irAEMM/pythonScripts/findCandidatesForSchedule.py

#date sorts studies from orthanc dataset into target study dataset

#takes transferQuery as the list of images that should be available on orthanc


import os
import json
import re
import sys
import datetime
import re

def main(parameterFile):
    fhome=os.path.expanduser('~')
    fsetup=os.path.join(fhome,'.labkey','setup.json')
    with open(fsetup,'r') as f:
        setup=json.load(f)

    sys.path.insert(0,setup['paths']['nixWrapper'])

    import nixWrapper

    nixWrapper.loadLibrary("labkeyInterface")

    import labkeyInterface
    import labkeyDatabaseBrowser
    import labkeyFileBrowser

    fconfig=os.path.join(fhome,'.labkey','network.json')

    net=labkeyInterface.labkeyInterface()
    net.init(fconfig)
    db=labkeyDatabaseBrowser.labkeyDB(net)
    fb=labkeyFileBrowser.labkeyFileBrowser(net)

    with open(parameterFile,'r') as f:
        pars=json.load(f)



    i=0
    #from orthancDatabase/Imaging dataset
    projectOrthanc=pars['Orthanc']['project']
    inputQuery=pars['Orthanc']['queryName']
    inputSchema=pars['Orthanc']['schemaName']
    inputParticipantField=pars['Orthanc']['participantField']

    #to target project dataset
    projectStudy=pars['Database']['project']
    #'iPNUMMretro/Study'
    #for prospective, set
    #projectStudy='IPNUMMprospektiva/Study'
    outputQuery=pars['Database']['queryName']
    outputSchema=pars['Database']['schemaName']
    #test for schedule entries which are scheduled
    scheduleCutOffDate=pars['Database']['scheduleCutOffDate']#format YYYY-MM-DD
    scheduleQuery=pars['Database']['scheduleQuery']
    scheduleToleranceDays=int(pars['Database']['scheduleToleranceDays'])
    dbParticipantField=pars['Database']['participantField']

    missingSchema=pars['Database']['missingImagesSchema']
    missingQuery=pars['Database']['missingImagesQuery']

    #make a list of images from transferQuery
    cutOffFilter={'variable':'actionDate','value':scheduleCutOffDate,'oper':'datelt'}
    #status of 1 is scheduled
    statusFilter={'variable':'actionStatus','value':'1','oper':'eq'}
    dsImage=db.selectRows(projectStudy,outputSchema,scheduleQuery,[cutOffFilter,statusFilter])

    #clear entries from missing list
    failureFilter={'variable':'failureDescription','value':'MISSING FORM','oper':'eq'}
    dsDelete=db.selectRows(projectStudy,missingSchema,missingQuery,[failureFilter])
    db.modifyRows('delete',projectStudy,missingSchema,missingQuery,dsDelete['rows'])


    for im in dsImage['rows']:

        print('{}: {} {}'.format(im[dbParticipantField],im['actionDate'],im['actionStatus']))       
        im['imagingVisitId']=im['visitId']
        actionDate=datetime.datetime.strptime(im['actionDate'],'%Y/%m/%d %H:%M:%S') 
        actionDateYMD=actionDate.strftime('%Y%m%d')
        im['imageDate']=actionDateYMD
        #this is still to be configured
        inputIdFilter={'variable':inputParticipantField,\
                'value':im[dbParticipantField],\
                'oper':'eq'}

        idFilter={'variable':dbParticipantField,\
                'value':im[dbParticipantField],\
                'oper':'eq'}
        #filter on series descripton - for PET, we should have 'PET WB'
        sdFilter={'variable':'seriesDescription','value':'PET WB','oper':'eq'}
        
        
        #have to convert from datetime to %Y%m%d format
        #dateFilter={'variable':'imageDate','value':im['imageDate'],'oper':'eq'}

        dsOrthanc=db.selectRows(projectOrthanc,inputSchema,inputQuery,[inputIdFilter,sdFilter])
        #what if dsOrthanc['rows'] is empty?
        #this is part of QA and is reported in missingImages Schema/Query

        uploadStatus="FAILED"
        imageDateMismatch=[]
        for im1 in dsOrthanc['rows']:

            date=datetime.datetime.strptime(im1['studyDate'],'%Y/%m/%d %H:%M:%S') 
            dt=date-actionDate
            if (abs(dt.days)>scheduleToleranceDays): 
                continue

            #convert date to %Y%m%d notation
            dateYMD=date.strftime('%Y%m%d')
            
            #enter this time difference to a list
            imFilter={'variable':'imagingVisitId',
                    'value':'{}'.format(im['imagingVisitId']),
                    'oper':'eq'}
            dsMissing=db.selectRows(projectStudy,missingSchema,\
                    missingQuery,[idFilter,imFilter])

            #already recorded
            vals=[dbParticipantField,'imagingVisitId','imageDate']
            mode='insert'
            if len(dsMissing['rows'])>0:
                mode='update'
                orow=dsMissing['rows'][0]
            else:
                orow={v:im[v] for v in vals}
            orow['imageDateMismatch']=dateYMD
            orow['failureDescription']='MISSING FORM'
            db.modifyRows(mode,projectStudy,missingSchema,\
                    missingQuery,[orow])
        
    print("Done: {}".format(len(dsImage['rows'])))

if __name__=='__main__':
    main(sys.argv[1])