def test_readConfig(self):
settings = gsm_lib.get_settings(self.setupFileFullPath)
gsm_lib.read_config(self.setupFolder, self.setupFileFullPath, settings)
self.assertEqual(settings.system_log_file, "log/rsm.log")
self.assertEqual(settings.source_data_schema_file,
"source_data_schema.xml")
self.assertEqual(settings.site_catalog, "site-catalog.xml")
def test_readConfig(self):
settings = gsm_lib.get_settings(self.setupFileFullPath)
gsm_lib.read_config(self.setupFolder, self.setupFileFullPath, settings)
self.assertEqual(settings.system_log_file, "log/rsm.log")
self.assertEqual(settings.source_data_schema_file,
"source_data_schema.xml")
self.assertEqual(settings.site_catalog, "site-catalog.xml")
def test_send(self):
conf_file = 'gsm-devconfig/settings.ini'
settings = gsm_lib.get_settings(conf_file)
props = EmailProps(settings.smtp_host, settings.smtp_port,
settings.sender_email, [settings.test_recipient],
[], 'Research Subject Mapper Notification',
'This is a test')
success = EmailSender().send(props)
self.assertEqual(True, success)
def test_send(self):
conf_file = 'gsm-devconfig/settings.ini'
settings = gsm_lib.get_settings(conf_file)
props = EmailProps(
settings.smtp_host,
settings.smtp_port,
settings.sender_email,
[settings.test_recipient],
[],
'Research Subject Mapper Notification',
'This is a test')
success = EmailSender().send(props)
self.assertEqual(True, success)
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
# obtaining command line arguments for path to config directory
args = parse_args()
configuration_directory = os.path.abspath(args['configuration_directory_path'])
do_keep_gen_files = args['keep']
# 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)
site_catalog_file = os.path.join(configuration_directory, settings.site_catalog)
# Initialize Redcap Interface
rt = redcap_transactions()
rt.configuration_directory = configuration_directory
properties = rt.init_redcap_interface(settings, logger)
# gets data from the person index for the fields listed in the source_data_schema.xml
response = rt.get_data_from_redcap(properties, logger)
xml_tree = etree.fromstring(response)
#XSL Transformation : transforms the person_index data
transform_xsl = proj_root + "bin/utils/person_index_transform.xsl"
xslt = etree.parse(transform_xsl)
transform = etree.XSLT(xslt)
person_index_data = transform(xml_tree)
# # # retrieve smi.xml from the sftp server
smi_path = get_smi_and_parse(site_catalog_file, settings, logger)
try:
smi_data = etree.parse(smi_path)
except IOError:
logger.exception("Could not open file: " + smi_path)
raise
#sorting both the xml files.
gsm_lib.sort_element_tree(smi_data)
gsm_lib.sort_element_tree(person_index_data)
#generating the person index dictionary
person_index_dict = {}
for item in person_index_data.iter('item'):
person_index_dict[item.findtext('research_subject_id')] = [
item.findtext('yob'),
item.findtext('mrn'),
item.findtext('facility_code')]
#iterate through the smi data and generate a
# new merged xml's for subject_map and subject_map_exceptions
subjectmap_root = etree.Element("subject_map_records")
subjectmap_exceptions_root = etree.Element("subject_map_exception_records")
exceptions = False
for item in smi_data.iter('item'):
if item.findtext('research_subject_id') in person_index_dict.keys():
logger.debug("Processing research_subject_id %s", item.findtext('research_subject_id'))
if (person_index_dict[item.findtext('research_subject_id')][0] == item.findtext('yob')):
logger.debug("yob matched for research_subject_id %s", item.findtext('research_subject_id'))
mrn = etree.SubElement(item, "mrn")
mrn.text = person_index_dict[item.findtext('research_subject_id')][1]
facility_code = etree.SubElement(item, "facility_code")
facility_code.text = person_index_dict[item.findtext('research_subject_id')][2]
item.remove(item.find('yob'))
subjectmap_root.append(item)
else:
logger.debug("yob not matched for research_subject_id %s", item.findtext('research_subject_id'))
exception_item = etree.Element("item")
research_subject_id = etree.SubElement(exception_item, "research_subject_id")
research_subject_id.text = item.findtext('research_subject_id')
if (research_subject_id.text is not None):
exceptions = True
pi_yob = etree.SubElement(exception_item, "Person_Index_YOB")
pi_yob.text = person_index_dict[item.findtext('research_subject_id')][0]
hcvt_yob = etree.SubElement(exception_item, "HCVTarget_YOB")
hcvt_yob.text = item.findtext('yob')
subjectmap_exceptions_root.append(exception_item)
#Below code transforms the xml files to csv files
transform_xsl = proj_root + "bin/utils/xml2csv.xsl"
xslt = etree.parse(transform_xsl)
transform = etree.XSLT(xslt)
tmp_folder = gsm_lib.get_temp_path(do_keep_gen_files)
subject_map_file = tmp_folder + "subject_map.csv"
logger.info('Using path subject map file path: ' + subject_map_file)
try:
subject_map_csv = open(subject_map_file, "w")
subject_map_csv.write("%s" % '"research_subject_id","start_date","end_date","mrn","facility_code"\n')
for item in subjectmap_root.iter("item"):
line = '"{0}","{1}","{2}","{3}","{4}"\n'.format(
gsm_lib.handle_blanks(item.findtext("research_subject_id")),
gsm_lib.handle_blanks(item.findtext("start_date")),
gsm_lib.handle_blanks(item.findtext("end_date")),
gsm_lib.handle_blanks(item.findtext("mrn")),
gsm_lib.handle_blanks(item.findtext("facility_code")))
subject_map_csv.write("%s" % line)
subject_map_csv.close()
except IOError:
logger.exception("Could not open file %s for write", subject_map_file)
raise
# remove the smi.xml from the folder because the XSLT process
# writes data to smi.xml
try:
os.remove(smi_path)
except OSError:
logger.exception("Could not remove file %s ", smi_path)
raise
# send the subject_map.csv to EMR team (sftp server)
parse_site_details_and_send(site_catalog_file, subject_map_file, 'sftp', settings, logger)
if do_keep_gen_files:
logger.info('Keeping the temporary file: ' + subject_map_file)
else:
logger.info('Removing the temporary file: ' + subject_map_file)
os.remove(subject_map_file)
# send subject_map_exceptions.csv as email attachment
if exceptions:
subject_map_exceptions_file = tmp_folder + 'subject_map_exceptions.csv'
try:
subject_map_exceptions_csv = open(subject_map_exceptions_file, "w")
except IOError:
logger.exception("Could not open file %s for write", subject_map_exceptions_file)
raise
subject_map_exceptions_csv.write("%s" % '"research_subject_id","person_index_yob","redcap_yob"\n')
for item in subjectmap_exceptions_root.iter("item"):
line = '"{0}","{1}","{2}"\n'.format(
gsm_lib.handle_blanks(item.find("research_subject_id").text),
gsm_lib.handle_blanks(item.find("Person_Index_YOB").text),
gsm_lib.handle_blanks(item.find("HCVTarget_YOB").text))
subject_map_exceptions_csv.write("%s" % line)
subject_map_exceptions_csv.close()
parse_site_details_and_send(site_catalog_file, subject_map_exceptions_file, 'email', settings, logger)
if do_keep_gen_files:
logger.info('Keeping the temporary file: ' + subject_map_exceptions_file)
else:
logger.info('Removing the temporary file: ' + subject_map_exceptions_file)
os.remove(subject_map_exceptions_file)
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)