From b1a898fa688a85a7eea08c16913cd44de61a9be4 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 5 Jul 2011 11:40:55 +0000
Subject: [PATCH] LMS-2333 Extended API to allow downloading transformed
images.
SVN: 21978
---
.../v1/IScreeningOpenbisServiceFacade.java | 42 ++++++----
.../api/v1/ScreeningOpenbisServiceFacade.java | 52 ++++++++++++
.../v1/ScreeningOpenbisServiceFacadeTest.java | 84 ++++++++++++++++---
3 files changed, 151 insertions(+), 27 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 92e8d670cb4..a758ecdd6cf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
@@ -64,7 +65,7 @@ public interface IScreeningOpenbisServiceFacade
/** Closes connection with the server. After calling this method this facade cannot be used. */
public void logout();
-
+
/**
* Removes all images loaded by {@link #loadImageWellCaching(PlateImageReference, ImageSize)}
* and {@link #loadThumbnailImageWellCaching(PlateImageReference)} from the image cache, thus
@@ -88,7 +89,7 @@ public interface IScreeningOpenbisServiceFacade
* Each returned plate has at least one data set with the specified analysis procedure.
*/
public List<Plate> listPlates(ExperimentIdentifier experiment, String analysisProcedure);
-
+
/**
* Return the list of all visible experiments, along with their hierarchical context (space,
* project).
@@ -126,7 +127,7 @@ public interface IScreeningOpenbisServiceFacade
*/
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
List<? extends PlateIdentifier> plates, String analysisProcedureOrNull);
-
+
/**
* For a given set of plates provides the list of all connected data sets containing images
* which are not segmentation images.
@@ -151,7 +152,7 @@ public interface IScreeningOpenbisServiceFacade
@Deprecated
public List<ImageDatasetReference> listSegmentationImageDatasets(
List<? extends PlateIdentifier> plates);
-
+
/**
* For a given set of plates provides the list of all connected data sets containing
* segmentation images (overlays) and calculated by specified analysis procedure.
@@ -211,7 +212,7 @@ public interface IScreeningOpenbisServiceFacade
public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException;
-
+
/**
* Gets proxies to the data sets owned by specified well and passing specified filter..
*
@@ -219,10 +220,9 @@ public interface IScreeningOpenbisServiceFacade
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
- IDataSetFilter dataSetFilter) throws IllegalStateException,
- EnvironmentFailureException;
-
+ public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier, IDataSetFilter dataSetFilter)
+ throws IllegalStateException, EnvironmentFailureException;
+
public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
EnvironmentFailureException;
@@ -267,9 +267,8 @@ public interface IScreeningOpenbisServiceFacade
* the server.
*/
public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
- IDataSetFilter dataSetFilter) throws IllegalStateException,
- EnvironmentFailureException;
-
+ IDataSetFilter dataSetFilter) throws IllegalStateException, EnvironmentFailureException;
+
/**
* Upload a new data set to the DSS for a plate.
*
@@ -440,7 +439,7 @@ public interface IScreeningOpenbisServiceFacade
public List<FeatureVectorWithDescription> loadFeaturesForPlateWells(
ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier,
String analysisProcedureOrNull, List<String> featureCodesOrNull);
-
+
/**
* For the given <var>materialIdentifier</var> find all plate locations that are connected to it
* and load the feature vectors for the given feature code if not <code>null</code>, or all
@@ -481,7 +480,7 @@ public interface IScreeningOpenbisServiceFacade
public List<FeatureVectorWithDescription> loadFeaturesForPlateWells(
MaterialIdentifier materialIdentifier, String analysisProcedureOrNull,
List<String> featureCodesOrNull);
-
+
/**
* Converts the given <var>WellIdentifiers</var> to <var>WellPositions</var>
*/
@@ -631,6 +630,19 @@ public interface IScreeningOpenbisServiceFacade
public void loadImages(List<PlateImageReference> imageReferences, ImageSize imageSizeOrNull,
IPlateImageHandler plateImageHandler) throws IOException;
+ /**
+ * Loads images where the desired properties of the images are specified by a
+ * LoadImageConfiguration. The options and their behavior are described in the
+ * {@link LoadImageConfiguration} documentation.
+ *
+ * @param configuration The configuration of the images to load.
+ * @param plateImageHandler Handler for the delivered images.
+ * @see LoadImageConfiguration
+ */
+ public void loadImages(List<PlateImageReference> imageReferences,
+ LoadImageConfiguration configuration, IPlateImageHandler plateImageHandler)
+ throws IOException;
+
/**
* Loads the PNG-encoded image for the specified <var>imageReference</var>.
