update workflow_process to handle Metagenome Sequencing

nmdc_automation/workflow_automation/workflow_process.py

@@ -8,6 +8,13 @@
 from nmdc_automation.models.nmdc import DataObject
 from nmdc_automation.models.workflow import WorkflowConfig, WorkflowProcessNode
 
+# Internal sequencing -> data_generation_set
+# External sequencing -> workflow_execution_set
+DATA_GENERATION_NAMES = [
+    "Sequencing Noninterleaved", "Sequencing Interleaved", "Metagenome Sequencing",
+    "Metatranscriptome Sequencing"
+]
+
 warned_objects = set()
 
 
@@ -99,20 +106,31 @@ def get_current_workflow_process_nodes(
     analyte_category = _determine_analyte_category(workflows)
 
     data_generation_ids = set()
-    data_generation_workflows = [wf for wf in workflows if wf.collection == "data_generation_set"]
-    workflow_execution_workflows = [wf for wf in workflows if wf.collection == "workflow_execution_set"]
+    data_generation_workflows = [wf for wf in workflows if wf.name in DATA_GENERATION_NAMES]
+    workflow_execution_workflows = [wf for wf in workflows if wf.name not in DATA_GENERATION_NAMES]
 
     # default query for data_generation_set records filtered by analyte category
     q = {"analyte_category": analyte_category}
     # override query with allowlist
     if allowlist:
         q["id"] = {"$in": list(allowlist)}
-    dg_execution_records = db["data_generation_set"].find(q)
-    dg_execution_records = list(dg_execution_records)
+        dg_records = db["data_generation_set"].find(q)
+        wfe_records = db["workflow_execution_set"].find(q)
+    else:
+        dg_records = db["data_generation_set"].find(q)
+        if analyte_category == "metagenome": # External sequencing - we only support metagenome for now
+            q2 = {"type": "nmdc:MetagenomeSequencing"}
+            wfe_records = db["workflow_execution_set"].find(q2)
+        else:
+            wfe_records = []
+
+    dg_records = list(dg_records)
+    wfe_records = list(wfe_records)
+    dg_records.extend(wfe_records)
 
     for wf in data_generation_workflows:
         # Sequencing workflows don't have a git repo
-        for rec in dg_execution_records:
+        for rec in dg_records:
             if _is_missing_required_input_output(wf, rec, data_objects_by_id):
                 continue
             data_generation_ids.add(rec["id"])