def test_research_id_to_redcap_id_converter_mail_key_error(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
email_settings = {}
redcap_settings = {}
redcap_settings['redcap_uri'] = 'https://example.org/redcap/api/'
redcap_settings['token'] = 'ABCDEF878D219CFA5D3ADF7F9AB12345'
self.assertRaises(Exception,redi.research_id_to_redcap_id_converter,self.data,redcap_settings,email_settings, self.research_id_to_redcap_id, False, self.configuration_directory)
def test_create_empty_event_tree_for_study_for_zero_subjects(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.zero_subjects = """<?xml version='1.0' encoding='US-ASCII'?>
<study></study>
"""
self.data_zero_subjects = etree.ElementTree(etree.fromstring(self.zero_subjects))
self.assertRaises(Exception,redi.create_empty_event_tree_for_study,self.data_zero_subjects,self.data_all_form_events)
def test_create_empty_events_for_one_subject_all_fields_input(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.result = etree.tostring(
redi.create_empty_events_for_one_subject(self.data1_test1,
self.data2_test1))
self.result = ''.join(self.result.split())
self.expect_test1 = ''.join(self.expect_test1.split())
self.assertEqual(self.expect_test1, self.result)
def test_create_empty_event_tree_for_study_for_zero_subjects(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.zero_subjects = """<?xml version='1.0' encoding='US-ASCII'?>
<study></study>
"""
self.data_zero_subjects = etree.ElementTree(
etree.fromstring(self.zero_subjects))
self.assertRaises(Exception, redi.create_empty_event_tree_for_study,
self.data_zero_subjects, self.data_all_form_events)
def test_parse_form_events(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
logger.info("Running " + __name__ +
"#test_person_form_event() using xml: ")
string_1_xml = """<?xml version="1.0" encoding="UTF-8"?>
<redcapProject>
<name>Project</name>
<form>
<name>cbc</name>
<formDateField>cbc_lbdtc</formDateField>
<formCompletedFieldName>cbc_complete</formCompletedFieldName>
<formImportedFieldName>cbc_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
<event>
<name>2_arm_1</name>
</event>
<event>
<name>3_arm_1</name>
</event>
</form>
<form>
<name>chemistry</name>
<formDateField>chem_lbdtc</formDateField>
<formCompletedFieldName>chemistry_complete</formCompletedFieldName>
<formImportedFieldName>chem_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
<event>
<name>2_arm_1</name>
</event>
</form>
</redcapProject>
"""
temp_file = 'tmp.xml'
fh = open(temp_file, 'w')
fh.write(string_1_xml)
fh.close()
etree_1 = etree.ElementTree(etree.fromstring(string_1_xml))
result_tree = redi.parse_form_events(temp_file)
result_xml = etree.tostring(result_tree)
par = etree.XMLParser(remove_blank_text=True)
clean_tree = etree.XML(string_1_xml, parser=par)
clean_result = etree.XML(result_xml, parser=par)
self.assertEqual(etree.tostring(clean_tree),
etree.tostring(clean_result))
os.remove(temp_file)
def test_research_id_to_redcap_id_converter(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
email_settings = {}
redcap_settings = {}
redcap_settings['redcap_uri'] = 'https://example.org/redcap/api/'
redcap_settings['token'] = 'ABCDEF878D219CFA5D3ADF7F9AB12345'
redcap_settings['verify_ssl'] = False
redi.research_id_to_redcap_id_converter(self.data, redcap_settings, email_settings, self.research_id_to_redcap_id, False, self.configuration_directory)
result = etree.tostring(self.data)
self.assertEqual(self.expect, result)
def test_parse_form_events(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
logger.info("Running " + __name__
+ "#test_person_form_event() using xml: " )
string_1_xml = """<?xml version="1.0" encoding="UTF-8"?>
<redcapProject>
<name>Project</name>
<form>
<name>cbc</name>
<formDateField>cbc_lbdtc</formDateField>
<formCompletedFieldName>cbc_complete</formCompletedFieldName>
<formImportedFieldName>cbc_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
<event>
<name>2_arm_1</name>
</event>
<event>
<name>3_arm_1</name>
</event>
</form>
<form>
<name>chemistry</name>
<formDateField>chem_lbdtc</formDateField>
<formCompletedFieldName>chemistry_complete</formCompletedFieldName>
<formImportedFieldName>chem_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
<event>
<name>2_arm_1</name>
</event>
</form>
</redcapProject>
"""
temp_file = 'tmp.xml'
fh = open(temp_file, 'w')
fh.write(string_1_xml)
fh.close()
etree_1 = etree.ElementTree(etree.fromstring(string_1_xml))
result_tree = redi.parse_form_events(temp_file)
result_xml = etree.tostring(result_tree)
par = etree.XMLParser(remove_blank_text = True)
clean_tree = etree.XML(string_1_xml, parser = par)
clean_result = etree.XML(result_xml, parser = par)
self.assertEqual(etree.tostring(clean_tree), etree.tostring(clean_result))
os.remove(temp_file)
def test_create_empty_event_tree_for_study_for_one_subjects(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.one_subject = """<?xml version='1.0' encoding='US-ASCII'?>
<study>
<subject>
<NAME>TestSubject</NAME>
<loinc_code>123456</loinc_code>
<RESULT>123</RESULT>
<REFERENCE_LOW>12.3</REFERENCE_LOW>
<REFERENCE_HIGH>12.3</REFERENCE_HIGH>
<REFERENCE_UNIT>g/dL</REFERENCE_UNIT>
<DATE_TIME_STAMP/>
<STUDY_ID>123</STUDY_ID>
<timestamp/><redcapFormName>cbc</redcapFormName><eventName/><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>hemo_lborres</redcapFieldNameValue><redcapFieldNameUnits>hemo_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>hemo_lbstat</redcapFieldNameStatus></subject>
</study>
"""
self.data_one_subject = etree.ElementTree(
