Adding copyAnonymizedDataset.py

pythonScripts/copyAnonymizedDataset.py

@@ -19,14 +19,17 @@ fconfig=os.path.join(fhome,'.labkey','network.json')
 net=labkeyInterface.labkeyInterface()
 net.init(fconfig)
 db=labkeyDatabaseBrowser.labkeyDB(net)
+fb=labkeyFileBrowser.labkeyFileBrowser(net)
 
-
+tempDir=os.path.join(os.path.expanduser('~'),'temp')
 #also need merlin credentials
 
 fconfigMerlin=os.path.join(fhome,'.labkey','merlin.json')
 netMerlin=labkeyInterface.labkeyInterface()
 netMerlin.init(fconfigMerlin)
 dbMerlin=labkeyDatabaseBrowser.labkeyDB(netMerlin)
+fbMerlin=labkeyFileBrowser.labkeyFileBrowser(netMerlin)
+
 
 
 
@@ -48,6 +51,32 @@ for row in ds['rows']:
     outRow=copy.deepcopy(row)
     outRow['PatientId']='{}-{}'.format(nixID,row['PatientId'])
     dbMerlin.modifyRows('insert',merlinProject,'study',merlinDataset,[outRow])
-
+    
+#
 print('Done')
+quit()
+
+imagingDataset="AnonymousImaging1?"
+merlinImagingDataset="Imaging1"
+imageDir="preprocessedImages"
+ds=db.selectRows(project,'study',imagingDataset,[],)
+for row in ds['rows']:
+    ofiles=[row['preprocessedCT'],row['preprocessedPET']]
+    pCode=row['PatientCode']
+    vCode=row['visitCode']
+    for ofile in ofiles:
+        xPath=[imageDir,pCode,vCode]
+        xPath.append(ofile)
+        path='/'.join(xPath)
+        localPath=os.path.join(tempDir,ofile)
+        remotePath=fb.formatPathURL(project,path)
+        fb.readFileToFile(remotePath,localPath)
+        merlinPath=fbMerlin.buildPathURL(merlinProject,xPath)
+        fbMerlin.writeFileToFile(localPath,merlinPath)
+    outRow=copy.deepcopy(row)
+    outRow['PatientId']='{}-{}'.format(nixID,row['PatientId'])
+    dbMerlin.modifyRows('insert',merlinProject,'study',merlinImagingDataset,[outRow])
+
+    
+