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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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def get_data(study_id_list): |
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ct = ClinicalTrials() |
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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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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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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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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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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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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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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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return ostmt |
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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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return ostmt |
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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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return ostmt |
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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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return ostmt |
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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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return ostmt |
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