def test_logging(self):
logger = UtilsLogging.getLogger('DEBUG')
logger.debug("Test message debug")
logger.info("Test message info")
logger.warning("Test message warning")
logger.error("Test message error")
logger.critical("Test message critical")
logger.fatal("Test message fatal")
def setImageQualityIndicatorsPlot(dataCollectionId, plotFile, csvFile):
logger = UtilsLogging.getLogger()
client = getCollectionWebService()
if client is None:
logger.error(
"No web service client available, cannot contact setImageQualityIndicatorsPlot web service."
)
returnDataCollectionId = client.service.setImageQualityIndicatorsPlot(
dataCollectionId, plotFile, csvFile)
return returnDataCollectionId
def getTransport():
transport = None
logger = UtilsLogging.getLogger()
if not "ISPyB_user" in os.environ:
logger.error("No ISPyB user name defined as environment variable!")
elif not "ISPyB_pass" in os.environ:
logger.error("No ISPyB password defined as environment variable!")
else:
ispybUserName = os.environ["ISPyB_user"]
ispybPassword = os.environ["ISPyB_pass"]
transport = HttpAuthenticated(username=ispybUserName,
password=ispybPassword)
return transport
def getCollectionWebService():
logger = UtilsLogging.getLogger()
collectionWdsl = getToolsForCollectionWebService()
transport = getTransport()
if transport is None:
logger.error(
"No transport defined, ISPyB web service client cannot be instantiated."
)
collectionWSClient = None
else:
collectionWSClient = Client(collectionWdsl,
transport=transport,
cache=None)
return collectionWSClient
def findDataCollectionFromFileLocationAndFileName(imagePath, client=None):
logger = UtilsLogging.getLogger()
dataCollectionWS3VO = None
noTrials = 10
fileLocation = os.path.dirname(imagePath)
fileName = os.path.basename(imagePath)
if fileName.endswith(".h5"):
prefix = UtilsImage.getPrefix(fileName)
imageNumber = UtilsImage.getImageNumber(fileName)
fileName = "{0}_{1:04d}.h5".format(prefix, imageNumber)
try:
if client is None:
client = getCollectionWebService()
if client is None:
logger.error(
"No web service client available, cannot contact findDataCollectionFromFileLocationAndFileName web service."
)
elif fileLocation is None:
logger.error(
"No fileLocation given, cannot contact findDataCollectionFromFileLocationAndFileName web service."
)
elif fileName is None:
logger.error(
"No fileName given, cannot contact findDataCollectionFromFileLocationAndFileName web service."
)
else:
dataCollectionWS3VO = client.service.findDataCollectionFromFileLocationAndFileName(
fileLocation, fileName)
except Exception as e:
logger.error(
"ISPyB error for findDataCollectionFromFileLocationAndFileName: {0}, {1} trials left"
.format(e, noTrials))
raise e
if dataCollectionWS3VO is None:
time.sleep(1)
if noTrials == 0:
raise RuntimeError(
"ISPyB error for findDataCollectionFromFileLocationAndFileName - no data collections found for path {0}"
.format(imagePath))
else:
logger.warning(
"Cannot find {0} in ISPyB - retrying, {1} trials left".format(
imagePath, noTrials))
return dataCollectionWS3VO
def findDataCollection(dataCollectionId, client=None):
e = None
dataCollectionWS3VO = None
noTrials = 5
logger = UtilsLogging.getLogger()
try:
if client is None:
client = getCollectionWebService()
if client is None:
logger.error(
"No web service client available, cannot contact findDataCollection web service."
)
elif dataCollectionId is None:
logger.error(
"No dataCollectionId given, cannot contact findDataCollection web service."
)
else:
dataCollectionWS3VO = client.service.findDataCollection(
dataCollectionId)
except Exception as e:
logger.error(
"ISPyB error for findDataCollection: {0}, {1} trials left".format(
e, noTrials))
return dataCollectionWS3VO
# 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.
#
__authors__ = ['O. Svensson']
__license__ = 'MIT'
__date__ = '21/04/2019'
from edna2.utils import UtilsLogging
from edna2.tasks.AbstractTask import AbstractTask
from edna2.tasks.test.ParallelTasks.ExampleTask import ExampleTask
logger = UtilsLogging.getLogger()
class ControlTestTask(AbstractTask):
"""
Control task for testing parallel execution
"""
def run(self, inData):
numberOfTasks = inData['numberOfTasks']
startNumber = inData['startNumber']
listTasks = []
for taskNumber in range(startNumber, startNumber + numberOfTasks):
testTaskInData = {'taskNumber': taskNumber}
testTask = ExampleTask(inData=testTaskInData)
logger.info(testTask)
listTasks.append(testTask)
if taskName is None:
parser.print_help()
sys.exit(1)
elif inData is None and inDataFile is not None:
with open(inDataFile) as fd:
inData = fd.read()
else:
print("Error - no indata provided!")
parser.print_help()
sys.exit(1)
# Set up logging
if errorLogLevel:
logger = UtilsLogging.getLogger('ERROR')
elif warningLogLevel:
logger = UtilsLogging.getLogger('WARNING')
elif debugLogLevel:
logger = UtilsLogging.getLogger('DEBUG')
else:
logger = UtilsLogging.getLogger('INFO')
# Load and run EDNA2 task
edna2 = __import__('edna2.tasks.{0}'.format(taskName))
tasks = getattr(edna2, "tasks")
tasksModule = getattr(tasks, taskName)
TaskClass = getattr(tasksModule, taskName)
task = TaskClass(inData=json.loads(inData))
task.execute()
