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diff --git a/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/hcs-dropbox.py b/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/hcs-dropbox.py
new file mode 100644
index 0000000000000000000000000000000000000000..ff5c73762570f2475ef219dbf644ea84e51618ba
--- /dev/null
+++ b/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/hcs-dropbox.py
@@ -0,0 +1,85 @@
+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')
+ exp.setPropertyValue('DESCRIPTION', 'A test 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, 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)
+ imageDataset.addGeneratedImageRepresentationWithResolution("512x512")
+ plate = create_plate_if_needed(transaction)
+ dataset = transaction.createNewImageDataSet(imageDataset, incoming);
+ dataset.setSample(plate)
+ transaction.moveFile(incoming.getPath(), dataset);
diff --git a/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/plugin.properties b/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..50d92e632822afd673a407aced7285cb44b0ffa1
--- /dev/null
+++ b/screening/sourceTest/core-plugins/SimpleImageDropboxTest/1/dss/drop-boxes/SimpleImageDropboxTest-drop-box/plugin.properties
@@ -0,0 +1,13 @@
+#
+# Drop box for HCS data sets
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${root-dir}/incoming-SimpleImageDropboxTest
+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
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
index 1c92e2390f246a3d67e8fa5e61f6c9a374519e6e..16c95b8b7031a774ea40145f4b27346a465bd071 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
@@ -254,14 +254,14 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
ImageHistogram actualHistogram = ImageHistogram.calculateHistogram(actualImage);
String expectedRenderedHistogram = expectedHistogram.renderAsASCIIChart(49, 9);
String actualRenderedHistogram = actualHistogram.renderAsASCIIChart(49, 9);
- if (expectedHistogram.equals(actualRenderedHistogram))
+ if (expectedRenderedHistogram.equals(actualRenderedHistogram))
{
return;
}
// difference can be caused by a value close to discretization border. Thus try another height.
expectedRenderedHistogram = expectedHistogram.renderAsASCIIChart(49, 10);
actualRenderedHistogram = actualHistogram.renderAsASCIIChart(49, 10);
- if (expectedHistogram.equals(actualRenderedHistogram))
+ if (expectedRenderedHistogram.equals(actualRenderedHistogram))
{
return;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/SimpleImageDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/SimpleImageDropboxTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d91b9cbd238939cff0e042b6a554a6a41386d71c
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/SimpleImageDropboxTest.java
@@ -0,0 +1,95 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * 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.List;
+
+import org.apache.commons.io.FileUtils;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
+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.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SimpleImageDropboxTest extends AbstractScreeningSystemTestCase
+{
+
+ @BeforeTest
+ public void dropAnExampleDataSet() throws Exception
+ {
+ File exampleDataSet = createTestDataContents();
+ moveFileToIncoming(exampleDataSet);
+ waitUntilDataSetImported(FINISHED_POST_REGISTRATION_CONDITION);
+ }
+
+ private File createTestDataContents() throws IOException
+ {
+ File destination = new File(workingDirectory, "test-data");
+ destination.mkdirs();
+ FileUtils.copyDirectory(new File(getTestDataFolder(), "PLATE1"), destination);
+ return destination;
+ }
+
+ private String getTestDataFolder()
+ {
+ return "../screening/resource/test-data/" + getClass().getSimpleName();
+ }
+
+ @Override
+ protected int dataSetImportWaitDurationInSeconds()
+ {
+ return 60;
+ }
+
+ @Test
+ public void test() throws Exception
+ {
+ ExperimentIdentifier identifier = ExperimentIdentifierFactory.parse("/TEST/TEST-PROJECT/DEMO-EXP-HCS");
+ Experiment experiment = commonServer.getExperimentInfo(sessionToken, identifier);
+ ListSampleCriteria sampleCriteria = ListSampleCriteria.createForExperiment(TechId.create(experiment));
+ List<Sample> samples = commonServer.listSamples(sessionToken, sampleCriteria);
+ Sample plate = samples.get(0);
+ assertEquals("/TEST/PLATE1", plate.getIdentifier());
+ assertEquals(1, samples.size());
+ List<AbstractExternalData> dataSets2
+ = commonServer.listRelatedDataSets(sessionToken, new DataSetRelatedEntities(samples), false);
+ AbstractExternalData dataSet = dataSets2.get(0);
+ assertEquals(1, dataSets2.size());
+ ImageChecker imageChecker = new ImageChecker();
+ imageChecker.check(new File(getTestDataFolder(), "1_1_Merged_Default.png"),
+ new ImageLoader(dataSet, sessionToken));
+ imageChecker.check(new File(getTestDataFolder(), "1_1_DAPI_Default.png"),
+ new ImageLoader(dataSet, sessionToken).channel("DAPI"));
+ imageChecker.check(new File(getTestDataFolder(), "1_3_DAPI_CY3_256x191.png"),
+ new ImageLoader(dataSet, sessionToken).tileColumn(3).channel("DAPI").channel("CY3").mode("thumbnail256x191"));
+ imageChecker.assertNoFailures();
+ }
+
+}