def __init__(self, ReportService, ReportExecution, user, key_password, verbose=True):
self.verbose = verbose
service_cred = dict(username=user, password=key_password)
service_cred = HttpAuthenticated(**service_cred)
exec_cred = dict(username=user, password=key_password)
exec_cred = HttpAuthenticated(**exec_cred)
log.basicConfig(filename='SSRS.log', level=log.INFO)
try:
self.ServiceClient = Client(ReportService, transport=service_cred)
self.ExecutionClient = Client(ReportExecution, transport=exec_cred)
except BaseException as e:
msg = "Error during connection: %s" % e.fault.faultstring
log.error(msg)
if self.verbose:
print(msg)
exit()
def get_soap_client(wsdl,
cache_requests=True,
max_age=MAX_AGE_DEFAULT,
minimum_spacing=0):
"""
Creates and returns a suds/SOAP client instance bound to the
provided ``WSDL``. If ``cache_requests`` is True, then the
client is configured to use a :class:`CachedThrottledTransport`.
The transport is constructed to use :data:`SOAP_CACHE` as the
cache folder, along with the ``max_age`` and ``minimum_spacing``
parameters if provided.
If ``cache_requests`` is ``False``, the client uses the default
:class:`suds.transport.http.HttpAuthenticated` transport.
"""
if cache_requests is True:
if proxy_dict is None:
soap_transport = CachedThrottledTransport(
cache_dir=SOAP_CACHE,
max_age=max_age,
minimum_spacing=minimum_spacing,
)
else:
soap_transport = CachedThrottledTransport(
cache_dir=SOAP_CACHE,
max_age=max_age,
minimum_spacing=minimum_spacing,
proxy=proxy_dict,
)
else:
if proxy_dict is None:
soap_transport = HttpAuthenticated()
else:
soap_transport = HttpAuthenticated(proxy=proxy_dict)
return Client(wsdl, transport=soap_transport)
def __init__(self, wsdl_url, username, password, servicename=None):
#create parser and download the WSDL document
self.url = wsdl_url
self.username = username
self.password = password
self.servicename = servicename
if servicename:
self.url = self.get_service_url()
if is_https(self.url):
logger.info("Creating secure connection")
from suds.transport.http import HttpAuthenticated
http_transport = HttpAuthenticated(username=self.username,
password=self.password)
else:
from suds.transport.http import HttpAuthenticated
http_transport = HttpAuthenticated(username=self.username,
password=self.password)
#Client.__init__(self, self.url, transport=http_transport, plugins=[SoapFixer()]) # uncomment after testing
#schema_import = Import(schema_url)
#schema_doctor = ImportDoctor(schema_import)
Client.__init__(self,
self.url,
transport=http_transport,
plugins=[SoapFixer()]) # added for testing purpose
def process(self, _edObject=None):
"""
First uses the ImageService to find the imageId.
