From 8dbaec5133725af6a5b74cc082d7f330d51318a9 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 21 Apr 2010 09:52:23 +0000
Subject: [PATCH] LMS-1491 screening API: fetching images, API improvements
SVN: 15557
---
screening/.classpath | 1 +
screening/etc/service.properties | 6 +-
.../server/DssScreeningApiServlet.java | 47 +++++
.../server/DssServiceRpcScreening.java | 196 ++++++++++++++++++
.../shared/api/IDssServiceRpcScreening.java | 64 ++++++
.../api/v1/ScreeningOpenbisServiceFacade.java | 161 +++++++++++---
.../screening/server/ScreeningServer.java | 26 ++-
.../server/ScreeningServerLogger.java | 37 ++--
.../server/logic/ScreeningApiImpl.java | 95 +++++++--
.../shared/api/IGenedataDssServer.java | 83 --------
.../shared/api/IScreeningApiServer.java | 23 +-
.../ScreenerDatasetPredicate.java | 44 ----
.../ScreenerReadonlyPlatePredicate.java | 6 +-
.../authorization/ScreenerWellPredicate.java | 44 ----
.../screening/shared/api/dto/Dataset.java | 50 -----
.../shared/api/dto/DatasetIdentifier.java | 58 ++++++
.../shared/api/dto/DatasetReference.java | 33 +++
.../dto/FeatureVectorDatasetReference.java | 34 +++
.../shared/api/dto/IDatasetIdentifier.java | 21 +-
.../dto/IFeatureVectorDatasetIdentifier.java | 26 +++
.../api/dto/IImageDatasetIdentifier.java | 26 +++
.../shared/api/dto/IPlateIdentifier.java | 15 --
.../shared/api/dto/ImageDatasetMetadata.java | 15 +-
.../shared/api/dto/ImageDatasetReference.java | 33 +++
.../screening/shared/api/dto/Plate.java | 27 +--
.../shared/api/dto/PlateIdentifier.java | 52 +++++
.../shared/api/dto/PlateImageReference.java | 53 +++++
.../shared/api/dto/PlateSingleImage.java | 22 +-
.../shared/api/dto/WellFeaturesReference.java | 35 ----
.../shared/api/dto/WellPosition.java | 6 +
.../java/screening-dssApplicationContext.xml | 36 ++++
.../screening/ScreeningClientApiTest.java | 84 +++++++-
32 files changed, 1056 insertions(+), 403 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssScreeningApiServlet.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/IDssServiceRpcScreening.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IGenedataDssServer.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerDatasetPredicate.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerWellPredicate.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Dataset.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetIdentifier.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/FeatureVectorDatasetReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IFeatureVectorDatasetIdentifier.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IImageDatasetIdentifier.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IPlateIdentifier.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateIdentifier.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateImageReference.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellFeaturesReference.java
create mode 100644 screening/source/java/screening-dssApplicationContext.xml
diff --git a/screening/.classpath b/screening/.classpath
index 4f56ff96ea0..e9814e6ef45 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -38,5 +38,6 @@
<attribute name="javadoc_location" value="jar:platform:/resource/libraries/jfreechart/jfreechart-1.0.13-javadocs.zip!/jfreechart-1.0.13-javadocs"/>
</attributes>
</classpathentry>
+ <classpathentry kind="lib" path="/libraries/spring/third-party/stream-supporting-httpinvoker.jar" sourcepath="/libraries/spring/third-party/stream-supporting-httpinvoker-src.zip"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 36f93e28c1d..79fbef37f27 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -140,7 +140,7 @@ hierarchical-storage-updater.hierarchy-root-dir = targets/hierarchical-store
# ---------------------------------------------------------------------------
# list of additional web servlets which will be exposed
-plugin-services = screening-image-download-servlet, tabular-data-graph-servlet
+plugin-services = screening-image-download-servlet, tabular-data-graph-servlet, screening-dss-api-exporter-servlet
# class of the web servlet
#screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.SplittingImagesDownloadServlet
@@ -152,6 +152,10 @@ tabular-data-graph-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.T
tabular-data-graph-servlet.path = /datastore_server_graph/*
tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties
+# expose an DSS API interface with RPC
+screening-dss-api-exporter-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.DssScreeningApiServlet
+screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api/*
+
# ---------------------------------------------------------------------------
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssScreeningApiServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssScreeningApiServlet.java
new file mode 100644
index 00000000000..f30dcb10876
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssScreeningApiServlet.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright 2010 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.dss.generic.server;
+
+import org.springframework.beans.factory.BeanFactory;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+import com.marathon.util.spring.StreamSupportingHttpInvokerServiceExporter;
+
+/**
+ * A servlet which exposes the spring bean with the HTTP Invoker
+ * @author Tomasz Pylak
+ */
+public class DssScreeningApiServlet extends HttpInvokerServlet
+{
+ private static final long serialVersionUID = 1L;
+
+ private static final BeanFactory APPLICATION_CONTEXT =
+ new ClassPathXmlApplicationContext(new String[]
+ { "screening-dssApplicationContext.xml" }, true);
+
+ private static StreamSupportingHttpInvokerServiceExporter getDssScreeningService()
+ {
+ return ((StreamSupportingHttpInvokerServiceExporter) APPLICATION_CONTEXT
+ .getBean("data-store-rpc-service-screening"));
+ }
+
+ public DssScreeningApiServlet()
+ {
+ super(getDssScreeningService(), "rmi-screening-dss-api");
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
new file mode 100644
index 00000000000..7bf7c0ec85e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -0,0 +1,196 @@
+/*
+ * Copyright 2010 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.dss.screening.server;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.util.Collection;
+import java.util.List;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IFeatureVectorDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IImageDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Implementation of the screening API interface using RPC. The instance will be created in spring
+ * and published as a HTTP invoker servlet configured in service.properties.
