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+#date sorts studies from orthanc dataset into target study dataset
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+
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+#takes transferQuery as the list of images that should be available on orthanc
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+
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+
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+import os
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+import json
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+import re
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+import sys
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+import datetime
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+import re
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+
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+def main(parameterFile):
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+ fhome=os.path.expanduser('~')
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+ fsetup=os.path.join(fhome,'.labkey','setup.json')
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+ with open(fsetup,'r') as f:
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+ setup=json.load(f)
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+
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+ sys.path.insert(0,setup['paths']['nixWrapper'])
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+
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+ import nixWrapper
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+
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+ nixWrapper.loadLibrary("labkeyInterface")
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+
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+ import labkeyInterface
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+ import labkeyDatabaseBrowser
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+ import labkeyFileBrowser
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+
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+ fconfig=os.path.join(fhome,'.labkey','network.json')
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+
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+ net=labkeyInterface.labkeyInterface()
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+ net.init(fconfig)
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+ db=labkeyDatabaseBrowser.labkeyDB(net)
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+ fb=labkeyFileBrowser.labkeyFileBrowser(net)
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+
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+ with open(parameterFile,'r') as f:
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+ pars=json.load(f)
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+
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+
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+
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+ i=0
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+ #from orthancDatabase/Imaging dataset
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+ projectOrthanc=pars['Orthanc']['project']
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+ inputQuery=pars['Orthanc']['queryName']
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+ inputSchema=pars['Orthanc']['schemaName']
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+ inputParticipantField=pars['Orthanc']['participantField']
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+
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+ #to target project dataset
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+ projectStudy=pars['Database']['project']
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+ #'iPNUMMretro/Study'
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+ #for prospective, set
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+ #projectStudy='IPNUMMprospektiva/Study'
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+ outputQuery=pars['Database']['queryName']
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+ outputSchema=pars['Database']['schemaName']
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+ #test for schedule entries which are scheduled
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+ scheduleCutOffDate=pars['Database']['scheduleCutOffDate']#format YYYY-MM-DD
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+ scheduleQuery=pars['Database']['scheduleQuery']
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+ scheduleToleranceDays=int(pars['Database']['scheduleToleranceDays'])
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+ dbParticipantField=pars['Database']['participantField']
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+
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+ missingSchema=pars['Database']['missingImagesSchema']
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+ missingQuery=pars['Database']['missingImagesQuery']
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+
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+ #make a list of images from transferQuery
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+ cutOffFilter={'variable':'actionDate','value':scheduleCutOffDate,'oper':'datelt'}
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+ #status of 1 is scheduled
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+ statusFilter={'variable':'actionStatus','value':'1','oper':'eq'}
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+ dsImage=db.selectRows(projectStudy,outputSchema,scheduleQuery,[cutOffFilter,statusFilter])
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+
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+ #clear entries from missing list
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+ failureFilter={'variable':'failureDescription','value':'MISSING FORM','oper':'eq'}
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+ dsDelete=db.selectRows(projectStudy,missingSchema,missingQuery,[failureFilter])
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+ db.modifyRows('delete',projectStudy,missingSchema,missingQuery,dsDelete['rows'])
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+
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+
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+ for im in dsImage['rows']:
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+
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+ print('{}: {} {}'.format(im[dbParticipantField],im['actionDate'],im['actionStatus']))
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+ im['imagingVisitId']=im['visitId']
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+ actionDate=datetime.datetime.strptime(im['actionDate'],'%Y/%m/%d %H:%M:%S')
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+ actionDateYMD=actionDate.strftime('%Y%m%d')
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+ im['imageDate']=actionDateYMD
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+ #this is still to be configured
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+ inputIdFilter={'variable':inputParticipantField,\
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+ 'value':im[dbParticipantField],\
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+ 'oper':'eq'}
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+
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+ idFilter={'variable':dbParticipantField,\
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+ 'value':im[dbParticipantField],\
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+ 'oper':'eq'}
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+ #filter on series descripton - for PET, we should have 'PET WB'
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+ sdFilter={'variable':'seriesDescription','value':'PET WB','oper':'eq'}
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+
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+
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+ #have to convert from datetime to %Y%m%d format
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+ #dateFilter={'variable':'imageDate','value':im['imageDate'],'oper':'eq'}
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+
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+ dsOrthanc=db.selectRows(projectOrthanc,inputSchema,inputQuery,[inputIdFilter,sdFilter])
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+ #what if dsOrthanc['rows'] is empty?
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+ #this is part of QA and is reported in missingImages Schema/Query
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+
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+ uploadStatus="FAILED"
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+ imageDateMismatch=[]
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+ for im1 in dsOrthanc['rows']:
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+
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+ date=datetime.datetime.strptime(im1['studyDate'],'%Y/%m/%d %H:%M:%S')
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+ dt=date-actionDate
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+ if (abs(dt.days)>scheduleToleranceDays):
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+ continue
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+
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+ #convert date to %Y%m%d notation
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+ dateYMD=date.strftime('%Y%m%d')
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+
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+ #enter this time difference to a list
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+ imFilter={'variable':'imagingVisitId',
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+ 'value':'{}'.format(im['imagingVisitId']),
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+ 'oper':'eq'}
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+ dsMissing=db.selectRows(projectStudy,missingSchema,\
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+ missingQuery,[idFilter,imFilter])
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+
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+ #already recorded
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+ vals=[dbParticipantField,'imagingVisitId','imageDate']
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+ mode='insert'
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+ if len(dsMissing['rows'])>0:
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+ mode='update'
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+ orow=dsMissing['rows'][0]
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+ else:
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+ orow={v:im[v] for v in vals}
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+ orow['imageDateMismatch']=dateYMD
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+ orow['failureDescription']='MISSING FORM'
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+ db.modifyRows(mode,projectStudy,missingSchema,\
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+ missingQuery,[orow])
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+
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+ print("Done: {}".format(len(dsImage['rows'])))
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+
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+if __name__=='__main__':
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+ main(sys.argv[1])
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Andrej Studen