def data_pipeline():
reqdat = dict(request.form)
print(reqdat)
print(reqdat['record'])
# Check the format returned sent by the REDCap server to determine if the values in the dict are lists or strings
if type(reqdat['record']) is str:
recordid = reqdat['record']
instr = reqdat['instrument']
elif type(reqdat['record']) is list:
recordid = reqdat['record'][0]
instr = reqdat['instrument'][0]
if instr == 'demographics' or instr == 'enrollment':
# Check to see if a new family member has been added by pulling the Enrollment table from the Data Collection project
rep = reqdat['redcap_repeat_instance'][0]
enroll = NDDdb.pullRCRecords(rc_api_url, rc_data_apikey, 'enrollment', recordid, 'redcap_id,demo_dateadded,demo_relation')
enroll.set_index(keys='redcap_repeat_instance', drop = False, inplace = True, verify_integrity = True)
lkid = enroll.loc[rep,'labkey_subjid']
reln = enroll.loc[rep,'demo_relation']
if reln!='':
if lkid=='': # Assign LabKey ID by querying LabKey for next available integer
lkid = str(NDDdb.getNextLabKeyID(server_context))
NDDdb.assignLabKeyID(rc_api_url, rc_data_apikey, server_context, recordid, rep, lkid, reln_map[reln], enroll.loc[rep,'demo_dateadded'])
idnum = enroll.loc[rep,'idnum']
if idnum=='': # Assign individual number by pulling family record and checking for next available value--or, if relation is one of {Proband, Mother, Father}, assign designated numbers
famdat = NDDdb.pullRCRecords(rc_api_url, rc_data_apikey, 'family_enrollment', recordid, '')
fnrow = famdat.loc[famdat['redcap_event_name']=='family_data_arm_1',].index
fnum = famdat.loc[fnrow,'fnum'].values[0]
if fnum != '':
print('Checking for next Ind num')
idnum = NDDdb.getNextIndNum(reln,enroll['idnum'])
print('Assigninf F-idnum')
NDDdb.assignFindivID(rc_api_url, rc_refer_apikey, rc_data_apikey, server_context, None, recordid, rep, lkid, fnum, idnum)
# Check to see if 'copy contact from' field has been set
if instr == 'demographics':
demo = NDDdb.pullRCRecords(rc_api_url, rc_data_apikey, 'demographics', recordid,'redcap_id')
reptocopy = demo.loc[demo['redcap_repeat_instance']==rep]['demo_copycontactfrom'].values[0]
if reptocopy != '':
copyfrom = demo.loc[demo['redcap_repeat_instance']==reptocopy]
pasteto = copyfrom[['redcap_id','demo_address1','demo_address2','demo_apt','demo_city','demo_state','demo_zip','demo_email','demo_email2','demo_phone','demo_phone2']]
pasteto['demo_copycontactfrom'] = ''
pasteto['redcap_event_name'] = 'family_member_arm_1'
pasteto['redcap_repeat_instance'] = rep
updateres = NDDdb.pushRCRecord(rc_api_url, rc_data_apikey, '', pasteto)
# If the saved record is the proband's, copy his/her email to the family contact email
if rep == '1':
NDDdb.setFamEmail(rc_api_url, rc_data_apikey, demo.loc[demo['redcap_repeat_instance']=='1','demo_email'].values[0], recordid)
sys.stdout.flush()
return
def referral_pipeline():
reqdat = dict(request.form)
# Check the format returned sent by the REDCap server to determine if the values in the dict are lists or strings
if type(reqdat['record']) is str:
recordid = reqdat['record']
instr = reqdat['instrument']
elif type(reqdat['record']) is list:
recordid = reqdat['record'][0]
instr = reqdat['instrument'][0]
# Pull record
referral = NDDdb.pullRCRecords(rc_api_url, rc_refer_apikey, instr, recordid,'pintoreferral_stat,apptdate,idnum,f_idnum,dataproj_id,physician_referral_form_complete')
referral = referral.loc[referral['redcap_repeat_instrument']==''] # TODO deprecate this temporary code
referral.set_index(keys='redcap_id', drop = False, inplace = True, verify_integrity = True)
# Fill in provider email if it hasn't been set already
if instr == 'physician_referral_form':
if referral.loc[recordid,'provider_email']=='':
if referral.loc[recordid,'sinaistatus']!='':
if referral.loc[recordid,'sinaistatus']=='1':
provider_email = NDDdict.mshprovider2email[referral.loc[recordid,'sinaiprovider']]
elif referral.loc[recordid,'sinaistatus']=='2':
provider_email = NDDdict.nyuprovider2email[referral.loc[recordid,'nyuprovider']]
else:
provider_email = ''
update = pd.DataFrame(data={'redcap_id':[recordid], 'provider_email':[provider_email]})
updatereferreq = NDDdb.pushRCRecord(rc_api_url, rc_refer_apikey, '', update)
# Get data collection id
dcid = referral.loc[recordid,'dataproj_id']
# If the data collection id is blank, query RedCap for the next one and set the 'I'm new here' flag
imnewhere = False
if dcid == '':
imnewhere = True
dcid = str(NDDdb.getNextDCID(rc_api_url, rc_data_apikey))
# Get individual #
idnum = referral.loc[recordid,'idnum']
# then check value of 'referral_triggerenroll' and 'referral_id'
# finally write new project id back to 'referral_id'
if referral.loc[recordid,'referral_triggerenroll'] == '1' and referral.loc[recordid,'verifiedunique']=='1':
idnum = NDDdb.pushToDC(rc_api_url, rc_refer_apikey, rc_data_apikey, referral, recordid, dcid, idnum, imnewhere)
if imnewhere:
lkupdate = pd.DataFrame(data={'id':[dcid], 'referralid':[recordid]})
NDDdb.LKinsertRow(lkupdate.iloc[0], 'Families', 'lists', server_context)
lkid = str(NDDdb.getNextLabKeyID(server_context))
NDDdb.assignLabKeyID(rc_api_url, rc_data_apikey, server_context, dcid, '1', lkid, 'Proband', dt.datetime.today().strftime('%Y-%m-%d'))
# Check if this subject was referred to Pinto study and has an appointment date
# how to check for fam's record here?
apptdate = referral.loc[recordid,'apptdate']
if referral.loc[recordid,'pintoreferral_stat']=='1' and apptdate != '' and idnum == '01':
# Assign F# if this subject does not have one already
dc = NDDdb.pullRCRecords(rc_api_url, rc_data_apikey, 'family_enrollment', '', '')
if len(dc) > 0:
dc = dc.loc[dc['redcap_event_name']=='family_data_arm_1']
dc.set_index(keys='redcap_id', drop = False, inplace = True, verify_integrity = True)
fnum = dc.loc[str(dcid),'fnum']
# Assign F# if this subject does not have one already
if fnum == '':
myfam = NDDdb.pullRCRecords(rc_api_url, rc_data_apikey, 'enrollment', dcid, '')
myfam.set_index(keys='idnum', drop = False, inplace = True, verify_integrity = False)
lkid = myfam.loc[idnum,'labkey_subjid']
fnum = NDDdb.getNextFnum(apptdate,dc)
NDDdb.assignFID(rc_api_url, rc_data_apikey, server_context, dcid, fnum)
NDDdb.assignFindivID(rc_api_url, rc_refer_apikey, rc_data_apikey, server_context, recordid, dcid, '1', lkid, fnum, idnum)
sys.stdout.flush()
return ''