def main():
# obtaining command line arguments for path to config directory
args = parse_args()
configuration_directory = os.path.abspath(
args['configuration_directory_path'])
# Configure logging
logger = configure_logging(args['verbose'], args['logfile'])
conf_file = os.path.join(configuration_directory, 'settings.ini')
settings = gsm_lib.get_settings(conf_file)
gsm_lib.read_config(configuration_directory, conf_file, settings)
# Check if xml_formatting_transform.xsl file is present/properly set in
# setting.ini
message2 = "Please set it with appropriate value and restart execution. " \
"For assistance refer config-example-gsm-input/settings.ini." \
"\nProgram will now terminate..."
if not settings.hasoption('xml_formatting_transform_xsl'):
message = "Required parameter xml_formatting_transform_xsl is missing " \
"in settings.ini. " + message2
logger.error(message)
raise gsm_lib.ConfigurationError(message)
elif settings.xml_formatting_transform_xsl == "":
message = "Required parameter xml_formatting_transform_xsl does not " \
"have a value in settings.ini. " + message2
logger.error(message)
raise gsm_lib.ConfigurationError(message)
elif not os.path.exists(
os.path.join(configuration_directory,
settings.xml_formatting_transform_xsl)):
message = "Required file xml_formatting_transform.xsl does not exist " \
"in {0}. Please make sure this file is included in the " \
"configuration directory and restart execution. For " \
"assistance refer config-example-gsm-input/xml_formatting_transform.xsl." \
"\nProgram will now terminate...".format(configuration_directory)
logger.error(message)
raise gsm_lib.ConfigurationError(message)
# Initialize Redcap Interface
rt = redcap_transactions()
rt.configuration_directory = configuration_directory
properties = rt.init_redcap_interface(settings, logger)
#get data from the redcap for the fields listed in the source_data_schema.xml
response = rt.get_data_from_redcap(properties, logger)
logger.debug(response)
xml_tree = etree.fromstring(response)
#XSL Transformation 1: This transformation removes junk data, rename elements and extracts site_id and adds new tag site_id
transform_xsl = os.path.join(configuration_directory,
settings.xml_formatting_transform_xsl)
xslt = etree.parse(transform_xsl)
transform = etree.XSLT(xslt)
xml_transformed = transform(xml_tree)
xml_str = etree.tostring(xml_transformed, method='xml', pretty_print=True)
#XSL Transformation 2: This transformation groups the data based on site_id
transform2_xsl = proj_root + 'bin/utils/groupby_siteid_transform.xsl'
xslt = etree.parse(transform2_xsl)
transform = etree.XSLT(xslt)
xml_transformed2 = transform(xml_transformed)
#XSL Transformation 3: This transformation removes all the nodes which are not set
transform3_xsl = proj_root + 'bin/utils/remove_junktags_transform.xsl'
xslt = etree.parse(transform3_xsl)
transform = etree.XSLT(xslt)
xml_transformed3 = transform(xml_transformed2)
#Prettifying the output generated by XSL Transformation
xml_str2 = etree.tostring(xml_transformed3,
method='xml',
pretty_print=True)
tree = etree.fromstring(xml_str2, etree.XMLParser(remove_blank_text=True))
# Loop through the start_date elements and update theur values
for k in tree.iter('start_date'):
d = datetime.datetime.strptime(k.text,
"%Y-%m-%d").date() - timedelta(days=365)
k.text = str(d)
#writing data to smi+site_code.xml. This xml will be saved to sftp of the site as smi.xml
do_keep_gen_files = args['keep']
tmp_folder = gsm_lib.get_temp_path(do_keep_gen_files)
subject_map_input = {}
for k in tree:
site_code = k.attrib['id']
file_name = tmp_folder + 'smi' + site_code + '.xml'
gsm_lib.write_element_tree_to_file(ET.ElementTree(k), file_name)
subject_map_input[site_code] = file_name
site_catalog_file = os.path.join(configuration_directory,
settings.site_catalog)
parse_site_details_and_send(site_catalog_file, subject_map_input, logger,
settings, do_keep_gen_files)
def main():
# obtaining command line arguments for path to config directory
args = parse_args()
configuration_directory = os.path.abspath(args['configuration_directory_path'])
if 'debug' in args:
if args['debug']:
debugging = args['debug']
else:
debugging = False
else:
debugging = False
# Configure logging
logger = configure_logging(args['verbose'], args['logfile'])
conf_file = os.path.join(configuration_directory, 'settings.ini')
settings = gsm_lib.get_settings(conf_file)
gsm_lib.read_config(configuration_directory, conf_file, settings)
if debugging:
if settings.redcap_log_file:
redcap_log_file = os.path.join(configuration_directory, settings.redcap_log_file)
else:
redcap_log_file = 'redcap.log.xml'
# Check if xml_formatting_transform.xsl file is present/properly set in
# setting.ini
message2 = "Please set it with appropriate value and restart execution. " \
"For assistance refer config-example-gsm-input/settings.ini." \
"\nProgram will now terminate..."
