MINOR : Add dss to v4 of the screening core plugin

SVN: 28336

screening/source/core-plugins/screening/4/dss/data-sources/imaging-db/plugin.properties

+#
+# Data source for the database storing image meta data.
+#
+# Variables:
+#   imaging-database.url-host-part
+#     The host and optionally port. Default is 'localhost'. 
+#   imaging-database.kind
+#     Second part of the database name. Default value is 'prod'.
+#   screening-sql-root-folder
+#     Path to root folder of SQL scripts. Default value is an empty string.
+#
+version-holder-class = ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseVersionHolder
+databaseEngineCode = postgresql
+basicDatabaseName = imaging
+urlHostPart = ${imaging-database.url-host-part:localhost}
+databaseKind = ${imaging-database.kind:prod}
+scriptFolder = ${screening-sql-root-folder:}sql/imaging
+owner =
+password = 
+# Credentials of a database user which is able to create a new database or roles in it.
+# Leave empty to use the db engines defaults.
+# Used only during the first start of the server or when server is upgraded to a new version.
+adminUser = 
+adminPassword =
+

screening/source/core-plugins/screening/4/dss/drop-boxes/hcs-dropbox/hcs-dropbox.py

+import os
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageMetadata
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+
+SPACE_CODE = "TEST"
+PROJECT_CODE = "TEST-PROJECT"
+PROJECT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s" % vars()
+EXPERIMENT_CODE = "DEMO-EXP-HCS"
+EXPERIMENT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s/%(EXPERIMENT_CODE)s" % vars()
+
+PLATE_CODE = "PLATE1"
+PLATE_ID = "/%(SPACE_CODE)s/%(PLATE_CODE)s" % vars()
+PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+
+def create_space_if_needed(transaction):
+    space = transaction.getSpace(SPACE_CODE)
+    if None == space:
+        space = transaction.createNewSpace(SPACE_CODE, None)
+        space.setDescription("A demo space")
+
+def create_project_if_needed(transaction):
+    project = transaction.getProject(PROJECT_ID)
+    if None == project:
+        create_space_if_needed(transaction)
+        project = transaction.createNewProject(PROJECT_ID)
+        project.setDescription("A demo project")
+        
+def create_experiment_if_needed(transaction):
+    """ Get the specified experiment or register it if necessary """
+    exp = transaction.getExperiment(EXPERIMENT_ID)
+    if None == exp:
+        create_project_if_needed(transaction)
+        print 'Creating new experiment : ' + EXPERIMENT_ID
+        exp = transaction.createNewExperiment(EXPERIMENT_ID, 'SIRNA_HCS')
+        
+    return exp
+    
+def create_plate_if_needed(transaction):
+    """ Get the specified sample or register it if necessary """
+
+    samp = transaction.getSample(PLATE_ID)
+
+    if None == samp:
+        exp = create_experiment_if_needed(transaction)
+        samp = transaction.createNewSample(PLATE_ID, 'PLATE')
+        samp.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+        samp.setExperiment(exp)
+        
+    return samp
+
+     
+class MyImageDataSetConfig(SimpleImageDataConfig):
+    def extractImageMetadata(self, imagePath):
+     
+        basename = os.path.splitext(imagePath)[0]
+        (plate, well, tile, channelCode) = basename.split("_")
+         
+        image_tokens = ImageMetadata()
+        image_tokens.well = well
+        try:
+            image_tokens.tileNumber = int(tile)
+        except ValueError:
+            raise Exception("Cannot parse field number from '" + tile + "' in '" + basename + "' file name.")
+     
+        image_tokens.channelCode = channelCode
+        return image_tokens
+    
+    def getTileGeometry(self, imageTokens, maxTileNumber):
+        return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3)    
+
+def process(transaction): 
+    incoming = transaction.getIncoming()
+    if incoming.isDirectory():
+        imageDataset = MyImageDataSetConfig()
+        imageDataset.setRawImageDatasetType()
+        imageDataset.setGenerateThumbnails(True)
+        imageDataset.setUseImageMagicToGenerateThumbnails(False)
+        plate = create_plate_if_needed(transaction)
+        dataset = transaction.createNewImageDataSet(imageDataset, incoming);
+        dataset.setSample(plate)
+        transaction.moveFile(incoming.getPath(), dataset);

screening/source/core-plugins/screening/4/dss/drop-boxes/hcs-dropbox/plugin.properties

+# 
+# Drop box for HCS data sets 
+#
+# Variables:
+#   incoming-root-dir
+#     Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/incoming-hcs
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
+script-path = hcs-dropbox.py
+storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+storage-processor.data-source = imaging-db
+storage-processor.define-channels-per-experiment = false

screening/source/core-plugins/screening/4/dss/drop-boxes/simple-dropbox/plugin.properties

+# 
+# Simple drop box which registers any file/folder 
+#
+#
+# Variables:
+#   incoming-root-dir
+#     Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/incoming-simple
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = simple-dropbox.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor

screening/source/core-plugins/screening/4/dss/drop-boxes/simple-dropbox/simple-dropbox.py

+#! /usr/bin/env python
+def process(transaction):
+    expid = "/TEST/TEST-PROJECT/DEMO-EXP-SIMPLE"
+    exp = transaction.getExperiment(expid)
+     
+    if None == exp:
+        exp = transaction.createNewExperiment(expid, "TEST-EXPERIMENT")
+   
+    dataSet = transaction.createNewDataSet()
+          
+    dataSet.setDataSetType("UNKNOWN")
+    dataSet.setExperiment(exp)
+    transaction.moveFile(transaction.getIncoming().getAbsolutePath(), dataSet)

screening/source/core-plugins/screening/4/dss/image-overview-plugins/microscopy-image-overview/plugin.properties

+class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
+dataset-types = MICROSCOPY_IMAGE

screening/source/core-plugins/screening/4/dss/maintenance-tasks/imaging-db-clean-up/plugin.properties

+#
+# Maintenance task which does a database clean up by deleting all data sets deleted in application server. 
+# This task assumes that data source 'imaging-db' has been defined. 
+#
+class = ch.systemsx.cisd.openbis.dss.etl.DeleteFromImagingDBMaintenanceTask
+# specified in seconds. Here : every day
+interval = 86400
+data-source = imaging-db

screening/source/core-plugins/screening/4/dss/reporting-plugins/default-plate-image-analysis/plugin.properties

+label = Image Analysis Results
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
+dataset-types = HCS_ANALYSIS_.*WELL_FEATURES
+properties-file =

screening/source/core-plugins/screening/4/dss/reporting-plugins/feature-lists-aggregation-service/plugin.properties

+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.FeatureListsAggregationServicePlugin
+label = Features Lists
\ No newline at end of file

screening/source/core-plugins/screening/4/dss/services/screening-dss-api-json/plugin.properties

+class = ch.systemsx.cisd.openbis.dss.generic.server.DssScreeningApiJsonServlet
+path = /rmi-datastore-server-screening-api-v1.json/*

screening/source/core-plugins/screening/4/dss/services/screening-dss-api/plugin.properties

+class = ch.systemsx.cisd.openbis.dss.generic.server.DssScreeningApiServlet
+path = /rmi-datastore-server-screening-api-v1/*

screening/source/core-plugins/screening/4/dss/services/screening-images/plugin.properties

+#
+# Image service 
+#
+class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
+path = /datastore_server_screening/*