Updated version that is based of labkeyInterface

slicerModule/iraemmBrowser.py

@@ -2,10 +2,9 @@ import os
 import unittest
 from __main__ import vtk, qt, ctk, slicer
 from slicer.ScriptedLoadableModule import *
-import slicerNetwork
-import loadDicom
 import json
 import datetime
+import sys
 
 #
 # labkeySlicerPythonExtension
@@ -42,12 +41,41 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     print("Setting up iraemmBrowserWidget")
     ScriptedLoadableModuleWidget.setup(self)
     # Instantiate and connect widgets ...
-    self.network=slicerNetwork.labkeyURIHandler()
+    
+    fhome=os.path.expanduser('~')
+    fsetup=os.path.join(fhome,'.labkey','setup.json')
+    try:
+        with open(fsetup) as f:
+            self.setup=json.load(f)
+    except FileNotFoundError:
+        self.setup={}
+
+    try:
+        pt=self.setup['paths']
+    except KeyError:
+        self.setup['paths']={}
+
+    try:    
+        sys.path.append(self.setup['paths']['labkeyInterface'])
+    except KeyError:
+        self.setup['paths']['labkeyInterface']=loadLibrary('labkeyInterface')
+        with open(fsetup,'w') as f:
+            json.dump(self.setup,f,indent='\t')
+    
+    import labkeyInterface
+    import labkeyDatabaseBrowser
+    import labkeyFileBrowser
+
+
+    self.network=labkeyInterface.labkeyInterface() 
 
     fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')
-    self.network.parseConfig(fconfig)
-    self.network.initRemote()
+    self.network.init(fconfig)
+
+    self.db=labkeyDatabaseBrowser.labkeyDB(self.network)
+    self.fb=labkeyFileBrowser.labkeyFileBrowser(self.network)
     self.project="iPNUMMretro/Study"
+    self.schema='study'
     self.dataset="Imaging1"
     self.reviewDataset="ImageReview"
     self.aeDataset="PET"
@@ -55,7 +83,7 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
 
     
 
-    ds=self.network.filterDataset(self.project,self.dataset,[])
+    ds=self.db.selectRows(self.project,self.schema,self.dataset,[])
     ids=[row['PatientId'] for row in ds['rows']]
     ids=list(set(ids))
 
@@ -80,7 +108,10 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
 
     self.segmentationField=qt.QLabel("Segmentation")
     setupFormLayout.addRow("Data field (Segmentation):",self.segmentationField)
-    
+   
+
+    self.idField=qt.QLabel(self.network.getUserId()['displayName'])
+    setupFormLayout.addRow("ID",self.idField)
     self.logic=iraemmBrowserLogic(self)
 
 
@@ -194,7 +225,7 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
 
   def onPatientListChanged(self,i):
       idFilter={'variable':'PatientId','value':self.patientList.currentText,'oper':'eq'}
-      ds=self.network.filterDataset(self.project,self.dataset, [idFilter])
+      ds=self.db.selectRows(self.project,self.schema,self.dataset, [idFilter])
       seq=[int(row['SequenceNum']) for row in ds['rows']]
       self.visitList.clear()  
             
@@ -211,7 +242,7 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       idFilter={'variable':'PatientId',\
               'value':self.patientList.currentText,'oper':'eq'}
       sFilter={'variable':'SequenceNum','value':s,'oper':'eq'}
-      ds=self.network.filterDataset(self.project,self.dataset,[idFilter,sFilter])
+      ds=self.db.selectRows(self.project,self.schema,self.dataset,[idFilter,sFilter])
       if not len(ds['rows'])==1:
           print("Found incorrect number {} of matches for [{}]/[{}]".\
                   format(len(ds['rows']),\
@@ -374,7 +405,10 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           #assume parent has the network set up
           self.parent=parent
           self.net=parent.network
+          self.db=parent.db
+          self.fb=parent.fb
           self.project=parent.project
+          self.schema=parent.schema
           self.participantField=parent.participantField.text
           self.segmentList=parent.segmentList
 
@@ -396,33 +430,44 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
 
   def loadImage(self,row,keepCached):
       
+      tempDir=os.path.join(os.path.expanduser('~'),'temp')
+      if not os.path.isdir(tempDir):
+          os.mkdir(tempDir)
       
