Updating populateImageFromTransferList to update failureStatus

pythonScripts/populateImagingFromTransferList.py

@@ -1,5 +1,8 @@
 #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
@@ -13,7 +16,12 @@ def main(parameterFile):
     with open(fsetup,'r') as f:
         setup=json.load(f)
 
-    sys.path.insert(0,setup['paths']['labkeyInterface'])
+    sys.path.insert(0,setup['paths']['nixWrapper'])
+
+    import nixWrapper
+
+    nixWrapper.loadLibrary("labkeyInterface")
+
     import labkeyInterface
     import labkeyDatabaseBrowser
     import labkeyFileBrowser
@@ -48,17 +56,29 @@ def main(parameterFile):
     transferQuery=pars['Database']['transferQuery']
     dbParticipantField=pars['Database']['participantField']
 
-    #make a list of images
+    missingSchema=pars['Database']['missingImagesSchema']
+    missingQuery=pars['Database']['missingImagesQuery']
+
+    #make a list of images from transferQuery
     dsImage=db.selectRows(projectStudy,outputSchema,transferQuery,[])
 
     for im in dsImage['rows']:
-        idFilter={'variable':inputParticipantField,'value':im[dbParticipantField],\
-            'oper':'eq'}
+        inputIdFilter={'variable':inputParticipantField,\
+                'value':im[dbParticipantField],\
+                'oper':'eq'}
+
+        idFilter={'variable':dbParticipantField,\
+                'value':im[dbParticipantField],\
+                '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,[idFilter])
+        dsOrthanc=db.selectRows(projectOrthanc,inputSchema,inputQuery,[inputIdFilter])
+        #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') 
@@ -66,6 +86,7 @@ def main(parameterFile):
             dateYMD=date.strftime('%Y%m%d')
             if dateYMD!=im['imageDate']:
                 print('Rejecting mismatch: {}/{}'.format(dateYMD,im['imageDate']))
+                imageDateMismatch.append(dateYMD)
                 continue
         
             outvar='NONE'
@@ -84,10 +105,10 @@ def main(parameterFile):
 
             #figure out which row in output study to update
             filters=[]
-            idFilter={'variable':dbParticipantField,'value':im[dbParticipantField],'oper':'eq'}
             seqNum=im['imagingVisitId']
             seqFilter={'variable':'SequenceNum','value':str(seqNum),'oper':'eq'}
-            print('Participant {} Sequence number {}'.format(im[dbParticipantField],str(seqNum)))
+            print('Participant {} Sequence number {}'.\
+                    format(im[dbParticipantField],str(seqNum)))
             #ds1 are the matching outputs in target dataset
             ds1=db.selectRows(projectStudy,outputSchema,outputQuery,\
                 [idFilter,seqFilter])
@@ -95,6 +116,7 @@ def main(parameterFile):
             if len(ds1['rows'])>1:
                 print('ERROR: too many matches for {}/{}'.\
                     format(im[dbParticipantField],seqNum))
+                status="MULTIPLE MATCHES"
                 continue
 
             mode='update'
@@ -114,9 +136,34 @@ def main(parameterFile):
             outRow['imagingVisitId']=im['imagingVisitId']
             outRow['visitCode']='VISIT_'+str(im['imagingVisitId'])
 
-            status=db.modifyRows(mode,projectStudy,outputSchema,outputQuery,[outRow])
-            print('{}'.format(status))
+            modifyStatus=db.modifyRows(mode,projectStudy,outputSchema,\
+                    outputQuery,[outRow])
+            print('{}'.format(modifyStatus))
+            uploadStatus="LOADED"
         
+        if uploadStatus=="FAILED":
+            #standard spiel - find if already present; if so, skip, if not, add
+            imFilter={'variable':'imagingVisitId',
+                    'value':'{}'.format(im['imagingVisitId']),
+                    'oper':'eq'}
+            dsMissing=db.selectRows(projectStudy,missingSchema,\
+                    missingQuery,[idFilter,imFilter])
+
+            #already recorded
+            imageDateMismatch=list(set(imageDateMismatch))
+            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']=','.join(imageDateMismatch)
+            orow['failureDescription']='MISSING DICOM'
+            db.modifyRows(mode,projectStudy,missingSchema,\
+                    missingQuery,[orow])
+            
+       
     print("Done")
 
 if __name__=='__main__':