Then uses ToolsForCollectionWebService for storing the image quality indicators.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreImageQualityIndicatorsv1_4.process")
# First get the image ID
xsDataImageQualityIndicators = self.getDataInput().getImageQualityIndicators()
strPathToImage = xsDataImageQualityIndicators.getImage().getPath().getValue()
strDirName = os.path.dirname(strPathToImage)+os.sep
strFileName = os.path.basename(strPathToImage)
if strDirName.endswith(os.sep):
strDirName = strDirName[:-1]
self.DEBUG("Looking for ISPyB imageId for dir %s name %s" % (strDirName, strFileName))
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(self.strToolsForCollectionWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService)
iDataCollectionId = clientToolsForCollectionWebService.service.findDataCollectionFromFileLocationAndFileName(
strDirName, \
strFileName, \
)
print iDataCollectionId
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(self.strToolsForAutoprocessingWebServiceWsdl, transport=httpAuthenticatedToolsForAutoprocessingWebService)
iImageId = 0
iAutoProcProgramId = self.iAutoProcProgramId
iSpotTotal = xsDataImageQualityIndicators.getSpotTotal().getValue()
iInResTotal = xsDataImageQualityIndicators.getInResTotal().getValue()
iGoodBraggCandidates = xsDataImageQualityIndicators.getGoodBraggCandidates().getValue()
iIceRings = xsDataImageQualityIndicators.getIceRings().getValue()
fMethod1res = xsDataImageQualityIndicators.getMethod1Res().getValue()
fMethod2res = xsDataImageQualityIndicators.getMethod2Res().getValue()
fMaxUnitCell = xsDataImageQualityIndicators.getMaxUnitCell().getValue()
fPctSaturationTop50peaks = xsDataImageQualityIndicators.getPctSaturationTop50Peaks().getValue()
iInResolutionOvrlSpots = xsDataImageQualityIndicators.getInResolutionOvrlSpots().getValue()
fBinPopCutOffMethod2res = xsDataImageQualityIndicators.getBinPopCutOffMethod2Res().getValue()
providedDate = Date(datetime.datetime.now())
self.iImageQualityIndicatorsId = clientToolsForAutoprocessingWebService.service.storeImageQualityIndicators(
strDirName, \
strFileName, \
iImageId, \
iAutoProcProgramId, \
iSpotTotal, \
iInResTotal, \
iGoodBraggCandidates, \
iIceRings, \
fMethod1res, \
fMethod2res, \
fMaxUnitCell, \
fPctSaturationTop50peaks, \
iInResolutionOvrlSpots, \
fBinPopCutOffMethod2res, \
providedDate)
self.DEBUG("EDPluginISPyBStoreImageQualityIndicatorsv1_4.process: imageQualityIndicatorsId=%d" % self.iImageQualityIndicatorsId)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreGridInfov1_4.process")
# First get the image ID
xsDataInputGridInfo = self.getDataInput()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService)
gridInfoWS3VO = clientToolsForCollectionWebService.factory.create(
'gridInfoWS3VO')
gridInfoWS3VO.gridInfoId = self.getXSValue(
xsDataInputGridInfo.gridInfoId)
gridInfoWS3VO.workflowMeshId = self.getXSValue(
xsDataInputGridInfo.workflowMeshId)
gridInfoWS3VO.dx_mm = self.getXSValue(xsDataInputGridInfo.dx_mm)
gridInfoWS3VO.dy_mm = self.getXSValue(xsDataInputGridInfo.dy_mm)
gridInfoWS3VO.xOffset = self.getXSValue(xsDataInputGridInfo.xOffset)
gridInfoWS3VO.yOffset = self.getXSValue(xsDataInputGridInfo.yOffset)
gridInfoWS3VO.steps_x = self.getXSValue(xsDataInputGridInfo.steps_x)
gridInfoWS3VO.steps_y = self.getXSValue(xsDataInputGridInfo.steps_y)
gridInfoWS3VO.meshAngle = self.getXSValue(
xsDataInputGridInfo.meshAngle)
# print gridInfoWS3VO
self.iGridInfoId = clientToolsForCollectionWebService.service.storeOrUpdateGridInfo(
gridInfoWS3VO)
self.DEBUG("EDPluginISPyBStoreGridInfov1_4.process: WorkflowId=%d" %
self.iGridInfoId)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBSetDataCollectionPositionv1_4.process")
# Get the workflow ID and status
strImagePath = self.dataInput.fileName.path.value
xsDataStartPosition = self.dataInput.startPosition
xsDataEndPosition = self.dataInput.endPosition
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService)
startMotorPosition3VO = self.createMotorPosition3VO(
clientToolsForCollectionWebService, xsDataStartPosition)
if xsDataEndPosition is not None:
endMotorPosition3VO = self.createMotorPosition3VO(
clientToolsForCollectionWebService, xsDataEndPosition)
else:
endMotorPosition3VO = None
self.iDataCollectionId = clientToolsForCollectionWebService.service.setDataCollectionPosition(
fileLocation = os.path.dirname(strImagePath), \
fileName = os.path.basename(strImagePath), \
startPosition = startMotorPosition3VO, \
endPosition = endMotorPosition3VO)
self.DEBUG(
"EDPluginISPyBSetDataCollectionPositionv1_4.process: DataCollectionId=%r"
% self.iDataCollectionId)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBSetImageQualityIndicatorsPlotv1_4.process")
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
# Loop over all positions
xsDataInputISPyBSetImageQualityIndicatorsPlot = self.getDataInput()
iDataCollectionId = self.getXSValue(
xsDataInputISPyBSetImageQualityIndicatorsPlot.dataCollectionId)
imageQualityIndicatorsPlotPath = self.getXSValue(
xsDataInputISPyBSetImageQualityIndicatorsPlot.
