From 0da45e96d0556acc762c95b2f140a10af6a9dce9 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Wed, 7 May 2014 11:29:29 +0000
Subject: [PATCH] script for uploading FACS data for Yeastlab
SVN: 31464
---
.../facs_data/BDLSRFortessaDropbox.py | 589 ++++++++++++++++++
.../drop-boxes/facs_data/import_facs.py | 105 ++++
.../drop-boxes/facs_data/plugin.properties | 19 +
3 files changed, 713 insertions(+)
create mode 100644 plasmid/source/drop-boxes/facs_data/BDLSRFortessaDropbox.py
create mode 100644 plasmid/source/drop-boxes/facs_data/import_facs.py
create mode 100644 plasmid/source/drop-boxes/facs_data/plugin.properties
diff --git a/plasmid/source/drop-boxes/facs_data/BDLSRFortessaDropbox.py b/plasmid/source/drop-boxes/facs_data/BDLSRFortessaDropbox.py
new file mode 100644
index 00000000000..57ffbe2b18e
--- /dev/null
+++ b/plasmid/source/drop-boxes/facs_data/BDLSRFortessaDropbox.py
@@ -0,0 +1,589 @@
+"""
+@author: Aaron Ponti
+"""
+import re
+import os
+import logging
+import xml.etree.ElementTree as xml
+from datetime import datetime
+
+class Processor:
+ """The Processor class performs all steps required for registering datasets
+ from the assigned dropbox folder."""
+
+ # A transaction object passed by openBIS
+ transaction = None
+
+ # The incoming folder to process (a java.io.File object)
+ incoming = ""
+
+ # Constructor
+ def __init__(self, transaction, logFile):
+
+ self.transaction = transaction
+ self.incoming = transaction.getIncoming()
+
+ # Set up logging
+ logging.basicConfig(filename=logFile, level=logging.DEBUG)
+
+ def createExperiment(self, expId, expName,
+ expType="LSR_FORTESSA_EXPERIMENT"):
+ """Create an experiment with given Experiment ID extended with the addition
+ of a string composed from current date and time.
+
+ @param expID, the experiment ID
+ @param expName, the experiment name
+ @param expType, the experiment type that must already exist; optional,
+ default is "LSR_FORTESSA_EXPERIMENT"
+ """
+
+ # Make sure to keep the code length within the limits imposed by
+ # openBIS for codes
+ if len(expId) > 41:
+ expId = expId[0:41]
+
+ # Create univocal ID
+ expId = expId + "_" + self.getCustomTimeStamp()
+
+ # Create the experiment
+ logging.info("Register experiment %s" % expId)
+ exp = self.transaction.createNewExperiment(expId, expType)
+ if not exp:
+ msg = "Could not create experiment " + expId + "!"
+ logging.error(msg)
+ raise Exception(msg)
+ else:
+ logging.info("Created experiment with ID " + expId + ".")
+
+ # Store the name
+ exp.setPropertyValue("LSR_FORTESSA_EXPERIMENT_NAME", expName)
+
+ return exp
+
+ def createSampleWithGenCode(self, spaceCode,
+ sampleType="LSR_FORTESSA_PLATE"):
+ """Create a sample with automatically generated code.
+
+ @param spaceCode, the code of the space
+ @param sampleType, the sample type that must already exist
+ @return sample An ISample
+ """
+
+ # Make sure there are not slashes in the spaceCode
+ spaceCode = spaceCode.replace("/", "")
+
+ # Create the sample
+ sample = self.transaction.createNewSampleWithGeneratedCode(spaceCode, sampleType)
+ if not sample:
+ msg = "Could not create sample with generated code"
+ logging.error(msg)
+ raise Exception(msg)
+
+ return sample
+
+ def formatExpDateForPostgreSQL(self, expDate):
+ """Format the experiment date to be compatible with postgreSQL's
+ 'timestamp' data type
+
+ @param Date stored in the FCS file, in the form 01-JAN-2013
+ @return Date in the form 2013-01-01
+ """
+
+ monthMapper = {'JAN': '01', 'FEB': '02', 'MAR': '03', 'APR': '04',
+ 'MAY': '05', 'JUN': '06', 'JUL': '07', 'AUG': '08',
+ 'SEP': '09', 'OCT': '10', 'NOV': '11', 'DEC': '12'}
+
+ # Separate the date into day, month, and year
+ (day, month, year) = expDate.split("-")
+
+ # Try mapping the month to digits (e.g. "06"). If the mapping does
+ # not work, return "NOT_FOUND"
+ month = monthMapper.get(month, "NOT_FOUND")
+
+ # Build the date in the correct format. If the month was not found,
+ # return 01-01-1970
+ if (month == "NOT_FOUND"):
+ logging.info("Invalid experiment date %s found. " \
+ "Reverting to 1970/01/01." % expDate)
+ return "1970-01-01"
+ else:
+ return (year + "-" + month + "-" + day)
+
+ def getCustomTimeStamp(self):
+ """Create an univocal time stamp based on the current date and time
+ (works around incomplete API of Jython 2.5).