+ *
+ * @author Tomasz Pylak
+ */
+public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
+ IDssServiceRpcScreening
+{
+
+ public DssServiceRpcScreening(String storeRootDir)
+ {
+ super(ServiceProvider.getOpenBISService());
+ setStoreDirectory(new File(storeRootDir));
+ operationLog.info("Started RPC V1 screening service.");
+ }
+
+ public int getMinClientVersion()
+ {
+ return 1;
+ }
+
+ public int getVersion()
+ {
+ return 1;
+ }
+
+ // ------------------ impl -----------------
+
+ public List<String> listAvailableFeatureNames(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
+ {
+ // TODO Auto-generated method stub
+
+ return null;
+ }
+
+ public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
+ List<? extends IImageDatasetIdentifier> imageDatasets)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public List<FeatureVectorDataset> loadFeatures(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets,
+ List<String> featureNames)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public InputStream loadImage(String sessionToken, PlateImageReference imageReference)
+ {
+ ExternalData imageDataset =
+ tryFindImageDataset(sessionToken, imageReference.getDatasetCode());
+ if (imageDataset != null)
+ {
+ return getImageStream(imageDataset, imageReference);
+ } else
+ {
+ return null;
+ }
+ }
+
+ private InputStream getImageStream(ExternalData imageDataset, PlateImageReference imageRef)
+ {
+ HCSDatasetLoader imageAccessor = createImageLoader(imageRef.getDatasetCode());
+ Location wellLocation = asLocation(imageRef.getWellPosition());
+ Location tileLocation =
+ getTileLocation(imageRef.getTile(), imageAccessor.getWellGeometry());
+ try
+ {
+ File path =
+ ImageChannelsUtils.getImagePath(imageAccessor, wellLocation, tileLocation,
+ imageRef.getChannel());
+ return new FileInputStream(path);
+ } catch (EnvironmentFailureException e)
+ {
+ throw createNoImageException(imageRef);
+ } catch (FileNotFoundException ex)
+ {
+ throw createNoImageException(imageRef);
+ } finally
+ {
+ imageAccessor.close();
+ }
+ }
+
+ private static IllegalArgumentException createNoImageException(PlateImageReference imageRef)
+ {
+ return new IllegalArgumentException("No image found: " + imageRef);
+ }
+
+ private static Location getTileLocation(int tile, Geometry wellGeometry)
+ {
+ int row = ((tile - 1) / wellGeometry.getColumns()) + 1;
+ int col = ((tile - 1) % wellGeometry.getColumns()) + 1;
+ return new Location(row, col);
+ }
+
+ private static Location asLocation(WellPosition wellPosition)
+ {
+ return new Location(wellPosition.getWellColumn(), wellPosition.getWellRow());
+ }
+
+ private HCSDatasetLoader createImageLoader(String datasetCode)
+ {
+ HCSDatasetLoader loader;
+ File datasetRoot = getRootDirectoryForDataSet(datasetCode);
+ loader = new HCSDatasetLoader(datasetRoot);
+ return loader;
+ }
+
+ private ExternalData tryFindImageDataset(String sessionToken, String datasetCode)
+ {
+ ExternalData dataset = tryGetDataSet(sessionToken, datasetCode);
+ if (dataset == null)
+ {
+ throw new IllegalArgumentException("Dataset " + datasetCode + " cannot be found.");
+ }
+ if (isImageDataset(dataset))
+ {
+ return dataset;
+ }
+ // it may be the feature dataset
+ Collection<ExternalData> parents = dataset.getParents();
+ if (parents.size() > 1)
+ {
+ throw new IllegalArgumentException("Dataset " + datasetCode
+ + " should have at most 1 parent, but has: " + parents.size());
+ }
+ if (parents.size() == 1)
+ {
+ ExternalData parent = parents.iterator().next();
+ if (isImageDataset(parent))
+ {
+ return parent;
+ } else
+ {
+ return null;
+ }
+ } else
+ {
+ return null;
+ }
+ }
+
+ private boolean isImageDataset(ExternalData dataset)
+ {
+ return dataset.getDataSetType().getCode().equals(ScreeningConstants.IMAGE_DATASET_TYPE);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/IDssServiceRpcScreening.java
new file mode 100644
index 00000000000..0c68e4c6e7f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/IDssServiceRpcScreening.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2010 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.dss.screening.shared.api;
+
+import java.io.InputStream;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IFeatureVectorDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IImageDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateImageReference;
+
+/**
+ * Public DSS API for screening. Non-compatible changes without consultation are forbidden.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IDssServiceRpcScreening
+{
+ /**
+ * For a given set of feature vector data sets provide the list of all available features. This
+ * is just the name of the feature. If for different data sets different sets of features are
+ * available, provide the union of the features of all data sets.
+ */
+ List<String> listAvailableFeatureNames(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+
+ /**
+ * For a given set of data sets and a set of features (given by their name), provide the feature
+ * matrix. Each column in that matrix is one feature, each row is one well in one data set.
+ */
+ List<FeatureVectorDataset> loadFeatures(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets,
+ List<String> featureNames);
+
+ /**
+ * Provide image for a given image reference (given by data set code, well position, channel and
+ * tile).
+ */
+ InputStream loadImage(String sessionToken, PlateImageReference imageReferences);
+
+ /**
+ * For a given set of image data sets, provide all image channels that have been acquired and
+ * the available (natural) image size(s).
+ */
+ List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
+ List<? extends IImageDatasetIdentifier> imageDatasets);
+
+}
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 8fa7b2004df..87100c3d2fb 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
@@ -1,20 +1,28 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.IScreeningApiServer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IFeatureVectorDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IImageDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateSingleImage;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.WellFeaturesReference;
/**
- * A facade of openBIS and Datastore Server API.
+ * A client side facade of openBIS and Datastore Server API.