if not settings.hasoption('xml_formatting_transform_xsl'):
message = "Required parameter xml_formatting_transform_xsl is missing " \
"in settings.ini. " + message2
logger.error(message)
raise gsm_lib.ConfigurationError(message)
elif settings.xml_formatting_transform_xsl == "":
message = "Required parameter xml_formatting_transform_xsl does not " \
"have a value in settings.ini. " + message2
logger.error(message)
raise gsm_lib.ConfigurationError(message)
elif not os.path.exists(os.path.join(configuration_directory, settings.xml_formatting_transform_xsl)):
message = "Required file xml_formatting_transform.xsl does not exist " \
"in {0}. Please make sure this file is included in the " \
"configuration directory and restart execution. For " \
"assistance refer config-example-gsm-input/xml_formatting_transform.xsl." \
"\nProgram will now terminate...".format(configuration_directory)
logger.error(message)
raise gsm_lib.ConfigurationError(message)
# Initialize Redcap Interface
rt = redcap_transactions()
rt.configuration_directory = configuration_directory
properties = rt.init_redcap_interface(settings, logger)
#get data from the redcap for the fields listed in the source_data_schema.xml
response = rt.get_data_from_redcap(properties, logger)
if debugging:
try:
print('Writing REDCap response to file: ')
with open(redcap_log_file, 'w') as log_file:
log_file.write(response)
except:
print('Unable to write the REDCap response to ' + redcap_log_file)
try:
logger.debug(response)
xml_tree = etree.fromstring(response)
#XSL Transformation 1: This transformation removes junk data, rename elements and extracts site_id and adds new tag site_id
logger.debug("Beginning XSL Transformation 1: This transformation removes junk data, rename elements and extracts site_id and adds new tag site_id")
transform_xsl = os.path.join(configuration_directory, settings.xml_formatting_transform_xsl)
xslt = etree.parse(transform_xsl)
transform = etree.XSLT(xslt)
xml_transformed = transform(xml_tree)
xml_str = etree.tostring(xml_transformed, method='xml', pretty_print=True)
logger.debug("XSL Transformation 1 completed.")
#XSL Transformation 2: This transformation groups the data based on site_id
logger.debug("Beginning XSL Transformation 2: This transformation groups the data based on site_id")
transform2_xsl = proj_root + 'rsm/utils/groupby_siteid_transform.xsl'
xslt = etree.parse(transform2_xsl)
transform = etree.XSLT(xslt)
xml_transformed2 = transform(xml_transformed)
logger.debug("XSL Transformation 2 completed.")
#XSL Transformation 3: This transformation removes all the nodes which are not set
logger.debug("Beginning XSL Transformation 3: This transformation removes all the nodes which are not set")
transform3_xsl = proj_root + 'rsm/utils/remove_junktags_transform.xsl'
xslt = etree.parse(transform3_xsl)
transform = etree.XSLT(xslt)
xml_transformed3 = transform(xml_transformed2)
logger.debug("XSL Transformation 3 completed.")