imageQualityIndicatorsPlotPath)
imageQualityIndicatorsCSVPath = self.getXSValue(
xsDataInputISPyBSetImageQualityIndicatorsPlot.
imageQualityIndicatorsCSVPath)
self.dataCollectionId = clientToolsForCollectionWebService.service.setImageQualityIndicatorsPlot(
arg0=iDataCollectionId, \
imageQualityIndicatorsPlotPath=imageQualityIndicatorsPlotPath, \
imageQualityIndicatorsCSVPath=imageQualityIndicatorsCSVPath, \
)
self.DEBUG(
"EDPluginISPyBSetImageQualityIndicatorsPlotv1_4.process: dataCollectionId=%r"
% self.dataCollectionId)
def run(self, inData):
dictConfig = UtilsConfig.getTaskConfig('ISPyB')
username = dictConfig['username']
password = dictConfig['password']
httpAuthenticated = HttpAuthenticated(username=username,
password=password)
wdsl = dictConfig['ispyb_ws_url'] + '/ispybWS/ToolsForCollectionWebService?wsdl'
client = Client(wdsl, transport=httpAuthenticated, cache=None)
if 'image' in inData:
path = pathlib.Path(inData['image'])
indir = path.parent.as_posix()
infilename = path.name
dataCollection = client.service.findDataCollectionFromFileLocationAndFileName(
indir,
infilename
)
elif 'dataCollectionId' in inData:
dataCollectionId = inData['dataCollectionId']
dataCollection = client.service.findDataCollection(dataCollectionId)
else:
errorMessage = 'Neither image nor data collection id given as input!'
logger.error(errorMessage)
raise BaseException(errorMessage)
if dataCollection is not None:
outData = Client.dict(dataCollection)
else:
outData = {}
return outData
def process(self, _edObject=None):
"""
First uses the ImageService to find the imageId.
Then uses ToolsForCollectionWebService for storing the image quality indicators.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process")
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(self.strToolsForAutoprocessingWebServiceWsdl, transport=httpAuthenticatedToolsForAutoprocessingWebService)
# Loop over all input image quality indicators:
listImageQualityIndicatorsForWS = []
for xsDataImageQualityIndicators in self.dataInput.imageQualityIndicators:
#print xsDataImageQualityIndicators.marshal()
imageQualityIndicatorsWS3VO = clientToolsForAutoprocessingWebService.factory.create('imageQualityIndicatorsWS3VO')
strPathToImage = xsDataImageQualityIndicators.getImage().getPath().getValue()
imageQualityIndicatorsWS3VO.fileName = os.path.basename(strPathToImage)
imageQualityIndicatorsWS3VO.fileLocation = os.path.dirname(strPathToImage)
# imageQualityIndicatorsWS3VO.imageId = 0
imageQualityIndicatorsWS3VO.autoProcProgramId = self.iAutoProcProgramId
imageQualityIndicatorsWS3VO.spotTotal = self.getXSValue(xsDataImageQualityIndicators.spotTotal)
imageQualityIndicatorsWS3VO.inResTotal = self.getXSValue(xsDataImageQualityIndicators.inResTotal)
imageQualityIndicatorsWS3VO.goodBraggCandidates = self.getXSValue(xsDataImageQualityIndicators.goodBraggCandidates)
imageQualityIndicatorsWS3VO.iceRings = self.getXSValue(xsDataImageQualityIndicators.iceRings)
imageQualityIndicatorsWS3VO.method1Res = self.getXSValue(xsDataImageQualityIndicators.method1Res)
imageQualityIndicatorsWS3VO.method2Res = self.getXSValue(xsDataImageQualityIndicators.method2Res)
imageQualityIndicatorsWS3VO.maxUnitCell = self.getXSValue(xsDataImageQualityIndicators.maxUnitCell)
imageQualityIndicatorsWS3VO.pctSaturationTop50Peaks = self.getXSValue(xsDataImageQualityIndicators.pctSaturationTop50Peaks)
imageQualityIndicatorsWS3VO.inResolutionOvrlSpots = self.getXSValue(xsDataImageQualityIndicators.inResolutionOvrlSpots)
imageQualityIndicatorsWS3VO.binPopCutOffMethod2Res = self.getXSValue(xsDataImageQualityIndicators.binPopCutOffMethod2Res)
imageQualityIndicatorsWS3VO.totalIntegratedSignal = self.getXSValue(xsDataImageQualityIndicators.totalIntegratedSignal)
imageQualityIndicatorsWS3VO.recordTimeStamp = DateTime(datetime.datetime.now())
listImageQualityIndicatorsForWS.append(imageQualityIndicatorsWS3VO)
self.listImageQualityIndicatorsId = clientToolsForAutoprocessingWebService.service.storeOrUpdateImageQualityIndicatorsForFileNames(
listImageQualityIndicatorsForWS = listImageQualityIndicatorsForWS)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process: listImageQualityIndicatorsId=%r" % self.listImageQualityIndicatorsId)
def init_connection(self, company):
t = HttpAuthenticated(
username=company.postlogistics_username,
password=company.postlogistics_password)
self.client = Client(
company.postlogistics_wsdl_url,
transport=t)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBSetImagesPositionsv1_4.process")
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
# Loop over all positions
listImagePosition = []
for xsDataImagePosition in self.dataInput.imagePosition:
imagePosition = clientToolsForCollectionWebService.factory.create('imagePosition')
# Get the workflow ID and status
imagePosition.fileName = os.path.basename(xsDataImagePosition.fileName.path.value)
imagePosition.fileLocation = os.path.dirname(xsDataImagePosition.fileName.path.value)
if xsDataImagePosition.jpegFileFullPath is not None:
imagePosition.jpegFileFullPath = xsDataImagePosition.jpegFileFullPath.path.value
if xsDataImagePosition.jpegThumbnailFileFullPath is not None:
imagePosition.jpegThumbnailFileFullPath = xsDataImagePosition.jpegThumbnailFileFullPath.path.value
listImagePosition.append(imagePosition)
self.listImageCreation = clientToolsForCollectionWebService.service.setImagesPositions(
listImagePosition=listImagePosition)
self.DEBUG("EDPluginISPyBSetImagesPositionsv1_4.process: listImageCreation=%r" % self.listImageCreation)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBStoreWorkflowv1_4.process")
# First get the image ID
xsDataWorkflow = self.getDataInput().getWorkflow()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
workflow3VO = clientToolsForCollectionWebService.factory.create('workflow3VO')
workflow3VO.comments = self.getXSValue(xsDataWorkflow.comments)
workflow3VO.logFilePath = self.getXSValue(xsDataWorkflow.logFilePath)
workflow3VO.recordTimeStamp = self.getDateValue(xsDataWorkflow.recordTimeStamp, "%a %b %d %H:%M:%S %Y", DateTime(datetime.datetime.now()))
workflow3VO.resultFilePath = self.getXSValue(xsDataWorkflow.resultFilePath)
workflow3VO.status = self.getXSValue(xsDataWorkflow.status)
workflow3VO.workflowId = self.getXSValue(xsDataWorkflow.workflowId)
workflow3VO.workflowTitle = self.getXSValue(xsDataWorkflow.workflowTitle)
workflow3VO.workflowType = self.getXSValue(xsDataWorkflow.workflowType)
# print workflow3VO
self.iWorkflowId = clientToolsForCollectionWebService.service.storeOrUpdateWorkflow(workflow3VO)
self.DEBUG("EDPluginISPyBStoreWorkflowv1_4.process: WorkflowId=%d" % self.iWorkflowId)
def _get_suds_client(self, url, **kw):
"""
Make a suds client for a specifij WSDL (via url).
Added new Suds cache features. Warning: These don't work on
Windows. *nix should be fine. Also exposed general kwargs to pass
down to Suds for advance users who don't want to deal with set_options().
"""
if self.fromurl == False:
# We're file:// access, so don't use https transport.
t = HttpAuthenticated(username=self.username,
password=self.password)
c = Client(url, transport=t, doctor=DOCTOR, **kw)
else:
try:
c = Client(url,
username=self.username,
password=self.password,
doctor=DOCTOR,
**kw)
except URLError as e:
t = HTTPSUnVerifiedCertTransport(username=self.username,
password=self.password)
c = Client(url,
username=self.username,
password=self.password,
doctor=DOCTOR,
transport=t,
**kw)
return c
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBGroupDataCollectionsv1_4.process")
xsDataInput = self.getDataInput()
arrayOfFileLocation = []
arrayOfFileName = []
for xsDataStringFilePath in xsDataInput.filePath:
strFilePath = xsDataStringFilePath.value
arrayOfFileLocation.append(os.path.dirname(strFilePath))
arrayOfFileName.append(os.path.basename(strFilePath))
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
self.listDataCollectionIds = clientToolsForCollectionWebService.service.groupDataCollections(\
dataCollectionGroupId=self.getXSValue(xsDataInput.dataCollectionGroupId), \
arrayOfFileLocation=arrayOfFileLocation, \
arrayOfFileName=arrayOfFileName, \
)
self.DEBUG(
"EDPluginISPyBGroupDataCollectionsv1_4.process: listDataCollectionIds=%r"
% self.listDataCollectionIds)
def _wsdl_client(self, service_name):
# Handling of redirection at soleil needs cookie handling
cj = CookieJar()
url_opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj))
trans = HttpAuthenticated(username=self.ws_username,
password=self.ws_password)
logging.info('_wsdl_client service_name %s - trans %s' %
(service_name, trans))
print '_wsdl_client service_name %s - trans %s' % (service_name, trans)
trans.urlopener = url_opener
urlbase = service_name + "?wsdl"
locbase = service_name
ws_root = self.ws_root.strip()
url = ws_root + urlbase
loc = ws_root + locbase
print '_wsdl_client, url', url
ws_client = Client(url, transport=trans, timeout=3, \
location=loc, cache = None)
return ws_client
def process(self, _edObject=None):
"""
Stores the contents of the AutoProcContainer in ISPyB.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreAutoProcStatusv1_4.process")
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(
self.strToolsForAutoprocessingWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService)
xsDataInputStoreAutoProcStatus = self.getDataInput()
if xsDataInputStoreAutoProcStatus.dataCollectionId is not None:
iDataCollectionId = xsDataInputStoreAutoProcStatus.dataCollectionId
if xsDataInputStoreAutoProcStatus.autoProcIntegrationId is not None:
self.iAutoProcIntegrationId = xsDataInputStoreAutoProcStatus.autoProcIntegrationId
if xsDataInputStoreAutoProcStatus.autoProcStatusId is not None:
self.iAutoProcStatusId = xsDataInputStoreAutoProcStatus.autoProcStatusId
# If autoProcIntegrationId is not given a dataCollectionId must be present:
if (self.iAutoProcIntegrationId is None) and (iDataCollectionId is
None):
strErrorMessage = "Either data collection id or auto proc integration id must be given as input!"
