Add a helper script to submit a single experiment

scripts/submit-experiment

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+import os
+from contextlib import contextmanager
+
+import luigi
+
+from rnaseq_pipeline.tasks import SubmitExperimentToGemma
+
+@contextmanager
+def umask(umask):
+    print(f'Setting umask to 0x{umask:03o}')
+    prev_umask = os.umask(umask)
+    try:
+        yield None
+    finally:
+        print(f'Restoring umask to 0x{prev_umask:03o}')
+        os.umask(prev_umask)
+
+def parse_octal(s):
+    return int(s, 8)
+
+def main(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma')
+    parser.add_argument('--resubmit-batch-info', action='store_false', help='Only resubmit batch information')
+    parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)')
+    parser.add_argument('--workers', type=int, default=100, help='Number of workers to use (defaults to 100)')
+    args = parser.parse_args(argv)
+    with umask(args.umask):
+        if args.batch_info:
+            task = SubmitExperimentBatchInfoToGemma(experiment_id=args.experiment_id, rerun=True)
+        else:
+            task = SubmitExperimentToGemma(experiment_id=args.experiment_id)
+        results = luigi.build([task], workers=args.workers, detailed_summary=True)
+    print(results.summary_text)
+
+if __name__ == '__main__':
+    sys.exit(main(sys.argv[1:]))

scripts/submit-experiments-from-gsheet

@@ -24,11 +24,11 @@ def parse_octal(s):
 
 def main(argv):
     parser = argparse.ArgumentParser()
-    parser.add_argument('--spreadsheet-id')
-    parser.add_argument('--sheet-name')
-    parser.add_argument('--umask', type=parse_octal, default='002')
-    parser.add_argument('--workers', type=int, default=100)
-    parser.add_argument('--ignore-priority', action='store_true')
+    parser.add_argument('--spreadsheet-id', required=True, help='Spreadsheet ID')
+    parser.add_argument('--sheet-name', required=True, help='Sheet name')
+    parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)')
+    parser.add_argument('--workers', type=int, default=100, help='Number of workers to use (defaults to 100)')
+    parser.add_argument('--ignore-priority', action='store_true', help='Ignore the priority column in the spreadsheet')
     args = parser.parse_args(argv)
     with umask(args.umask):
         results = luigi.build([SubmitExperimentsFromGoogleSpreadsheetToGemma(args.spreadsheet_id, args.sheet_name, ignore_priority=args.ignore_priority)], workers=args.workers, detailed_summary=True)

setup.py

@@ -15,4 +15,4 @@
       extras_require={
           'gsheet': ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'],
           'webviewer': ['Flask', 'gunicorn']},
-      scripts=['scripts/luigi-wrapper', 'scripts/submit-experiments-from-gsheet'])
+      scripts=['scripts/luigi-wrapper', 'scripts/submit-experiments-from-gsheet', 'scripts/submit-experiment'])