How to use dax - 10 common examples

dax_settings = dax.DAX_Settings()
    logger = setup_info_logger()
    parser = configure_parser()
    parsed_args = parser.parse_args()
    logger.info('testing logger')

    #argument checks do their own logging
    if not check_arguments(logger, parsed_args):
        exit(-1)

    if not dax_settings.is_cluster_valid(logger):
        exit(-1)

    launcher = bin.read_settings(parsed_args.settings, logger, exe='patch assessors')

    with XnatUtils.get_interface(launcher.xnat_host, launcher.xnat_user,
                                 launcher.xnat_pass) as intf:
        print 'intf=', intf

        print 'launcher process dict=', launcher.project_process_dict

        project_list = set(launcher.project_process_dict.keys())
        if parsed_args.projects:
            for p in project_list:
                if p not in project_list:
                    msg = "project {} is not in the list of projects defined in {} ({})"
                    logger.warning(msg.format(p, parsed_args.settings, project_list))

        for p in project_list:
            project_processors = launcher.project_process_dict.get(p, None)
            if project_processors is None:
                logger.info("Procject '{}' has no processors - skipping")

"""
    Main function to upload the results / PBS / OUTLOG of assessors
     from the queue folder

    :param upload_settings: dictionary defining the upload information
    :return: None
    """
    if len(os.listdir(RESULTS_DIR)) == 0:
        LOGGER.warn('No data need to be uploaded.\n')
        sys.exit()

    warnings = list()

    for upload_dict in upload_settings:
        try:
            with XnatUtils.get_interface(host=upload_dict['host'],
                                         user=upload_dict['username'],
                                         pwd=upload_dict['password']) as intf:
                LOGGER.info('='*50)
                proj_str = (upload_dict['projects'] if upload_dict['projects']
                            else 'all')
                LOGGER.info('Connecting to XNAT <%s>, upload for projects:%s' %
                            (upload_dict['host'], proj_str))
                if not XnatUtils.has_dax_datatypes(intf):
                    msg = 'dax datatypes are not installed on xnat <%s>.'
                    raise DaxUploadError(msg % (upload_dict['host']))

                # 1) Upload the assessor data
                # For each assessor label that need to be upload :
                LOGGER.info('Uploading results for assessors')
                if DAX_SETTINGS.get_use_reference():
                    LOGGER.info('using upload by reference, dir is:{}'.format(

import pandas
import pyxnat
from dax import XnatUtils
from dax import utilities

if len(sys.argv)!=4 :
    print('Usage:')
    print('python Xnatreport_assessor.py   ')
    sys.exit()


project = sys.argv[1]
proctype = sys.argv[2]
outfile = sys.argv[3]

xnat = XnatUtils.get_interface()

Assrs = xnat.list_project_assessors(project)

R = list()
for assr in Assrs :

    if assr.get('proctype') != proctype : continue

    #print(assr['assessor_label'])

    # Get desired fields
    thisR = {}
    for key in ('project_label','subject_label','session_label','proctype',
                'assessor_id','procstatus','qcstatus','assessor_label') :
        thisR[key] = assr[key]

host=_host, user=_user)))
        # set test object:
        tests.set_tobj(test_obj)

        # Make the temp dir:
        if not os.path.isdir(DAX_TEST_DIR):
            os.makedirs(DAX_TEST_DIR)

        # Set the log of any dax function to a temp file for user:
        if hide:
            logfile = os.path.join(DAX_TEST_DIR, 'dax_test.log')
        else:
            logfile = None
        log.setup_debug_logger('dax', logfile)

        with XnatUtils.get_interface(host=_host, user=username) as intf:
            tests.set_xnat(intf)
            tests.run_test(project, sessions, nb_sess)

    print((TD_END.format(nb_test=tests.get_number(),
                        time="%.3f" % tests.get_time(),
                        state=tests.get_test_state())))

    if do_not_remove:
        if 'OK' == tests.get_test_state()[:2]:
            shutil.rmtree(DAX_TEST_DIR)

elif f_settings.endswith('.csv'):
            with open(up_file, 'rb') as csvfileread:
                csvreader = csv.reader(csvfileread, delimiter=',')
                for index, row in (csvreader):
                    if len(row) < 4:
                        raise DaxError("error: could not read the csv row. \
Missing args. 4 needed, %s found at line %s." % (str(len(row)), str(index)))
                    else:
                        if row != DEFAULT_HEADER:
                            host_projs.append(dict(list(zip(DEFAULT_HEADER,
                                                        row[:4]))))
        elif f_settings.endswith('.yaml'):
            doc = utilities.read_yaml(f_settings)
            host_projs = doc.get('settings')
        else:
            raise DaxError("error: doesn't recognize the file format for the \
settings file. Please use either JSON/PYTHON/CSV format.")
    else:  # if not file, use the environment variables and options
        _host = os.environ['XNAT_HOST']
        if host:
            _host = host
        if projects:
            projects = projects.split(',')
        else:
            projects = []
        if username:
            username = username
            if not password:
                MSG = "Please provide the password for user <%s> on xnat(%s):"
                password = getpass.getpass(prompt=MSG % (username, _host))
                if not password:
                    raise DaxError('empty password entered')