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
else:
if self.iAutoProcIntegrationId is None:
# If no autoProcessingId is given create a dummy entry in the integration table
self.iAutoProcIntegrationId = self.storeOrUpdateAutoProcIntegration(
clientToolsForAutoprocessingWebService,
_iDataCollectionId=iDataCollectionId)
# Store the AutoProcStatus
self.iAutoProcStatusId = self.storeOrUpdateAutoProcStatus(clientToolsForAutoprocessingWebService, \
_xsDataAutoProcStatus = xsDataInputStoreAutoProcStatus.getAutoProcStatus(), \
_iAutoProcIntegrationId = self.iAutoProcIntegrationId, \
_iAutoProcStatusId = self.iAutoProcStatusId)
def __init__(self, url, username, password):
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(
username=username, password=password)
self.client = Client(
url,
transport=httpAuthenticatedToolsForAutoprocessingWebService,
cache=None,
timeout=15)
def main():
url = 'https://blah.com/soap/sp/Services?wsdl'
credentials = dict(username='******', password='******')
t = HttpAuthenticated(**credentials)
client = Client(url,
location='https://blah.com/soap/sp/Services',
transport=t)
print(client.last_sent())
def send(self, xml):
t = HttpAuthenticated(username='******', password='******')
client = Client(
url='http://test3.alignetsac.com/sfewsperu/ws/invoker?wsdl',
transport=t)
response = client.service.invoke(xml)
_logger.info('resultado ' + response)
return self
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG(
"EDPluginISPyBUpdateDataCollectionGroupWorkflowIdv1_4.process")
xsDataInput = self.getDataInput()
newComment = xsDataInput.newComment.value
# print xsDataInput.marshal()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
if xsDataInput.dataCollectionId is None:
self.ERROR("No input data collection id")
self.setFailure()
return
dataCollectionId = xsDataInput.dataCollectionId.value
dataCollectionWS3VO = clientToolsForCollectionWebService.service.findDataCollection(
dataCollectionId)
if dataCollectionWS3VO is None:
self.ERROR(
"No data collection corresponding to data collection id {0}".
format(dataCollectionId))
self.setFailure()
return
dataCollectionGroupId = dataCollectionWS3VO.dataCollectionGroupId
if dataCollectionGroupId is None:
self.ERROR(
"No data collection group corresponding to data collection id {0}"
.format(dataCollectionId))
self.setFailure()
return
dataCollectionGroupWS3VO = clientToolsForCollectionWebService.service.findDataCollectionGroup(
dataCollectionGroupId)
if not newComment in str(dataCollectionGroupWS3VO.comments):
dataCollectionGroupWS3VO.comments = newComment
self.iDataCollectionGroupId = clientToolsForCollectionWebService.service.storeOrUpdateDataCollectionGroup(
dataCollectionGroupWS3VO)
# Make sure the comments hasn't already been added by ISPyB:
dataCollectionWS3VO = clientToolsForCollectionWebService.service.findDataCollection(
dataCollectionId)
if hasattr(dataCollectionWS3VO, "comments"):
if not newComment in dataCollectionWS3VO.comments:
dataCollectionWS3VO.comments += " " + newComment
dataCollectionId = clientToolsForCollectionWebService.service.storeOrUpdateDataCollection(
dataCollectionWS3VO)
else:
dataCollectionWS3VO.comments = newComment
dataCollectionId = clientToolsForCollectionWebService.service.storeOrUpdateDataCollection(
dataCollectionWS3VO)
self.DEBUG(
"EDPluginISPyBUpdateDataCollectionGroupWorkflowIdv1_4.process: DataCollectionGroupId=%r"
% self.iDataCollectionGroupId)
def __initWebservice(self):
self.httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(
username=self.user, password=self.password)
self.client = Client(
self.URL,
transport=self.httpAuthenticatedToolsForAutoprocessingWebService,
cache=None,
timeout=self.timeout)
self.experiments = []
self.response = None
def __init__(self, **kwargs):
if 'url' not in kwargs.keys():
self.complain(self.parameter_error, 'url')
self.__dict__.update(kwargs)
t = HttpAuthenticated(username=self.username, password=self.password)
#self.client = Client(self.url, transport=t)
self.client = Client(self.url)
self.service = self.client.service
self.session = self.service.login(self.username, self.password)
def init_app(self, app):
"""Initializes user office class.