etree.fromstring(self.one_subject))
self.output_one_subject = """<person_form_event><person><study_id>123</study_id><all_form_events><form>
<name>cbc</name>
<event>
<name>1_arm_1</name>
<field><name>lymce_lborres</name><value/></field><field><name>lymce_lborresu</name><value/></field><field><name>hemo_lborresu</name><value/></field><field><name>cbc_lbdtc</name><value/></field><field><name>cbc_nximport</name><value/></field><field><name>lymce_lbstat</name><value/></field><field><name>cbc_complete</name><value/></field><field><name>hemo_lbstat</name><value/></field><field><name>hemo_lborres</name><value/></field></event>
</form>
<form>
<name>chemistry</name>
<event>
<name>1_arm_1</name>
<field><name>k_lborres</name><value/></field><field><name>chem_lbdtc</name><value/></field><field><name>sodium_lborresu</name><value/></field><field><name>k_lbstat</name><value/></field><field><name>sodium_lbstat</name><value/></field><field><name>chem_nximport</name><value/></field><field><name>chemistry_complete</name><value/></field><field><name>k_lborresu</name><value/></field><field><name>sodium_lborres</name><value/></field></event>
</form>
<form>
<name>inr</name>
<event>
<name>1_arm_1</name>
<field><name>inr_lbdtc</name><value/></field><field><name>inr_complete</name><value/></field><field><name>inr_nximport</name><value/></field></event>
</form>
</all_form_events></person></person_form_event>
"""
self.expect_one_subject = etree.tostring(
etree.fromstring(self.output_one_subject))
self.result = etree.tostring(
redi.create_empty_event_tree_for_study(self.data_one_subject,
self.data_all_form_events))
self.assertEqual(self.expect_one_subject, self.result)
def test_empty_event(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
logger.info("Running " + __name__
+ "#test_empty_event() using study_id: " + `self.CONST_STUDY_ID`)
# Case 1 input string
string_1_empty_event = """
<event>
</event>
"""
out_dict_1 = {'study_id':self.CONST_STUDY_ID}
etree_1 = etree.ElementTree(etree.fromstring(string_1_empty_event))
self.assertRaises(Exception, redi_lib.create_import_data_json, out_dict_1, etree_1)
def test_update_status_field_value_when_one_subject_with_no_form(self):
redi.configure_logging(proj_root+'log/redi.log')
self.source = """<person_form_event>
<person>
<study_id>99</study_id>
<all_form_events>
</all_form_events>
</person>
</person_form_event>
"""
self.source_tree = etree.ElementTree(etree.fromstring(self.source))
self.input = """
<rediFieldMap>
<clinicalComponent>
<redcapFormName>cbc</redcapFormName>
<redcapFieldNameValue>wbc_lborres</redcapFieldNameValue>
<redcapFieldNameUnits>wbc_lborresu</redcapFieldNameUnits>
<redcapStatusFieldName>wbc_lbstat</redcapStatusFieldName>
<redcapStatusFieldValue>NOT_DONE</redcapStatusFieldValue>
</clinicalComponent>
<clinicalComponent>
<redcapFormName>cbc</redcapFormName>
<redcapFieldNameValue>neut_lborres</redcapFieldNameValue>
<redcapFieldNameUnits>neut_lborresu</redcapFieldNameUnits>
</clinicalComponent>
<clinicalComponent>
<redcapFormName>inr</redcapFormName>
<redcapFieldNameValue>inr_lborres</redcapFieldNameValue>
<redcapStatusFieldName>inr_lbstat</redcapStatusFieldName>
<redcapStatusFieldValue>NOT_DONE</redcapStatusFieldValue>
</clinicalComponent>
</rediFieldMap>
"""
self.input_tree = etree.ElementTree(etree.fromstring(self.input))
self.output = """<person_form_event>
<person>
<study_id>99</study_id>
<all_form_events>
</all_form_events>
</person>
</person_form_event>
"""
self.expect = etree.tostring(etree.fromstring(self.output))
redi.updateStatusFieldValueInPersonFormEventTree(self.source_tree, self.input_tree)
result = etree.tostring(self.source_tree)
self.assertEqual(self.expect, result)
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.CONST_STUDY_ID = 73
global logger
logger = logging.getLogger('redi')
logging.basicConfig(filename=proj_root + 'log/redi.log',
format='%(asctime)s - %(levelname)s - \
%(name)s - %(message)s',
datefmt='%m/%d/%Y %H:%M:%S',
filemode='w',
level=logging.DEBUG)
return ()
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.CONST_STUDY_ID = 73
global logger
logger = logging.getLogger('redi')
logging.basicConfig(filename=proj_root+'log/redi.log',
format='%(asctime)s - %(levelname)s - \
%(name)s - %(message)s',
datefmt='%m/%d/%Y %H:%M:%S',
filemode='w',
level=logging.DEBUG)
return()
def setUp(self):
redi.configure_logging()
self.test_form_data = {'cbc': 'cbc_complete', 'chemistry': 'chemistry_complete'}
self.expect = """record,redcap_event_name,field_name,value\n001-0001,"3_arm_1",hemo_lborres,12.3\n001-0001,"3_arm_1",hemo_lborresu,"g/dL"\n001-0001,"3_arm_1",plat_lborres,92\n001-0001,"3_arm_1",plat_lborresu,"thou/cu mm"\n001-0001,"3_arm_1",neut_lborres,52.8\n001-0001,"3_arm_1",neut_lborresu,"%"\n001-0001,"3_arm_1",anc_lbstat,"NOT_DONE"\n001-0001,"3_arm_1",lym_lbstat,"NOT_DONE"\n001-0001,"3_arm_1",lymce_lbstat,"NOT_DONE"\n001-0001,"3_arm_1",wbc_lbstat,"NOT_DONE"\n001-0001,"3_arm_1",cbc_lbdtc,"1908-08-11"\n001-0001,"3_arm_1",cbc_complete,2\n001-0001,"3_arm_1",cbc_nximport,"Y"\n"""
self.output_date_format = "%Y-%m-%d"
self.test_xml = """<?xml version='1.0' encoding='US-ASCII'?>
<study>
<subject>
<NAME>WHITE BLOOD CELL COUNT</NAME>
<COMPONENT_ID>1577876</COMPONENT_ID>
<ORD_VALUE>6.0</ORD_VALUE>
<REFERENCE_LOW>4.0</REFERENCE_LOW>
<REFERENCE_HIGH>10.0</REFERENCE_HIGH>
<REFERENCE_UNIT>thou/cu mm</REFERENCE_UNIT>
<SPECIMN_TAKEN_TIME>1908-08-11 10:05:00</SPECIMN_TAKEN_TIME>
<STUDY_ID>001-0001</STUDY_ID>
