Changes

Readme.md

@@ -1,14 +0,0 @@
-## Labkey Python interface ##
-A Python3 urllib3 based interface for communication with the LabKey server. Update over official LabKey version is the use of client certificates to access potentially sensitive sites.
-
-### Setup ###
-Update `network-config-sample.json` with personal information needed to access the site (certificates, keys, username and password)
-When using labkeyInterface, use the updated file as input to labkeyInterface constructor, ie
-```python
-ifc=labkeyInterface.labkeyInterface('/path/to/network-config.json')
-```
-
-### Use ###
-`getFile.py` illustrates use to connect to site, collect image and perform image analysis.
-
-

getFile.py

@@ -1,75 +0,0 @@
-import labkeyInterface
-import labkeyFileBrowser
-import io
-import pydicom
-import numpy
-import itk
-
-net=labkeyInterface.labkeyInterface()
-net.init('/home/studen/.labkey/merlin.json')
-b=labkeyFileBrowser.labkeyFileBrowser(net)
-
-url=b.formatPathURL('DORA/Radiomics',"")
-ok,dirs=b.listRemoteDir(url)
-url=dirs[10]
-
-ok,dirs=b.listRemoteDir(url)
-url=dirs[0]
-
-ok,dirs=b.listRemoteDir(url)
-fileUrl=dirs[0]
-
-resp=net.get(fileUrl)
-fileObj=io.BytesIO(resp.data)
-
-#get dcm representation of the file
-dcm=pydicom.dcmread(fileObj)
-
-#matrix dimension
-ConstPixelDims = (int(dcm.Rows), int(dcm.Columns))
-npArray = numpy.zeros(ConstPixelDims, dtype=dcm.pixel_array.dtype)
-
-npArray[:, :] = dcm.pixel_array
-
-#get it to itk
-itkImg=itk.GetImageFromArray(npArray)
-
-
-#works for DORA dicoms, but it would be great to be able to get that from itkImg
-InputPixelType = itk.SS
-#required by Canny
-OutputPixelType = itk.F
-
-Dimension = 2
-
-InputImageType = itk.Image[InputPixelType, Dimension]
-OutputImageType = itk.Image[OutputPixelType, Dimension]
-
-#recast to F
-castImageFilter = itk.CastImageFilter[InputImageType, OutputImageType].New()
-castImageFilter.SetInput(itkImg)
-
-#for debugging
-
-castImageFilter.Update()
-itkImg1=castImageFilter.GetOutput()
-
-variance=2
-upperThreshold=5
-lowerThreshold=0.4*upperThreshold
-
-cannyFilter = itk.CannyEdgeDetectionImageFilter[
-    OutputImageType,
-    OutputImageType].New()
-cannyFilter.SetInput(castImageFilter.GetOutput())
-cannyFilter.SetVariance(variance)
-cannyFilter.SetLowerThreshold(lowerThreshold)
-cannyFilter.SetUpperThreshold(upperThreshold)
-
-cannyFilter.Update()
-
-canny=cannyFilter.GetOutput()
-
-npCanny=itk.GetArrayFromImage(canny)
-
-

labkeyDatabaseBrowser.py

@@ -1,33 +0,0 @@
-import labkeyInterface
-import json
-
-class labkeyDB:
-    def __init__(self,net):
-        self.net=net
-
-    def selectRows(self,project,schemaName, queryName,qfilter):
-
-        debug=False
-        url=self.net.GetLabkeyUrl()+'/'+project
-        url+='/query-selectRows.api?schemaName='+schemaName+\
-                '&query.queryName='+queryName
-        for f in qfilter:
-            url+="&query."+f['variable']+"~"+f['oper']+"="+f['value']
-        if debug:
-            print("Sending {}").format(url)
-        response=self.net.get(url)
-        return json.loads(response.data)
-
-    def modifyRows(self,mode, project,schemaName, queryName, rows):
-        #mode can be insert/update/delete
-        debug=True
-        data={}
-        data['schemaName']=schemaName
-        data['queryName']=queryName
-        data['rows']=rows
-        url=self.net.GetLabkeyUrl()+'/'+project
-        url+='/query-'+mode+'Rows.api?'
-        response=self.net.post(url,json.dumps(data))
-        return response.data
-
-

