Merge branch '134-RCB.RMB.error' into 'develop'

Resolve "Server changing... need to change .insert calls"

Closes #134

See merge request !92

CHANGELOG.md

@@ -9,6 +9,8 @@
 * Use CI staging RIDs for CI unit tests: getBag, uploadInputBag, uploadExecutionRun, uploadQC, uploadProcessedFiles, uploadOutputBag (#133)
 * Add `-u "F"` to CI unit test uploadOutputBag `upload_output_bag.py`
 * Remove "fail" integration CI tests (#133 addendum)
+* Add licence header to nf file,  R and python scriptsand pytest scripts
+* Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134)
 
 # v2.0.0
 **User Facing**

rna-seq.nf

 #!/usr/bin/env nextflow
+//rna-seq.nf
+//*
+//* --------------------------------------------------------------------------
+//* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+//* --------------------------------------------------------------------------
+//*
 
 //  ########  ####  ######  ########
 //  ##     ##  ##  ##    ## ##

workflow/scripts/calculateTPM.R

+#!/usr/bin/env R
+#calculateTPM.R
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 gc()
 library(optparse)
 

workflow/scripts/convertGeneSymbols.R

+#!/usr/bin/env R
+#convertGeneSymbols.R
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 gc()
 library(optparse)
 

workflow/scripts/delete_entry.py

+#!/usr/bin/env python3
+#delete_entry.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -34,4 +42,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)

workflow/scripts/extract_ref_data.py

 #!/usr/bin/env python3
+#extract_ref_data.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd

workflow/scripts/generate_references.py

@@ -2,7 +2,7 @@
 #generate_references.py
 #*
 #* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
 #* --------------------------------------------------------------------------
 #*
 

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-#
-# * --------------------------------------------------------------------------
-# * Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/master/LICENSE)
-# * --------------------------------------------------------------------------
-#
+#generate_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 '''Make YAML of software versions.'''
 

workflow/scripts/parse_meta.py

 #!/usr/bin/env python3
+#parse_meta.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd

workflow/scripts/tin_hist.py

 #!/usr/bin/env python3
+#tin_hist.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd

workflow/scripts/upload_execution_run.py

+#!/usr/bin/env python3
+#upload_execution_run.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -33,7 +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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
     else:
         run_data = {
@@ -58,4 +66,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)

workflow/scripts/upload_input_bag.py

+#!/usr/bin/env python3
+#upload_input_bag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -31,7 +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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
     rid = entities[0]["RID"]
 
     print(rid)
@@ -43,4 +51,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credential = {"cookie": args.cookie}
-    main(host, 2, credential)
\ No newline at end of file
+    main(host, 2, credential)

workflow/scripts/upload_output_bag.py

+#!/usr/bin/env python3
+#upload_output_bag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -34,7 +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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
 
     else:
@@ -42,7 +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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
 
     print(rid)
@@ -54,4 +62,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credential = {"cookie": args.cookie}
-    main(host, 2, credential)
\ No newline at end of file
+    main(host, 2, credential)

workflow/scripts/upload_qc.py

+#!/usr/bin/env python3
+#upload_qc.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -37,14 +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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         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], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
     else:
         run_data = {
@@ -72,4 +80,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)

workflow/scripts/utils.py

 #!/usr/bin/env python3
+#utils.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import shlex
 import logging

workflow/tests/test_alignReads.py

 #!/usr/bin/env python3
+#test_alignReads.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd

workflow/tests/test_completion.py

 #!/usr/bin/env python3
+#test_completion.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -12,4 +18,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.completionMultiqc
 def test_multiqcExist(filename):
     assert os.path.exists(os.path.join(
-        test_output_path, filename))
\ No newline at end of file
+        test_output_path, filename))

workflow/tests/test_consistency.py

 #!/usr/bin/env python3
+#test_consistency.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd

workflow/tests/test_dataQC.py

 #!/usr/bin/env python3
+#test_dataQC.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd

workflow/tests/test_dedupReads.py

 #!/usr/bin/env python3
+#test_dedupReads.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd