A thin version of labkeyBrowser relying completely on labkeyInterface

labkeyBrowser/CMakeLists.txt

@@ -4,8 +4,6 @@ set(MODULE_NAME labkeySlicerPythonExtension)
 #-----------------------------------------------------------------------------
 set(MODULE_PYTHON_SCRIPTS
   ${MODULE_NAME}.py
-  fileIO.py
-  slicerNetwork.py
   )
 
 set(MODULE_PYTHON_RESOURCES

labkeyBrowser/labkeyBrowser.py

@@ -2,12 +2,13 @@ import os
 import unittest
 from __main__ import vtk, qt, ctk, slicer
 from slicer.ScriptedLoadableModule import *
-import slicerNetwork
-import loadDicom
+#import slicerNetwork
 import json
 import zipfile
 import pathlib
-
+import sys
+import urllib3
+import string
 #
 # labkeySlicerPythonExtension
 #
@@ -43,7 +44,38 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
     ScriptedLoadableModuleWidget.setup(self)
     # Instantiate and connect widgets ...
     self.logic=labkeyBrowserLogic(self)
-    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=slicerNetwork.labkeyURIHandler()
+    self.network=labkeyInterface.labkeyInterface()
+    fconfig=os.path.join(fhome,'.labkey','network.json')
+    self.network.init(fconfig)
+    self.db=labkeyDatabaseBrowser.labkeyDB(self.network)
+    self.fb=labkeyFileBrowser.labkeyFileBrowser(self.network)
+
     #
     # Parameters Area
     #
@@ -134,7 +166,8 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
     self.fileList=qt.QListWidget()
     self.fileList.toolTip="Select remote file"
     self.fileList.itemDoubleClicked.connect(self.onFileListDoubleClicked)
-    self.currentRemoteDir=''
+    #remote dir is a list
+    self.currentRemoteDir=[]
 
     #add dummy entry
     items=('.','..')
@@ -152,7 +185,8 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
     self.fileTypeSelector=qt.QComboBox()
     self.fileTypeSelector.toolTip="Select file type"
 
-    items=self.network.fileTypesAvailable()
+    items=('VolumeFile','SegmentationFile','TransformFile')
+
     self.populateFileTypeSelector(items)
 
     fileDialogFormLayout.addRow("File type :",self.fileTypeSelector)
@@ -264,7 +298,24 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
   def onLoadConfigButtonClicked(self):
        filename=qt.QFileDialog.getOpenFileName(None,'Open configuration file (JSON)',
             self.configDir, '*.json')
-       self.network.parseConfig(filename,self)
+ 
+        
+       self.network.init(filename)
+
+       cfg=self.network.connectionConfig
+
+       if 'SSL' in cfg:
+           sslSetup=cfg['SSL']
+           self.privateKeyButton.setText(sslSetup['key'])
+           self.userCertButton.setText(sslSetup['user'])
+           self.caCertButton.setText(sslSetup['ca'])
+      
+       self.serverURL.setText(cfg['host'])
+       if 'labkey' in cfg:
+           labkey=cfg['labkey']
+           self.authName.setText(labkey['user'])
+           self.authPass.setText(labkey['password'])
+
        #self.serverURL.setText(self.network.hostname)
        #self.authName.setText(self.network.auth_name)
        #self.authPass.setText(self.network.auth_pass)
@@ -392,24 +443,24 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
         iText=item.text()
         print("Selected items: {0} ".format(iText))
 