settings file. Please use either JSON/PYTHON/CSV format.")
    else:  # if not file, use the environment variables and options
        _host = os.environ['XNAT_HOST']
        if host:
            _host = host
        if projects:
            projects = projects.split(',')
        else:
            projects = []
        if username:
            username = username
            if not password:
                MSG = "Please provide the password for user <%s> on xnat(%s):"
                password = getpass.getpass(prompt=MSG % (username, _host))
                if not password:
                    raise DaxError('empty password entered')
        else:
            netrc_obj = DAX_Netrc()
            username, password = netrc_obj.get_login(_host)
        host_projs.append(dict(list(zip(DEFAULT_HEADER, [_host, username,
                                                         password,
                                                         projects]))))
    return host_projs

def download_xnat_file(self, src, dst):
        """Download XNAT specific file."""
        results = None
        with XnatUtils.get_interface(host=self.host, user=self.user,
                                     pwd=self.pwd) as xnat:
            try:
                _res, _file = src.split('/files/')
                res = xnat.select(_res)
                if not res.exists():
                    msg = 'resources specified by %s not found on XNAT.'
                    raise AutoSpiderError(msg % src)
            except Exception:
                msg = 'resources can not be checked because the path given is \
wrong for XNAT. Please check https://wiki.xnat.org/display/XNAT16/\
XNAT+REST+API+Directory for the path.'
                raise AutoSpiderError(msg % src)
            try:
                results = res.file(_file).get(dst)
            except Exception:
                raise AutoSpiderError('downloading files from XNAT failed.')

        return results

pwd=self.pwd) as xnat:
            try:
                _res, _file = src.split('/files/')
                res = xnat.select(_res)
                if not res.exists():
                    msg = 'resources specified by %s not found on XNAT.'
                    raise AutoSpiderError(msg % src)
            except Exception:
                msg = 'resources can not be checked because the path given is \
wrong for XNAT. Please check https://wiki.xnat.org/display/XNAT16/\
XNAT+REST+API+Directory for the path.'
                raise AutoSpiderError(msg % src)
            try:
                results = res.file(_file).get(dst)
            except Exception:
                raise AutoSpiderError('downloading files from XNAT failed.')

        return results

def download_xnat_file(self, src, dst):
        """Download XNAT specific file."""
        results = None
        with XnatUtils.get_interface(host=self.host, user=self.user,
                                     pwd=self.pwd) as xnat:
            try:
                _res, _file = src.split('/files/')
                res = xnat.select(_res)
                if not res.exists():
                    msg = 'resources specified by %s not found on XNAT.'
                    raise AutoSpiderError(msg % src)
            except Exception:
                msg = 'resources can not be checked because the path given is \
wrong for XNAT. Please check https://wiki.xnat.org/display/XNAT16/\
XNAT+REST+API+Directory for the path.'
                raise AutoSpiderError(msg % src)
            try:
                results = res.file(_file).get(dst)
            except Exception:
                raise AutoSpiderError('downloading files from XNAT failed.')

def upload_assessor_snapshots(assessor_obj, original, thumbnail):
    """
    Upload the snapshots of the assessor PDF.
     (both the original and the thumbnail)

    :param assessor_obj: pyxnat EObject of the assessor to upload the snapshots
    :param original: The original file (full size)
    :param thumbnail: The thumbnail of the original file
    :return: True if it uploaded OK, False if it failed.

    """
    if not os.path.isfile(original) or not os.path.isfile(thumbnail):
        err = "%s: original or thumbnail snapshots don't exist."
        raise XnatUtilsError(err % ('upload_assessor_snapshots'))

    assessor_obj.out_resource('SNAPSHOTS')\
                .file(os.path.basename(thumbnail))\
                .put(thumbnail, thumbnail.split('.')[1].upper(), 'THUMBNAIL',
                     overwrite=True,
                     params={"event_reason": "DAX uploading file"})
    assessor_obj.out_resource('SNAPSHOTS')\
                .file(os.path.basename(original))\
                .put(original, original.split('.')[1].upper(), 'ORIGINAL',
                     overwrite=True,
                     params={"event_reason": "DAX uploading file"})
    return True