Adding findCandidatesForSchedule.py

pythonScripts/findCandidatesForSchedule.py

@@ -0,0 +1,137 @@
+#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])