Making populateImagingFromOrthance.py use Analysis/Run infrastructure

pythonScripts/populateImagingFromOrthanc.py

@@ -16,36 +16,50 @@ sys.path.insert(0,setup['paths']['labkeyInterface'])
 import labkeyInterface
 import labkeyDatabaseBrowser
 
+sys.path.insert(0,setup['paths']['analysisInterface'])
+import analysisInterface
+
 fconfig=os.path.join(fhome,'.labkey','network.json')
 
 net=labkeyInterface.labkeyInterface()
 net.init(fconfig)
 db=labkeyDatabaseBrowser.labkeyDB(net)
+fb=labkeyFileBrowser.labkeyFileBrowser(net)
+
+parameterFile=sys.argv[1]
+runid=sys.argv[2];
+
+ana=analysisInterface.analysisInterface(db,fb,runid)
+ana.updateStatus(2)
+pars=ana.getParameters(parameterFile)
+
+if pars==None:
+    sys.exit()
+
 
 
 i=0
 #from orthancDatabase/Imaging dataset
-projectOrthanc='Orthanc/Database'
-inputDataset='Imaging'
+projectOrthanc=pars['Orthanc']['project']
+inputQuery=pars['Orthanc']['queryName']
+inputSchema=pars['Orthanc']['schemaName']
+inputParticipantField=pars['Orthanc']['participantField']
+
 #to target project dataset
-projectStudy='iPNUMMretro/Study'
+projectStudy=pars['Database']['project']
+#'iPNUMMretro/Study'
 #for prospective, set
-projectStudy='IPNUMMprospektiva/Study'
-outputDataset='Imaging1'
+#projectStudy='IPNUMMprospektiva/Study'
+outputQuery=pars['Database']['queryName']
+outputSchema=pars['Database']['schemaName']
 #select patientId that are contained in the demographics dataset
-demographicDataset='ClinicalData'
-#for prospective
-demographicDataset='demographicData'
-
+listQuery=pars['Database']['listQuery']
+dbParticipantField=pars['Database']['participantField']
 
-orthancParticipantField='PatientId'
-participantField='PatientId'
-#for prospective
-participantField='ParticipantId'
 
 #make a list of patients
-dsDemo=db.selectRows(projectStudy,'study',demographicDataset,[])
-patients=[row[participantField] for row in dsDemo['rows']]
+dsDemo=db.selectRows(projectStudy,outputSchema,listQuery,[])
+patients=[row[dbParticipantField] for row in dsDemo['rows']]
 patients=list(set(patients))
 
 patientListStr=""
@@ -55,15 +69,15 @@ for p in patients:
     patientListStr+=p
 
 
-patientFilter={'variable':orthancParticipantField,
+patientFilter={'variable':inputParticipantField,
         'value':patientListStr,'oper':'in'}
 
 #takes orthanc as the baseline, selects from patient list
-ds=db.selectRows(projectOrthanc,'study',inputDataset,[patientFilter])
+ds=db.selectRows(projectOrthanc,inputSchema,inputQuery,[patientFilter])
 
 
 #single entry for the patientId/dicomStudy pair
-selectVars={participantField:orthancParticipantField,\
+selectVars={dbParticipantField:inputParticipantField,\
         'dicomStudy':'dicomStudy'}
 
 dates=[datetime.datetime.strptime(row['studyDate'],'%Y/%m/%d %H:%M:%S') \
@@ -97,22 +111,22 @@ for j in range(len(dates)):
                 'value':row[selectVars[v]],'oper':'eq'})
 
     #ds2 are all studies by patient from sorted dataset
-    ds2=db.selectRows(projectStudy,'study',outputDataset,
-            [{'variable':participantField,\
-                    'value':row[orthancParticipantField],'oper':'eq'}])
+    ds2=db.selectRows(projectStudy,outputSchema,outputQuery,
+            [{'variable':dbParticipantField,\
+                    'value':row[inputParticipantField],'oper':'eq'}])
     
     #ds1 is the matching row from output dataset 
-    ds1=db.selectRows(projectStudy,'study',outputDataset,filters)
+    ds1=db.selectRows(projectStudy,outputSchema,outputQuery,filters)
     if len(ds1['rows'])>1:
         print('ERROR: too many matches for {}/{}'.\
-                format(row[orthancParticipantField],row['dicomStudy']))
+                format(row[inputParticipantField],row['dicomStudy']))
         continue
 
     mode='update'
     outRow={}
     if len(ds1['rows'])==0:
         mode='insert'
-        outRow[participantField]=row[orthancParticipantField]
+        outRow[dbParticipantField]=row[inputParticipantField]
         
         #setting sequence number to length of already included studies
         #sorted by date makes it historically incremental
@@ -125,7 +139,7 @@ for j in range(len(dates)):
     outRow[outvar]=row['orthancSeries']
     outRow['studyDate']=row['studyDate']
 
-    status=db.modifyRows(mode,projectStudy,'study',outputDataset,[outRow])
+    status=db.modifyRows(mode,projectStudy,outputSchema,outputQuery,[outRow])
     print('{}'.format(status))
     if j==50:
         break