Merge pull request #961 from satra/enh/pdb

enh: add debugging mode to nipype display crash

Author: satra

CHANGES

@@ -31,6 +31,7 @@ Next Release
 * ENH: Added ANTS based openfmri workflow
 * ENH: MapNode now supports flattening of nested lists 
 * ENH: Support for headless mode using Xvfb
+* ENH: nipype_display_crash has a debugging mode
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
 * FIX: FNIRT registration pathway and associated OpenFMRI example script
 * FIX: spm12b compatibility for Model estimate

bin/nipype_display_crash

@@ -1,53 +1,86 @@
 #!/usr/bin/env python
 """Displays crash information from Nipype crash files. For certain crash files,
 one can rerun a failed node in a temp directory.
-"""
 
-import argparse
-from nipype.utils.filemanip import loadcrash
+Examples:
+
+nipype_display_crash crashfile.pklz
+nipype_display_crash crashfile.pklz -r -i
+nipype_display_crash crashfile.pklz -r -i
+
+"""
 
-def display_crash_files(crashfile, rerun):
+def display_crash_files(crashfile, rerun, debug, directory):
     """display crash file content and rerun if required"""
 
+    from nipype.utils.filemanip import loadcrash
     crash_data = loadcrash(crashfile)
     node = None
     if 'node' in crash_data:
         node = crash_data['node']
     tb = crash_data['traceback']
-    print "\n"
-    print "File: %s"%crashfile
+    print("\n")
+    print("File: %s" % crashfile)
     if node:
-        print "Node: %s"%node
+        print("Node: %s" % node)
         if node.base_dir:
-            print "Working directory: %s"%node.output_dir()
+            print("Working directory: %s" % node.output_dir())
         else:
-            print "Node crashed before execution"
-        print "\n"
-        print "Node inputs:"
-        print node.inputs
-        print "\n"
-    print "Traceback: "
-    print ''.join(tb)
-    print "\n"
+            print("Node crashed before execution")
+        print("\n")
+        print("Node inputs:")
+        print(node.inputs)
+        print("\n")
+    print("Traceback: ")
+    print(''.join(tb))
+    print ("\n")
 
     if rerun:
         if node is None:
-            print "No node in crashfile. Cannot rerun"
+            print("No node in crashfile. Cannot rerun")
             return
-        print "Rerunning node"
-        node.base_dir = None
+        print("Rerunning node")
+        node.base_dir = directory
         node.config = {'execution': {'crashdump_dir': '/tmp'}}
-        node.run()
-        print "\n"
+        try:
+            node.run()
+        except:
+            if debug and debug != 'ipython':
+                import pdb
+                pdb.post_mortem()
+            else:
+                raise
+        print("\n")
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(prog='nipype_display_crash',
-                                     description=__doc__)
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_display_crash',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
     parser.add_argument('crashfile', metavar='f', type=str,
-                   help='crash file to display')
+                        help='crash file to display')
     parser.add_argument('-r','--rerun', dest='rerun',
                         default=False, action="store_true",
-                        help='rerun crashed node')
+                        help='rerun crashed node' + defstr)
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument('-d','--debug', dest='debug',
+                        default=False, action="store_true",
+                        help='enable python debugger when re-executing' + defstr)
+    group.add_argument('-i','--ipydebug', dest='ipydebug',
+                        default=False, action="store_true",
+                        help='enable ipython debugger when re-executing' + defstr)
+    parser.add_argument('--dir', dest='directory',
+                        default=None,
+                        help='Directory to run the node in' + defstr)
     args = parser.parse_args()
-
-    display_crash_files(args.crashfile, args.rerun)
+    print args.debug, args.ipydebug
+    debug = 'ipython' if args.ipydebug else args.debug
+    if debug == 'ipython':
+        import sys
+        from IPython.core import ultratb
+        sys.excepthook = ultratb.FormattedTB(mode='Verbose',
+                                             color_scheme='Linux',
+                                             call_pdb=1)
+    display_crash_files(args.crashfile, args.rerun,
+                        debug, args.directory)