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UPENN datatype to pull information from two redcap projects #147

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UPENN datatype to pull information from two redcap projects #147

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24 changes: 17 additions & 7 deletions lochness/redcap/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,8 @@ def initialize_metadata(Lochness: 'Lochness object',
f'redcap.{project_name}:{subject_id}'
subject_dict['REDCap'] += \
f';redcap.UPENN:{row[redcap_id_colname]}' # UPENN REDCAP
subject_dict['REDCap'] += \
f';redcap.UPENN_new:{row[redcap_id_colname]}' # UPENN REDCAP
subject_dict['Box'] = f'box.{study_name}:{subject_id}'
subject_dict['XNAT'] = f'xnat.{study_name}:*:{subject_id}'

Expand Down Expand Up @@ -679,6 +681,13 @@ def sync(Lochness, subject, dry=False):
_debug_tup = (redcap_instance, redcap_project, redcap_subject)

if 'UPENN' in redcap_instance:
print(redcap_instance)
if redcap_instance == 'redcap.UPENN':
upenn_id_colname = 'session_subid'
elif redcap_instance == 'redcap.UPENN_new':
upenn_id_colname = 'src_subject_id'
else:
logger.warning('Wrong upenn_id_colname. Check REDCap code')
# UPENN REDCap is set up with its own record_id, but have added
# "session_subid" field to note AMP-SCZ ID
redcap_subject_sl = redcap_subject.lower()
Expand All @@ -687,20 +696,21 @@ def sync(Lochness, subject, dry=False):
contains_logic = []
for subject_id in [redcap_subject, redcap_subject_sl]:
contains_logic += [
f"contains([session_subid], '{subject_id}_{x}')"
for x in digits_str]
f"contains([{upenn_id_colname}], '{subject_id}_{x}')"
for x in digits_str]
contains_logic += [
f"contains([session_subid], '{subject_id}={x}')"
for x in digits_str]
f"contains([{upenn_id_colname}], '{subject_id}={x}')"
for x in digits_str]


record_query = {
'token': api_key,
'content': 'record',
'format': 'json',
'filterLogic': f"[session_subid] = '{redcap_subject}' or "
f"[session_subid] = '{redcap_subject_sl}' or "
f"{' or '.join(contains_logic)}"
'filterLogic':
f"[{upenn_id_colname}] = '{redcap_subject}' or "
f"[{upenn_id_colname}] = '{redcap_subject_sl}' or "
f"{' or '.join(contains_logic)}"
}
# f"[session_subid] = '{redcap_subject_sl}' or "
# f"{' or '.join(contains_logic)}"
Expand Down
2 changes: 2 additions & 0 deletions lochness/rpms/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -322,6 +322,8 @@ def initialize_metadata(Lochness: 'Lochness object',
if upenn:
subject_dict['REDCap'] = \
'redcap.UPENN:' + df_measure[rpms_id_colname]
subject_dict['REDCap'] += \
';redcap.UPENN_new:' + df_measure[rpms_id_colname]

df_tmp = pd.DataFrame.from_dict(subject_dict, orient='index')
df = pd.concat([df, df_tmp.T])
Expand Down