Moving wrapper to a separate project

wrapper/nixWrapper.py

@@ -1,244 +0,0 @@
-import sys
-import os
-import urllib3
-import shutil
-import zipfile
-import pathlib
-import json
-import getpass
-import chardet
-import base64
-
-#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 buildGITURL(server,project,path,branch='master'):
-    if server.find('wiscigt')>-1:
-        projectURL='%2f'.join(project)
-        pathURL='%2f'.join(path)
-        return server+'/api/v4/projects/'+projectURL+'/repository/files/'+pathURL+'?ref='+branch
-    if server.find('fmf.uni-lj.si')>-1:
-        projectURL='/'.join(project)#studen/nixSuite
-        pathURL='/'.join(path)
-        return '/'.join([server,projectURL,'raw',branch,pathURL])
-
-
-
-def getResources():
-    server='http://wiscigt.powertheword.com'
-    project=['labkey','nixsuite']
-    path=['remoteResources','resources.json']
-
-    server='https://git0.fmf.uni-lj.si'
-    project=['studen','nixSuite']
-    
-    remoteSourcesURL=buildGITURL(server,project,path)
-    print('remoteSourcesURL {}'.format(remoteSourcesURL))
-    http = urllib3.PoolManager()
-    r = http.request('GET', remoteSourcesURL)
-    #returns a JSON
-    encoding=chardet.detect(r.data)['encoding']
-    dataDecoded=r.data.decode(encoding)
-    jsonData=json.loads(dataDecoded)
-    print(jsonData)
-
-    #since gogs drops raw data, we already did the hard part 
-    if server.find('fmf.uni-lj.si')>-1:
-        return jsonData
-
-    #on gitlab a further decoding step is required
-    #we are interested in content, do looped way of decoding it 
-    b64_bytes=jsonData['content'].encode('ascii')
-    m_bytes=base64.b64decode(b64_bytes)
-    m=m_bytes.decode('ascii')
-    return json.loads(m)
-
-def loadModule(slicer,qt,name,moduleName):
-    loadLibrary(name)
-    modulePath=os.path.join(getSuitePath(),name,'slicerModules',moduleName+'.py')
-    factoryManager = slicer.app.moduleManager().factoryManager()
-
-    factoryManager.registerModule(qt.QFileInfo(modulePath))
-
-    factoryManager.loadModules([moduleName,])
-    slicer.util.selectModule(moduleName)
-
-
-def loadLibrary(name,doReload=True):
-    print('loadLibrary')
-    installDir=getSuitePath()
-    finalName=os.path.join(installDir,name)
-    if os.path.isdir(finalName):
-        if not doReload:
-            #1 keep existing copy, return
-            sys.path.append(finalName)
-            return
-        else:
-            #1 remove existing copy
-            shutil.rmtree(finalName)
-    
-    #load library from git, store it at a default location and 
-    #add path to the python sys
-    remoteSources=getResources()
-
-    #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()
-
-    rsource=remoteSources[name]
-    print(rsource)
-    r = http.request('GET', rsource['url'], 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()
-    print('File  {}: {}'.format(tempFile,os.path.isfile(tempFile)))
-    #2 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
-    try:
-        zipName=name.lower()+'-'+rsource['branch']
-        os.rename(os.path.join(installDir,zipName),finalName)
-    except FileNotFoundError:
-        try:
-            zipName=name+'-'+rsource['branch']
-            os.rename(os.path.join(installDir,zipName),finalName)
-        except FileNotFoundError:
-            #git0/gogs
-            zipName=name.lower()
-            os.rename(os.path.join(installDir,zipName),finalName)
-
-    
-    sys.path.append(finalName)
-    updateSetup(name,finalName)
-    return finalName
-
-def updateSetup(name,path):
-
-    #update setup.json
-    #set paths[name]=finalName
-    #for use in slicer, use .labkey/slicer/setup.json
-    setupDir=os.path.join(os.path.expanduser('~'),'.labkey','slicer')
-    if not os.path.isdir(setupDir):
-        os.makedirs(setupDir)
-    setupFile=os.path.join(setupDir,'setup.json')
-    
-    #if f is not there, create an empty json
-    try:
-        with open(setupFile,'r') as f:
-            setup=json.load(f)
-    except OSError:
-        setup={}
-
-    try:
-        setup['paths'][name]=path
-    except KeyError:
-        setup['paths']={}
-        setup['paths'][name]=path
-
-    with open(setupFile,'w') as f:
-        json.dump(setup,f)
-    
-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')
-