*
* @author Tomasz Pylak
*/
@@ -22,7 +30,9 @@ public class ScreeningOpenbisServiceFacade
{
private static final int SERVER_TIMEOUT_MIN = 5;
- private final IScreeningApiServer screeningServer;
+ private final IScreeningApiServer openbisScreeningServer;
+
+ private final Map<String/* url */, IDssServiceRpcScreening> dssScreeningServerCache;
private final String sessionToken;
@@ -35,31 +45,38 @@ public class ScreeningOpenbisServiceFacade
public static ScreeningOpenbisServiceFacade tryCreate(String userId, String userPassword,
String serverUrl)
{
- IScreeningApiServer server = createScreeningServer(serverUrl);
- String sessionToken = server.tryLoginScreening(userId, userPassword);
+ IScreeningApiServer openbisServer = createScreeningOpenbisServer(serverUrl);
+ String sessionToken = openbisServer.tryLoginScreening(userId, userPassword);
if (sessionToken == null)
{
return null;
}
- return new ScreeningOpenbisServiceFacade(server, sessionToken);
+ return new ScreeningOpenbisServiceFacade(openbisServer, sessionToken);
}
- private static IScreeningApiServer createScreeningServer(String serverUrl)
+ private static IScreeningApiServer createScreeningOpenbisServer(String serverUrl)
{
return HttpInvokerUtils.createServiceStub(IScreeningApiServer.class, serverUrl
+ "/rmi-screening-api", SERVER_TIMEOUT_MIN);
}
+ private static IDssServiceRpcScreening createScreeningDssServer(String serverUrl)
+ {
+ return HttpInvokerUtils.createStreamSupportingServiceStub(IDssServiceRpcScreening.class,
+ serverUrl + "/rmi-datastore-server-screening-api", SERVER_TIMEOUT_MIN);
+ }
+
private ScreeningOpenbisServiceFacade(IScreeningApiServer screeningServer, String sessionToken)
{
- this.screeningServer = screeningServer;
+ this.openbisScreeningServer = screeningServer;
+ this.dssScreeningServerCache = new HashMap<String, IDssServiceRpcScreening>();
this.sessionToken = sessionToken;
}
/** Closes connection with the server. After calling this method this facade cannot be used. */
public void logout()
{
- screeningServer.logoutScreening(sessionToken);
+ openbisScreeningServer.logoutScreening(sessionToken);
}
/**
@@ -68,24 +85,34 @@ public class ScreeningOpenbisServiceFacade
*/
public List<Plate> listPlates()
{
- return screeningServer.listPlates(sessionToken);
+ return openbisScreeningServer.listPlates(sessionToken);
}
/**
* For a given set of plates provides the list of all connected data sets containing feature
* vectors.
*/
- public List<Dataset> listFeatureVectorDatasets(List<? extends IPlateIdentifier> plates)
+ public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
+ List<? extends PlateIdentifier> plates)
{
- return screeningServer.listFeatureVectorDatasets(sessionToken, plates);
+ return openbisScreeningServer.listFeatureVectorDatasets(sessionToken, plates);
}
/**
* For a given set of plates provides the list of all connected data sets containing images.
*/
- public List<Dataset> listImageDatasets(List<? extends IPlateIdentifier> plates)
+ public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
+ {
+ return openbisScreeningServer.listImageDatasets(sessionToken, plates);
+ }
+
+ /**
+ * Converts a given list of dataset codes to dataset identifiers which can be used in other API
+ * calls.
+ */
+ public List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes)
{
- return screeningServer.listImageDatasets(sessionToken, plates);
+ return openbisScreeningServer.getDatasetIdentifiers(sessionToken, datasetCodes);
}
/**
@@ -93,34 +120,57 @@ public class ScreeningOpenbisServiceFacade
* is just the name of the feature. If for different data sets different sets of features are
* available, provides the union of the feature names of all data sets.
*/
- public List<String> listAvailableFeatureNames(List<? extends IDatasetIdentifier> featureDatasets)
+ public List<String> listAvailableFeatureNames(
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
{
- // TODO 2010-04-16, Tomasz Pylak:
- return null;
+ if (featureDatasets.size() == 0)
+ {
+ return new ArrayList<String>();
+ }
+ IDssServiceRpcScreening dssServer = getScreeningDssServer(featureDatasets);
+ return dssServer.listAvailableFeatureNames(sessionToken, featureDatasets);
}
/**
* For a given set of data sets and a set of features (given by their name), provide all the
* feature vectors.
*/
- // Q: what result structure do you prefer? The one below is the easiest to use in Java,
- // but it could be also a simple String[][] table like:
- // plate-barcode well-row well-column feature1 feature2 ....
public List<FeatureVectorDataset> loadFeatures(
- List<? extends IDatasetIdentifier> featureDatasets, List<String> featureNames)
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets,
+ List<String> featureNames)
{
- // TODO 2010-04-16, Tomasz Pylak:
- return null;
+ if (featureDatasets.size() == 0)
+ {
+ return new ArrayList<FeatureVectorDataset>();
+ }
+ if (featureNames.size() == 0)
+ {
+ throw new IllegalArgumentException("no feature names has been specified");
+ }
+ IDssServiceRpcScreening dssServer = getScreeningDssServer(featureDatasets);
+ return dssServer.loadFeatures(sessionToken, featureDatasets, featureNames);
}
/**
- * For a given set of wells (given by feature vector data set code and well position), provide
- * all images for all channels and tiles.
+ * Provide images for a given set of image references (given by data set code, well position,
+ * channel and tile).
*/
- public List<PlateSingleImage> loadWellImages(List<WellFeaturesReference> wells)
+ public List<PlateSingleImage> loadImages(List<PlateImageReference> imageReferences)
{
- // TODO 2010-04-16, Tomasz Pylak:
- return null;
+ if (imageReferences.size() == 0)
+ {
+ return new ArrayList<PlateSingleImage>();
+ }
+ String datastoreServerUrl = extractDatastoreServerUrl(imageReferences);
+ IDssServiceRpcScreening dssServer = getScreeningDssServer(datastoreServerUrl);
+
+ List<PlateSingleImage> images = new ArrayList<PlateSingleImage>();
+ for (PlateImageReference imageRef : imageReferences)
+ {
+ InputStream stream = dssServer.loadImage(sessionToken, imageRef);
+ images.add(new PlateSingleImage(imageRef, stream));
+ }
+ return images;
}
/**
@@ -128,10 +178,55 @@ public class ScreeningOpenbisServiceFacade
* the available (natural) image size(s).