+ """
+
+ t = datetime.now()
+ return (t.strftime("%y%d%m%H%M%S") + unicode(t)[20:])
+
+ def getSubFolders(self):
+ """Returns a list of subfolders of the passed incoming directory.
+
+ @return list of subfolders (String)
+ """
+
+ incomingStr = self.incoming.getAbsolutePath()
+ return [name for name in os.listdir(incomingStr)
+ if os.path.isdir(os.path.join(incomingStr, name))]
+
+ def processExperiment(self, experimentNode,
+ openBISExpType="LSR_FORTESSA_EXPERIMENT"):
+ """Register an IExperimentUpdatable based on the Experiment XML node.
+
+ @param experimentNode An XML node corresponding to an Experiment
+ @param openBISExpType The experiment type
+ @return IExperimentUpdatable experiment
+ """
+
+ # Get the openBIS identifier
+ openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
+
+ # Get the experiment name
+ expName = experimentNode.attrib.get("name")
+
+ # Get the experiment date and reformat it to be compatible
+ # with postgreSQL
+ expDate = self.formatExpDateForPostgreSQL(experimentNode.attrib.get("date"))
+
+ # Get the description
+ description = experimentNode.attrib.get("description")
+
+ # Get the acquisition hardware
+ acqHardware = experimentNode.attrib.get("acq_hardware")
+
+ # Get the acquisition software
+ acqSoftware = experimentNode.attrib.get("acq_software")
+
+ # Get the owner name
+ owner = experimentNode.attrib.get("owner_name")
+
+ # Create the experiment (with corrected ID if needed: see above)
+ openBISExperiment = self.createExperiment(openBISIdentifier,
+ expName, openBISExpType)
+ if not openBISExperiment:
+ msg = "Could not create experiment " + openBISIdentifier
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the date
+ openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DATE",
+ expDate)
+ # Set the description
+ openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DESCRIPTION",
+ description)
+
+ # Set the acquisition hardware
+ openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_HARDWARE",
+ acqHardware)
+
+ # Set the acquisition software
+ openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_SOFTWARE",
+ acqSoftware)
+
+ # Set the experiment owner
+ openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_OWNER",
+ owner)
+
+ # Return the openBIS Experiment object
+ return openBISExperiment
+
+ def processFCSFile(self, fcsFileNode, openBISTube, openBISExperiment):
+ """Register the FCS File using the parsed properties file
+
+ @param fcsFileNode An XML node corresponding to an FCS file (dataset)
+ @param openBISTube An ISample object representing a Tube or Well
+ @param openBISExperiment An ISample object representing an Experiment
+ """
+
+ # Dataset type
+ datasetType = "LSR_FORTESSA_FCSFILE"
+
+ # Create a new dataset
+ dataset = self.transaction.createNewDataSet()
+ if not dataset:
+ msg = "Could not get or create dataset"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the dataset type
+ dataset.setDataSetType(datasetType)
+
+ # Assign the dataset to the sample
+ dataset.setSample(openBISTube)
+
+ # Assign the dataset to the experiment
+ dataset.setExperiment(openBISExperiment)
+
+ # Set the file type
+ dataset.setFileFormatType("FCS")
+
+ # Assign the file to the dataset (we will use the absolute path)
+ fileName = fcsFileNode.attrib.get("relativeFileName")
+ fileName = os.path.join(self.incoming.getAbsolutePath(), fileName)
+
+ # Log
+ logging.info("PROCESSFCSFILE: Registering file: " + fileName)
