Initial import of packaged nixWrapper

LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# NIX Suite
+
+A set of tools used to format NIX compatible databases. 
+
+## Installation
+
+```bash
+pip install nixWrapper 
+```
+
+##Usage
+
+```python
+import nixWrapper
+nixWrapper.loadLibrary('labkeyInterface')
+import labkeyInterface
+...
+```
+## Developer notes
+
+[Packaging][pypiTutorial] howto.
+
+[pypiTutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/
+

pyproject.toml

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+[build-system]
+requires= ["setuptools>=77.0.3"]
+build-backend="setuptools.build_meta"
+
+[project]
+name="nixWrapper"
+version="1.1.2"
+authors=[{name="Andrej Studen", email="andrej.studen@fmf.uni-lj.si"},]
+description="portal to Network of Imaging Excellence (NIX) utilities"
+readme="README.md"
+requires-python = ">=3.7"
+classifiers = [
+"Programming Language :: Python :: 3",
+"Operating System :: OS Independent",
+]
+
+license = "MIT"
+license-files = ["LICEN[CS]E"]
+dependencies=[
+"urllib3 >= 1.26.0",
+"chardet >= 3.0.0",
+]
+
+[project.urls]
+"Homepage" = "https://git0.fmf.uni-lj.si/studen/nixSuite"
+"Bug Tracker" = "https://git0.fmf.uni-lj.si/studen/nixSuite"
+

src/nixWrapper/__init__.py

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+from nixWrapper.nixWrapper import loadLibrary

src/nixWrapper/nixWrapper.py

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+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')
+