*/
public List<ImageDatasetMetadata> listImageMetadata(
- List<? extends IDatasetIdentifier> imageDatasets)
+ List<? extends IImageDatasetIdentifier> imageDatasets)
{
- // TODO 2010-04-16, Tomasz Pylak:
- return null;
+ if (imageDatasets.size() == 0)
+ {
+ return new ArrayList<ImageDatasetMetadata>();
+ }
+ IDssServiceRpcScreening dssServer = getScreeningDssServer(imageDatasets);
+ return dssServer.listImageMetadata(sessionToken, imageDatasets);
}
+ // --------- helpers -----------
+
+ private static String extractDatastoreServerUrl(List<? extends IDatasetIdentifier> datasets)
+ {
+ assert datasets.size() > 0 : "no datasets specified";
+ String datastoreServerUrl = null;
+ for (IDatasetIdentifier dataset : datasets)
+ {
+ String url = dataset.getDatastoreServerUrl();
+ if (datastoreServerUrl == null)
+ {
+ datastoreServerUrl = url;
+ } else
+ {
+ if (datastoreServerUrl.equals(url) == false)
+ {
+ throw new IllegalArgumentException(
+ "Only datasets from one datastore server can be specified in one call. Datasets from two different servers have been found.");
+ }
+ }
+ }
+ return datastoreServerUrl;
+ }
+
+ private IDssServiceRpcScreening getScreeningDssServer(String serverUrl)
+ {
+ IDssServiceRpcScreening dssService = dssScreeningServerCache.get(serverUrl);
+ if (dssService == null)
+ {
+ dssService = createScreeningDssServer(serverUrl);
+ dssScreeningServerCache.put(serverUrl, dssService);
+ }
+ return dssService;
+ }
+
+ private IDssServiceRpcScreening getScreeningDssServer(
+ List<? extends IDatasetIdentifier> datasets)
+ {
+ String datastoreServerUrl = extractDatastoreServerUrl(datasets);
+ return getScreeningDssServer(datastoreServerUrl);
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index a2326db3ff6..47b3dfb5119 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -55,8 +55,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
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.api.IScreeningApiServer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -185,8 +187,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
// --------- IScreeningOpenbisServer - method signature should be changed with care
- public List<Dataset> listFeatureVectorDatasets(String sessionToken,
- List<? extends IPlateIdentifier> plates)
+ public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
{
try
{
@@ -197,8 +199,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
}
- public List<Dataset> listImageDatasets(String sessionToken,
- List<? extends IPlateIdentifier> plates)
+ public List<ImageDatasetReference> listImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
{
try
{
@@ -220,6 +222,18 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
}
+ public List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken,
+ List<String> datasetCodes)
+ {
+ try
+ {
+ return createScreeningApiImpl(sessionToken).getDatasetIdentifiers(datasetCodes);
+ } catch (UserFailureException e)
+ {
+ throw translateException(e);
+ }
+ }
+
private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
{
try
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index 06f4e0c8ceb..13fb260fab0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -35,9 +35,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.IScreeningApiServer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
@@ -128,17 +130,28 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
- // --- IGenedataScreeningServer
+ // --- IScreeningApiServer
- public List<Dataset> listFeatureVectorDatasets(String sessionToken,
- List<? extends IPlateIdentifier> plates)
+ public void logoutScreening(String sessionToken)
+ {
+ // No logging because already done by the session manager
+ }
+
+ public String tryLoginScreening(String userId, String userPassword)
+ {
+ // No logging because already done by the session manager
+ return null;
+ }
+
+ public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
{
logAccess(sessionToken, "listFeatureVectorDatasets", "plates(%s)", plates);
return null;
}
- public List<Dataset> listImageDatasets(String sessionToken,
- List<? extends IPlateIdentifier> plates)
+ public List<ImageDatasetReference> listImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
{
logAccess(sessionToken, "listImageDatasets", "plates(%s)", plates);
return null;
@@ -150,14 +163,10 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
- public void logoutScreening(String sessionToken)
+ public List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken,
+ List<String> datasetCodes)
{
- // No logging because already done by the session manager
- }
-
- public String tryLoginScreening(String userId, String userPassword)
- {
- // No logging because already done by the session manager
+ logAccess(sessionToken, "getDatasetIdentifiers", "datasets(%s)", datasetCodes);
return null;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index d4dd7b2edd8..7d1d8d0774c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
@@ -30,7 +31,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -40,8 +43,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentif
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.DatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -66,56 +72,90 @@ public class ScreeningApiImpl
this.daoFactory = daoFactory;
}
- public List<Dataset> listFeatureVectorDatasets(List<? extends IPlateIdentifier> plates)
+ public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
+ List<? extends PlateIdentifier> plates)
{
- return loadDatasets(plates, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
+ List<ExternalDataPE> datasets =
+ loadDatasets(plates, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
+ return asFeatureVectorDatasets(datasets);
}
- public List<Dataset> listImageDatasets(List<? extends IPlateIdentifier> plates)
+ public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
- return loadDatasets(plates, ScreeningConstants.IMAGE_DATASET_TYPE);
+ List<ExternalDataPE> datasets = loadDatasets(plates, ScreeningConstants.IMAGE_DATASET_TYPE);
+ return asImageDatasets(datasets);
}
// NOTE: this method is slow when a number of plates is big
- private List<Dataset> loadDatasets(List<? extends IPlateIdentifier> plates,
+ private List<ExternalDataPE> loadDatasets(List<? extends PlateIdentifier> plates,
String datasetTypeCode)
{
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
- List<Dataset> datasets = new ArrayList<Dataset>();
- for (IPlateIdentifier plate : plates)
+ List<ExternalDataPE> datasets = new ArrayList<ExternalDataPE>();
+ for (PlateIdentifier plate : plates)
{
- List<Dataset> plateDatasets = loadDatasets(plate, datasetTypeCode, sampleBO);
+ List<ExternalDataPE> plateDatasets = loadDatasets(plate, datasetTypeCode, sampleBO);
datasets.addAll(plateDatasets);
}
return datasets;
}
- private List<Dataset> loadDatasets(IPlateIdentifier plate, String datasetTypeCode,
+ private List<ExternalDataPE> loadDatasets(PlateIdentifier plate, String datasetTypeCode,
ISampleBO sampleBO)
{
sampleBO.loadBySampleIdentifier(createSampleIdentifier(plate));
SamplePE sample = sampleBO.getSample();
List<ExternalDataPE> datasets = daoFactory.getExternalDataDAO().listExternalData(sample);
datasets = ScreeningUtils.filterDatasetsByType(datasets, datasetTypeCode);
- return asDatasets(datasets, plate);
+ return datasets;
+ }
+
+ private static List<FeatureVectorDatasetReference> asFeatureVectorDatasets(
+ List<ExternalDataPE> datasets)
+ {
+ List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
+ for (ExternalDataPE externalData : datasets)
+ {
+ result.add(asFeatureVectorDataset(externalData));
+ }
+ return result;
+ }
+
+ private static FeatureVectorDatasetReference asFeatureVectorDataset(ExternalDataPE externalData)
+ {
+ DataStorePE dataStore = externalData.getDataStore();
+ return new FeatureVectorDatasetReference(externalData.getCode(),
+ dataStore.getDownloadUrl(), createPlateIdentifier(externalData));
}
- private static List<Dataset> asDatasets(List<ExternalDataPE> datasets, IPlateIdentifier plate)
+ private static List<ImageDatasetReference> asImageDatasets(List<ExternalDataPE> datasets)
{
- List<Dataset> result = new ArrayList<Dataset>();
+ List<ImageDatasetReference> result = new ArrayList<ImageDatasetReference>();
for (ExternalDataPE externalData : datasets)
{
- result.add(asDataset(externalData, plate));
+ result.add(asImageDataset(externalData));
}
return result;
}
- private static Dataset asDataset(ExternalDataPE externalData, IPlateIdentifier plate)
+ private static ImageDatasetReference asImageDataset(ExternalDataPE externalData)
{
- return new Dataset(externalData.getCode(), externalData.getDataStore().getCode(), plate);
+ DataStorePE dataStore = externalData.getDataStore();
+ return new ImageDatasetReference(externalData.getCode(), dataStore.getDownloadUrl(),
+ createPlateIdentifier(externalData));
}
- private static SampleIdentifier createSampleIdentifier(IPlateIdentifier plate)
+ private static PlateIdentifier createPlateIdentifier(ExternalDataPE externalData)
+ {
+ SamplePE sample = externalData.tryGetSample();
