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@s-emerson
s-emerson committed Nov 4, 2021
2 parents 5806b77 + 507df67 commit e720ccd
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11 changes: 11 additions & 0 deletions CHANGELOG
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@@ -1,5 +1,16 @@
Changelog
=========
## [1.8.1] - 2021-11-04
### Summary
This release provides one major bug fix in the FTLD follow-up packet, updated
installation instructions, and a few minor fixes for bugs in error logging
etc.

### Updated
* Fix cappy install instructions in README
* Update FTLD FVP Z1X with fixed column spacing


## [1.8.0] - 2021-09-13
### Summary

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -21,7 +21,7 @@ HOW TO Convert from REDCap to NACC

To install NACCulator, run:

$ python3 -m pip install git+https://github.com/ctsit/[email protected]#egg=cappy-2.0.0
$ python3 -m pip install git+https://github.com/ctsit/[email protected]
$ pip3 install git+https://github.com/ctsit/nacculator.git

Once the project data is exported from REDCap to the CSV file `data.csv`, run:
Expand Down Expand Up @@ -59,7 +59,7 @@ the `-file` flag._
[-lbd | -ftld] [-file FILE] [-meta FILTER_META] [-ptid PTID]
[-vnum VNUM] [-vtype VTYPE]

Process redcap form output to nacculator.
Process redcap export data through nacculator.