Args:
app (flask app): Flask app
"""
http_auth = HttpAuthenticated(username=app.config.get("SMIS_USERNAME"),
password=app.config.get("SMIS_PASSWORD"))
self.smis_ws = Client(app.config.get("SMIS_WS_URL"),
transport=http_auth,
cache=None,
timeout=180)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBUpdateWorkflowStatusv1_4.process")
# Get the workflow ID and status
iWorkflowId = self.dataInput.workflowId.value
strStatus = self.dataInput.newStatus.value
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(self.strToolsForCollectionWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService)
self.iWorkflowId = clientToolsForCollectionWebService.service.updateWorkflowStatus(iWorkflowId, strStatus)
self.DEBUG("EDPluginISPyBUpdateWorkflowStatusv1_4.process: WorkflowId=%d" % self.iWorkflowId)
def __init__(self, credentials):
# logging.basicConfig(level=logging.INFO)
# logging.getLogger('suds.client').setLevel(logging.DEBUG)
soap_url = 'http://api.rostelecontent.ru/server.services.php'
wsdl_url = 'http://api.rostelecontent.ru/services.wsdl'
transport = HttpAuthenticated(**credentials)
self.api = Client(url=wsdl_url,
location=soap_url,
transport=transport,
plugins=[NamespaceCorrectionPlugin()])
self.api.set_options(cache=None)
def main():
# Build transport and client objects using HttpAuth for authentication
# and MessagePlugin to allow the capturing of raw XML, necessary for
# extracting the IPControl session ID later
plugin = MyPlugin()
credentials = dict(username=user, password=pw)
transport = HttpAuthenticated(**credentials)
client = Client('http://ipcontrol.foobar.net/inc-ws/services/Exports?wsdl',
headers={
'username': user,
'password': pw
},
transport=transport,
plugins=[plugin])
query_parameters = ('ipaddress = 1.2.3.4', False
) # The boolean is for includeFreeBlocks
# Exports must be initialized first. The IPControl session ID can then
# be extracted from the raw reply data. This is necessary later when
# the export service is called.
context = client.service.initExportChildBlock(*query_parameters)
session_id_re = re.search(r'([0-9-]{19,20})',
str(plugin.last_received_raw), re.M)
if session_id_re:
session_id = session_id_re.group(1)
print("SESSION ID: {}".format(session_id))
else:
print("NO SESSION ID FOUND")
sys.exit()
# Build a new SOAP header where the 'sessionID' is set to the value extracted
# from the raw initialization reply data above, then apply the new
# header to the existing client object.
sid = Element(
'sessionID',
ns=('ns1', 'http://xml.apache.org/axis/session')).setText(session_id)
sid.set("SOAP-ENV:mustUnderstand", "0")
sid.set("SOAP-ENV:actor", "http://schemas.xmlsoap.org/soap/actor/next")
sid.set("xsi:type", "soapenc:long")
client.set_options(soapheaders=sid)
result = client.service.exportChildBlock(context)
print("RESULT: {}".format(result))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
# Initializing webservices
self.DEBUG("EDPluginBioSaxsISPyBv1_0.preProcess")
self.dataBioSaxsSample = self.dataInput.sample
user = None
password = ""
if self.dataBioSaxsSample:
if self.dataBioSaxsSample.login:
user = self.dataBioSaxsSample.login.value
password = self.dataBioSaxsSample.passwd.value
if not user:
self.ERROR(
"No login/password information in sample configuration. Giving up."
