Rename omics_processing endpoints to data_generation

nmdc_server/api.py

@@ -411,13 +411,18 @@ async def get_study_image(study_id: str, db: Session = Depends(get_db)):
     return StreamingResponse(BytesIO(image), media_type="image/jpeg")
 
 
-# omics_processing
+# data_generation
+# Note the intermingling of the terms "data generation" and "omics processing."
+# The Berkeley schema (NMDC schema v11) did away with the phrase "omics processing."
+# As a result, public-facing uses of "omics processing" should be replaced with
+# "data generation."
+# Future work should go in to a more thorough conversion of omics process to data generation.
 @router.post(
-    "/omics_processing/search",
+    "/data_generation/search",
     response_model=query.OmicsProcessingSearchResponse,
-    tags=["omics_processing"],
-    name="Search for omics processings",
-    description="Faceted search of omics_processing data.",
+    tags=["data_generation"],
+    name="Search for data generations",
+    description="Faceted search of data_generation data.",
 )
 async def search_omics_processing(
     query: query.SearchQuery = query.SearchQuery(),
@@ -428,19 +433,19 @@ async def search_omics_processing(
 
 
 @router.post(
-    "/omics_processing/facet",
+    "/data_generation/facet",
     response_model=query.FacetResponse,
-    tags=["omics_processing"],
+    tags=["data_generation"],
     name="Get all values of an attribute",
 )
 async def facet_omics_processing(query: query.FacetQuery, db: Session = Depends(get_db)):
     return crud.facet_omics_processing(db, query.attribute, query.conditions)
 
 
 @router.post(
-    "/omics_processing/binned_facet",
+    "/data_generation/binned_facet",
     response_model=query.BinnedFacetResponse,
-    tags=["omics_processing"],
+    tags=["data_generation"],
     name="Get all values of a non-string attribute with binning",
 )
 async def binned_facet_omics_processing(
@@ -450,26 +455,26 @@ async def binned_facet_omics_processing(
 
 
 @router.get(
-    "/omics_processing/{omics_processing_id}",
+    "/data_generation/{data_generation_id}",
     response_model=schemas.OmicsProcessing,
-    tags=["omics_processing"],
+    tags=["data_generation"],
 )
-async def get_omics_processing(omics_processing_id: str, db: Session = Depends(get_db)):
-    db_omics_processing = crud.get_omics_processing(db, omics_processing_id)
+async def get_omics_processing(data_generation_id: str, db: Session = Depends(get_db)):
+    db_omics_processing = crud.get_omics_processing(db, data_generation_id)
     if db_omics_processing is None:
         raise HTTPException(status_code=404, detail="OmicsProcessing not found")
     return db_omics_processing
 
 
 @router.get(
-    "/omics_processing/{omics_processing_id}/outputs",
+    "/data_generation/{data_generation_id}/outputs",
     response_model=List[schemas.DataObject],
-    tags=["omics_processing"],
+    tags=["data_generation"],
 )
 async def list_omics_processing_data_objects(
-    omics_processing_id: str, db: Session = Depends(get_db)
+    data_generation_id: str, db: Session = Depends(get_db)
 ):
-    return crud.list_omics_processing_data_objects(db, omics_processing_id).all()
+    return crud.list_omics_processing_data_objects(db, data_generation_id).all()
 
 
 # data object

tests/test_app.py

@@ -153,7 +153,7 @@ def test_get_environmental_aggregation(db: Session, client: TestClient):
 @pytest.mark.parametrize(
     "endpoint",
     [
-        "omics_processing",
+        "data_generation",
     ],
 )
 def test_list_data_objects(db: Session, client: TestClient, endpoint: str):

web/src/data/api.ts

@@ -402,7 +402,7 @@ async function searchStudy(params: SearchParams) {
 }
 
 async function searchOmicsProcessing(params: SearchParams) {
-  return _search<OmicsProcessingResult>('omics_processing', params);
+  return _search<OmicsProcessingResult>('data_generation', params);
 }
 
 async function searchReadsQC(params: SearchParams) {
@@ -483,7 +483,7 @@ async function getFacetSummary(
   field: string,
   conditions: Condition[],
 ): Promise<FacetSummaryResponse[]> {
-  const path = type;
+  const path = type === 'omics_processing' ? 'data_generation' : type;
   const { data } = await client.post<{ facets: Record<string, number> }>(`${path}/facet`, {
     conditions, attribute: field,
   });
@@ -504,7 +504,8 @@ async function getBinnedFacet<T = string | number>(
   numBins: number,
   resolution: 'day' | 'week' | 'month' | 'year' = 'month',
 ) {
-  const { data } = await client.post<BinResponse<T>>(`${table}/binned_facet`, {
+  const path = table === 'omics_processing' ? 'data_generation' : table;
+  const { data } = await client.post<BinResponse<T>>(`${path}/binned_facet`, {
     attribute,
     conditions,
     resolution,
@@ -588,7 +589,8 @@ async function getDataObjectList(
     'metaproteomic_analysis',
   ];
   if (supportedTypes.indexOf(type) >= 0) {
-    const { data } = await client.get<DataObjectSearchResult[]>(`${type}/${parentId}/outputs`);
+    const path = type === 'omics_processing' ? 'data_generation' : type;
+    const { data } = await client.get<DataObjectSearchResult[]>(`${path}/${parentId}/outputs`);
     return data;
   }
   return [];