+ assert sample != null : "dataset not connected to a sample: " + externalData;
+ final String plateCode = sample.getCode();
+ GroupPE group = sample.getGroup();
+ final String spaceCodeOrNull = (group != null) ? group.getCode() : null;
+ return new PlateIdentifier(plateCode, spaceCodeOrNull);
+ }
+
+ private static SampleIdentifier createSampleIdentifier(PlateIdentifier plate)
{
SampleOwnerIdentifier owner;
String spaceCode = plate.tryGetSpaceCode();
@@ -171,4 +211,23 @@ public class ScreeningApiImpl
assert plateTypePE != null : "plate type not found";
return SampleTypeTranslator.translate(plateTypePE, null);
}
+
+ public List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes)
+ {
+ IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ List<IDatasetIdentifier> identifiers = new ArrayList<IDatasetIdentifier>();
+ for (String datasetCode : datasetCodes)
+ {
+ identifiers.add(getDatasetIdentifier(externalDataBO, datasetCode));
+ }
+ return identifiers;
+ }
+
+ private IDatasetIdentifier getDatasetIdentifier(IExternalDataBO externalDataBO,
+ String datasetCode)
+ {
+ externalDataBO.loadByCode(datasetCode);
+ ExternalDataPE externalData = externalDataBO.getExternalData();
+ return new DatasetIdentifier(datasetCode, externalData.getDataStore().getDownloadUrl());
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IGenedataDssServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IGenedataDssServer.java
deleted file mode 100644
index c9b0fa5ccff..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IGenedataDssServer.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2010 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.plugin.screening.shared.api;
-
-import java.util.List;
-
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreenerDatasetPredicate;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreenerWellPredicate;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDataset;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetMetadata;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateSingleImage;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.WellFeaturesReference;
-
-/**
- * @author Tomasz Pylak
- */
-public interface IGenedataDssServer
-{
- /**
- * For a given set of feature vector data sets provide the list of all available features. This
- * is just the name of the feature. If for different data sets different sets of features are
- * available, provide the union of the features of all data sets.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- List<String> listAvailableFeatureNames(
- String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerDatasetPredicate.class) List<IDatasetIdentifier> featureDatasets);
-
- /**
- * For a given set of data sets and a set of features (given by their name), provide the feature
- * matrix. Each column in that matrix is one feature, each row is one well in one data set.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- List<FeatureVectorDataset> loadFeatures(
- String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerDatasetPredicate.class) List<IDatasetIdentifier> featureDatasets,
- List<String> featureNames);
-
- /**
- * For a given set of wells (given by data set code / well position), provide all images for all
- * channels and tiles. To be more precise: find the image parent data set for each feature
- * vector data set given by data set code and then provide the images for a sub set of the wells
- * of this image data set. Do this for all feature vector data sets.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- List<PlateSingleImage> loadWellImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerWellPredicate.class) List<WellFeaturesReference> wells);
-
- /**
- * For a given set of image data sets, provide all image channels that have been acquired and
- * the available (natural) image size(s).
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- List<ImageDatasetMetadata> listImageMetadata(
- String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerDatasetPredicate.class) List<IDatasetIdentifier> imageDatasets);
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IScreeningApiServer.java
index e744e3186f3..ecc24d346d0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/IScreeningApiServer.java
@@ -24,11 +24,14 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Authoriz
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreenerPlateValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreenerReadonlyPlatePredicate;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
/**
* This interface is a part of the official public screening API. It is forbidden to change it in a
@@ -67,9 +70,9 @@ public interface IScreeningApiServer
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.OBSERVER)
- List<Dataset> listFeatureVectorDatasets(
+ List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerReadonlyPlatePredicate.class) List<? extends IPlateIdentifier> plates)
+ @AuthorizationGuard(guardClass = ScreenerReadonlyPlatePredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
/**
@@ -78,8 +81,16 @@ public interface IScreeningApiServer
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.OBSERVER)
- List<Dataset> listImageDatasets(
+ List<ImageDatasetReference> listImageDatasets(
String sessionToken,
- @AuthorizationGuard(guardClass = ScreenerReadonlyPlatePredicate.class) List<? extends IPlateIdentifier> plates)
+ @AuthorizationGuard(guardClass = ScreenerReadonlyPlatePredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
+
+ /**
+ * Converts a given list of dataset codes to dataset identifiers.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> datasetCodes);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerDatasetPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerDatasetPredicate.java
deleted file mode 100644
index 95be78bcf54..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerDatasetPredicate.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2010 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.plugin.screening.shared.api.authorization;
-
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DelegatedPredicate;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Dataset;
-
-/**
- * @author Tomasz Pylak
- */
-public class ScreenerDatasetPredicate extends DelegatedPredicate<String, Dataset>
-{
- public ScreenerDatasetPredicate()
- {
- super(new DataSetCodePredicate());
- }
-
- @Override
- public String convert(Dataset value)
- {
- return value.getDatasetCode();
- }
-
- @Override
- public String getCandidateDescription()
- {
- return "dataset";
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerReadonlyPlatePredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerReadonlyPlatePredicate.java
index c7597dd532e..7505500d63e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerReadonlyPlatePredicate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerReadonlyPlatePredicate.java
@@ -21,13 +21,13 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwn
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateIdentifier;
/**
* @author Tomasz Pylak
*/
public class ScreenerReadonlyPlatePredicate extends
- DelegatedPredicate<SampleOwnerIdentifier, IPlateIdentifier>
+ DelegatedPredicate<SampleOwnerIdentifier, PlateIdentifier>
{
public ScreenerReadonlyPlatePredicate()
@@ -36,7 +36,7 @@ public class ScreenerReadonlyPlatePredicate extends
}
@Override
- public SampleOwnerIdentifier convert(IPlateIdentifier value)
+ public SampleOwnerIdentifier convert(PlateIdentifier value)
{
return new SampleOwnerIdentifier(new SpaceIdentifier(DatabaseInstanceIdentifier
.createHome(), value.tryGetSpaceCode()));
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerWellPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerWellPredicate.java
deleted file mode 100644
index 390e87f2d4d..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/ScreenerWellPredicate.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2010 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.plugin.screening.shared.api.authorization;
-
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DelegatedPredicate;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.WellFeaturesReference;
-
-/**
- * @author Tomasz Pylak
- */
-public class ScreenerWellPredicate extends DelegatedPredicate<String, WellFeaturesReference>
-{
- public ScreenerWellPredicate()
- {
- super(new DataSetCodePredicate());
- }
-
- @Override
- public String getCandidateDescription()
- {
- return "well";
- }
-
- @Override
- public String convert(WellFeaturesReference value)
- {
- return value.getFeatureVectorDataset().getDatasetCode();
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Dataset.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Dataset.java
deleted file mode 100644
index c9acb66258f..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Dataset.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
-
-import java.io.Serializable;
-
-/**
- * Description of one dataset.
