hcs_image_raw.py

#! /usr/bin/env python

import commonImageDropbox
import commonDropbox

reload(commonImageDropbox)
reload(commonDropbox)

""" sample type code of the plate, needed if a new sample is registered automatically """
PLATE_TYPE_CODE = "PLATE"
SIRNA_EXP_TYPE = "SIRNA_HCS"
PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"

iBrain2DatasetId = None

def createPlateWithExperimentIfNeeded(transaction, assayParser, plateCode, spaceCode, plateGeometry):
    projectCode = assayParser.get(assayParser.EXPERIMENTER_PROPERTY)
    experiment = assayParser.get(assayParser.ASSAY_ID_PROPERTY)
    experimentDesc = assayParser.get(assayParser.ASSAY_DESC_PROPERTY)   
    experimentType = assayParser.get(assayParser.ASSAY_TYPE_PROPERTY)
    
    if transaction.getSpace(spaceCode) == None:
        transaction.createNewSpace(spaceCode, None)
    
    sampleIdentifier = "/"+spaceCode+"/"+plateCode
    plate = transaction.getSample(sampleIdentifier)
    if plate == None:
        projectIdent = "/" + spaceCode +"/" + projectCode
        if transaction.getProject(projectIdent) == None:
            transaction.createNewProject(projectIdent)
        expIdentifier = projectIdent + "/"+experiment
        experiment = transaction.getExperiment(expIdentifier)
        if experiment == None:
            experiment = transaction.createNewExperiment(expIdentifier, SIRNA_EXP_TYPE)
            openbisExpDesc = experimentDesc + " (type: "+experimentType + ")"
            experiment.setPropertyValue("DESCRIPTION", openbisExpDesc)

        plate = transaction.createNewSample(sampleIdentifier, PLATE_TYPE_CODE)
        plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, plateGeometry)
        plate.setExperiment(experiment)
    return plate

def rollback_service(service, throwable):
    global iBrain2DatasetId
    commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
        
def rollback_transaction(service, transaction, algorithmRunner, throwable):
    rollback_service(service, throwable)
    
if incoming.isDirectory():
    incomingPath = incoming.getPath()
    metadataParser = commonDropbox.AcquiredDatasetMetadataParser(incomingPath)
    iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
    assayParser = commonDropbox.AssayParser(incomingPath)

    imageDataset = commonImageDropbox.IBrain2ImageDataSetConfig()
    imageDataset.setRawImageDatasetType()
    imageDataset.setFileFormatType("TIFF")
    imageDataset.setRecognizedImageExtensions(["tif", "tiff"])    
    imageDataset.setStoreChannelsOnExperimentLevel(False)
    imageDataset.setGenerateThumbnails(True)
    imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)

    imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
    for propertyCode, value in metadataParser.getDatasetPropertiesIter():
		imageRegistrationDetails.setPropertyValue(propertyCode, value)
    
    tr = service.transaction(incoming, factory)

    plate = metadataParser.getPlateCode()
    space = assayParser.get(assayParser.LAB_LEADER_PROPERTY)
    plateGeometry = factory.figureGeometry(imageRegistrationDetails)
    plate = createPlateWithExperimentIfNeeded(tr, assayParser, plate, space, plateGeometry)	    

    dataset = tr.createNewDataSet(imageRegistrationDetails)
    dataset.setSample(plate)
    imageDataSetFolder = tr.moveFile(incomingPath, dataset)
    if tr.commit():
        commonDropbox.createSuccessStatus(iBrain2DatasetId, dataset, incomingPath)