Merge pull request #297 from microbiomedata/280-log-update-query

280 fix update query syntax
microbiomedata · Nov 22, 2024 · b79eb3c · b79eb3c
2 parents 7213e8b + f241a2f
commit b79eb3c
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Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/nmdc_automation/import_automation/activity_mapper.py b/nmdc_automation/import_automation/activity_mapper.py
@@ -120,9 +120,10 @@ def map_sequencing_data(self) -> Tuple[nmdc.Database, Dict]:
                     db.data_object_set.append(DataObject(**do_record))
                     has_output.append(data_object_id)
         update = {
-            "collection": "data_generation_set",
-            "filter": {"id": self.nucelotide_sequencing_id},
-            "update": {"$addToSet": {"has_output": has_output}}
+            "update": "data_generation_set",
+            "updates": [
+                {"q": {"id": self.nucelotide_sequencing_id}, "u": {"$addToSet": {"has_output": has_output[0]}}}
+            ]
         }
         # update self.data_object_map
         if len(has_output) > 1:

diff --git a/nmdc_automation/run_process/run_import.py b/nmdc_automation/run_process/run_import.py
@@ -85,6 +85,7 @@ def import_projects(import_file, import_yaml, site_configuration, iteration):
             runtime.run_query(data_generation_update)
         except Exception as e:
             logger.error(f"Error applying update to sequencing data generation: {e}")
+            logger.error(data_generation_update)
             raise e
 
 

diff --git a/tests/test_imports.py b/tests/test_imports.py
@@ -42,9 +42,10 @@ def test_gold_mapper_map_sequencing_data(gold_mapper):
     exp_dobj_type = "Metagenome Raw Reads"  # From the gold_import_files fixture
     exp_nucleotide_sequencing_id = "nmdc:omprc-11-importT"  # From the gold mapper fixture
     exp_update = {
-        "collection": "data_generation_set",
-        "filter": {"id": exp_nucleotide_sequencing_id},
-        "update": {"$addToSet": {"has_output": [exp_dobj_id]}}
+        "update": "data_generation_set",
+        "updates": [
+            {"q": {"id": exp_nucleotide_sequencing_id}, "u": {"$addToSet": {"has_output": exp_dobj_id}}}
+        ],
     }
     # Sequencing data does not get a URL
     exp_url = None