optional arguments:
-h, --help show this help message and exit
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8 changes: 4 additions & 4 deletions nacc/ftld/fvp/builder.py
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Expand Up @@ -124,12 +124,12 @@ def add_z1x(record, packet):
Z1X.B6LNOT = record['fu_b6lnot']
except KeyError:
try:
if record['fu_lbudspch'] is not None:
Z1X.B2LSUB = '1'
Z1X.B2LNOT = ''
if record['fu_lbspcgim'] is not None:
if record['fu_lbudspch'] in ['0', '1']:
Z1X.B2LSUB = '1'
Z1X.B2LNOT = ''
if record['fu_lbspcgim'] in ['0', '1']:
Z1X.B6LSUB = '1'
Z1X.B6LNOT = ''
# And leave the LBD fields blank if the project does not contain the
# LBD module
except KeyError:
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32 changes: 16 additions & 16 deletions nacc/ftld/fvp/forms.py
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Expand Up @@ -46,21 +46,22 @@ def __init__(self):
self.fields['LANGA4'] = nacc.uds3.Field(name='LANGA4', typename='Num', position=(61, 61), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 4b A4SUB = 0 (No)'])
self.fields['A4SUB'] = nacc.uds3.Field(name='A4SUB', typename='Num', position=(63, 63), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['A4NOT'] = nacc.uds3.Field(name='A4NOT', typename='Num', position=(65, 66), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 4b A4SUB = 1 (Yes)'])
self.fields['LANGB1'] = nacc.uds3.Field(name='LANGB1', typename='Num', position=(70, 70), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 6b B1SUB = 0 (No)'])
self.fields['B1SUB'] = nacc.uds3.Field(name='B1SUB', typename='Num', position=(72, 72), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B1NOT'] = nacc.uds3.Field(name='B1NOT', typename='Num', position=(74, 75), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 6b B1SUB = 1 (Yes)'])
self.fields['LANGB4'] = nacc.uds3.Field(name='LANGB4', typename='Num', position=(77, 77), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGB5'] = nacc.uds3.Field(name='LANGB5', typename='Num', position=(79, 79), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 8b B5SUB = 0 (No)'])
self.fields['B5SUB'] = nacc.uds3.Field(name='B5SUB', typename='Num', position=(81, 81), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B5NOT'] = nacc.uds3.Field(name='B5NOT', typename='Num', position=(83, 84), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 8b B5SUB = 1 (Yes)'])
self.fields['LANGB6'] = nacc.uds3.Field(name='LANGB6', typename='Num', position=(86, 86), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 9b B6SUB = 0 (No)'])
self.fields['B6SUB'] = nacc.uds3.Field(name='B6SUB', typename='Num', position=(88, 88), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B6NOT'] = nacc.uds3.Field(name='B6NOT', typename='Num', position=(90, 91), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 9b B6SUB = 1 (Yes)'])
self.fields['LANGB7'] = nacc.uds3.Field(name='LANGB7', typename='Num', position=(93, 93), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 10b B7SUB = 0 (No)'])
self.fields['B7SUB'] = nacc.uds3.Field(name='B7SUB', typename='Num', position=(95, 95), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B7NOT'] = nacc.uds3.Field(name='B7NOT', typename='Num', position=(97, 98), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 10b B7SUB = 1 (Yes)'])
self.fields['LANGB8'] = nacc.uds3.Field(name='LANGB8', typename='Num', position=(100, 100), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGB9'] = nacc.uds3.Field(name='LANGB9', typename='Num', position=(102, 102), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGB1'] = nacc.uds3.Field(name='LANGB1', typename='Num', position=(68, 68), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 6b B1SUB = 0 (No)'])
self.fields['B1SUB'] = nacc.uds3.Field(name='B1SUB', typename='Num', position=(70, 70), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B1NOT'] = nacc.uds3.Field(name='B1NOT', typename='Num', position=(72, 73), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 6b B1SUB = 1 (Yes)'])
self.fields['LANGB4'] = nacc.uds3.Field(name='LANGB4', typename='Num', position=(75, 75), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGB5'] = nacc.uds3.Field(name='LANGB5', typename='Num', position=(77, 77), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 8b B5SUB = 0 (No)'])
self.fields['B5SUB'] = nacc.uds3.Field(name='B5SUB', typename='Num', position=(79, 79), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B5NOT'] = nacc.uds3.Field(name='B5NOT', typename='Num', position=(81, 82), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 8b B5SUB = 1 (Yes)'])
self.fields['LANGB6'] = nacc.uds3.Field(name='LANGB6', typename='Num', position=(84, 84), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 9b B6SUB = 0 (No)'])
self.fields['B6SUB'] = nacc.uds3.Field(name='B6SUB', typename='Num', position=(86, 86), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B6NOT'] = nacc.uds3.Field(name='B6NOT', typename='Num', position=(88, 89), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 9b B6SUB = 1 (Yes)'])
self.fields['LANGB7'] = nacc.uds3.Field(name='LANGB7', typename='Num', position=(91, 91), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 10b B7SUB = 0 (No)'])
self.fields['B7SUB'] = nacc.uds3.Field(name='B7SUB', typename='Num', position=(93, 93), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B7NOT'] = nacc.uds3.Field(name='B7NOT', typename='Num', position=(95, 96), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98'], blanks=['Blank if Question 10b B7SUB = 1 (Yes)'])
self.fields['LANGB8'] = nacc.uds3.Field(name='LANGB8', typename='Num', position=(98, 98), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGB9'] = nacc.uds3.Field(name='LANGB9', typename='Num', position=(100, 100), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGC1'] = nacc.uds3.Field(name='LANGC1', typename='Num', position=(102, 102), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['LANGC2'] = nacc.uds3.Field(name='LANGC2', typename='Num', position=(104, 104), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGD1'] = nacc.uds3.Field(name='LANGD1', typename='Num', position=(106, 106), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGD2'] = nacc.uds3.Field(name='LANGD2', typename='Num', position=(108, 108), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
Expand All @@ -85,7 +86,6 @@ def __init__(self):
self.fields['LANGE3F'] = nacc.uds3.Field(name='LANGE3F', typename='Num', position=(150, 150), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=[])
self.fields['LANGCLS'] = nacc.uds3.Field(name='LANGCLS', typename='Num', position=(152, 152), length=1, inclusive_range=(1, 2), allowable_values=['1', '2'], blanks=['Blank if Question 27b CLSSUB = 0 (No)'])
self.fields['CLSSUB'] = nacc.uds3.Field(name='CLSSUB', typename='Num', position=(154, 154), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['CLSSUB'] = nacc.uds3.Field(name='CLSSUB', typename='Num', position=(154, 154), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B2LSUB'] = nacc.uds3.Field(name='B2LSUB', typename='Num', position=(156, 156), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
self.fields['B2LNOT'] = nacc.uds3.Field(name='B2LNOT', typename='Num', position=(158, 159), length=2, inclusive_range=None, allowable_values=['95', '96', '97', '98', '99'], blanks=['Blank if Question 28b B2LSUB = 1 (Yes)'])
self.fields['B6LSUB'] = nacc.uds3.Field(name='B6LSUB', typename='Num', position=(161, 161), length=1, inclusive_range=(0, 1), allowable_values=['0', '1'], blanks=[])
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8 changes: 4 additions & 4 deletions nacc/ftld/ivp/builder.py
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Expand Up @@ -125,12 +125,12 @@ def add_z1x(record, packet):
Z1X.B6LNOT = record['b6lnot']
except KeyError:
try:
if record['lbudspch'] is not None:
Z1X.B2LSUB = '1'
Z1X.B2LNOT = ''
if record['lbspcgim'] is not None:
if record['lbudspch'] in ['0', '1']:
Z1X.B2LSUB = '1'
Z1X.B2LNOT = ''
if record['lbspcgim'] in ['0', '1']:
Z1X.B6LSUB = '1'
Z1X.B6LNOT = ''
# And leave the LBD fields blank if the project does not contain the
# LBD module
except KeyError:
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6 changes: 3 additions & 3 deletions nacc/redcap2nacc.py
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Expand Up @@ -167,7 +167,7 @@ def check_for_bad_characters(field: Field) -> typing.List:
return incompatible