<timestamp>1908-08-11</timestamp><redcapFormName>cbc</redcapFormName><eventName>3_arm_1</eventName><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>wbc_lborres</redcapFieldNameValue><redcapFieldNameUnits>wbc_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>wbc_lbstat</redcapFieldNameStatus></subject>
<subject>
<NAME>HEMOGLOBIN</NAME>
<COMPONENT_ID>1534435</COMPONENT_ID>
<ORD_VALUE>12.3</ORD_VALUE>
<REFERENCE_LOW>12.0</REFERENCE_LOW>
<REFERENCE_HIGH>16.0</REFERENCE_HIGH>
<REFERENCE_UNIT>g/dL</REFERENCE_UNIT>
<SPECIMN_TAKEN_TIME>1908-08-11 10:05:00</SPECIMN_TAKEN_TIME>
<STUDY_ID>001-0001</STUDY_ID>
<timestamp>1908-08-11</timestamp><redcapFormName>cbc</redcapFormName><eventName>3_arm_1</eventName><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>hemo_lborres</redcapFieldNameValue><redcapFieldNameUnits>hemo_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>hemo_lbstat</redcapFieldNameStatus></subject>
<subject>
<NAME>PLATELET COUNT</NAME>
<COMPONENT_ID>1009</COMPONENT_ID>
<ORD_VALUE>92</ORD_VALUE>
<REFERENCE_LOW>150</REFERENCE_LOW>
<REFERENCE_HIGH>450</REFERENCE_HIGH>
<REFERENCE_UNIT>thou/cu mm</REFERENCE_UNIT>
<SPECIMN_TAKEN_TIME>1908-08-11 10:05:00</SPECIMN_TAKEN_TIME>
<STUDY_ID>001-0001</STUDY_ID>
<timestamp>1908-08-11</timestamp><redcapFormName>cbc</redcapFormName><eventName>3_arm_1</eventName><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>plat_lborres</redcapFieldNameValue><redcapFieldNameUnits>plat_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>plat_lbstat</redcapFieldNameStatus></subject>
<subject>
<NAME>NEUTROPHILS RELATIVE PERCENT</NAME>
<COMPONENT_ID>1539315</COMPONENT_ID>
<ORD_VALUE>52.8</ORD_VALUE>
<REFERENCE_LOW>40.0</REFERENCE_LOW>
<REFERENCE_HIGH>80.0</REFERENCE_HIGH>
<REFERENCE_UNIT>%</REFERENCE_UNIT>
<SPECIMN_TAKEN_TIME>1908-08-11 10:05:00</SPECIMN_TAKEN_TIME>
<STUDY_ID>001-0001</STUDY_ID>
<timestamp>1908-08-11</timestamp><redcapFormName>cbc</redcapFormName><eventName>3_arm_1</eventName><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>neut_lborres</redcapFieldNameValue><redcapFieldNameUnits>neut_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>neut_lbstat</redcapFieldNameStatus></subject>
</study>
"""
self.translationTableXml = '''<rediFieldMap>
def test_empty_event(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
logger.info("Running " + __name__ +
"#test_empty_event() using study_id: " +
` self.CONST_STUDY_ID `)
# Case 1 input string
string_1_empty_event = """
<event>
</event>
"""
out_dict_1 = {'study_id': self.CONST_STUDY_ID}
etree_1 = etree.ElementTree(etree.fromstring(string_1_empty_event))
self.assertRaises(Exception, redi_lib.create_import_data_json,
out_dict_1, etree_1)
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY, False)
self.form_event_tree = """<?xml version='1.0' encoding='US-ASCII'?>
<redcapProject>
<name>Project</name>
<form>
<name>cbc</name>
<formDateField>cbc_lbdtc</formDateField>
<formCompletedFieldName>cbc_complete</formCompletedFieldName>
<formImportedFieldName>cbc_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
</form>
<form>
<name>chemistry</name>
<formDateField>chem_lbdtc</formDateField>
<formCompletedFieldName>chemistry_complete</formCompletedFieldName>
<formImportedFieldName>chem_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
</form>
<form>
<name>inr</name>
<formDateField>inr_lbdtc</formDateField>
<formCompletedFieldName>inr_complete</formCompletedFieldName>
<formImportedFieldName>inr_nximport</formImportedFieldName>
<formCompletedFieldValue>2</formCompletedFieldValue>
<formImportedFieldValue>Y</formImportedFieldValue>
<event>
<name>1_arm_1</name>
</event>
</form>
</redcapProject>
"""
self.data_form_event_tree = etree.ElementTree(etree.fromstring(self.form_event_tree))
return()
def test_create_empty_event_tree_for_study_for_one_subjects(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.one_subject = """<?xml version='1.0' encoding='US-ASCII'?>
<study>
<subject>
<NAME>TestSubject</NAME>
<loinc_code>123456</loinc_code>
<RESULT>123</RESULT>
<REFERENCE_LOW>12.3</REFERENCE_LOW>
<REFERENCE_HIGH>12.3</REFERENCE_HIGH>
<REFERENCE_UNIT>g/dL</REFERENCE_UNIT>
<DATE_TIME_STAMP/>
<STUDY_ID>123</STUDY_ID>
<timestamp/><redcapFormName>cbc</redcapFormName><eventName/><formDateField>cbc_lbdtc</formDateField><formCompletedFieldName>cbc_complete</formCompletedFieldName><formImportedFieldName>cbc_nximport</formImportedFieldName><redcapFieldNameValue>hemo_lborres</redcapFieldNameValue><redcapFieldNameUnits>hemo_lborresu</redcapFieldNameUnits><redcapFieldNameStatus>hemo_lbstat</redcapFieldNameStatus></subject>
</study>
"""
self.data_one_subject= etree.ElementTree(etree.fromstring(self.one_subject))
self.output_one_subject = """<person_form_event><person><study_id>123</study_id><all_form_events><form>
<name>cbc</name>
<event>
<name>1_arm_1</name>
<field><name>lymce_lborres</name><value/></field><field><name>lymce_lborresu</name><value/></field><field><name>hemo_lborresu</name><value/></field><field><name>cbc_lbdtc</name><value/></field><field><name>cbc_nximport</name><value/></field><field><name>lymce_lbstat</name><value/></field><field><name>cbc_complete</name><value/></field><field><name>hemo_lbstat</name><value/></field><field><name>hemo_lborres</name><value/></field></event>
</form>
<form>
<name>chemistry</name>
<event>
<name>1_arm_1</name>
<field><name>k_lborres</name><value/></field><field><name>chem_lbdtc</name><value/></field><field><name>sodium_lborresu</name><value/></field><field><name>k_lbstat</name><value/></field><field><name>sodium_lbstat</name><value/></field><field><name>chem_nximport</name><value/></field><field><name>chemistry_complete</name><value/></field><field><name>k_lborresu</name><value/></field><field><name>sodium_lborres</name><value/></field></event>
