wip: move first nipype commands to a group command

Author: alexsavio

bin/nipype_cmd

@@ -1,8 +1,11 @@
 #!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+
 import sys
 from nipype.utils.nipype_cmd import main
 
+import click
+
 if __name__ == '__main__':
     main(sys.argv)

bin/nipype_crash_search

@@ -0,0 +1 @@
+

bin/nipype_display_crash

@@ -0,0 +1,82 @@
+#!python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import click
+
+
+@click.group()
+def cli():
+    pass
+
+
+@cli.command()
+@click.argument('logdir', type=str)
+@click.option('-r', '--regex', type=str, default='*',
+              help='Regular expression to be searched in each traceback.')
+def search(logdir, regex):
+    """Search for tracebacks content.
+
+    Search for traceback inside a folder of nipype crash log files that match
+    a given regular expression.
+
+    Examples:
+    nipype search -d nipype/wd/log -r '.*subject123.*'
+    """
+    import re
+    from .crash_files import iter_tracebacks
+
+    rex = re.compile(regex, re.IGNORECASE)
+    for file, trace in iter_tracebacks(logdir):
+        if rex.search(trace):
+            click.echo("-" * len(file))
+            click.echo(file)
+            click.echo("-" * len(file))
+            click.echo(trace)
+
+
+@cli.command()
+@click.argument('crashfile', type=str)
+@click.option('-r', '--rerun', is_flag=True, flag_value=True,
+              help='Rerun crashed node.')
+@click.option('-d', '--debug', is_flag=True, flag_value=True,
+              help='Enable Python debugger when re-executing.')
+@click.option('-i', '--ipydebug', is_flag=True, flag_value=True,
+              help='Enable IPython debugger when re-executing.')
+@click.option('--dir', type=str,
+              help='Directory where to run the node in.')
+def crash(crashfile, rerun, debug, ipydebug, directory):
+    """Display Nipype crash files.
+
+    For certain crash files, one can rerun a failed node in a temp directory.
+
+    Examples:
+    nipype crash crashfile.pklz
+    nipype crash crashfile.pklz -r -i
+    nipype crash crashfile.pklz -r -i
+    """
+    from .crash_files import display_crash_file
+
+    debug = 'ipython' if ipydebug else 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_file(crashfile, rerun, debug, directory)
+
+
+@cli.command()
+@click.argument('pklz_file', type=str)
+def show(pklz_file):
+    """Print the content of Nipype node .pklz file.
+
+    Examples:
+    nipype show node.pklz
+    """
+    from pprint import pprint
+    from ..utils.filemanip import loadpkl
+
+    pkl_data = loadpkl(pklz_file)
+    pprint(pkl_data)

bin/nipype_display_pklz

@@ -0,0 +1,88 @@
+"""Utilities to manipulate and search through .pklz crash files."""
+
+import re
+import sys
+import os.path as op
+from glob import glob
+
+from traits.trait_errors import TraitError
+from nipype.utils.filemanip import loadcrash
+
+
+def load_pklz_traceback(crash_filepath):
+    """Return the traceback message in the given crash file."""
+    try:
+        data = loadcrash(crash_filepath)
+    except TraitError as te:
+        return str(te)
+    except:
+        raise
+    else:
+        return '\n'.join(data['traceback'])
+
+
+def iter_tracebacks(logdir):
+    """Return an iterator over each file path and
+    traceback field inside `logdir`.
+    Parameters
+    ----------
+    logdir: str
+        Path to the log folder.
+
+    field: str
+        Field name to be read from the crash file.
+
+    Yields
+    ------
+    path_file: str
+
+    traceback: str
+    """
+    crash_files = sorted(glob(op.join(logdir, '*.pkl*')))
+
+    for cf in crash_files:
+        yield cf, load_pklz_traceback(cf)
+
+
+def display_crash_file(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)
+
+    if node:
+        print("Node: %s" % node)
+        if node.base_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")
+
+    if rerun:
+        if node is None:
+            print("No node in crashfile. Cannot rerun")
+            return
+        print("Rerunning node")
+        node.base_dir = directory
+        node.config = {'execution': {'crashdump_dir': '/tmp'}}
+        try:
+            node.run()
+        except:
+            if debug and debug != 'ipython':
+                import pdb
+                pdb.post_mortem()
+            else:
+                raise
+        print("\n")