 
 import strawberry
 from fastapi import FastAPI, Request
+from fastapi.middleware.cors import CORSMiddleware
 from strawberry.fastapi import GraphQLRouter
 
 from src.api_adapters.strawberry_models.pharos_query_models import Query as pharosQuery
 from src.api_adapters.strawberry_models.pounce_query_models import Query as pounceQuery
-from fastapi.middleware.cors import CORSMiddleware
 
 from src.use_cases.build_from_yaml import HostDashboardFromYaml