</form>
<form>
<name>inr</name>
<event>
<name>1_arm_1</name>
<field><name>inr_lbdtc</name><value/></field><field><name>inr_complete</name><value/></field><field><name>inr_nximport</name><value/></field></event>
</form>
</all_form_events></person></person_form_event>
"""
self.expect_one_subject = etree.tostring(etree.fromstring(self.output_one_subject))
self.result = etree.tostring(redi.create_empty_event_tree_for_study(self.data_one_subject,self.data_all_form_events))
self.assertEqual(self.expect_one_subject, self.result)
def test_log(self):
import os.path
file_name = self.file_name
sys.path.append('log')
# remove any existing log file in log/ folder
#if os.path.isfile(file_name):
# with open(file_name):
#print "here"
# os.remove(file_name)
#print os.path.isfile(file_name)
# call the configure logging function
redi.configure_logging()
#print os.path.isfile(file_name)
# check if the file is created
assert os.path.isfile(file_name) == True
# remove the file created through testing
os.remove(file_name)
def test_update_formdatefield(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
redi.update_formdatefield(self.data, self.form_events_tree)
# output raw file to check it
#redi.write_element_tree_to_file(self.data, 'rawData.xml')
# initialize a dictionary for the formdatefield
# [key, value] = [formdatefield, filled or not?(0/1)]
isFormDateFieldFilled = {}
for subject in self.data.iter('subject'):
form_date_field = subject.find('formDateField').text
if not form_date_field:
isFormDateFieldFilled[form_date_field] = 1
status=1
for key,value in isFormDateFieldFilled.items():
if value != status:
status = 0
break
self.assertEqual(status,1)
def test_log(self):
import os.path
file_name = self.file_name
sys.path.append('log')
# remove any existing log file in log/ folder
#if os.path.isfile(file_name):
# with open(file_name):
#print "here"
# os.remove(file_name)
#print os.path.isfile(file_name)
# call the configure logging function
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
#print 'checking if log file was created: ' + file_name
# check if the file is created
assert os.path.isfile(file_name) == True
# remove the file created through testing
os.remove(file_name)
def setUp(self):
# initialize the data with element tree
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_xml = """<?xml version="1.0" encoding="utf8"?>
<study>
<subject>
<NAME>TSH REFLEX</NAME>
<loinc_code>1552152</loinc_code>
<RESULT>0.74</RESULT>
<REFERENCE_LOW>0.27</REFERENCE_LOW>
<REFERENCE_HIGH>4.20</REFERENCE_HIGH>
<REFERENCE_UNIT>mIU/L</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
<subject>
<NAME>HEP C RNA, QUANT REAL-TIME</NAME>
<loinc_code>740</loinc_code>
<RESULT>5.8</RESULT>
<REFERENCE_LOW></REFERENCE_LOW>
<REFERENCE_HIGH></REFERENCE_HIGH>
<REFERENCE_UNIT>log IU</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
<subject>
<NAME>HCV QUANTITATIVE INTERPRETATION</NAME>
<loinc_code>1534483</loinc_code>
<RESULT>Detected</RESULT>
<REFERENCE_LOW></REFERENCE_LOW>
<REFERENCE_HIGH></REFERENCE_HIGH>
<REFERENCE_UNIT></REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
</study>"""
self.data = etree.ElementTree(etree.fromstring(self.test_xml))
self.input_date_format = "%Y-%m-%d %H:%M:%S"
self.output_date_format = "%Y-%m-%d"
def setUp(self):
# initialize the data with element tree
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_xml = """<?xml version="1.0" encoding="utf8"?>
<study>
<subject>
<NAME>TSH REFLEX</NAME>
<loinc_code>1552152</loinc_code>
<RESULT>0.74</RESULT>
<REFERENCE_LOW>0.27</REFERENCE_LOW>
<REFERENCE_HIGH>4.20</REFERENCE_HIGH>
<REFERENCE_UNIT>mIU/L</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
<subject>
<NAME>HEP C RNA, QUANT REAL-TIME</NAME>
<loinc_code>740</loinc_code>
<RESULT>5.8</RESULT>
<REFERENCE_LOW></REFERENCE_LOW>
<REFERENCE_HIGH></REFERENCE_HIGH>
<REFERENCE_UNIT>log IU</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
<subject>
<NAME>HCV QUANTITATIVE INTERPRETATION</NAME>
<loinc_code>1534483</loinc_code>
<RESULT>Detected</RESULT>
<REFERENCE_LOW></REFERENCE_LOW>
<REFERENCE_HIGH></REFERENCE_HIGH>
<REFERENCE_UNIT></REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>59</STUDY_ID>
</subject>
</study>"""
self.data = etree.ElementTree(etree.fromstring(self.test_xml))
self.input_date_format = "%Y-%m-%d %H:%M:%S"
self.output_date_format = "%Y-%m-%d"
def test_research_id_to_redcap_id_converter(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
class MockRedcapClient(RedcapClient):
def __init__(self, context):
self.__context = context
def send_data_to_redcap(self, data, overwrite=False):
raise NotImplementedError()
def get_data_from_redcap(self, records_to_fetch=None,
events_to_fetch=None, fields_to_fetch=None,
forms_to_fetch=None, return_format='xml'):
return self.__context.dummy_get_data_from_redcap(
records_to_fetch, events_to_fetch, fields_to_fetch,
forms_to_fetch, return_format)
redi.research_id_to_redcap_id_converter(self.data,
MockRedcapClient(self),
self.research_id_to_redcap_id,
self.configuration_directory)
result = etree.tostring(self.data)
self.assertEqual(self.expect, result)
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
def test_update_form_imported(self):
redi.configure_logging()
redi.update_form_imported_field(self.data, self.form_events_tree, 'undefined')
