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diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index f22766dcd323a7cdc9946cb13d07899a22e53f58..4ab4ab7905eef383e653d87d457642b6cc72078a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/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;
diff --git a/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/data-set-handler.py b/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/data-set-handler.py
new file mode 100644
index 0000000000000000000000000000000000000000..8bb3826f3bb12ef8ee87eb12787ac67884b7bd8f
--- /dev/null
+++ b/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/data-set-handler.py
@@ -0,0 +1,87 @@
+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);
diff --git a/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/plugin.properties b/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..1e7a5a4bbf727102249de8432d2fafafb84018d9
--- /dev/null
+++ b/screening/sourceTest/core-plugins/MiscellaneousDropBoxApiV2FeaturesTest/1/dss/drop-boxes/MiscellaneousDropBoxApiV2FeaturesTest-drop-box/plugin.properties
@@ -0,0 +1,7 @@
+incoming-dir = ${root-dir}/incoming-MiscellaneousDropBoxApiV2FeaturesTest
+incoming-dir-create = true
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
+script-path = data-set-handler.py
+storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+storage-processor.data-source = imaging-db
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MiscellaneousDropBoxApiV2FeaturesTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MiscellaneousDropBoxApiV2FeaturesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..42935e802eec20ea8a215d1f81f09c79cf607808
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MiscellaneousDropBoxApiV2FeaturesTest.java
@@ -0,0 +1,165 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.screening.systemtests;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.springframework.mock.web.MockHttpServletRequest;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.servlet.SpringRequestContextProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Test(groups =
+ { "slow", "systemtest" })
+public class MiscellaneousDropBoxApiV2FeaturesTest extends AbstractScreeningSystemTestCase
+{
+ private MockHttpServletRequest request;
+ private String sessionToken;
+
+ private ICommonServer commonServer;
+ private IScreeningClientService screeningClientService;
+ private IScreeningServer screeningServer;
+
+ @BeforeTest
+ public void dropAnExampleDataSet() throws IOException, Exception
+ {
+ File exampleDataSet = createTestDataContents();
+ moveFileToIncoming(exampleDataSet);
+ waitUntilDataSetImported();
+ }
+
+ @BeforeMethod
+ public void setUp() throws Exception
+ {
+ commonServer =
+ (ICommonServer) applicationContext
+ .getBean(ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER);
+ screeningClientService =
+ (IScreeningClientService) applicationContext
+ .getBean(ResourceNames.SCREENING_PLUGIN_SERVICE);
+ request = new MockHttpServletRequest();
+ ((SpringRequestContextProvider) applicationContext.getBean("request-context-provider"))
+ .setRequest(request);
+ Object bean = applicationContext.getBean(ResourceNames.SCREENING_PLUGIN_SERVER);
+ screeningServer = (IScreeningServer) bean;
+ sessionToken = screeningClientService.tryToLogin("admin", "a").getSessionID();
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ File[] files = getIncomingDirectory().listFiles();
+ for (File file : files)
+ {
+ FileUtilities.deleteRecursively(file);
+ }
+ }
+
+ @Test
+ public void testSettingPlateGeometryByFigureGeometry()
+ {
+ Experiment experiment =
+ commonServer.getExperimentInfo(sessionToken,
+ ExperimentIdentifierFactory.parse("/TEST/TEST-PROJECT/TEST-EXP-HCS"));
+ List<Sample> samples =
+ commonServer.listSamples(sessionToken,
+ ListSampleCriteria.createForExperiment(new TechId(experiment.getId())));
+
+ Sample sample = samples.get(0);
+ assertEquals("/TEST/PLATE1", sample.getIdentifier());
+ assertEquals("[$PLATE_GEOMETRY: 24_WELLS_4X6]", sample.getProperties().toString());
+ assertEquals(1, samples.size());
+ }
+
+ @Test
+ public void testImageResolutions()
+ {
+ Experiment experiment =
+ commonServer.getExperimentInfo(sessionToken,
+ ExperimentIdentifierFactory.parse("/TEST/TEST-PROJECT/TEST-EXP-HCS"));
+ List<Sample> samples =
+ commonServer.listSamples(sessionToken,
+ ListSampleCriteria.createForExperiment(new TechId(experiment.getId())));
+ Sample sample = samples.get(0);
+
+ PlateContent plateContent = screeningServer.getPlateContent(sessionToken, new TechId(sample.getId()));
+
+ PlateMetadata plateMetadata = plateContent.getPlateMetadata();
+ assertEquals(4, plateMetadata.getRowsNum());
+ assertEquals(6, plateMetadata.getColsNum());
+ assertEquals(0, plateMetadata.getWells().size());
+ List<ImageDatasetEnrichedReference> imageDatasets = plateContent.getImageDatasets();
+ DatasetImagesReference imageDataset = imageDatasets.get(0).getImageDataset();
+ assertEquals("/TEST/TEST-PROJECT/TEST-EXP-HCS", imageDataset.getDatasetReference().getExperimentIdentifier());
+ assertEquals(1, imageDatasets.size());
+ List<ImageResolution> imageDatasetResolutions =
+ screeningServer.getImageDatasetResolutions(sessionToken,
+ imageDataset.getDatasetCode(), imageDataset.getDatastoreCode());
+ Collections.sort(imageDatasetResolutions);
+ assertEquals("[256x191, 1392x1040]", imageDatasetResolutions.toString());
+ }
+
+ private File createTestDataContents() throws IOException
+ {
+ File dest = new File(workingDirectory, "TEST-PLATE1");
+ dest.mkdirs();
+ File src = new File(getTestDataFolder(), "PLATE1");
+
+ // Copy the test data set to the location for processing
+ FileUtils.copyDirectory(src, dest);
+ return dest;
+ }
+
+ private String getTestDataFolder()
+ {
+ return "../screening/resource/test-data/" + getClass().getSimpleName() + "/";
+ }
+
+ @Override
+ protected int dataSetImportWaitDurationInSeconds()
+ {
+ return 60;
+ }
+}