From 8995bdbd74ceeedd946fa468239bf41fa9b2ce78 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 22 Jul 2021 13:27:49 -0500
Subject: [PATCH] Add nodefaults to all inserts calls with deriva.core
---
workflow/scripts/upload_execution_run.py | 2 +-
workflow/scripts/upload_input_bag.py | 2 +-
workflow/scripts/upload_output_bag.py | 4 ++--
workflow/scripts/upload_qc.py | 4 ++--
4 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/upload_execution_run.py b/workflow/scripts/upload_execution_run.py
index 5fd0cf4..7ba9ce2 100644
--- a/workflow/scripts/upload_execution_run.py
+++ b/workflow/scripts/upload_execution_run.py
@@ -41,7 +41,7 @@ def main(hostname, catalog_number, credential):
"Execution_Status": args.status,
"Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
}
- entities = run_table.insert([run_data])
+ entities = run_table.insert([run_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
else:
run_data = {
diff --git a/workflow/scripts/upload_input_bag.py b/workflow/scripts/upload_input_bag.py
index 434129d..d2deca2 100644
--- a/workflow/scripts/upload_input_bag.py
+++ b/workflow/scripts/upload_input_bag.py
@@ -39,7 +39,7 @@ def main(hostname, catalog_number, credential):
"Bag_Type": "Replicate_Input_Seq"
}
- entities = inputBag_table.insert([inputBag_data])
+ entities = inputBag_table.insert([inputBag_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
print(rid)
diff --git a/workflow/scripts/upload_output_bag.py b/workflow/scripts/upload_output_bag.py
index a4ac630..1dce763 100644
--- a/workflow/scripts/upload_output_bag.py
+++ b/workflow/scripts/upload_output_bag.py
@@ -42,7 +42,7 @@ def main(hostname, catalog_number, credential):
"Notes": args.notes,
"Bag_Type": "mRNA_Replicate_Analysis"
}
- entities = outputBag_table.insert([outputBag_data])
+ entities = outputBag_table.insert([outputBag_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
else:
@@ -50,7 +50,7 @@ def main(hostname, catalog_number, credential):
"RID": args.update,
"Execution_Run": args.executionRunRID
}
- entities = outputBag_table.insert([outputBag_data])
+ entities = outputBag_table.insert([outputBag_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
print(rid)
diff --git a/workflow/scripts/upload_qc.py b/workflow/scripts/upload_qc.py
index 3c51bc8..ce12fb6 100644
--- a/workflow/scripts/upload_qc.py
+++ b/workflow/scripts/upload_qc.py
@@ -45,14 +45,14 @@ def main(hostname, catalog_number, credential):
"Median_TIN": args.tin,
"Notes": args.notes
}
- entities = run_table.insert([run_data])
+ entities = run_table.insert([run_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
elif args.update == "E":
run_data = {
"Execution_Run": args.executionRunRID,
"Replicate": args.repRID
}
- entities = run_table.insert([run_data])
+ entities = run_table.insert([run_data], nondefaults=["RCB", "RMB"])
rid = entities[0]["RID"]
else:
run_data = {
--
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