result = etree.tostring(self.data)
self.assertEqual(self.expect, result)
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
def test_create_empty_events_for_one_subject_all_fields_input(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.result = etree.tostring(redi.create_empty_events_for_one_subject(self.data1_test1,self.data2_test1))
self.result = ''.join(self.result.split())
self.expect_test1 = ''.join(self.expect_test1.split())
self.assertEqual(self.expect_test1, self.result)
def setUp(self):
# configure logging
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
# start a server in seperate thread
thread.start_new_thread(self.server_setup,())
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_raw_xml = """<?xml version='1.0' encoding='US-ASCII'?>
def test_create_empty_events_for_one_subject_no_fields_input(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.assertRaises(Exception,redi.create_empty_events_for_one_subject,self.data1_test2,self.data2_test2)
def setUp(self):
# configure logging
redi.configure_logging()
# start a server in seperate thread
thread.start_new_thread(self.server_setup,())
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_report_params = {
'project': 'hcvtarget-uf',
'report_file_path': proj_root + 'config/report.xml',
'redcap_uri': 'https://hostname.org'}
self.test_report_data = {
'total_subjects': 5,
'form_details': {
'Total_chemistry_Forms': 22,
'Total_cbc_Forms': 53
},
'subject_details': {
'60': {'cbc_Forms': 1, 'chemistry_Forms': 1},
'61': {'cbc_Forms': 2, 'chemistry_Forms': 1},
'63': {'cbc_Forms': 11, 'chemistry_Forms': 4},
'59': {'cbc_Forms': 39, 'chemistry_Forms': 16}
},
'errors' : [],
}
self.specimen_taken_time_summary = {'total': 15, 'blank': 3}
self.test_alert_summary = {
'multiple_values_alert': [
'This is multiple values alert 1',
'This is multiple values alert 2',
'This is multiple values alert 3'],
'max_event_alert': [
'This is max event alert 1',
'This is max event alert 2',
'This is max event alert 3']
}
self.expected_xml = '''
<report>
<header>
<project>hcvtarget-uf</project>
<date>'''+time.strftime("%m/%d/%Y")+'''</date>
<redcapServerAddress>https://hostname.org</redcapServerAddress>
</header>
<summary>
<subjectCount>5</subjectCount>
<forms>
<form>
<form_name>Total_cbc_Forms</form_name>
<form_count>53</form_count>
</form>
<form>
<form_name>Total_chemistry_Forms</form_name>
<form_count>22</form_count>
</form>
</forms>
</summary>
<alerts>
<tooManyForms>
<eventAlert>
<message>This is max event alert 1</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 2</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 3</message>
</eventAlert>
</tooManyForms>
<tooManyValues>
<valuesAlert>
<message>This is multiple values alert 1</message>
</valuesAlert>
<valuesAlert>
<message>This is multiple values alert 2</message>
</valuesAlert>
<valuesAlert><message>This is multiple values alert 3</message>
</valuesAlert></tooManyValues>
</alerts>
<subjectsDetails>
<Subject><ID>59</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>39</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>16</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>60</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>1</form_count></form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject><ID>61</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>2</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>63</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>11</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>4</form_count>
</form>
</forms>
</Subject>
</subjectsDetails>
<errors/>
<summaryOfSpecimenTakenTimes>
<total>15</total>
<blank>3</blank>
<percent>20.0</percent>
</summaryOfSpecimenTakenTimes>
</report>'''
self.schema_str = StringIO('''\
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="report">
<xs:complexType>
<xs:sequence>
<xs:element name="header">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="project"/>
<xs:element type="xs:string" name="date"/>
<xs:element type="xs:string" name="redcapServerAddress"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="summary">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="subjectCount"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="alerts">
<xs:complexType>
<xs:sequence>
<xs:element name="tooManyForms">
<xs:complexType>
<xs:sequence>
<xs:element name="eventAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="tooManyValues">
<xs:complexType>
<xs:sequence>
<xs:element name="valuesAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="subjectsDetails">
<xs:complexType>
<xs:sequence>
<xs:element name="Subject" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="ID"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="errors">
</xs:element>
<xs:element name="summaryOfSpecimenTakenTimes">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="total"/>
<xs:element type="xs:byte" name="blank"/>
<xs:element type="xs:float" name="percent"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>''')
return
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.sampleData = """<rediFieldMap>
def test_update_status_field_value_when_one_subject_with_two_forms_with_one_event_in_each_form(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.source = """<person_form_event>
<person>
<study_id>99</study_id>
<all_form_events>
<form>
<name>cbc</name>
<event>
<name>1_arm_1</name>
<field>
<name>cbc_lbdtc</name>
<value>1905-10-01</value>
</field>
<field>
<name>wbc_lborres</name>
<value>3.0</value>
</field>
<field>