labkeyFileBrowser.py

@@ -1,57 +0,0 @@
-import urllib3
-import xml.etree.ElementTree as ET
-
-
-class labkeyFileBrowser:
-
-    def __init__(self,net):
-        self.net=net
-
-    def GetRootUrl(self):
-        return self.net.GetLabkeyUrl()+"/_webdav"
-    
-    def listRemoteDir(self,url):
-        #input is remoteDir, result are remoteDirs
-
-        #r=MethodRequest(dirUrl,method="PROPFIND")
-        PROPFIND=u"""<?xml version="1.0" encoding="utf-8"?>\n
-                    <propfind xmlns="DAV:">\n
-                    <prop>\n
-                    <getetag/>\n
-                    </prop>\n
-                    </propfind>"""
-        headers=urllib3.util.make_headers(basic_auth=self.net.getBasicAuth())
-        headers["Content-Type"]='text/xml; charset="utf-8"'
-        headers['content-length']=str(len(PROPFIND))
-        headers['Depth']='1'
-        #add csrf
-        headers["X-LABKEY-CSRF"]=self.net.getCSRF()
-
-        try:
-            f=self.net.http.request('PROPFIND',url,headers=headers,body=PROPFIND)
-        #f contains json as a return value
-        except urllib3.exceptions.HTTPError as e:
-            print(e)
-            return False,dirs
-        
-        tree=ET.XML(f.data)
-        rps=tree.findall('{DAV:}response')
-        dirs=[]
-        for r in rps:
-            hr=r.find('{DAV:}href')
-            dirent=hr.text
-            #dirent=re.sub('/labkey/_webdav/','',dirent)
-            dirent=self.net.connectionConfig['host']+dirent
-            dirs.append(dirent)
-        del dirs[0]
-        return True,dirs
-
-    def readFileToBuffer(self, url):
-        return self.net.get(url)
-    
-    def formatPathURL(self,project,path):
-        url=self.GetRootUrl()+'/'+project+'/@files'
-        if len(path)==0:
-            return url
-        return url+'/'+path
-        

labkeyInterface.py

@@ -1,104 +0,0 @@
-import urllib3
-#requests doesnt work as it lacks key password checking
-import chardet
-import json
-
-
-class labkeyInterface:
-
-    def init(self,fname):
-        #fname is a file with configuration
-        try:
-            f=open(fname)
-        except OSError as e:
-            print("Confgiuration error: OS error({0}): {1}").format(e.errno, e.strerror)
-            raise
-
-        self.connectionConfig=json.load(f)
-        
-        self.http=urllib3.PoolManager()
-
-        if 'SSL' in self.connectionConfig:
-            self.http = urllib3.PoolManager(\
-                cert_file=self.connectionConfig['SSL']['user'],\
-                cert_reqs='CERT_REQUIRED',\
-                key_file=self.connectionConfig['SSL']['key'],\
-                ca_certs=self.connectionConfig['SSL']['ca'])
-
-    #password=self.connectionConfig['SSL']['keyPwd'],\ doesnt work until 1.25
-    def GetLabkeyUrl(self):
-        return self.connectionConfig['host']+"/labkey"
-
-    def GetLabkeyWebdavUrl(self):
-        return self.GetLabkeyUrl()+"/_webdav"
-
-    def getBasicAuth(self):
-        user=self.connectionConfig['labkey']['user']
-        pwd=self.connectionConfig['labkey']['password']
-        return user+":"+pwd
-        
-        
-
-
-
-    
-    def get(self,url):
-
-        debug=False
-        if debug:
-            print("GET: {0}").format(url)
-            print("as {0}").format(user)
-        headers=urllib3.util.make_headers(basic_auth=self.getBasicAuth())
-        try:
-            return self.http.request('GET',url,headers=headers)
-        #f contains json as a return value
-        except urllib3.exceptions.HTTPError as e:
-            print(e)
-
-    def post(self,url,data):
-
-        debug=False
-        headers=urllib3.util.make_headers(basic_auth=self.getBasicAuth())
-        headers["Content-Type"]="application/json"
-        #add csrf;also sets self.cookie
-        headers["X-LABKEY-CSRF"]=self.getCSRF()
-        headers["Cookie"]=self.cookie
-
-        try:
-            return self.http.request('POST',url,headers=headers,body=data)
-        #f contains json as a return value
-        except urllib3.exceptions.HTTPError as e:
-            print(e)
-
-    def put(self,url,data):
-
-        debug=False
-
-        if debug:
-            print("PUT: {}").format(url)
-
-        headers=urllib3.util.make_headers(basic_auth=self.getBasicAuth())
-        headers["Content-Type"]="application/octet-stream"
-        #add csrf
-        headers["X-LABKEY-CSRF"]=self.getCSRF()
-        headers["Cookie"]=self.cookie
-
-        try:
-            return self.http.request('PUT',url,headers=headers,body=data)
-        #f contains json as a return value
-        except urllib3.exceptions.HTTPError as e:
-            print(e)
-      
-
-            
-    def getCSRF(self):
-        url=self.GetLabkeyUrl()+'/login/whoAmI.view'
-        response=self.get(url)
-        self.cookie=response.getheader('Set-Cookie')
-        encoding=chardet.detect(response.data)['encoding']
-        jsonData=json.loads(response.data.decode(encoding))
-        return jsonData["CSRF"]
-
-
-
-