+
+ # Move the file
+ self.transaction.moveFile(fileName, dataset)
+
+
+ def processTray(self, trayNode, openBISExperiment):
+ """Register a Tray (Plate) based on the Tray XML node
+ and an IExperimentUpdatable object
+
+ @param trayNode An XML node corresponding to a Tray (Plate)
+ @param openBISExperiment An IExperimentUpdatable object
+ @param openBISSampleType sample type (default "LSR_FORTESSA_PLATE")
+ @return ISample sample, or null
+ """
+
+ # openBIS sample type
+ openBISSampleType = "LSR_FORTESSA_PLATE"
+
+ # Get the identifier of the space all relevant attributes
+ openBISSpaceIdentifier = \
+ trayNode.attrib.get("openBISSpaceIdentifier")
+
+ # Get the tray name
+ name = trayNode.attrib.get("name")
+
+ # Get the tray geometry
+ trayGeometry = trayNode.attrib.get("trayGeometry")
+
+ # Create the sample. The Plate is configured in openBIS to
+ # auto-generate its own identifier.
+ openBISTray = self.createSampleWithGenCode(openBISSpaceIdentifier,
+ openBISSampleType)
+ if not openBISTray:
+ msg = "Could not create plate sample."
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the experiment for the sample
+ openBISTray.setExperiment(openBISExperiment)
+
+ # Set the plate name
+ openBISTray.setPropertyValue("LSR_FORTESSA_PLATE_NAME", name)
+
+ # Set the tray geometry
+ openBISTray.setPropertyValue("LSR_FORTESSA_PLATE_GEOMETRY", trayGeometry)
+
+ # Return the openBIS ISample object
+ return openBISTray
+
+
+ def processTubeOrWell(self, tubeNode, openBISContainerSample,
+ specimenName, openBISExperiment):
+ """Register a Tube or Well (as a child of a Specimen) based on the Tube or
+ Well XML node and an ISample object.
+
+ The associated fcs file is attached as a IDataset
+
+ @param tubeNode An XML node corresponding to a Tube or Well
+ @param openBISContainerSample An ISample object that will contain
+ the Tube or Well
+ @param specimenName Name of the specimen associated to the Tube or Well
+ @param openBISExperiment The IExperiment to which the Tube belongs
+ @param openBISSpecimenType (default "LSR_FORTESSA_TUBE"), the
+ sample type. One of LSR_FORTESSA_TUBE and LSR_FORTESSA_WELL.
+ @return ISample sample, or null
+ """
+
+ # Get the name
+ name = tubeNode.attrib.get("name")
+
+ # openBIS type
+ if tubeNode.tag == "Tube":
+ openBISSpecimenType = "LSR_FORTESSA_TUBE"
+ elif tubeNode.tag == "Well":
+ openBISSpecimenType = "LSR_FORTESSA_WELL"
+ else:
+ msg = "Unknown tube type" + tubeNode.tag
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Build the openBIS Identifier
+ openBISSpaceIdentifier = \
+ tubeNode.attrib.get("openBISSpaceIdentifier")
+
+ # Create the sample. The Tube/Well is configured in openBIS to
+ # auto-generate its own identifier.
+ openBISTube = self.createSampleWithGenCode(openBISSpaceIdentifier,
+ openBISSpecimenType)
+ if not openBISTube:
+ msg = "Could not create sample with auto-generated identifier"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the experiment to which it belongs
+ openBISTube.setExperiment(openBISExperiment)
+
+ # Set the Specimen name as a property
+ openBISTube.setPropertyValue("LSR_FORTESSA_SPECIMEN", specimenName)
+
+ # Set the name
+ if openBISSpecimenType == "LSR_FORTESSA_TUBE":
+ openBISTube.setPropertyValue("LSR_FORTESSA_TUBE_NAME", name)
+ elif openBISSpecimenType == "LSR_FORTESSA_WELL":
+ openBISTube.setPropertyValue("LSR_FORTESSA_WELL_NAME", name)
+ else:
+ msg = "Unknown value for openBISSpecimenType."
