SP-179, BIS-21: More system tests.

SVN: 26056

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java

@@ -163,14 +163,18 @@ public class SimpleImageDataSetRegistrator
                 imageDatasetFactory.createDataSetRegistrationDetails();
         ImageDataSetInformation imageDataset = registrationDetails.getDataSetInformation();
         setImageDataset(incoming, imageDataset);
-        List<ChannelColorComponent> channelColorComponentsOrNull =
-                simpleImageConfig.getChannelColorComponentsOrNull();
-        if (channelColorComponentsOrNull == null)
+        List<Channel> channels = simpleImageConfig.getChannels();
+        if (channels != null)
         {
-            imageDataset.setChannels(simpleImageConfig.getChannels());
-        } else
-        {
-            imageDataset.setChannels(simpleImageConfig.getChannels(), channelColorComponentsOrNull);
+            List<ChannelColorComponent> channelColorComponentsOrNull =
+                    simpleImageConfig.getChannelColorComponentsOrNull();
+            if (channelColorComponentsOrNull == null)
+            {
+                imageDataset.setChannels(channels);
+            } else
+            {
+                imageDataset.setChannels(channels, channelColorComponentsOrNull);
+            }
         }
         setRegistrationDetails(registrationDetails, imageDataset);
         return registrationDetails;

screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/data-set-handler.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 = "TEST-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"
+
+
+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')
+        exp.setPropertyValue("DESCRIPTION", "A sample experiment")
+        
+    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, "384_WELLS_16X24")
+        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)
+        imageDataset.setPlate(SPACE_CODE, PLATE_CODE)
+        dataset = transaction.createNewImageDataSet(imageDataset, incoming);
+        plate = create_plate_if_needed(transaction)
+        plateGeometry = dataset.figureGeometry()
+        plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, plateGeometry)
+        dataset.setSample(plate)
+        transaction.moveFile(incoming.getPath(), dataset);