def check_redcap_event(options, record) -> bool:
def check_redcap_event(options, record, out=sys.stdout, err=sys.stderr) -> bool:
"""
Determines if the record's redcap_event_name and filled forms match the
options flag
Expand Down Expand Up @@ -230,7 +230,7 @@ def check_redcap_event(options, record) -> bool:
form_match_z1 = record['fvp_z1_complete']
except KeyError:
form_match_z1 = ''
record['ivp_z1_complete'] = ''
record['fvp_z1_complete'] = ''
form_match_z1x = record['fvp_z1x_complete']
if form_match_z1 in ['0', ''] and form_match_z1x in ['0', '']:
return False
Expand All @@ -256,7 +256,7 @@ def check_redcap_event(options, record) -> bool:
if followup_match in ['', '0']:
return False
except KeyError:
print("Could not find a REDCap field for TFP Z1X form.")
print("Could not find a REDCap field for TFP Z1X form.", file=err)
return False
elif options.tfp3:
event_name = 'tele'
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -6,7 +6,7 @@

from setuptools import setup, find_packages

VERSION = "1.8.0"
VERSION = "1.8.1"

setup(
name="nacculator",
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4 changes: 2 additions & 2 deletions tests/test_skip_optional_forms_ftld.py
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Expand Up @@ -14,7 +14,7 @@ def test_a3a_ivp_skip(self):

expected = record['ftdothis']
result = ivp_builder.build_ftld_ivp_form(record)
self.assertEqual(expected, result['FTDOThIS'])
self.assertEqual(expected, result['FTDOTHIS'])

def test_a3a_fvp_skip(self):
""" If the FVP A3a is not present in the csv, it should be skipped
Expand All @@ -24,7 +24,7 @@ def test_a3a_fvp_skip(self):

expected = record['fu_ftdothis']
result = fvp_builder.build_ftld_fvp_form(record)
self.assertEqual(expected, result['FTDOThIS'])
self.assertEqual(expected, result['FTDOTHIS'])

def test_ivp_b3f_not_skipped(self):
""" Form B3F is required and should never be skipped. """
Expand Down

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