- *
- * @author Tomasz Pylak
- */
-public class Dataset implements IDatasetIdentifier, Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private final String datasetCode;
-
- private final String datastoreCode;
-
- private final IPlateIdentifier plate;
-
- public Dataset(String datasetCode, String datastoreCode, IPlateIdentifier plate)
- {
- this.datasetCode = datasetCode;
- this.datastoreCode = datastoreCode;
- this.plate = plate;
- }
-
- /** a code of the dataset */
- public String getDatasetCode()
- {
- return datasetCode;
- }
-
- /** a code which points to the datastore server on which the dataset is accessible */
- public String getDatastoreCode()
- {
- return datastoreCode;
- }
-
- /** a pointer to a plate to which the dataset belongs */
- public IPlateIdentifier getPlate()
- {
- return plate;
- }
-
- @Override
- public String toString()
- {
- return datasetCode;
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetIdentifier.java
new file mode 100644
index 00000000000..3a666695f78
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetIdentifier.java
@@ -0,0 +1,58 @@
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
+
+import java.io.Serializable;
+
+/**
+ * Contains data which uniquely define a dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class DatasetIdentifier implements Serializable, IDatasetIdentifier
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String datasetCode;
+
+ // a.k.a. downloadURL
+ private final String datastoreServerUrl;
+
+ public DatasetIdentifier(String datasetCode, String datastoreServerUrl)
+ {
+ this.datasetCode = datasetCode;
+ this.datastoreServerUrl = datastoreServerUrl;
+ }
+
+ /** a code of the dataset */
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public String getDatastoreServerUrl()
+ {
+ return datastoreServerUrl;
+ }
+
+ @Override
+ public String toString()
+ {
+ return datasetCode;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || obj instanceof DatasetIdentifier == false)
+ {
+ return false;
+ }
+ DatasetIdentifier that = (DatasetIdentifier) obj;
+ return datasetCode.equals(that.datasetCode);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return datasetCode.hashCode();
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetReference.java
new file mode 100644
index 00000000000..a46585ae7a7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/DatasetReference.java
@@ -0,0 +1,33 @@
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
+
+import java.io.Serializable;
+
+/**
+ * Description of one dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class DatasetReference extends DatasetIdentifier implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private final PlateIdentifier plate;
+
+ public DatasetReference(String datasetCode, String datastoreServerUrl, PlateIdentifier plate)
+ {
+ super(datasetCode, datastoreServerUrl);
+ this.plate = plate;
+ }
+
+ /** a pointer to a plate to which the dataset belongs */
+ public PlateIdentifier getPlate()
+ {
+ return plate;
+ }
+
+ @Override
+ public String toString()
+ {
+ return super.toString() + " (plate: " + plate + ")";
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/FeatureVectorDatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/FeatureVectorDatasetReference.java
new file mode 100644
index 00000000000..ca950190a66
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/FeatureVectorDatasetReference.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.api.dto;
+
+/**
+ * Description of one feature vector dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class FeatureVectorDatasetReference extends DatasetReference implements
+ IFeatureVectorDatasetIdentifier
+{
+ private static final long serialVersionUID = 1L;
+
+ public FeatureVectorDatasetReference(String datasetCode, String datastoreServerUrl,
+ PlateIdentifier plate)
+ {
+ super(datasetCode, datastoreServerUrl, plate);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IDatasetIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IDatasetIdentifier.java
index 84b02780f0d..f6d5c2a908d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IDatasetIdentifier.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IDatasetIdentifier.java
@@ -1,3 +1,19 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.api.dto;
/**
@@ -8,8 +24,9 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
public interface IDatasetIdentifier
{
/** a code of the dataset */
- String getDatasetCode();
+ public String getDatasetCode();
/** a code which points to the datastore server on which the dataset is accessible */
- String getDatastoreCode();
+ public String getDatastoreServerUrl();
+
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IFeatureVectorDatasetIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IFeatureVectorDatasetIdentifier.java
new file mode 100644
index 00000000000..9747dce82ca
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IFeatureVectorDatasetIdentifier.java
@@ -0,0 +1,26 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.api.dto;
+
+/**
+ * Contains data which uniquely define a feature vector dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IFeatureVectorDatasetIdentifier extends IDatasetIdentifier
+{
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IImageDatasetIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IImageDatasetIdentifier.java
new file mode 100644
index 00000000000..093d1a4d70c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IImageDatasetIdentifier.java
@@ -0,0 +1,26 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.api.dto;
+
+/**
+ * Contains data which uniquely define an image dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IImageDatasetIdentifier extends IDatasetIdentifier
+{
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IPlateIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IPlateIdentifier.java
deleted file mode 100644
index e398a4b80c8..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/IPlateIdentifier.java
+++ /dev/null
@@ -1,15 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
-
-/**
- * Contains data which uniquely define a plate
- *
- * @author Tomasz Pylak
- */
-public interface IPlateIdentifier
-{
- /** a code of the plate */
- String getPlateCode();
-
- /** a code of the space to which the plate belongs or null if it is a shared plate */
- String tryGetSpaceCode();
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetMetadata.java
index 8ee5750525d..b8e7d956f1c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetMetadata.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetMetadata.java
@@ -15,15 +15,18 @@ public class ImageDatasetMetadata implements Serializable
private final int channelsNumber;
+ private final int tilesNumber;
+
private final int width;
private final int height;
- public ImageDatasetMetadata(IDatasetIdentifier dataset, int channelsNumber, int width,