       #fields={'ctResampled':True,'petResampled':False}
       fields={"CT":self.parent.ctField.text,\
               "PET":self.parent.petField.text,\
               "Segmentation":self.parent.segmentationField.text}
 
-      relativePaths={x:self.project+'/@files/preprocessedImages/'\
-             +row['patientCode']+'/'+row['visitCode']+'/'+row[y]\
+      relativePaths={x:['preprocessedImages',row['patientCode'],row['visitCode'],row[y]]\
              for (x,y) in fields.items()}
 
       self.volumeNode={}
       for f in relativePaths:
+
           p=relativePaths[f]
-          labkeyPath=self.net.GetLabkeyPathFromRelativePath(p)
-          rp=self.net.head(labkeyPath)
-          if not slicerNetwork.labkeyURIHandler.HTTPStatus(rp):
-              print("Failed to get {}".format(labkeyPath))
-              continue
+          
+          localPath=os.path.join(tempDir,p[-1])
+
+          if not os.path.isfile(localPath):
+              #download from server
+              remotePath=self.fb.formatPathURL(self.project,'/'.join(p))
+              if not self.fb.entryExists(remotePath):
+                  print("Failed to get {}".format(remotePath))
+                  continue
 
-          #pushes it to background
+              self.fb.readFileToFile(remotePath,localPath) 
+          
           properties={}
           #make sure segmentation gets loaded as a labelmap
           if f=="Segmentation":
               properties["labelmap"]=1
-
-          self.volumeNode[f]=self.net.loadNode(p,'VolumeFile',\
-                  properties=properties,returnNode=True,keepCached=keepCached)
+              
+          
+          self.volumeNode[f]=slicer.util.loadNodeFromFile(localPath,filetype='VolumeFile',properties=properties)
+          
+          if not keepCached:
+              os.remove(localPath)
 
       #mimic abdominalCT standardized window setting
       self.volumeNode['CT'].GetScalarVolumeDisplayNode().\
@@ -535,12 +580,13 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           filters.append({'variable':f,'value':str(inputRow[f]),'oper':'eq'})
       
       
-      ds=self.net.filterDataset(project,dataset,filters)
+      ds=self.db.selectRows(project,self.schema,dataset,filters)
       return ds['rows']
 
   def loadReview(self,currentRow):
 
       #see if we have already done a review
+      currentRow['ModifiedBy']=self.net.getUserId()['id']
       rows=self.getUniqueRows(self.parent.project,self.parent.reviewDataset,\
               [self.participantField,'visitCode','Segmentation','ModifiedBy'],currentRow)
 
@@ -559,6 +605,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
 
   #submit review to labkey
   def submitReview(self,currentRow,comment):
+      currentRow['ModifiedBy']=self.net.getUserId()['id']
       fields=[self.participantField,'visitCode','Segmentation','ModifiedBy']
       rows=self.getUniqueRows(self.parent.project,self.parent.reviewDataset,\
               fields,currentRow)
@@ -590,7 +637,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
 
       row['reviewComment']=comment
       row['Date']=datetime.datetime.now().ctime()
-      self.net.modifyDataset(mode,self.parent.project,\
+      self.db.modifyRows(mode,self.parent.project,self.parent.schema,\
               self.parent.reviewDataset,[row])
       
       print("review submitted")
@@ -617,6 +664,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
 
 
   def loadAE(self,currentRow):
+      currentRow['ModifiedBy']=self.net.getUserId()['id']
       fields=[self.participantField,'petResampled','ModifiedBy']
       rows=self.getUniqueRows(self.parent.project,self.parent.aeDataset,\
               fields,currentRow)
@@ -637,6 +685,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
               continue
 
   def submitAE(self,currentRow):
+      currentRow['ModifiedBy']=self.net.getUserId()['id']
       fields=[self.participantField,'petResampled','ModifiedBy']
       rows=self.getUniqueRows(self.parent.project,self.parent.aeDataset,\
               fields,currentRow)
@@ -661,7 +710,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           row[seg+'AE']=self.getAEResult(seg) 
 
       row['Date']=datetime.datetime.now().ctime()
-      resp=self.net.modifyDataset(mode,self.parent.project,\
+      resp=self.db.modifyRows(mode,self.parent.project,self.parent.schema,\
               self.parent.aeDataset,[row])
       print("Response {}".format(resp))
       print("AE submitted")