)
self.setFailure()
return
# I don't trust in this authentication.... but it is going to work soon
self.httpAuthenticatedToolsForBiosaxsWebService = HttpAuthenticated(
username=user, password=password)
self.client = Client(
self.URL,
transport=self.httpAuthenticatedToolsForBiosaxsWebService,
cache=None)
if self.dataInput.dammifAvg:
self.dammifAvg = self.dataInput.dammifAvg.value
if self.dataInput.dammifFilter:
self.dammifFilter = self.dataInput.dammifFilter.value
if self.dataInput.dammifStart:
self.dammifStart = self.dataInput.dammifStart.value
if self.dataInput.dammifJobs:
self.dammifJobs = self.dataInput.dammifJobs.value
if self.dataInput.scatterPlotFile:
self.scatterPlotFilePath = self.dataInput.scatterPlotFile.path.value
if self.dataInput.guinierPlotFile:
self.guinierPlotFilePath = self.dataInput.guinierPlotFile.path.value
if self.dataInput.kratkyPlotFile:
self.kratkyPlotFilePath = self.dataInput.kratkyPlotFile.path.value
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
# Initializing webservices
self.DEBUG("EDPluginBioSaxsISPyB_HPLCv1_0.preProcess")
self.dataBioSaxsSample = self.dataInput.sample
user = None
password = ""
if self.dataBioSaxsSample:
if self.dataBioSaxsSample.login:
user = self.dataBioSaxsSample.login.value
password = self.dataBioSaxsSample.passwd.value
if self.dataBioSaxsSample.ispybURL:
self.URL = self.dataBioSaxsSample.ispybURL.value
if not user:
self.ERROR(
"No login/password information in sample configuration. Giving up. falling back on test mode"
)
# self.setFailure()
# return
user = "******"
password = "******"
# construct code based on letters + numbers user concept
self.code = ''.join(i for i in user if i.isalpha())
self.number = ''.join(i for i in user if i.isdigit())
# I don't trust in this authentication.... but it is going to work soon
self.httpAuthenticatedToolsForBiosaxsWebService = HttpAuthenticated(
username=user, password=password)
self.client = Client(
self.URL,
transport=self.httpAuthenticatedToolsForBiosaxsWebService,
cache=None)
if (self.dataInput.hdf5File is not None):
if (self.dataInput.hdf5File.path is not None):
self.hdf5File = self.dataInput.hdf5File.path.value
if (self.dataInput.jsonFile is not None):
if (self.dataInput.jsonFile.path is not None):
self.jsonFile = self.dataInput.jsonFile.path.value
if (self.dataInput.hplcPlot is not None):
if (self.dataInput.hplcPlot.path is not None):
self.hplcPlot = self.dataInput.hplcPlot.path.value
def _get_suds_client(self, url):
"""
Make a suds client for a specific WSDL (via url).
For now, we have to work around a few minor issues with the Suds cache
and different authentication methods based on uri or file:// access.
"""
if self.fromurl == False:
# We're file:// access, so don't use https transport.
t = HttpAuthenticated(username = self.username, password = self.password)
# Suds will intermittantly throw a SAX exception trying to parse cached files.
# if it does this, retry.
c = Client(url, transport=t, doctor=DOCTOR)
else:
c = Client(url, username=self.username, password=self.password,doctor=DOCTOR)
return c
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBStoreWorkflowStepv1_4.process")
# First get the image ID
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService,
cache=None)
dictWorkflowStep = {
"workflowId":
self.getXSValue(self.dataInput.workflowId),
"workflowStepType":
self.getXSValue(self.dataInput.workflowStepType),
"status":
self.getXSValue(self.dataInput.status),
"folderPath":
self.getXSValue(self.dataInput.folderPath),
"imageResultFilePath":
self.getXSValue(self.dataInput.imageResultFilePath),
"htmlResultFilePath":
self.getXSValue(self.dataInput.htmlResultFilePath),
"resultFilePath":
self.getXSValue(self.dataInput.resultFilePath),
"comments":
self.getXSValue(self.dataInput.comments),
"crystalSizeX":
self.getXSValue(self.dataInput.crystalSizeX),
"crystalSizeY":
self.getXSValue(self.dataInput.crystalSizeY),
"crystalSizeZ":
self.getXSValue(self.dataInput.crystalSizeZ),
"maxDozorScore":
self.getXSValue(self.dataInput.maxDozorScore),
}
strDictWorkflowStep = json.dumps(dictWorkflowStep)
self.iWorkflowStepId = clientToolsForCollectionWebService.service.storeWorkflowStep(
strDictWorkflowStep)
self.DEBUG(
"EDPluginISPyBStoreWorkflowStepv1_4.process: WorkflowStepId = {0}".
format(self.iWorkflowStepId))
