def test_for_FTDPABVF_blank(self):
record = make_filled_form()
record['ftdpabvf'] = '9'
record['ftdbvft'] = ''
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'FTDPABVF' is '9' with length '1', but should be blank:"
" 'Blank if Question 22 FTDBVFT = blank'."
]
self.assertEqual(warnings, expected)
def test_for_filled_when_ruled_blank(self):
# Have it look for the langa4 error to see that general blanking rules
# are working (langa4 also comes before the variable (a4sub)
# it's dependent on)
record = make_filled_form()
record['a4sub'] = '0'
record['langa4'] = '1'
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'LANGA4' is '1' with length '1', but should be blank:"
" 'Blank if Question 4b A4SUB = 0 (No)'."
]
self.assertEqual(warnings, expected)
def test_for_special_case_FTDCPC2F(self):
'''
One packet of questions should be left blank if FTDCPC2F has a value
(anything between 95-98)
'''
record = make_filled_form()
record['ftdcpc2f'] = '95'
record['ftdhaird'] = '1'
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'FTDhAIRD' is '1' with length '1', but should be blank:"
" 'Blank if Question 0 FTDCPC2F = 95'."
]
self.assertEqual(warnings, expected)
def test_for_FTDPABVF_0(self):
'''
Have it make sure _blanking_rule_for_others_left_blank is working by
checking both 0 and False instances (it will skip if either of these
is the case for two questions)
'''
record = make_filled_form()
record['ftdpabvf'] = '9'
record['ftdcppa'] = '0'
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'FTDPABVF' is '9' with length '1', but should be blank:"
" 'Blank if Question 12 FTDCPPA = 0 (No) '."
]
self.assertEqual(warnings, expected)
def test_for_single_blanking_rule_returned(self):
'''
Have it make sure that only one error is returned from a list of
rules when not working with special cases (special cases need a
fix in a later feature branch)
'''
record = make_filled_form()
record['ftdcppas'] = '******'
record['ftdcppa'] = ''
record['ftdpabvf'] = ''
record['ftdppasl'] = '0'
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'FTDCPPAS' is '2' with length '1', but should be blank:"
" 'Blank if Question 1 FTDPPASL = 0 (No)'."
]
self.assertEqual(warnings, expected)
def test_for_special_case_or2(self):
'''
Have it make sure _blanking_rule_ftld_or2 works properly (and by
extension or3, or4, and or5) - This blanking rule depends on either
of two possible answers to questions, along with regular
blanking rules
'''
record = make_filled_form()
record['ftdmrirf'] = '0'
record['ftdmrifa'] = '9'
record['ftdmriob'] = ''
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
expected = [
"'FTDMRIRF' is '0' with length '1', but should be blank: "
"'Blank if Question 2a, FTDMRIFA, = 0 (No) or 9"
" (Unknown)'."
]
self.assertEqual(warnings, expected)
def test_for_special_case_FTDMRIOS(self):
'''
Have it make sure _blanking_rule_ftld_or2a works properly -
This blanking rule has an extra condition added to the or2 rules
(packet['FTDMRIOB'] != 1)
'''
record = make_filled_form()
record['ftdmrios'] = '1'
record['ftdmriob'] = '0'
ipacket = build_uds3_ftld_ivp_form(record)
warnings = []
warnings = redcap2nacc.check_blanks(ipacket, self.options)
# FTDMRIOS is a Char field with a length of 60 characters
expected = [
"'FTDMRIOS' is"
" '1 "
" ' with length '60', but should be blank:"
" 'Blank if Question 2a11 FTDMRIOB ne 1 (Yes)'."
]
self.assertEqual(warnings, expected)
def convert(fp, options, out=sys.stdout, err=sys.stderr):
"""Converts data in REDCap's CSV format to NACC's fixed-width format."""
reader = csv.DictReader(fp)
for record in reader:
# Right now the csf form is a single non-longitudinal form in a
# separate REDCap project with no redcap_event_name.
if not options.csf:
event_match = check_redcap_event(options, record)
if not event_match:
continue
print("[START] ptid : " + str(record['ptid']), file=err)
try:
if options.lbd and options.ivp:
packet = lbd_ivp_builder.build_uds3_lbd_ivp_form(record)
elif options.lbd and options.fvp:
packet = lbd_fvp_builder.build_uds3_lbd_fvp_form(record)
elif options.ftld and options.ivp:
packet = ftld_ivp_builder.build_uds3_ftld_ivp_form(record)
elif options.ftld and options.fvp:
packet = ftld_fvp_builder.build_uds3_ftld_fvp_form(record)
elif options.csf:
packet = csf_builder.build_uds3_csf_form(record)
elif options.ivp:
packet = ivp_builder.build_uds3_ivp_form(record)
elif options.np:
packet = np_builder.build_uds3_np_form(record)
elif options.fvp:
packet = fvp_builder.build_uds3_fvp_form(record)
elif options.tfp:
packet = tfp_builder.build_uds3_tfp_form(record)
elif options.m:
packet = m_builder.build_uds3_m_form(record)
except Exception:
if 'ptid' in record:
print("[SKIP] Error for ptid : " + str(record['ptid']),
file=err)
traceback.print_exc()
continue
if not options.np and not options.m and not options.tfp and not \
options.lbd and not options.ftld and not options.csf:
set_blanks_to_zero(packet)
if options.m:
blanks_uds3.set_zeros_to_blanks(packet)
warnings = []
try:
warnings += check_blanks(packet, options)
except KeyError:
print("[SKIP] Error for ptid : " + str(record['ptid']), file=err)
traceback.print_exc()
continue
try:
warnings += check_characters(packet)
if warnings:
print("[SKIP] Error for ptid : " + str(record['ptid']),
file=err)
warn = "\n".join(map(str, warnings))
warn = warn.replace("\\", "")
print(warn, file=err)
continue
except KeyError:
print("[SKIP] Error for ptid : " + str(record['ptid']), file=err)
traceback.print_exc()
continue
if not options.np and not options.m and not options.lbd and not \
options.ftld and not options.csf:
warnings += check_single_select(packet)
for form in packet:
try:
print(form, file=out)
except AssertionError:
print("[SKIP] Error for ptid : " + str(record['ptid']),
file=err)
traceback.print_exc()
continue