* <p>
@@ -707,7 +719,7 @@ public interface IScreeningOpenbisServiceFacade
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull);
-
+
/**
* Returns an alphabetically sorted list of analysis procedure codes of all data sets of the
* specified experiment.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 6f9fc4d0d10..e78e07db901 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetO
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
@@ -1686,4 +1687,55 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
}
+ public void loadImages(List<PlateImageReference> imageReferences,
+ final LoadImageConfiguration configuration, final IPlateImageHandler plateImageHandler)
+ throws IOException
+ {
+ plateImageReferencesMultiplexer.process(imageReferences,
+ new IReferenceHandler<PlateImageReference>()
+ {
+ public void handle(DssServiceRpcScreeningHolder dssService,
+ List<PlateImageReference> references)
+ {
+ checkDSSMinimalMinorVersion(dssService, "loadImages", List.class,
+ LoadImageConfiguration.class);
+ final InputStream stream =
+ dssService.getService().loadImages(sessionToken, references,
+ configuration);
+ try
+ {
+ final ConcatenatedFileOutputStreamWriter imagesWriter =
+ new ConcatenatedFileOutputStreamWriter(stream);
+ int index = 0;
+ long size;
+ do
+ {
+ final ByteArrayOutputStream outputStream =
+ new ByteArrayOutputStream();
+ size = imagesWriter.writeNextBlock(outputStream);
+ if (size > 0)
+ {
+ plateImageHandler.handlePlateImage(references.get(index),
+ outputStream.toByteArray());
+ }
+ index++;
+ } while (size >= 0);
+ } catch (IOException ex)
+ {
+ throw new WrappedIOException(ex);
+ } finally
+ {
+ try
+ {
+ stream.close();
+ } catch (IOException ex)
+ {
+ throw new WrappedIOException(ex);
+ }
+ }
+
+ }
+ });
+ }
+
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index 7058b3a14ca..41b058e6a37 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetO
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.dss.screening.server.DssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
@@ -629,8 +630,8 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
new ImageDatasetReference(DATA_SET1, null, URL1, plate, null, null, null,
properties, null);
final ImageDatasetReference r2 =
- new ImageDatasetReference(DATA_SET2, null, URL2, plate, null, null, null,
- null, null);
+ new ImageDatasetReference(DATA_SET2, null, URL2, plate, null, null, null, null,
+ null);
context.checking(new Expectations()
{
{
@@ -639,27 +640,28 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
}
});
- List<ImageDatasetReference> dataSets = facade.listSegmentationImageDatasets(plates, "AP-42");
+ List<ImageDatasetReference> dataSets =
+ facade.listSegmentationImageDatasets(plates, "AP-42");
assertSame(r1, dataSets.get(0));
assertEquals(1, dataSets.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testListSegmentationImageDataSetsWithUnspecifiedAnalysisProcedure()
{
final Plate plate =
- new Plate("p1", "s", "s-12", new ExperimentIdentifier("e", "p1", "s", "e-13"));
+ new Plate("p1", "s", "s-12", new ExperimentIdentifier("e", "p1", "s", "e-13"));
final List<Plate> plates = Arrays.asList(plate);
HashMap<String, String> properties = new HashMap<String, String>();
properties.put(ScreeningConstants.ANALYSIS_PROCEDURE, "AP-42");
final ImageDatasetReference r1 =
- new ImageDatasetReference(DATA_SET1, null, URL1, plate, null, null, null,
- properties, null);
+ new ImageDatasetReference(DATA_SET1, null, URL1, plate, null, null, null,
+ properties, null);
final ImageDatasetReference r2 =
- new ImageDatasetReference(DATA_SET2, null, URL2, plate, null, null, null,
- null, null);
+ new ImageDatasetReference(DATA_SET2, null, URL2, plate, null, null, null, null,
+ null);
context.checking(new Expectations()
{
{
@@ -667,15 +669,15 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
will(returnValue(Arrays.asList(r1, r2)));
}
});
-
+
List<ImageDatasetReference> dataSets = facade.listSegmentationImageDatasets(plates, null);
-
+
assertSame(r1, dataSets.get(0));
assertSame(r2, dataSets.get(1));
assertEquals(2, dataSets.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testListPlateWells()
{
@@ -740,6 +742,64 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
context.assertIsSatisfied();
}
+ @Test
+ public void testLoadImagesUsingConfiguration() throws IOException
+ {
+ final LoadImageConfiguration config = new LoadImageConfiguration();
+ config.setDesiredImageFormatPng(true);
+
+ final PlateImageReference r1 = new PlateImageReference(1, 2, 1, "c1", i1id);
+ final PlateImageReference r2 = new PlateImageReference(12, 22, 1, "c1", i2id);
+ final ByteArrayOutputStream stream1 = new ByteArrayOutputStream();
+ final ByteArrayOutputStream stream2 = new ByteArrayOutputStream();
+ context.checking(new Expectations()
+ {
+ {
+ one(dssService1).loadImages(SESSION_TOKEN, Arrays.asList(r1), config);
+ ConcatenatedContentInputStream s1 =
+ new ConcatenatedContentInputStream(true, Arrays
+ .<IContent> asList(new ByteArrayBasedContent("hello 1"
+ .getBytes(), "h1")));
+ will(returnValue(s1));
+
+ one(dssService2).loadImages(SESSION_TOKEN, Arrays.asList(r2), config);
+ ConcatenatedContentInputStream s2 =
+ new ConcatenatedContentInputStream(true, Arrays
+ .<IContent> asList(new ByteArrayBasedContent("hello 2"
+ .getBytes(), "h2")));
+ will(returnValue(s2));
+ }
+ });
+
+ IPlateImageHandler handler = new IPlateImageHandler()
+ {
+
+ public void handlePlateImage(PlateImageReference plateImageReference,
+ byte[] imageFileBytes)
+ {
+
+ try
+ {
+ if (r1.equals(plateImageReference))
+ {
+ stream1.write(imageFileBytes);
+ } else if (r2.equals(plateImageReference))
+ {
+ stream2.write(imageFileBytes);
+ }
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ };
+ facade.loadImages(Arrays.asList(r1, r2), config, handler);
+
+ assertEquals("hello 1", stream1.toString());
+ assertEquals("hello 2", stream2.toString());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testListImageMetaData()
{
--
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