BUG: Fixed typo in configFileParser.py

STYLE: Ran autopep8 on AutoWorkup.py
ENH: Added commandline testing for configFileParser.py

AutoWorkup/AutoWorkup.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python
 
+
 def load_modules(modules):
     """ The command 'module' is actually a script call in bash:
 
@@ -13,36 +14,38 @@ def load_modules(modules):
 
 def setup(argv):
     print "Configuring environment..."
-    import os, os.path
+    import os
+    import os.path
     from utilities.configFileParser import resolveDataSinkOption, parseFile
     from utilities.pathHandling import validatePath
     from utilities import misc
-    environment, experiment, pipeline, cluster = parseFile(argv["--ExperimentConfig"], argv["--pe"], argv["--workphase"])
+    environment, experiment, pipeline, cluster = parseFile(
+        argv["--ExperimentConfig"], argv["--pe"], argv["--workphase"])
     pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)
-
     if cluster is None:
         assert argv["--wf_template_runner"] in misc.WFRUN, \
-          "wf_template_runner options for clusters can only be given when the configuration file's CLUSTER option == True"
+            "wf_template_runner options for clusters can only be given when the configuration file's CLUSTER option == True"
         os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wf_template_runner"]))
     else:
         load_modules(cluster['modules'])  # Load modules if not already done  ## MODS PATH
         # print os.environ['LOADEDMODULES']
-    if environment['virtualenv_dir']:  ## MODS PATH
-        activate_this = validatePath(os.path.join(environment['virtualenv_dir'], 'bin', 'activate_this.py'), False, False)
+    if environment['virtualenv_dir'] is not None:  # MODS PATH
+        activate_this = validatePath(
+            os.path.join(environment['virtualenv_dir'], 'bin', 'activate_this.py'), False, False)
         execfile(activate_this, dict(__file__=activate_this))
     utilities_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'utilities')
     configure_env = validatePath(os.path.join(utilities_path, 'configure_env.py'), False, False)
     # Add the AutoWorkup directory to the PYTHONPATH every time - REQUIRED FOR CLUSTER DISPATCHING
-    environment['env']['PYTHONPATH'] =  environment['env']['PYTHONPATH'] + ":" + os.path.dirname(__file__)
+    environment['env']['PYTHONPATH'] = environment['env']['PYTHONPATH'] + ":" + os.path.dirname(__file__)
     execfile(configure_env, dict(__file__=__file__,
                                  append_os_path=environment['env']['PATH'],
                                  append_sys_path=environment['env']['PYTHONPATH'])
-        )  ## MODS PATH
+             )  # MODS PATH
     from nipype import config
     config.enable_debug_mode()
     from utilities.package_check import verify_packages
     verify_packages()
-    if 'FREESURFER' in experiment['components']:  ## FREESURFER MODS
+    if 'FREESURFER' in experiment['components']:  # FREESURFER MODS
         configure_FS = validatePath(os.path.join(utilities_path, 'utilities', 'configure_FS.py'), False, False)
         execfile(configure_FS, dict(FS_VARS=misc.FS_VARS, env=environment['env']))
         print "FREESURFER needs to check for sane environment here!"  # TODO: raise warning, write method, what???

AutoWorkup/utilities/configFileParser.py

@@ -5,17 +5,18 @@
 ===================
 
 Usage:
-  configFileParser.py [--debug] ENV FILE
+  configFileParser.py [--debug] ENV PHASE FILE
   configFileParser.py (-h | --help | -v | --version)
 
 Arguments:
   ENV            Environment name in configuration file
+  PHASE          Workflow phase to use: atlas-based-reference, subject-template-generation or subject-based-reference
   FILE           Configuration file
 
 Options:
   -h, --help     Print this and exit
   -v, --version  Print file version and exit
-  --debug        Run doctests for file
+  --debug        Run doctests for file  # TODO
 """
 from ConfigParser import ConfigParser
 import os
@@ -49,7 +50,7 @@ def parseEnvironment(parser, section):
     retval['prefix'] = validatePath(parser.get(section, 'MOUNT_PREFIX'), True, True)
     if retval['prefix'] is None:
         retval['prefix'] = ''
-    if parser.has_option(section, 'VIRTUALENV'):
+    if parser.has_option(section, 'VIRTUALENV_DIR'):
         retval['virtualenv_dir'] = validatePath(parser.get(section, 'VIRTUALENV_DIR'), False, True)
     else:
         retval['virtualenv_dir'] = None
@@ -253,7 +254,17 @@ def nipype_options(args, pipeline, cluster, experiment, environment):
 
 if __name__ == "__main__":
     from docopt import docopt
-
+    SILENT = True
     args = docopt(__doc__, version='0.1')  # Get argv as dictionary
-    # TODO: Add and run doctests!
-    print parseFile(args["FILE"], args["ENV"])
+    assert args["PHASE"] in ['atlas-based-reference',
+                             'subject-template-generation', 'subject-based-reference'], "Unknown phase!"
+    if args['--debug']:
+        # TODO: Add and run doctests!
+        pass
+    output = parseFile(args["FILE"], args["ENV"], args["PHASE"])
+    from pprint import pprint
+    print ""
+    print "**** OUTPUT ****"
+    for d in output:
+        pprint(d)
+        print ""