enh: option to save crash files as text

Author: mgxd

nipype/pipeline/plugins/base.py

@@ -23,7 +23,7 @@
 
 
 from ... import logging
-from ...utils.filemanip import savepkl, loadpkl
+from ...utils.filemanip import savepkl, loadpkl, crash2txt
 from ...utils.misc import str2bool
 from ..engine.utils import (nx, dfs_preorder, topological_sort)
 from ..engine import MapNode
@@ -58,7 +58,7 @@ def report_crash(node, traceback=None, hostname=None):
                                      exc_traceback)
     timeofcrash = strftime('%Y%m%d-%H%M%S')
     login_name = getpass.getuser()
-    crashfile = 'crash-%s-%s-%s-%s.pklz' % (timeofcrash,
+    crashfile = 'crash-%s-%s-%s-%s' % (timeofcrash,
                                             login_name,
                                             name,
                                             str(uuid.uuid4()))
@@ -68,10 +68,16 @@ def report_crash(node, traceback=None, hostname=None):
     if not os.path.exists(crashdir):
         os.makedirs(crashdir)
     crashfile = os.path.join(crashdir, crashfile)
+    if node.config['execution']['text_crashfiles']:
+        crashfile += '.txt'
+    else:
+        crashfile += '.pklz'
     logger.info('Saving crash info to %s' % crashfile)
     logger.info(''.join(traceback))
-    savepkl(crashfile, dict(node=node, traceback=traceback))
-    # np.savez(crashfile, node=node, traceback=traceback)
+    if node.config['execution']['text_crashfiles']:
+        crash_to_txt(crashfile, dict(node=node, traceback=traceback))
+    else:
+        savepkl(crashfile, dict(node=node, traceback=traceback))
     return crashfile
 
 

nipype/utils/config.py

@@ -55,6 +55,7 @@
 remove_unnecessary_outputs = true
 try_hard_link_datasink = true
 single_thread_matlab = true
+text_crashfiles = true
 stop_on_first_crash = false
 stop_on_first_rerun = false
 use_relative_paths = false

nipype/utils/filemanip.py

@@ -531,6 +531,18 @@ def loadpkl(infile):
     return unpkl
 
 
+def crash2txt(filename, record):
+    """ Write out plain text crash file """
+    with open(filename, 'w') as fp:
+        if 'node' in record:
+            node = record['node']
+            fp.write('Node: {}\n'.format(node.fullname))
+            fp.write('Working directory: {}\n'.format(node.output_dir()))
+            fp.write('\n')
+            fp.write('Node inputs:\n{}\n'.format(node.inputs))
+        fp.write(record['traceback'])
+
+
 def savepkl(filename, record):
     if filename.endswith('pklz'):
         pkl_file = gzip.open(filename, 'wb')