- int height)
+ public ImageDatasetMetadata(IDatasetIdentifier dataset, int channelsNumber, int tilesNumber,
+ int width, int height)
{
this.imageDataset = dataset;
this.channelsNumber = channelsNumber;
+ this.tilesNumber = tilesNumber;
this.width = width;
this.height = height;
}
@@ -42,6 +45,14 @@ public class ImageDatasetMetadata implements Serializable
return channelsNumber;
}
+ /**
+ * number of image tiles (aka fields) into which each well is splited
+ */
+ public int getTilesNumber()
+ {
+ return tilesNumber;
+ }
+
/** width of all the images in the described dataset */
public int getWidth()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetReference.java
new file mode 100644
index 00000000000..735ed66f9f4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/ImageDatasetReference.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.api.dto;
+
+/**
+ * Description of one image dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageDatasetReference extends DatasetReference implements IImageDatasetIdentifier
+{
+ private static final long serialVersionUID = 1L;
+
+ public ImageDatasetReference(String datasetCode, String datastoreServerUrl,
+ PlateIdentifier plate)
+ {
+ super(datasetCode, datastoreServerUrl, plate);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Plate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Plate.java
index 1bc1bd22d71..ed8ff9e3ef3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Plate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/Plate.java
@@ -7,24 +7,17 @@ import java.io.Serializable;
*
* @author Tomasz Pylak
*/
-public class Plate implements IPlateIdentifier, Serializable
+public class Plate extends PlateIdentifier implements Serializable
{
private static final long serialVersionUID = 1L;
- private String plateCode, experimentCode, projectCode, spaceCodeOrNull;
+ private String experimentCode, projectCode;
public Plate(String plateCode, String experimentCode, String projectCode, String spaceCodeOrNull)
{
- this.plateCode = plateCode;
+ super(plateCode, spaceCodeOrNull);
this.experimentCode = experimentCode;
this.projectCode = projectCode;
- this.spaceCodeOrNull = spaceCodeOrNull;
- }
-
- /** a code of the plate */
- public String getPlateCode()
- {
- return plateCode;
}
/** a code of the experiment to which the plate belongs */
@@ -38,18 +31,4 @@ public class Plate implements IPlateIdentifier, Serializable
{
return projectCode;
}
-
- /** a code of the space to which the plate belongs or null if it is a shared plate */
- public String tryGetSpaceCode()
- {
- return spaceCodeOrNull;
- }
-
- @Override
- public String toString()
- {
- return (spaceCodeOrNull != null ? "/" + spaceCodeOrNull : "shared") + "/" + projectCode
- + "/" + experimentCode + "/" + plateCode;
- }
-
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateIdentifier.java
new file mode 100644
index 00000000000..9d82e988d31
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateIdentifier.java
@@ -0,0 +1,52 @@
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
+
+import java.io.Serializable;
+
+/**
+ * Contains data which uniquely define a plate
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateIdentifier implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private String plateCode, spaceCodeOrNull;
+
+ public PlateIdentifier(String plateCode, String spaceCodeOrNull)
+ {
+ this.plateCode = plateCode;
+ this.spaceCodeOrNull = spaceCodeOrNull;
+ }
+
+ /** a code of the plate */
+ public String getPlateCode()
+ {
+ return plateCode;
+ }
+
+ /** a code of the space to which the plate belongs or null if it is a shared plate */
+ public String tryGetSpaceCode()
+ {
+ return spaceCodeOrNull;
+ }
+
+ @Override
+ public String toString()
+ {
+ return (spaceCodeOrNull != null ? "/" + spaceCodeOrNull : "") + "/" + plateCode;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || obj instanceof Plate == false)
+ {
+ return false;
+ }
+ Plate that = (Plate) obj;
+ return plateCode.equals(that.getPlateCode())
+ && ((spaceCodeOrNull != null && spaceCodeOrNull.equals(that.tryGetSpaceCode())) || (spaceCodeOrNull == null && that
+ .tryGetSpaceCode() == null));
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateImageReference.java
new file mode 100644
index 00000000000..c817c0f35e3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateImageReference.java
@@ -0,0 +1,53 @@
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
+
+import java.io.Serializable;
+
+/**
+ * Identifies one well in a dataset containing images.
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateImageReference extends DatasetIdentifier implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private final WellPosition wellPosition;
+
+ private final int tile;
+
+ private final int channel;
+
+ public PlateImageReference(int wellRow, int wellColumn, int tile, int channel,
+ IDatasetIdentifier dataset)
+ {
+ super(dataset.getDatasetCode(), dataset.getDatastoreServerUrl());
+ this.wellPosition = new WellPosition(wellRow, wellColumn);
+ this.tile = tile;
+ this.channel = channel;
+ }
+
+ /** well position on the plate */
+ public WellPosition getWellPosition()
+ {
+ return wellPosition;
+ }
+
+ /** a sequential number of an image tile, starts from 1 */
+ public int getTile()
+ {
+ return tile;
+ }
+
+ /** index of a channel in which an image has been taken, starts from 1 */
+ public int getChannel()
+ {
+ return channel;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Image for [dataset " + getDatasetCode() + ", well " + wellPosition + ", channel "
+ + channel + ", tile " + tile + "]";
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateSingleImage.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateSingleImage.java
index 08ac539a85d..e42e73bbd5f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateSingleImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/PlateSingleImage.java
@@ -13,41 +13,35 @@ public class PlateSingleImage implements Serializable
{
private static final long serialVersionUID = 1L;
- private final WellPosition wellPosition;
-
- private final int tile;
-
- private final int channel;
+ private final PlateImageReference imageReference;
private final InputStream image;
- public PlateSingleImage(WellPosition wellPosition, int tile, int channel, InputStream image)
+ public PlateSingleImage(PlateImageReference imageReference, InputStream image)
{
- this.wellPosition = wellPosition;
- this.tile = tile;
- this.channel = channel;
+ this.imageReference = imageReference;
this.image = image;
}
/** position of the well to which the image belongs */
public WellPosition getWellPosition()
{
- return wellPosition;
+ return imageReference.getWellPosition();
}
/**
- * tile (a.k.a. field) number. Each well can be separated into many tiles, for each tile one
- * image is acquired.
