Merge pull request #1433 from microbiomedata/1431-update-annotation-i…

…ngest Use correct slot when querying gene aggregations
microbiomedata · Nov 14, 2024 · 887530c · 887530c
2 parents 02ca10d + 9aa5e09
commit 887530c
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/nmdc_server/ingest/all.py b/nmdc_server/ingest/all.py
@@ -225,7 +225,7 @@ def load(db: Session, function_limit=None, skip_annotation=False):
             ),
             pipeline.load_mp_analysis,
             WorkflowActivityTypeEnum.metaproteomic_analysis.value,
-            annotations=mongodb["metap_gene_function_aggregation"],
+            annotations=mongodb["functional_annotation_agg"],
             function_limit=function_limit,
         )
         db.commit()

diff --git a/nmdc_server/ingest/pipeline.py b/nmdc_server/ingest/pipeline.py
@@ -31,15 +31,15 @@ def load_mg_annotation(db: Session, obj: Dict[str, Any], **kwargs) -> LoadObject
 
     query = annotations.find(
         {
-            "metagenome_annotation_id": pipeline.id,
+            "was_generated_by": pipeline.id,
             "gene_function_id": {
                 "$regex": gene_regex,
             },
         },
         no_cursor_timeout=True,
         projection={
             "_id": False,
-            "metagenome_annotation_id": True,
+            "was_generated_by": True,
             "count": True,
             "gene_function_id": True,
         },
@@ -88,7 +88,7 @@ def load_mp_analysis(db: Session, obj: Dict[str, Any], **kwargs) -> LoadObjectRe
 
     query = annotations.find(
         {
-            "metaproteomic_analysis_id": pipeline.id,
+            "was_generated_by": pipeline.id,
             "gene_function_id": {
                 "$regex": gene_regex,
             },
@@ -97,7 +97,7 @@ def load_mp_analysis(db: Session, obj: Dict[str, Any], **kwargs) -> LoadObjectRe
         no_cursor_timeout=True,
         projection={
             "_id": False,
-            "metaproteomic_analysis_id": True,
+            "was_generated_by": True,
             "count": True,
             "gene_function_id": True,
             "best_protein": True,
@@ -139,15 +139,15 @@ def load_mt_annotation(db: Session, obj: Dict[str, Any], **kwargs) -> LoadObject
     # Query gene function annotations from mongo and build the appropriate objects
     query = annotations.find(
         {
-            "metagenome_annotation_id": pipeline.id,
+            "was_generated_by": pipeline.id,
             "gene_function_id": {
                 "$regex": gene_regex,
             },
         },
         no_cursor_timeout=True,
         projection={
             "_id": False,
-            "metatranscriptome_annotation_id": True,
+            "was_generated_by": True,
             "count": True,
             "gene_function_id": True,
         },