diff --git a/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_1_GFP_OverlayDAPI_Default.png b/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_1_GFP_OverlayDAPI_Default.png
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diff --git a/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_CY3_Overlay2GFP_DAPI_256x256.png b/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_CY3_Overlay2GFP_DAPI_256x256.png
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diff --git a/screening/resource/test-data/PlatonicPlateImageDropboxTest/2_1_CY3_Overlay2GFP_Default.png b/screening/resource/test-data/PlatonicPlateImageDropboxTest/2_1_CY3_Overlay2GFP_Default.png
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diff --git a/screening/resource/test-data/PlatonicPlateImageDropboxTest/Platonic-Plate/bPLATE_wA1_s4_cRGB.png b/screening/resource/test-data/PlatonicPlateImageDropboxTest/Platonic-Plate/bPLATE_wA1_s4_cRGB.png
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diff --git a/screening/resource/test-data/Simple16BitImageDropboxTest/1_2_Merged_Overlay2CY3_256x256.png b/screening/resource/test-data/Simple16BitImageDropboxTest/1_2_Merged_Overlay2CY3_256x256.png
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diff --git a/screening/resource/test-data/Simple16BitImageDropboxTest/2_1_Merged_Default.png b/screening/resource/test-data/Simple16BitImageDropboxTest/2_1_Merged_Default.png
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diff --git a/screening/resource/test-data/Simple16BitImageDropboxTest/PLATE-16-BIT/PLATE-16-BIT_A01_04_DAPI.png b/screening/resource/test-data/Simple16BitImageDropboxTest/PLATE-16-BIT/PLATE-16-BIT_A01_04_DAPI.png
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diff --git a/screening/resource/test-data/Simple16BitImageDropboxTest/PLATE-16-BIT/PLATE-16-BIT_A01_04_GFP.png b/screening/resource/test-data/Simple16BitImageDropboxTest/PLATE-16-BIT/PLATE-16-BIT_A01_04_GFP.png
new file mode 100644
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diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractImageDropboxTestCase.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractImageDropboxTestCase.java
index 97b090bb7806cbf4b907dbf9a5e9a039a0e884a9..bb57b9c15ba1a3502e03bc6295ca531e09c248d8 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractImageDropboxTestCase.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractImageDropboxTestCase.java
@@ -20,6 +20,7 @@ import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
import org.apache.commons.io.FileUtils;
@@ -91,7 +92,16 @@ public abstract class AbstractImageDropboxTestCase extends AbstractScreeningSyst
protected AbstractExternalData getRegisteredContainerDataSet()
{
- List<AbstractExternalData> dataSets = getRegisteredDataSets();
+ Class<? extends AbstractImageDropboxTestCase> testClass = getClass();
+ AbstractExternalData containerDataSet = getRegisteredContainerDataSet(testClass);
+ assertNotNull("No container data set found for test " + testClass.getSimpleName(), containerDataSet);
+ return containerDataSet;
+ }
+
+ protected AbstractExternalData getRegisteredContainerDataSet(Class<? extends AbstractImageDropboxTestCase> testClass)
+ {
+ String experimentCode = translateIntoCamelCase(testClass.getSimpleName()).toUpperCase();
+ List<AbstractExternalData> dataSets = getRegisteredDataSets(experimentCode);
for (AbstractExternalData dataSet : dataSets)
{
if (dataSet.getDataSetType().getDataSetKind().equals(DataSetKind.CONTAINER))
@@ -99,18 +109,19 @@ public abstract class AbstractImageDropboxTestCase extends AbstractScreeningSyst
return dataSet;
}
}
- fail("No container data set found: " + dataSets);
- return null; // never reached but needed for the compiler
+ return null;
}
- protected List<AbstractExternalData> getRegisteredDataSets()
+ private List<AbstractExternalData> getRegisteredDataSets(String experimentCode)
{
- String code = translateIntoCamelCase(getClass().getSimpleName()).toUpperCase();
- ExperimentIdentifier identifier = ExperimentIdentifierFactory.parse("/TEST/TEST-PROJECT/" + code);
- Experiment experiment = commonServer.getExperimentInfo(sessionToken, identifier);
- List<AbstractExternalData> dataSets
- = commonServer.listRelatedDataSets(sessionToken, new DataSetRelatedEntities(Arrays.asList(experiment)), false);
- return dataSets;
+ ExperimentIdentifier identifier = ExperimentIdentifierFactory.parse("/TEST/TEST-PROJECT/" + experimentCode);
+ List<Experiment> experiments = commonServer.listExperiments(sessionToken, Arrays.asList(identifier));
+ if (experiments.isEmpty())
+ {
+ return Collections.emptyList();
+ }
+ Experiment experiment = experiments.get(0);
+ return commonServer.listRelatedDataSets(sessionToken, new DataSetRelatedEntities(Arrays.asList(experiment)), false);
