Exemplo n.º 1
0
def setup_environment(argv):
    print("Configuring environment...")
    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"])
    pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)
    if cluster is None:
        print("Running on local")
        #raise NotImplementedError("Running local has old code and has not been tested!")
        #assert argv["--wfrun"] in argvWFRUN, \
        #    "wfrun  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'] is not None:  # MODS PATH
        #activate_this = validatePath(
        #    os.path.join(environment['virtualenv_dir'], 'bin', 'activate_this.py'), False, False)
        #if os.path.exists( activate_this ) :
        #    exec(open(activate_this).read(), 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__)

    exec(open(configure_env).read() , dict(__file__=__file__,
                                 append_os_path=environment['env']['PATH'],
                                 append_sys_path=environment['env']['PYTHONPATH'])
             )  # MODS PATH

    print("@"*80)
    print(environment['env']['PYTHONPATH'])
    print("@"*80)
    print(environment['env']['PATH'])
    print("@"*80)

    from nipype import config
    config.enable_debug_mode()
    #config.enable_provenance()

    from utilities.package_check import verify_packages
    verify_packages()
    if 'FREESURFER' in experiment['components']:  # FREESURFER MODS
        configure_FS = validatePath(os.path.join(utilities_path, 'utilities', 'configure_FS.py'), False, False)
        exec(open(configure_FS).read(), dict(FS_VARS=misc.FS_VARS, env=environment['env']))
        print("FREESURFER needs to check for sane environment here!")  # TODO: raise warning, write method, what???
    for key, value in list(environment['env'].items()):
        if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
            pass
        else:
            os.environ[key] = value  # Do not use os.putenv (see Python documentation)
    return environment, experiment, pipeline, cluster
Exemplo n.º 2
0
def setup(argv):
    print "Configuring environment..."
    import os, 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"])
    pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)

    if cluster is None:
        assert argv["--wfrun"] in misc.WFRUN, \
          "wfrun options for clusters can only be given when the configuration file's CLUSTER option == True"
        os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wfrun"]))
    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)
        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__)
    execfile(
        configure_env,
        dict(__file__=__file__,
             append_os_path=environment['env']['PATH'],
             append_sys_path=environment['env']['PYTHONPATH']))  ## 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
        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???
    for key, value in environment['env'].items():
        if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
            pass
        else:
            os.environ[
                key] = value  # Do not use os.putenv (see Python documentation)
    return environment, experiment, pipeline, cluster
Exemplo n.º 3
0
def setup(argv):
    print "Configuring environment..."
    import os, 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['--wfrun'])
    pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)

    if cluster is None:
        assert argv["--wfrun"] in misc.WFRUN, \
          "wfrun options for clusters can only be given when the configuration file's CLUSTER option == True"
        os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wfrun"]))
    else:
        load_modules(cluster['modules'])  # Load modules if not already done  ## MODS PATH
        # print os.environ['LOADEDMODULES']
    if environment['virtualenv']:  ## MODS PATH
        activate_this = validatePath(os.path.join(environment['virtualenv'], 'bin', 'activate_this.py'))
        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'))
    execfile(configure_env, dict(__file__=__file__,
                                 append_os_path=environment['env']['PATH'],
                                 append_sys_path=environment['env']['PYTHONPATH'])
        )  ## 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
        configure_FS = validatePath(os.path.join(utilities_path, 'utilities', 'configure_FS.py'))
        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???
    for key, value in environment['env'].items():
        if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
            pass
        else:
            os.environ[key] = value  # Do not use os.putenv (see Python documentation)
    return environment, experiment, pipeline, cluster