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Upload summwrap.py

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  1. summwrap.py +182 -0
summwrap.py ADDED
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+ from utils.summarize_utils.summ_utils import *
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+ from utils.summarize_utils.ctwrap import ClinicalTrials
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+ import pandas as pd
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+
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+ # get data
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+ def get_data(study_id_list):
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+ # print(study_id_list)
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+ ct = ClinicalTrials()
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+
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+ fields=['NCTId','OfficialTitle','BriefSummary','DetailedDescription','LocationCountry',
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+ 'OrgStudyId','SecondaryId','Condition','InterventionName',
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+ 'DesignInterventionModel','BriefTitle','Phase', 'DesignAllocation',
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+ 'DesignMasking','OverallStatus', 'WhyStopped','EnrollmentCount', 'LastUpdatePostDate',
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+ 'InterventionDescription']
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+
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+
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+ column_names = ['Rank','NCTId','OfficialTitle','BriefSummary','DetailedDescription',
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+ 'LocationCountry' ,'OrgStudyId','SecondaryId','Condition','InterventionName',
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+ 'DesignInterventionModel', 'BriefTitle','Phase','DesignAllocation',
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+ 'DesignMasking', 'OverallStatus', 'WhyStopped','EnrollmentCount',
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+ 'LastUpdatePostDate','InterventionDescription']
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+ my_list =[]
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+ for ncid in study_id_list:
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+ nct_fields = ct.get_study_fields(
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+ search_expr= ncid,
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+ fields=fields,
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+ fmt="csv",
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+ )
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+ my_list.append(nct_fields[1:])
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+ flat_list = [item for sublist in my_list for item in sublist]
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+ d= [dict(zip(column_names, l)) for l in flat_list ]
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+ data = pd.DataFrame(d).fillna('')
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+ print('Data reading complete..')
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+ return data
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+
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+
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+ def get_summ(status, alloc, masking, phase, imodel, osid, sid, locations,pcount,otitle, bsumm,ddesc,ystop,nctid,lupd):
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+ locs = get_locs(locations)
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+ print(status)
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+
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+ if alloc.lower()!='n/a'and ystop =='' and pcount !='0' and status =='':
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+ print('first if - im inside alloc is not na & ystop is none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ alloc.lower() + ', ' + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ return ostmt
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+
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+ if alloc.lower()!='n/a'and ystop =='' and pcount !='0' and status =='Active, not recruiting' :
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+ print('second if - im inside alloc is not na & ystop is none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ alloc.lower() + ', ' + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ get_status(status) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+ if alloc.lower()!='n/a'and ystop =='' and pcount !='0' and status !='':
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+ print('third if - im inside alloc is not na & ystop is none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ alloc.lower() + ', ' + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))) )
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+ if alloc.lower()=='n/a' and ystop =='' and pcount !='0':
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+ print('fourth if - im alloc is na and ystop is none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_url(nctid,lupd)
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+ print(ostmt)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+
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+ if alloc.lower()=='n/a' and ystop !='' and pcount !='0':
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+ print('fifth if - im in alloc na; ystop not none; pcount not 0')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_ystop(ystop) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+
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+ if alloc.lower()!='n/a' and ystop !='' and pcount !='0':
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+ print('sixth if - im alloc not na and ystop is not none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ alloc.lower() + ', ' + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ ' in ' + pcount + ' subjects '+ \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_ystop(ystop) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+
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+ if alloc.lower()!='n/a' and ystop !='' and pcount =='0':
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+ print('seventh if - im alloc not na and ystop is not none')
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+ print(ystop)
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ alloc.lower() + ', ' + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_ystop(ystop) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+
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+ if alloc.lower()=='n/a' and ystop !='' and pcount =='0':
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+ print('eigth if - im alloc not na and ystop is not none')
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+ ostmt = get_first_word(alloc,masking,status) + \
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+ get_mask(masking) + \
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+ get_imodel(imodel) + \
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+ '/'.join(phase.lower().split('|')) + ' '+ \
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+ get_osid(osid,sid)+ \
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+ 'study ' + \
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+ get_locs(locations) + \
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+ get_obj(otitle,bsumm,ddesc) + \
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+ get_status(status) + \
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+ get_ystop(ystop) + \
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+ get_url(nctid,lupd)
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+ ostmt = repos_study_design(remove_period_spaces(map_terms(map_week_num(ostmt))))
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+ # ostmt = unique_list(ostmt)
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+ return ostmt
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+