Merge pull request #1885 from mgxd/enh/crashtxt

ENH: config option to write crashfiles in plain text

Author: satra

doc/users/config_file.rst

@@ -137,8 +137,15 @@ Execution
     schedulers the default is set to 2 seconds.
 
 *xvfb_max_wait*
-    Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x parameter of an Interface is True.
-
+    Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x
+    parameter of an Interface is True.
+
+*crashfile_format*
+    This option controls the file type of any crashfile generated. Pklz
+    crashfiles allow interactive debugging and rerunning of nodes, while text
+    crashfiles allow portability across machines and shorter load time.
+    (possible values: ``pklz`` and ``txt``; default value: ``pklz``)
+    
 Example
 ~~~~~~~
 

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']['crashfile_format'].lower() in ['text', 'txt']:
+        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']['crashfile_format'].lower() in ['text', 'txt']:
+        crash2txt(crashfile, dict(node=node, traceback=traceback))
+    else:
+        savepkl(crashfile, dict(node=node, traceback=traceback))
     return crashfile
 
 

nipype/pipeline/plugins/tests/test_base.py

@@ -26,7 +26,8 @@ def test_report_crash():
             mock_node._id = 'an_id'
             mock_node.config = {
                 'execution' : {
-                    'crashdump_dir' : '.'
+                    'crashdump_dir' : '.',
+                    'crashfile_format' : 'pklz',
                 }
             }
 

nipype/utils/config.py

@@ -55,6 +55,7 @@
 remove_unnecessary_outputs = true
 try_hard_link_datasink = true
 single_thread_matlab = true
+crashfile_format = pklz
 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(''.join(record['traceback']))
+
+
 def savepkl(filename, record):
     if filename.endswith('pklz'):
         pkl_file = gzip.open(filename, 'wb')