#Prettifying the output generated by XSL Transformation
xml_str2 = etree.tostring(xml_transformed3, method='xml', pretty_print=True)
tree = etree.fromstring(xml_str2, etree.XMLParser(remove_blank_text=True))
# Loop through the start_date elements and update their values
for k in tree.iter('start_date'):
d = datetime.datetime.strptime(k.text, "%Y-%m-%d").date()-timedelta(days=365)
k.text = str(d)
#writing data to smi+site_code.xml. This xml will be saved to sftp of the site as smi.xml
do_keep_gen_files = args['keep']
tmp_folder = gsm_lib.get_temp_path(do_keep_gen_files)
subject_map_input = {}
for k in tree:
site_code = k.attrib['id']
file_name = tmp_folder + 'smi' + site_code + '.xml'
gsm_lib.write_element_tree_to_file(ET.ElementTree(k), file_name)
subject_map_input[site_code] = file_name
site_catalog_file = os.path.join(configuration_directory, settings.site_catalog)
parse_site_details_and_send(site_catalog_file, subject_map_input, logger, settings, do_keep_gen_files)
except Exception as xe:
if debugging:
print('Unable to transform data returned by REDCap:')
print('REDCap response logged to ' + redcap_log_file)
print('Ecountered the following error:')
print(xe)
exit()
else:
print('Unable to transform data returned by REDCap:')
exit()
def main():
global configuration_directory
global do_keep_gen_files
global tmp_folder
# obtaining command line arguments for path to config directory
parser = argparse.ArgumentParser()
parser.add_argument(
'-c', dest='configuration_directory_path',
default=default_configuration_directory,
required=False,
help='Specify the path to the configuration directory')
# read the optional argument `-k` for keeping the generated files
parser.add_argument(
'-k', '--keep',
default=default_do_keep_gen_files,
required=False,
help = 'Specify `yes` to preserve the files generated during execution')
args = vars(parser.parse_args())
configuration_directory = args['configuration_directory_path'] + '/'
do_keep_gen_files = False if args['keep'] is None else True
#setup_json = configuration_directory + 'setup.json'
global setup
setup = gsm_lib.read_config(configuration_directory, 'setup.json')
site_catalog_file = configuration_directory + setup['site_catalog']
system_log_file = setup['system_log_file']
# Configure logging
global gsmlogger
gsmlogger = GSMLogger()
gsmlogger.configure_logging(system_log_file)
# Initialize Redcap Interface
rt = redcap_transactions()
rt.configuration_directory = configuration_directory
properties = rt.init_redcap_interface(setup, gsmlogger.logger)
transform_xsl = configuration_directory + setup['xml_formatting_tranform_xsl']
#get data from the redcap for the fields listed in the source_data_schema.xml
response = rt.get_data_from_redcap(properties, gsmlogger.logger)
#XSL Transformation 1: This transformation removes junk data, rename elements and extracts site_id and adds new tag site_id
xml_tree = etree.fromstring(response)
xslt = etree.parse(transform_xsl)
transform = etree.XSLT(xslt)
xml_transformed = transform(xml_tree)
xml_str = etree.tostring(xml_transformed, method='xml', pretty_print=True)
#XSL Transformation 2: This transformation groups the data based on site_id
transform2_xsl = proj_root + 'bin/utils/groupby_siteid_transform.xsl'
xslt = etree.parse(transform2_xsl)
transform = etree.XSLT(xslt)
xml_transformed2 = transform(xml_transformed)
#XSL Transformation 3: This transformation removes all the nodes which are not set
transform3_xsl = proj_root + 'bin/utils/remove_junktags_transform.xsl'
xslt = etree.parse(transform3_xsl)
transform = etree.XSLT(xslt)
xml_transformed3 = transform(xml_transformed2)
#Prettifying the output generated by XSL Transformation
xml_str2 = etree.tostring(xml_transformed3, method='xml', pretty_print=True)
tree = etree.fromstring(xml_str2, etree.XMLParser(remove_blank_text=True))
# Loop through the start_date elements and update theur values
for k in tree.iter('start_date'):
d = datetime.datetime.strptime(k.text, "%Y-%m-%d").date()-timedelta(days=180)
k.text = str(d)
#writing data to smi+site_id.xml. This xml will be saved to sftp of the site as smi.xml
smi_filenames = []
smi_ids = []
tmp_folder = gsm_lib.get_temp_path(do_keep_gen_files)
for k in tree:
file_name = tmp_folder + 'smi' + k.attrib['id']+'.xml'
gsm_lib.write_element_tree_to_file(ET.ElementTree(k), file_name)
smi_filenames.append(file_name)
smi_ids.append(k.attrib['id'])
print 'Using smi_filenames: '
pprint.pprint(smi_filenames)
parse_site_details_and_send(site_catalog_file, smi_filenames, smi_ids, gsmlogger)