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the TubeSet container
+ openBISTube.setContainer(openBISContainerSample)
+
+ # Return the openBIS ISample
+ return openBISTube
+
+ def processTubeSet(self, experimentNode, openBISExperiment):
+ """Register a TubeSet (virtual tube container).
+
+ @param experimentNode An XML node corresponding to an Experiment
+ @param openBISExperiment An IExperimentUpdatable object
+ @param openBISSampleType The TubeSet sample type
+ @return ISample sample, or null
+ """
+
+ # Sample type
+ openBISSampleType = "LSR_FORTESSA_TUBESET"
+
+ # Get the identifier of the space all relevant attributes
+ openBISSpaceIdentifier = \
+ experimentNode.attrib.get("openBISSpaceIdentifier")
+
+ # Create the sample. The Tubeset is configured in openBIS to
+ # auto-generate its own identifier.
+ openBISTubeSet = self.createSampleWithGenCode(openBISSpaceIdentifier,
+ openBISSampleType)
+ if not openBISTubeSet:
+ msg = "Could not get or create TubeSet"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the experiment for the sample
+ openBISTubeSet.setExperiment(openBISExperiment)
+
+ logging.info("PROCESS_TUBESET: Created new TubeSet " \
+ "with identifier %s, sample type %s" \
+ % (openBISTubeSet.getSampleIdentifier(),
+ openBISSampleType))
+
+ # Return the openBIS ISample object
+ return openBISTubeSet
+
+ def register(self, tree):
+ """Register the Experiment using the parsed properties file.
+
+ @param tree ElementTree parsed from the properties XML file
+ """
+
+ # Get the root node (obitXML)
+ root = tree.getroot()
+
+ # Create a virtual TubeSet
+ openBISTubeSet = None
+
+ # Iterate over the children (Experiments)
+ for experimentNode in root:
+
+ # The tag of the immediate children of the root experimentNode
+ # must be Experiment
+ if experimentNode.tag != "Experiment":
+ msg = "Expected Experiment node, found " + experimentNode.tag
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Process an Experiment XML node and get/create an IExperimentUpdatable
+ openBISExperiment = self.processExperiment(experimentNode,
+ "LSR_FORTESSA_EXPERIMENT")
+
+ # Process children of the Experiment
+ for childNode in experimentNode:
+
+ # The child of an Experiment can be a Tray or a Specimen
+ nodeType = childNode.tag
+
+ if nodeType == "Specimen":
+
+ # A specimen is a direct child of an experiment if there
+ # is no plate, and the FCS files are therefore associated
+ # to tubes. In this case, we create a virtual TubeSet
+ # sample container (one for all Tubes in the experiment).
+ if openBISTubeSet is None:
+ openBISTubeSet = self.processTubeSet(experimentNode,
+ openBISExperiment)
+
+ # The only information we need from the Specimen is its
+ # name to associate to the Tubes as property
+ specimenNameProperty = childNode.attrib.get("name")
+
+ # Now iterate over the children of the Specimen
+ for tubeNode in childNode:
+
+ # The child of a Specimen is a Tube
+ if tubeNode.tag != "Tube":
+ msg = "Expected Tube node!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Process the tube node and get the openBIS object
+ openBISTube = self.processTubeOrWell(tubeNode,
+ openBISTubeSet,
+ specimenNameProperty,
+ openBISExperiment)
+
+ # Now process the FCS file
+ for fcsNode in tubeNode:
+
+ # The child of a Tube is an FCSFile
+ if fcsNode.tag != "FCSFile":
+ msg = "Expected FSC File node!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Process the FCS file node
+ self.processFCSFile(fcsNode, openBISTube,
+ openBISExperiment)
+
+ elif nodeType == "Tray":
+
+ # Process the tray node and get the openBIS object
+ openBISTray = self.processTray(childNode,
+ openBISExperiment)
+
+ # Now iterate over the children of the Tray
+ for specimenNode in childNode:
+
+ # The child of a Tray is a Specimen
+ if specimenNode.tag != "Specimen":
+ msg = "Expected Specimen node!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # The only information we need from the Specimen is its
+ # name to associate to the Wells as property
+ specimenNameProperty = specimenNode.attrib.get("name")
+
+ for wellNode in specimenNode:
+
+ # The child of a Specimen is a Tube
+ if wellNode.tag != "Well":
+ msg = "Expected Well node!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Process the tube node and get the openBIS object
+ openBISWell = self.processTubeOrWell(wellNode,
+ openBISTray,
+ specimenNameProperty,
+ openBISExperiment)
+
+ # Now process the FCS file
+ for fcsNode in wellNode:
+
+ # The child of a Tube is an FCSFile
+ if fcsNode.tag != "FCSFile":
+ msg = "Expected FSC File node!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Process the FCS file node
+ self.processFCSFile(fcsNode, openBISWell,
+ openBISExperiment)
+
+ else:
+
+ msg = "The Node must be either a Specimen or a Tray"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Log that we are finished with the registration
+ logging.info("REGISTER: Registration completed")
+
+
+ def run(self):
+ """Run the registration."""
