nixSuite/wrapper/nixWrapper.py

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'):
    projectURL='%2f'.join(project)
    pathURL='%2f'.join(path)
    return server+'/api/v4/projects/'+projectURL+'/repository/files/'+pathURL+'?ref='+branch


def getResources():
    server='http://wiscigt.powertheword.com'
    project=['labkey','nixsuite']
    path=['remoteResources','resources.json']

    remoteSourcesURL=buildGITURL(server,project,path)
    http = urllib3.PoolManager()
    r = http.request('GET', remoteSourcesURL)
    #returns a JSON
    encoding=chardet.detect(r.data)['encoding']
    jsonData=json.loads(r.data.decode(encoding))

    #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):

    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]
    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()
    
    #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:
        zipName=name+'-'+rsource['branch']
        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')