-
+        
         #this is hard -> compose path string from currentRemoteDir and selection
         if item.text().find('..')==0:
             #one up
-            idx=self.currentRemoteDir.rfind('/')
-            if idx<0:
-                self.currentRemoteDir=''
-            else:
-                self.currentRemoteDir=self.currentRemoteDir[:idx]
+            try:
+                self.currentRemoteDir.pop()
+            except IndexError:
+                pass
         elif item.text().find('.')==0:
             pass
         else:
-            if len(self.currentRemoteDir)>0:
-                self.currentRemoteDir+='/'
-            self.currentRemoteDir+=item.text()
-        print("Listing {0}".format(self.currentRemoteDir))
-        flist=self.network.toRelativePath(
-            self.network.listRelativeDir(self.currentRemoteDir))
+            self.currentRemoteDir.append(item.text())
+        print("Listing {}".format(self.currentRemoteDir))
+        remoteDirString=self.fb.GetRootUrl()
+        if len(self.currentRemoteDir):
+            remoteDirString+='/'+'/'.join(self.currentRemoteDir)
+        ok,lst=self.fb.listRemoteDir(remoteDirString)
+        flist=[self.fb.baseDir(f) for f in lst] 
         print("Got")
         print(flist)
         flist.insert(0,'..')
@@ -419,20 +470,32 @@ class labkeyBrowserWidget(ScriptedLoadableModuleWidget):
 
   def onLoadFileButtonClicked(self):
       properties={}
-      localPath=self.network.DownloadFileToCache(self.selectedFile.text)
+      
+      #local path
+      tempDir=os.path.join(os.path.expanduser('~'),'temp')
+      if not os.path.isdir(tempDir):
+          os.mkdir(tempDir)
+      localPath=os.path.join(tempDir,self.currentRemoteDir[-1])
+
+      print(localPath)
+
+      #remote path
+      remotePath=self.fb.GetRootUrl()+'/'+'/'.join(self.currentRemoteDir)
+      print(remotePath)
+
+      #copy over
+      self.fb.readFileToFile(remotePath,localPath)
+      
+      #do slicer magic
       slicer.util.loadNodeFromFile(localPath,self.fileTypeSelector.currentText,
         properties,returnNode=False)
-      if not self.keepCachedFileCheckBox.isChecked():
-              os.remove(localPath)
+      
+      #if not self.keepCachedFileCheckBox.isChecked():
+      os.remove(localPath)
 
   def onLoadDirButtonClicked(self):
-    #dir=self.network.loadDir(self.selectedFile.text)
-    dir=self.selectedFile.text
-    try:
-        self.loadDicomLogic.load(self.network,dir)
-    except:
-        self.loadDicomLogic=loadDicom.loadDicomLogic(self)
-        self.loadDicomLogic.load(self.network,dir)
+
+    print('Not implemented')
 
 # labkeySlicerPythonExtensionLogic
 #
@@ -578,3 +641,45 @@ def getHomeDir():
     except:
       fhome=os.environ['HOMEDRIVE']+os.environ['HOMEPATH']
       return fhome
+
+
+def loadLibrary(name):
+    #load library from git, store it at a default location and return path to the stored location
+    remoteSources={
+            "labkeyInterface":\
+                    "http://wiscigt.powertheword.com/labkey/labkeyinterface/-/archive/master/labkeyinterface-master.zip"
+    }
+    #two steps:
+    #1 Download
+
+    tempDir=os.path.join(os.path.expanduser('~'),'temp')
+    if not os.path.isdir(tempDir):
+        os.mkdir(tempDir)
+    tempFile=os.path.join(tempDir,name+'.zip')
+    
+    http = urllib3.PoolManager()
+    r = http.request('GET', remoteSources[name], preload_content=False)
+    chunk_size=65536 
+    with open(tempFile, 'wb') as out:
+        while True:
+            data = r.read(chunk_size)
+            if not data:
+                break
+            out.write(data)
+
+    r.release_conn()
+    
+    #2 Unzip
+    installDir=os.path.join(os.path.expanduser('~'),'.labkey','software','src')
+    if not os.path.isdir(installDir):
+        os.makedirs(installDir)
+    
+    with zipfile.ZipFile(tempFile,'r') as zip_ref:
+        zip_ref.extractall(installDir)
+    #cleanup
+    os.remove(tempFile)
+
+    zipName=name.lower()+'-master'
+    os.rename(os.path.join(installDir,zipName),os.path.join(installDir,name))
+
+    return os.path.join(installDir,name)