+
+ # Make sure that incoming is a folder
+ if not self.incoming.isDirectory():
+ msg = "Incoming MUST be a folder!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Log
+ logging.info("Incoming folder: " + self.incoming.getAbsolutePath())
+
+ # There must be just one subfolder: the user subfolder
+ subFolders = self.getSubFolders()
+ if len(subFolders) != 1:
+ msg = "Expected user subfolder!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Set the user folder
+ userFolder = os.path.join(self.incoming.getAbsolutePath(),
+ subFolders[0])
+
+ # In the user subfolder we must find the data_structure.ois file
+ dataFileName = os.path.join(userFolder, "data_structure.ois")
+ if not os.path.exists(dataFileName):
+ msg = "File data_structure.ois not found!"
+ logging.error(msg)
+ raise Exception(msg)
+
+ # Now read the data structure file and store all the pointers to
+ # the properties files. The paths are stored relative to self.incoming,
+ # so we can easily build the full file paths.
+ propertiesFileList = []
+ f = open(dataFileName)
+ try:
+ for line in f:
+ line = re.sub('[\r\n]', '', line)
+ propertiesFile = os.path.join(self.incoming.getAbsolutePath(),
+ line)
+ propertiesFileList.append(propertiesFile)
+ finally:
+ f.close()
+
+ # Process (and ultimately register) all experiments
+ for propertiesFile in propertiesFileList:
+
+ # Log
+ logging.info("* * * Processing: " + propertiesFile)
+
+ # Read the properties file into an ElementTree
+ tree = xml.parse(propertiesFile)
+
+ # Now register the experiment
+ self.register(tree)
+
+
+def process(transaction):
+ """Dropbox entry point.
+
+ @param transaction, the transaction object
+ """
+
+ # Get path to containing folder
+ # __file__ does not work (reliably) in Jython
+ dbPath = "../core-plugins/microscopy/1/dss/drop-boxes/BDLSRFortessaDropbox"
+
+ # Path to the logs subfolder
+ logPath = os.path.join(dbPath, "logs")
+
+ # Make sure the logs subforder exist
+ if not os.path.exists(logPath):
+ os.makedirs(logPath)
+
+ # Path for the log file
+ logFile = os.path.join(logPath, "registration_log.txt")
+
+ # Create a Processor
+ processor = Processor(transaction, logFile)
+
+ # Run
+ processor.run()
diff --git a/plasmid/source/drop-boxes/facs_data/import_facs.py b/plasmid/source/drop-boxes/facs_data/import_facs.py
new file mode 100644
index 00000000000..e9a6e693c29
--- /dev/null
+++ b/plasmid/source/drop-boxes/facs_data/import_facs.py
@@ -0,0 +1,105 @@
+#! /usr/bin/env python
+"""
+ Script for uploading FACS data for the YeastLab.
+
+ FACS data are organized in one main folder which contains a folder with the username. Inside this folder there are folders and subfolders that correspond
+ to different FACS experiments. Inside the username folder there is a file called data_structure.ois which contains the structure of the FACS experiments.
+ This script creates a sample in openBIS for each FACS experiment and uploads the corresponding data in one dataset connected to the samples.