<name>wbc_lbstat</name>
<value/>
</field>
<field>
<name>neut_lborres</name>
<value>500</value>
</field>
<field>
<name>neut_lbstat</name>
<value/>
</field>
</event>
</form>
<form>
<name>inr</name>
<event>
<name>1_arm_1</name>
<field>
<name>inr_lbdtc</name>
<value>1906-12-01</value>
</field>
<field>
<name>inr_lborres</name>
<value/>
</field>
<field>
<name>inr_lbstat</name>
<value/>
</field>
</event>
</form>
</all_form_events>
</person>
</person_form_event>
"""
self.source_tree = etree.ElementTree(etree.fromstring(self.source))
self.input = """
<rediFieldMap>
<clinicalComponent>
<redcapFormName>cbc</redcapFormName>
<redcapFieldNameValue>wbc_lborres</redcapFieldNameValue>
<redcapFieldNameUnits>wbc_lborresu</redcapFieldNameUnits>
<redcapStatusFieldName>wbc_lbstat</redcapStatusFieldName>
<redcapStatusFieldValue>NOT_DONE</redcapStatusFieldValue>
</clinicalComponent>
<clinicalComponent>
<redcapFormName>cbc</redcapFormName>
<redcapFieldNameValue>neut_lborres</redcapFieldNameValue>
<redcapFieldNameUnits>neut_lborresu</redcapFieldNameUnits>
</clinicalComponent>
<clinicalComponent>
<redcapFormName>inr</redcapFormName>
<redcapFieldNameValue>inr_lborres</redcapFieldNameValue>
<redcapStatusFieldName>inr_lbstat</redcapStatusFieldName>
<redcapStatusFieldValue>NOT_DONE</redcapStatusFieldValue>
</clinicalComponent>
</rediFieldMap>
"""
self.input_tree = etree.ElementTree(etree.fromstring(self.input))
self.output = """<person_form_event>
<person>
<study_id>99</study_id>
<all_form_events>
<form>
<name>cbc</name>
<event>
<name>1_arm_1</name>
<field>
<name>cbc_lbdtc</name>
<value>1905-10-01</value>
</field>
<field>
<name>wbc_lborres</name>
<value>3.0</value>
</field>
<field>
<name>wbc_lbstat</name>
<value/>
</field>
<field>
<name>neut_lborres</name>
<value>500</value>
</field>
<field>
<name>neut_lbstat</name>
<value/>
</field>
</event>
</form>
<form>
<name>inr</name>
<event>
<name>1_arm_1</name>
<field>
<name>inr_lbdtc</name>
<value>1906-12-01</value>
</field>
<field>
<name>inr_lborres</name>
<value/>
</field>
<field>
<name>inr_lbstat</name>
<value>NOT_DONE</value>
</field>
</event>
</form>
</all_form_events>
</person>
</person_form_event>
"""
self.expect = etree.tostring(etree.fromstring(self.output))
redi.updateStatusFieldValueInPersonFormEventTree(self.source_tree, self.input_tree)
result = etree.tostring(self.source_tree)
self.assertEqual(self.expect, result)
def test_update_event_name(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
redi.update_event_name(self.data, self.form_events_tree, 'undefined')
result = etree.tostring(self.data)
self.assertEqual(self.expect, result)
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_report_params = {
"project": "hcvtarget-uf",
"report_file_path": proj_root + "config/report.xml",
"redcap_server": "https://hostname.org",
}
self.test_report_data = {
"total_subjects": 5,
"form_details": {"Total_chemistry_Forms": 22, "Total_cbc_Forms": 53},
"subject_details": {
"60": {"cbc_Forms": 1, "chemistry_Forms": 1},
"61": {"cbc_Forms": 2, "chemistry_Forms": 1},
"63": {"cbc_Forms": 11, "chemistry_Forms": 4},
"59": {"cbc_Forms": 39, "chemistry_Forms": 16},
},
"errors": [],
}
self.specimen_taken_time_summary = {"total": 15, "blank": 3}
self.test_alert_summary = {
"multiple_values_alert": [
"This is multiple values alert 1",
"This is multiple values alert 2",
"This is multiple values alert 3",
],
"max_event_alert": ["This is max event alert 1", "This is max event alert 2", "This is max event alert 3"],
}
self.expected_xml = (
"""
<report>
<header>
<project>hcvtarget-uf</project>
<date>"""
+ time.strftime("%m/%d/%Y")
+ """</date>
<redcapServerAddress>https://hostname.org</redcapServerAddress>
</header>
<summary>
<subjectCount>5</subjectCount>
<forms>
<form>
<form_name>Total_cbc_Forms</form_name>
<form_count>53</form_count>
</form>
<form>
<form_name>Total_chemistry_Forms</form_name>
<form_count>22</form_count>
</form>
</forms>
</summary>
<alerts>
<tooManyForms>
<eventAlert>
<message>This is max event alert 1</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 2</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 3</message>
</eventAlert>
</tooManyForms>
<tooManyValues>
<valuesAlert>
<message>This is multiple values alert 1</message>
</valuesAlert>
<valuesAlert>
<message>This is multiple values alert 2</message>
</valuesAlert>
<valuesAlert><message>This is multiple values alert 3</message>
</valuesAlert></tooManyValues>
</alerts>
<subjectsDetails>
<Subject><ID>59</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>39</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>16</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>60</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>1</form_count></form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject><ID>61</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>2</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>63</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>11</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>4</form_count>
</form>
</forms>
</Subject>
</subjectsDetails>
<errors/>
<summaryOfSpecimenTakenTimes>
<total>15</total>
<blank>3</blank>
<percent>20.0</percent>
</summaryOfSpecimenTakenTimes>
</report>"""
)
self.schema_str = StringIO(
"""\
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="report">
<xs:complexType>
<xs:sequence>
<xs:element name="header">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="project"/>
<xs:element type="xs:string" name="date"/>