}
private String translateIntoCamelCase(String string)
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 8270cb500045290516fca04fe521c80663c6f1ce..f76b4800a1d6df97d3a1becd4102627d6ed21018 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
@@ -106,8 +106,21 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
*/
protected static final class ImageLoader implements IImageLoader
{
+ private static final class OverlayChannel
+ {
+ private String dataSetCode;
+ private String channel;
+
+ OverlayChannel(String dataSetCode, String channel)
+ {
+ this.dataSetCode = dataSetCode;
+ this.channel = channel;
+ }
+ }
+
private final URLMethodWithParameters url;
private final List<String> channels = new ArrayList<String>();
+ private final List<OverlayChannel> overlayChannels = new ArrayList<OverlayChannel>();
private final Map<String, String> transformationsByChannel = new HashMap<String, String>();
private boolean mergeChannels = true;
private boolean microscopy = false;
@@ -149,6 +162,11 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
url.addParameter(ImageServletUrlParameters.CHANNEL_PARAM, channel);
}
}
+ for (OverlayChannel overlayChannel : overlayChannels)
+ {
+ String name = ImageServletUrlParameters.OVERLAY_CHANNEL_PREFIX_PARAM + overlayChannel.dataSetCode;
+ url.addParameter(name, overlayChannel.channel);
+ }
if (microscopy == false)
{
url.addParameter(ImageServletUrlParameters.WELL_ROW_PARAM, Integer.toString(wellRow));
@@ -214,6 +232,12 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
return this;
}
+ public ImageLoader overlay(String dataSetCode, String channel)
+ {
+ overlayChannels.add(new OverlayChannel(dataSetCode, channel));
+ return this;
+ }
+
public ImageLoader rescaling(String channel, int low, int high)
{
transformationsByChannel.put(channel,
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/PlatonicPlateImageDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/PlatonicPlateImageDropboxTest.java
index 2c64ca33420025bd9e892cc0055ce742f243686c..ec690821d3e1e43478f363d2f59cf735ac6852e6 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/PlatonicPlateImageDropboxTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/PlatonicPlateImageDropboxTest.java
@@ -60,6 +60,20 @@ public class PlatonicPlateImageDropboxTest extends AbstractImageDropboxTestCase
new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("GFP").mode("thumbnail64x64"));
imageChecker.check(new File(getTestDataFolder(), "1_1_Merged_Default_GFP_0_100.png"),
new ImageLoader(dataSet, sessionToken).rescaling("GFP", 0, 100));
+ imageChecker.check(new File(getTestDataFolder(), "1_1_GFP_OverlayDAPI_Default.png"),
+ new ImageLoader(dataSet, sessionToken).channel("GFP").overlay(dataSet.getCode(), "DAPI"));
+ // Because all data sets are registered before the actual test methods are executed we can
+ // use images from another data set as an overlay image
+ AbstractExternalData dataSet2 = getRegisteredContainerDataSet(Simple16BitImageDropboxTest.class);
+ if (dataSet2 != null)
+ {
+ imageChecker.check(new File(getTestDataFolder(), "1_2_CY3_Overlay2GFP_DAPI_256x256.png"),
+ new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("CY3")
+ .overlay(dataSet2.getCode(), "GFP").overlay(dataSet2.getCode(), "DAPI").mode("thumbnail256x256"));
+ imageChecker.check(new File(getTestDataFolder(), "2_1_CY3_Overlay2GFP_Default.png"),
+ new ImageLoader(dataSet, sessionToken).tileRow(2).tileColumn(1).channel("CY3")
+ .overlay(dataSet2.getCode(), "GFP"));
+ }
imageChecker.assertNoFailures();
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java
index d3b9d4356dde634ef847a9f56ddddb76d017cae2..3f6ab2ea0ecf2dd9b5c9e0ac792bbfdc230d049f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java
@@ -58,6 +58,17 @@ public class Simple16BitImageDropboxTest extends AbstractImageDropboxTestCase
new ImageLoader(dataSet, sessionToken).tileColumn(2).mode("thumbnail1392x1040"));
imageChecker.check(new File(getTestDataFolder(), "1_2_GFP_thumbnail1392x1040.png"),
new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("GFP").mode("thumbnail1392x1040"));
+ imageChecker.check(new File(getTestDataFolder(), "2_1_Merged_Default.png"),
+ new ImageLoader(dataSet, sessionToken).tileRow(2).tileColumn(1));
+ // Because all data sets are registered before the actual test methods are executed we can
+ // use images from another data set as an overlay image
+ AbstractExternalData dataSet2 = getRegisteredContainerDataSet(PlatonicPlateImageDropboxTest.class);
+ if (dataSet2 != null)
+ {
+ imageChecker.check(new File(getTestDataFolder(), "1_2_Merged_Overlay2CY3_256x256.png"),
+ new ImageLoader(dataSet, sessionToken).tileColumn(2)
+ .overlay(dataSet2.getCode(), "CY3").mode("thumbnail256x256"));
+ }
imageChecker.assertNoFailures();
}
}