first pass at autopsy

dSQAutopsy

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+dSQAutopsy.py

dSQAutopsy.py

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+#!/usr/bin/env python
+from __future__ import print_function #to make printing stderr work cleanly
+import sys
+import argparse
+#from dSQ import __version__
+__version__ = 0.4
+desc = """Dead Simple Queue Autopsy v{}
+https://github.com/ycrc/dSQ
+A helper script for analyzing the success state of your tasks after a dSQ 
+run has completed. Specify the taskfile and the status.tsv file generated 
+by the dSQ job and dSQAutopsy will print the tasks that didn't run or 
+completed with non-zero exit codes. It will also report count of each to 
+stderr.
+
+""".format(__version__)
+
+# argument parsing
+parser = argparse.ArgumentParser(description=desc,
+                                 usage='%(prog)s taskfile status.tsv', 
+                                 formatter_class=argparse.RawTextHelpFormatter,
+                                 prog='dSQAutopsy')
+parser.add_argument('-v','--version',
+                    action='version',
+                    version='%(prog)s {}'.format(__version__))
+parser.add_argument('taskfile',
+                    nargs=1,
+                    type=argparse.FileType('r'),
+                    help='Task file, one task per line')
+parser.add_argument('statusfile',
+                    nargs=1,
+                    type=argparse.FileType('r'),
+                    help='The status.tsv file generated from your dSQ run')
+
+args = parser.parse_args()
+
+try:
+    succeeded = set()
+    failed = set()
+    norun = set()
+    for i,l in enumerate(args.statusfile[0]):
+        print(l)
+        exit_code = l.split('\t',2)[1]
+        if exit_code == "0":
+            succeeded.add(i)
+        else:
+            failed.add(i)
+
+    for i,l in enumerate(args.taskfile[0]):
+        if i not in succeeded:
+            if i not in failed:
+                norun.add(i)
+            print(l, end='')
+    print("Autopsy Task Report:\n{} succeeded\n{} failed\n{} didn't run.".format(len(succeeded), len(failed), len(norun)), file=sys.stderr)
+except Exception as e:
+    print ("Something went wrong. Did you specify the right files?")
+    sys.exit(1)