<xs:element type="xs:string" name="redcapServerAddress"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="summary">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="subjectCount"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="alerts">
<xs:complexType>
<xs:sequence>
<xs:element name="tooManyForms">
<xs:complexType>
<xs:sequence>
<xs:element name="eventAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="tooManyValues">
<xs:complexType>
<xs:sequence>
<xs:element name="valuesAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="subjectsDetails">
<xs:complexType>
<xs:sequence>
<xs:element name="Subject" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="ID"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="errors">
</xs:element>
<xs:element name="summaryOfSpecimenTakenTimes">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="total"/>
<xs:element type="xs:byte" name="blank"/>
<xs:element type="xs:float" name="percent"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>"""
)
return
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_report_params = {'project': 'hcvtarget-uf',
'report_file_path': proj_root + 'config/report.xml',
'redcap_server': 'https://hostname.org'}
self.test_report_data = {
'total_subjects': 5,
'form_details': {
'Total_chemistry_Forms': 22,
'Total_cbc_Forms': 53
},
'subject_details': {
'60': {'cbc_Forms': 1, 'chemistry_Forms': 1},
'61': {'cbc_Forms': 2, 'chemistry_Forms': 1},
'63': {'cbc_Forms': 11, 'chemistry_Forms': 4},
'59': {'cbc_Forms': 39, 'chemistry_Forms': 16}
},
'errors' : [],
}
self.specimen_taken_time_summary = {'total': 15, 'blank': 3}
self.test_alert_summary = {
'multiple_values_alert': [
'This is multiple values alert 1',
'This is multiple values alert 2',
'This is multiple values alert 3'],
'max_event_alert': [
'This is max event alert 1',
'This is max event alert 2',
'This is max event alert 3']
}
self.expected_xml = '''
<report>
<header>
<project>hcvtarget-uf</project>
<date>'''+time.strftime("%m/%d/%Y")+'''</date>
<redcapServerAddress>https://hostname.org</redcapServerAddress>
</header>
<summary>
<subjectCount>5</subjectCount>
<forms>
<form>
<form_name>Total_cbc_Forms</form_name>
<form_count>53</form_count>
</form>
<form>
<form_name>Total_chemistry_Forms</form_name>
<form_count>22</form_count>
</form>
</forms>
</summary>
<alerts>
<tooManyForms>
<eventAlert>
<message>This is max event alert 1</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 2</message>
</eventAlert>
<eventAlert>
<message>This is max event alert 3</message>
</eventAlert>
</tooManyForms>
<tooManyValues>
<valuesAlert>
<message>This is multiple values alert 1</message>
</valuesAlert>
<valuesAlert>
<message>This is multiple values alert 2</message>
</valuesAlert>
<valuesAlert><message>This is multiple values alert 3</message>
</valuesAlert></tooManyValues>
</alerts>
<subjectsDetails>
<Subject><ID>59</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>39</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>16</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>60</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>1</form_count></form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject><ID>61</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>2</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>1</form_count>
</form>
</forms>
</Subject>
<Subject>
<ID>63</ID>
<forms>
<form>
<form_name>cbc_Forms</form_name>
<form_count>11</form_count>
</form>
<form>
<form_name>chemistry_Forms</form_name>
<form_count>4</form_count>
</form>
</forms>
</Subject>
</subjectsDetails>
<errors/>
<summaryOfSpecimenTakenTimes>
<total>15</total>
<blank>3</blank>
<percent>20.0</percent>
</summaryOfSpecimenTakenTimes>
</report>'''
self.schema_str = StringIO('''\
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="report">
<xs:complexType>
<xs:sequence>
<xs:element name="header">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="project"/>
<xs:element type="xs:string" name="date"/>
<xs:element type="xs:string" name="redcapServerAddress"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="summary">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="subjectCount"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="alerts">
<xs:complexType>
<xs:sequence>
<xs:element name="tooManyForms">
<xs:complexType>
<xs:sequence>
<xs:element name="eventAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="tooManyValues">
<xs:complexType>
<xs:sequence>
<xs:element name="valuesAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="subjectsDetails">
<xs:complexType>
<xs:sequence>
<xs:element name="Subject" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="ID"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="errors">
</xs:element>
<xs:element name="summaryOfSpecimenTakenTimes">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="total"/>
<xs:element type="xs:byte" name="blank"/>
<xs:element type="xs:float" name="percent"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>''')
return
def setUp(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.test_raw_xml = """<?xml version='1.0' encoding='US-ASCII'?>
def test_update_event_name(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
redi.update_event_name(self.data, self.form_events_tree, 'undefined')
result = etree.tostring(self.data)
self.assertEqual(self.expect, result)
def setUp(self):
redi.configure_logging()
self.test_raw_xml = """<?xml version='1.0' encoding='US-ASCII'?>
def setUp(self):
redi.configure_logging()
self.test_report_params = {'project': 'hcvtarget-uf',
