From 3b7cf08e7840397ecc43e93e111c2cc7f8aacc67 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Fri, 22 Nov 2024 09:35:00 -0800
Subject: [PATCH 1/4] dump failing update query to the log

---
 nmdc_automation/run_process/run_import.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nmdc_automation/run_process/run_import.py b/nmdc_automation/run_process/run_import.py
index 922765d3..970f3791 100644
--- 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
 
 

From ff45e202aa82c03b95d3e533dc5fa85e87ac46c0 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Fri, 22 Nov 2024 10:34:34 -0800
Subject: [PATCH 2/4] fix incorrect update query syntax

---
 nmdc_automation/import_automation/activity_mapper.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nmdc_automation/import_automation/activity_mapper.py b/nmdc_automation/import_automation/activity_mapper.py
index a3e97ba5..d1930d16 100644
--- 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}}}
+            ]
         }
         # update self.data_object_map
         if len(has_output) > 1:

From 360fb576a9585473a635c7bd834605657687a8f2 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Fri, 22 Nov 2024 10:45:25 -0800
Subject: [PATCH 3/4] fix update query

---
 nmdc_automation/import_automation/activity_mapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nmdc_automation/import_automation/activity_mapper.py b/nmdc_automation/import_automation/activity_mapper.py
index d1930d16..87970b51 100644
--- a/nmdc_automation/import_automation/activity_mapper.py
+++ b/nmdc_automation/import_automation/activity_mapper.py
@@ -122,7 +122,7 @@ def map_sequencing_data(self) -> Tuple[nmdc.Database, Dict]:
         update = {
             "update": "data_generation_set",
             "updates": [
-                {"q": {"id": self.nucelotide_sequencing_id}, "u": {"$addToSet": {"has_output": has_output}}}
+                {"q": {"id": self.nucelotide_sequencing_id}, "u": {"$addToSet": {"has_output": has_output[0]}}}
             ]
         }
         # update self.data_object_map

From f241a2f224109e7ece3c0abbd782a468cb80e004 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Fri, 22 Nov 2024 10:57:30 -0800
Subject: [PATCH 4/4] update unit test

---
 tests/test_imports.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/test_imports.py b/tests/test_imports.py
index 2ef2a40d..29b2c637 100644
--- 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