def test_get_emr_data(self):
temp_folder = tempfile.mkdtemp('/')
input_string = '''"NAME","COMPONENT_ID","RESULT","REFERENCE_UNIT","DATE_TIME_STAMP","STUDY_ID"
"RNA","1905","<5","IU/mL","1907-05-21 05:50:00","999-0059"
"EGFR","1740200","eGFR result is => 60 ml/min/1.73M2","ml/min/1.73M2","1903-11-27 15:13:00","999-0059"
"HEMATOCRIT","1534436",">27&<30","%","","999-0059"'''
with open(temp_folder+"raw.txt", 'w+') as f:
f.write(input_string)
props = EmrConnectionDetails('fake.server',
'username',
'password',
'tmp',
'output.csv'
)
GetEmrData.get_emr_data(temp_folder, props)
with open(temp_folder + 'raw.xml') as f:
result = f.read()
expected = '''<?xml version="1.0" encoding="utf8"?>
<study>
<subject>
<NAME>RNA</NAME>
<COMPONENT_ID>1905</COMPONENT_ID>
<RESULT><5</RESULT>
<REFERENCE_UNIT>IU/mL</REFERENCE_UNIT>
<DATE_TIME_STAMP>1907-05-21 05:50:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>EGFR</NAME>
<COMPONENT_ID>1740200</COMPONENT_ID>
<RESULT>eGFR result is => 60 ml/min/1.73M2</RESULT>
<REFERENCE_UNIT>ml/min/1.73M2</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>HEMATOCRIT</NAME>
<COMPONENT_ID>1534436</COMPONENT_ID>
<RESULT>>27&<30</RESULT>
<REFERENCE_UNIT>%</REFERENCE_UNIT>
<DATE_TIME_STAMP></DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
</study>
'''
self.assertEqual(result, expected)
shutil.rmtree(temp_folder)
def test_get_emr_data(self):
temp_folder = tempfile.mkdtemp('/')
input_string = '''"NAME","COMPONENT_ID","RESULT","REFERENCE_UNIT","DATE_TIME_STAMP","STUDY_ID"
"RNA","1905","<5","IU/mL","1907-05-21 05:50:00","999-0059"
"EGFR","1740200","eGFR result is => 60 ml/min/1.73M2","ml/min/1.73M2","1903-11-27 15:13:00","999-0059"
"HEMATOCRIT","1534436",">27&<30","%","","999-0059"'''
with open(temp_folder + "raw.txt", 'w+') as f:
f.write(input_string)
props = EmrConnectionDetails('fake.server', 'username', 'password',
'tmp', 'output.csv')
GetEmrData.get_emr_data(temp_folder, props)
with open(temp_folder + 'raw.xml') as f:
result = f.read()
expected = '''<?xml version="1.0" encoding="utf8"?>
<study>
<subject>
<NAME>RNA</NAME>
<COMPONENT_ID>1905</COMPONENT_ID>
<RESULT><5</RESULT>
<REFERENCE_UNIT>IU/mL</REFERENCE_UNIT>
<DATE_TIME_STAMP>1907-05-21 05:50:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>EGFR</NAME>
<COMPONENT_ID>1740200</COMPONENT_ID>
<RESULT>eGFR result is => 60 ml/min/1.73M2</RESULT>
<REFERENCE_UNIT>ml/min/1.73M2</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>HEMATOCRIT</NAME>
<COMPONENT_ID>1534436</COMPONENT_ID>
<RESULT>>27&<30</RESULT>
<REFERENCE_UNIT>%</REFERENCE_UNIT>
<DATE_TIME_STAMP></DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
</study>
'''
self.assertEqual(result, expected)
shutil.rmtree(temp_folder)
def test_get_emr_data(self):
"""
This test verifies only that the csv file on the sftp server
can be transformed to an xml file.
Note: This test is not concerned with testing the sftp communication"""
temp_folder = tempfile.mkdtemp('/')
temp_txt_file = os.path.join(temp_folder, "raw.txt")
temp_xml_file = os.path.join(temp_folder, "raw.xml")
input_string = '''"NAME","COMPONENT_ID","RESULT","REFERENCE_UNIT","DATE_TIME_STAMP","STUDY_ID"
"RNA","1905","<5","IU/mL","1907-05-21 05:50:00","999-0059"
"EGFR","1740200","eGFR result is => 60 ml/min/1.73M2","ml/min/1.73M2","1903-11-27 15:13:00","999-0059"
"HEMATOCRIT","1534436",">27&<30","%","","999-0059"'''
with open(temp_txt_file, 'w+') as f:
f.write(input_string)
props = EmrFileAccessDetails(
emr_download_file='raw.csv',
emr_host='localhost',
emr_username='******',
emr_password='******',
emr_port='7788',
emr_private_key=None,
emr_private_key_pass=None,
)
GetEmrData.get_emr_data(temp_folder, props)
with open(temp_xml_file) as f:
result = f.read()
expected = '''<?xml version="1.0" encoding="utf8"?>
<study>
<subject>
<NAME>RNA</NAME>
<COMPONENT_ID>1905</COMPONENT_ID>
<RESULT><5</RESULT>
<REFERENCE_UNIT>IU/mL</REFERENCE_UNIT>
<DATE_TIME_STAMP>1907-05-21 05:50:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>EGFR</NAME>
<COMPONENT_ID>1740200</COMPONENT_ID>
<RESULT>eGFR result is => 60 ml/min/1.73M2</RESULT>
<REFERENCE_UNIT>ml/min/1.73M2</REFERENCE_UNIT>
<DATE_TIME_STAMP>1903-11-27 15:13:00</DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
<subject>
<NAME>HEMATOCRIT</NAME>
<COMPONENT_ID>1534436</COMPONENT_ID>
<RESULT>>27&<30</RESULT>
<REFERENCE_UNIT>%</REFERENCE_UNIT>
<DATE_TIME_STAMP></DATE_TIME_STAMP>
<STUDY_ID>999-0059</STUDY_ID>
</subject>
</study>
'''
self.assertEqual(result, expected)
shutil.rmtree(temp_folder)