'report_file_path': proj_root + 'config/report.xml',
'redcap_server': 'https://hostname.org'}
self.test_report_data = {'total_subjects': 5,
'cumulative_end_date': '1907-08-24',
'total_unique_dates': 52,
'cumulative_start_date': '1904-02-17',
'Total_chemistry_Forms': 22,
'subject_details': {'60': {'earliestdate': datetime.date(1905, 3, 9), 'latestdate': datetime.date(1905, 6, 4), 'cbc_Forms': 1, 'chemistry_Forms': 1, 'StudyPeriod': 270},
'61': {'earliestdate': datetime.date(1905, 3, 8), 'latestdate': datetime.date(1905, 2, 23), 'cbc_Forms': 2, 'chemistry_Forms': 1, 'StudyPeriod': 75},
'63': {'earliestdate': datetime.date(1905, 2, 20), 'latestdate': datetime.date(1905, 1, 28), 'cbc_Forms': 11, 'chemistry_Forms': 4, 'StudyPeriod': 92},
'59': {'earliestdate': datetime.date(1905, 1, 30), 'latestdate': datetime.date(1905, 6, 10), 'cbc_Forms': 39, 'chemistry_Forms': 16, 'StudyPeriod': 318}},
'Total_cbc_Forms': 53}
self.test_alert_summary = {'multiple_values_alert': ['This is multiple values alert 1',
'This is multiple values alert 2',
'This is multiple values alert 3'],
'max_event_alert': ['This is max event alert 1',
'This is max event alert 2',
'This is max event alert 3']}
self.test_form_data = {'cbc': 'cbc_complete', 'chemistry': 'chemistry_complete'}
self.expected_xml = '''<report><header><project>hcvtarget-uf</project><date>'''+time.strftime("%m/%d/%Y")+'''</date><redcapServerAddress>https://hostname.org</redcapServerAddress></header><summary><subjectCount>5</subjectCount><forms><form><form_name>Total_cbc_Forms</form_name><form_count>53</form_count></form><form><form_name>Total_chemistry_Forms</form_name><form_count>22</form_count></form></forms><total_unique_dates>52</total_unique_dates><dates><earliestDate>1904-02-17</earliestDate><latestDate>1907-08-24</latestDate></dates></summary><alerts><tooManyForms><eventAlert><message>This is max event alert 1</message></eventAlert><eventAlert><message>This is max event alert 2</message></eventAlert><eventAlert><message>This is max event alert 3</message></eventAlert></tooManyForms><tooManyValues><valuesAlert><message>This is multiple values alert 1</message></valuesAlert><valuesAlert><message>This is multiple values alert 2</message></valuesAlert><valuesAlert><message>This is multiple values alert 3</message></valuesAlert></tooManyValues></alerts><subjectsDetails><Subject><ID>60</ID><forms><form><form_name>cbc_Forms</form_name><form_count>1</form_count></form><form><form_name>chemistry_Forms</form_name><form_count>1</form_count></form></forms><StudyPeriod>270</StudyPeriod><earliestdate>1905-03-09</earliestdate><latestdate>1905-06-04</latestdate></Subject><Subject><ID>61</ID><forms><form><form_name>cbc_Forms</form_name><form_count>2</form_count></form><form><form_name>chemistry_Forms</form_name><form_count>1</form_count></form></forms><StudyPeriod>75</StudyPeriod><earliestdate>1905-03-08</earliestdate><latestdate>1905-02-23</latestdate></Subject><Subject><ID>63</ID><forms><form><form_name>cbc_Forms</form_name><form_count>11</form_count></form><form><form_name>chemistry_Forms</form_name><form_count>4</form_count></form></forms><StudyPeriod>92</StudyPeriod><earliestdate>1905-02-20</earliestdate><latestdate>1905-01-28</latestdate></Subject><Subject><ID>59</ID><forms><form><form_name>cbc_Forms</form_name><form_count>39</form_count></form><form><form_name>chemistry_Forms</form_name><form_count>16</form_count></form></forms><StudyPeriod>318</StudyPeriod><earliestdate>1905-01-30</earliestdate><latestdate>1905-06-10</latestdate></Subject></subjectsDetails></report>'''
self.schema_str = StringIO('''\
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="report">
<xs:complexType>
<xs:sequence>
<xs:element name="header">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="project"/>
<xs:element type="xs:string" name="date"/>
<xs:element type="xs:string" name="redcapServerAddress"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="summary">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="subjectCount"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element type="xs:byte" name="total_unique_dates"/>
<xs:element name="dates">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:date" name="earliestDate"/>
<xs:element type="xs:date" name="latestDate"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="alerts">
<xs:complexType>
<xs:sequence>
<xs:element name="tooManyForms">
<xs:complexType>
<xs:sequence>
<xs:element name="eventAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="tooManyValues">
<xs:complexType>
<xs:sequence>
<xs:element name="valuesAlert" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="message"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="subjectsDetails">
<xs:complexType>
<xs:sequence>
<xs:element name="Subject" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:byte" name="ID"/>
<xs:element name="forms">
<xs:complexType>
<xs:sequence>
<xs:element name="form" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="form_name"/>
<xs:element type="xs:byte" name="form_count"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element type="xs:short" name="StudyPeriod"/>
<xs:element type="xs:date" name="earliestdate"/>
<xs:element type="xs:date" name="latestdate"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>''')
return
def test_create_empty_events_for_one_subject_no_fields_input(self):
redi.configure_logging(DEFAULT_DATA_DIRECTORY)
self.assertRaises(Exception, redi.create_empty_events_for_one_subject,
self.data1_test2, self.data2_test2)