Initial import

remoteResources/resources.json

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+{
+	"labkeyInterface":"http://wiscigt.powertheword.com/labkey/labkeyinterface/-/archive/master/labkeyinterface-master.zip",
+	"irAEMM":"http://wiscigt.powertheword.com/oil/iraemm/-/archive/master/iraemm-master.zip"
+}

wrapper/nixWrapper.py

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+import sys
+import os
+import urllib3
+import shutil
+import zipfile
+import pathlib
+import json
+import getpass
+#this is meant to be used as a startup script
+#all commands will be executed when python -m script -i is used
+
+
+#generic function to load library from gitlab
+def getSuitePath():
+    installDir=os.path.join(os.path.expanduser('~'),'.labkey','software','src')
+    if not os.path.isdir(installDir):
+        os.makedirs(installDir)
+    return installDir
+
+
+def loadModule(slicer,name,moduleName):
+    loadLibrary(name)
+    modulePath=os.path.join(getSuitePath(),name,'slicerModule',moduleName+'.py')
+    factoryManager = slicer.app.moduleManager().factoryManager()
+
+    factoryManager.registerModule(qt.QFileInfo(modulePath))
+
+    factoryManager.loadModules([moduleName,])
+    slicer.util.selectModule(moduleName)
+
+
+def loadLibrary(name):
+    #load library from git, store it at a default location and 
+    #add path to the python sys
+    
+    remoteSourcesURL={
+            "labkeyInterface":\
+                    "http://wiscigt.powertheword.com/labkey/labkeyinterface/-/archive/master/labkeyinterface-master.zip"
+            "iraeMM":
+
+    }
+    #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=getSuitePath()
+
+    #3 remove existing copy
+    finalName=os.path.join(installDir,name)
+    if os.path.isdir(finalName):
+        shutil.rmtree(finalName)
+
+    #unzip
+    with zipfile.ZipFile(tempFile,'r') as zip_ref:
+        zip_ref.extractall(installDir)
+    
+    #cleanup
+    os.remove(tempFile)
+
+    #rename
+    #this is the best guess of the relation between zip directory and name
+    zipName=name.lower()+'-master'
+    os.rename(os.path.join(installDir,zipName),finalName)
+    
+    sys.path.append(finalName)
+
+def setConfig(labkeyUser,labkeyServer='https://merlin.fmf.uni-lj.si',\
+        certificateZip=None):
+    connectionConfig={}
+    if certificateZip!=None:
+        zpath=pathlib.Path(certificateZip)
+        user=zpath.stem
+        userDir=os.path.join(os.path.expanduser('~'),'.labkey',user)
+        if not os.path.isdir(userDir):
+            os.makedirs(userDir)
+        caName=None
+        with zipfile.ZipFile(certificateZip,'r') as zipObj:
+            zipObj.extract(user+'.crt',userDir)
+            zipObj.extract(user+'.key',userDir)
+            zipList=zipObj.namelist()
+            for f in zipList:
+                if f.find('CA')>-1:
+                    caName=f
+                    zipObj.extract(f,userDir)
+    
+        #setup SSL
+        sslSetup={}
+        sslSetup['user']=os.path.join(userDir,user+'.crt')
+        sslSetup['key']=os.path.join(userDir,user+'.key')
+        sslSetup['ca']=os.path.join(userDir,caName)
+        sslSetup['keyPwd']='notUsed'
+        connectionConfig['SSL']=sslSetup
+
+    connectionConfig["host"]=labkeyServer
+    connectionConfig["context"]="labkey"
+    labkeySetup={}
+    labkeySetup['user']=labkeyUser
+    labkeyPwd='guest'
+    if not labkeyUser=='guest':
+        labkeyPwd=getpass.getpass(prompt='Enter labkey password:')
+    labkeySetup['password']=labkeyPwd 
+    connectionConfig['labkey']=labkeySetup
+
+    orthancSetup={}
+    if connectionConfig['host'].find('merlin')>-1:
+        orthancSetup['server']='https://orthanc.fmf.uni-lj.si'
+    if connectionConfig['host'].find('onko-nix')>-1:
+        orthancSetup['server']='http://onko-nix.onko-i.si:8042'
+    orthancSetup['user']='ask'
+    orthancSetup['password']='askPassword'
+    connectionConfig['orthanc']=orthancSetup
+    net=labkeyInterface.labkeyInterface()
+    net.connectionConfig=connectionConfig
+    net.initRemote()
+    print(net.getUserId())
+    return net
+
+def testCertificate(certificateZip):
+    return setConfig('guest',certificateZip=certificateZip)
+
+def testConnection(labkeyUser,labkeyServer='https://merlin.fmf.uni-lj.si',\
+        certificateZip=None):
+    return setConfig(labkeyUser,labkeyServer,certificateZip)
+
+def getDefaultConfig(configFile):
+    #if configFile is None, this will set it to default and leave unchanged otherwise
+    if configFile==None:
+        return os.path.join(os.path.expanduser('~'),'.labkey','network.json')
+    return configFile
+
+def storeConfig(net,configFile=None):
+    #if configFile is None, this will set it to default and leave unchanged otherwise
+    with open(getDefaultConfig(configFile),'w') as f:
+        json.dump(net.connectionConfig,f,indent='\t')
+
+def getInterface(configFile=None):
+    net=labkeyInterface.labkeyInterface()
+    #if configFile is None, this will set it to default and leave unchanged otherwise
+    net.init(getDefaultConfig(configFile))
+    return net
+
+#loadLibrary('labkeyInterface')
+