+ The space where the sample should go is detected from the username. The project and experiment are detected from the name of the folders given by the user.
+ The FACS experiment should be named by the users as PROJECT-EXPERIMENT-SAMPLE.
+
+"""
+
+import os, glob, re, csv, time, shutil
+from java.io import File
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageContainerDataConfig, ChannelColor
+from loci.formats import ImageReader
+from time import *
+from datetime import *
+
+
+def process(transaction):
+ incoming = transaction.getIncoming()
+
+ projectNameList=[]
+ experimentNameList=[]
+ sampleNameList=[]
+ directoryToImportList=[]
+ userNameList=[]
+
+
+ # read the data_structure.ois file to get the structure of the FACS experiment. The name of the FACS experiment contains project, experiment, sample info for openBIS.
+ def getProjExpSample(incoming):
+ for userName in os.listdir(incoming):
+ if not userName.startswith('.'):
+ dataStructure = incoming + "/" + userName + "/data_structure.ois"
+ f = open(dataStructure)
+ lines=f.readlines()
+ for line in lines:
+ path = re.split("/", line)
+ directoryToImport= incoming +"/"+ "/".join(path[:-1])
+ projectName = re.split("-",path[-1])[0]
+ if len(re.split("-",path[-1])) == 3:
+ experimentName = re.split("-",path[-1])[1]
+ sampleNameFile = re.split("-",path[-1])[2]
+ sampleName = re.split("_properties.oix", sampleNameFile)[0]
+ elif len(re.split("-",path[-1]))==2:
+ experimentNameProp = re.split("-",path[-1])[1]
+ experimentName = re.split("_properties.oix", experimentNameProp)[0]
+ sampleName = "na"
+
+
+ projectNameList.append(projectName)
+ experimentNameList.append(experimentName)
+ sampleNameList.append(sampleName)
+ directoryToImportList.append(directoryToImport)
+ userNameList.append(userName)
+
+ return userNameList, projectNameList, experimentNameList, sampleNameList, directoryToImportList
+
+
+ getProjExpSample(incoming.getPath())
+
+
+ for user in set (userNameList):
+ if user == "pontia":
+ space = "AARON"
+ elif user == "ottozd":
+ space = "DIANA"
+ elif user == "elfstrok":
+ space = "KRISTINA"
+
+
+ for proj in set(projectNameList):
+ print space
+ project = transaction.getProject("/" + space + "/" + proj)
+ if not project:
+ project = transaction.createNewProject("/" + space + "/" + proj)
+
+ for exp in set(experimentNameList):
+ experiment = transaction.getExperiment("/" + space + "/" + proj + "/" + exp)
+ if not experiment:
+ experiment = transaction.createNewExperiment("/" + space + "/" + proj + "/" + exp, "FACS_DATA")
+
+ for sample, directory in zip(sampleNameList,directoryToImportList):
+ if sample == "na":
+ sampleNew = transaction.createNewSampleWithGeneratedCode(space, "FACS_DATA")
+ sampleNew.setExperiment(experiment)
+ else:
+ sampleNew = transaction.createNewSample("/" + space + "/" + sample, "FACS_DATA" )
+ sampleNew.setExperiment(experiment)
+
+ dataSet = transaction.createNewDataSet()
+ dataSet.setDataSetType("FACS_DATA")
+ dataSet.setSample(sampleNew)
+ transaction.moveFile(directory, dataSet)
+
+
+
+
+
+
+
+
diff --git a/plasmid/source/drop-boxes/facs_data/plugin.properties b/plasmid/source/drop-boxes/facs_data/plugin.properties
new file mode 100644
index 00000000000..d7b020e7b35
--- /dev/null
+++ b/plasmid/source/drop-boxes/facs_data/plugin.properties
@@ -0,0 +1,19 @@
+#
+# Image drop box which registers a dataset from the webUI
+#
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+
+#input = image-dropbox
+dropbox-name = facs_data
+
+incoming-dir = /Users/barillac/openbis-screening2/data/incoming-facs
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = import_facs.py
+#script-path =BDLSRFortessaDropbox.py
+program-class = ch.systemsx.cisd.etlserver.registrator.api.v2.ExampleJavaDataSetRegistrationDropboxV2
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
--
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