+ * tile (aka field) number, each well can be separated into many tiles, for each tile one image
+ * is acquired.
*/
public int getTile()
{
- return tile;
+ return imageReference.getTile();
}
/** Index of the channel. Starts from 1. */
public int getChannel()
{
- return channel;
+ return imageReference.getChannel();
}
/** stream with a png image */
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellFeaturesReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellFeaturesReference.java
deleted file mode 100644
index c00df8e4b4a..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellFeaturesReference.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto;
-
-import java.io.Serializable;
-
-/**
- * Identifies one well in a dataset containing feature vectors.
- *
- * @author Tomasz Pylak
- */
-public class WellFeaturesReference implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private final WellPosition wellPosition;
-
- private final IDatasetIdentifier featureVectorDataset;
-
- public WellFeaturesReference(WellPosition wellPosition, IDatasetIdentifier featureVectorDataset)
- {
- this.wellPosition = wellPosition;
- this.featureVectorDataset = featureVectorDataset;
- }
-
- /** well position on the plate */
- public WellPosition getWellPosition()
- {
- return wellPosition;
- }
-
- /** identifier of the dataset containing feature vectors */
- public IDatasetIdentifier getFeatureVectorDataset()
- {
- return featureVectorDataset;
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellPosition.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellPosition.java
index be7f8a3d756..79472517672 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellPosition.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/dto/WellPosition.java
@@ -30,4 +30,10 @@ public class WellPosition implements Serializable
{
return wellColumn;
}
+
+ @Override
+ public String toString()
+ {
+ return "[" + wellRow + ", " + wellColumn + "]";
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/screening-dssApplicationContext.xml b/screening/source/java/screening-dssApplicationContext.xml
new file mode 100644
index 00000000000..1342c06b707
--- /dev/null
+++ b/screening/source/java/screening-dssApplicationContext.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-2.5.xsd">
+
+ <!--
+ // Replaces ${...} with corresponding values found in 'location' property. A value
+ // can be overridden by setting a corresponding system property.
+ -->
+ <bean id="propertyConfigurer"
+ class="ch.systemsx.cisd.common.spring.ExposablePropertyPaceholderConfigurer">
+ <property name="location" value="file:etc/service.properties" />
+ <property name="systemPropertiesModeName" value="SYSTEM_PROPERTIES_MODE_OVERRIDE" />
+ <property name="ignoreUnresolvablePlaceholders" value="true" />
+ </bean>
+
+ <!--
+ // Screening specific configuration
+ -->
+
+ <bean id="data-store-rpc-service-screening"
+ class="com.marathon.util.spring.StreamSupportingHttpInvokerServiceExporter">
+ <property name="service">
+ <bean class="ch.systemsx.cisd.openbis.dss.screening.server.DssServiceRpcScreening" >
+ <constructor-arg value="${storeroot-dir}" />
+ </bean>
+ </property>
+ <property name="serviceInterface" value="ch.systemsx.cisd.openbis.dss.screening.shared.api.IDssServiceRpcScreening" />
+ </bean>
+
+
+</beans>
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/ScreeningClientApiTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/ScreeningClientApiTest.java
index e22b5c6f174..2e3a6217b8d 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/ScreeningClientApiTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/ScreeningClientApiTest.java
@@ -16,30 +16,96 @@
package ch.systemsx.cisd.openbis.plugin.screening;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
+import org.apache.log4j.lf5.util.StreamUtils;
+
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.PlateSingleImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.WellPosition;
/**
* @author Tomasz Pylak
*/
public class ScreeningClientApiTest
{
- private static final String USER_ID = "tpylak";
+ private static final String USER_ID = "a";
private static final String USER_PASSWORD = "x";
- private static final String SERVER_URL = "http://localhost:8888/openbis";
+ private static final String OPENBIS_SERVER_URL = "http://localhost:8888/openbis";
- public static void main(String[] args)
+ public static void main(String[] args) throws IOException
{
ScreeningOpenbisServiceFacade facade =
- ScreeningOpenbisServiceFacade.tryCreate(USER_ID, USER_PASSWORD, SERVER_URL);
- List<Plate> plates = facade.listPlates();
- System.out.println("Plates: " + plates);
- System.out.println("Image datasets: " + facade.listImageDatasets(plates));
- System.out.println("Feature vector datasets: " + facade.listFeatureVectorDatasets(plates));
+ ScreeningOpenbisServiceFacade.tryCreate(USER_ID, USER_PASSWORD, OPENBIS_SERVER_URL);
+ // List<Plate> plates = facade.listPlates();
+ // System.out.println("Plates: " + plates);
+ // List<ImageDatasetReference> imageDatasets = facade.listImageDatasets(plates);
+ // System.out.println("Image datasets: " + imageDatasets);
+ // List<FeatureVectorDatasetReference> featureVectorDatasets =
+ // facade.listFeatureVectorDatasets(plates);
+ // System.out.println("Feature vector datasets: " + featureVectorDatasets);
+
+ // test for feature vector dataset
+ // String datasetCode = "20091214153212961-474922"; // feature vector
+ String datasetCode = "20091216162628729-475111"; // image
+ IDatasetIdentifier datasetIdentifier = getDatasetIdentifier(facade, datasetCode);
+ loadImages(facade, datasetIdentifier);
+
+ facade.logout();
+ }
+ private static IDatasetIdentifier getDatasetIdentifier(ScreeningOpenbisServiceFacade facade,
+ String datasetCode)
+ {
+ IDatasetIdentifier datasetIdentifier =
+ facade.getDatasetIdentifiers(Arrays.asList(datasetCode)).get(0);
+ return datasetIdentifier;
+ }
+
+ private static void loadImages(ScreeningOpenbisServiceFacade facade,
+ IDatasetIdentifier datasetIdentifier) throws FileNotFoundException, IOException
+ {
+ for (int channel = 1; channel <= 2; channel++)
+ {
+ for (int tile = 4; tile <= 6; tile++)
+ {
+ List<PlateImageReference> imageRefs = new ArrayList<PlateImageReference>();
+ imageRefs.add(new PlateImageReference(1, 3, tile, channel, datasetIdentifier));
+ List<PlateSingleImage> images = facade.loadImages(imageRefs);
+ saveImages(images);
+ }
+ }
+
+ }
+
+ private static void saveImages(List<PlateSingleImage> images) throws FileNotFoundException,
+ IOException
+ {
+ for (PlateSingleImage image : images)
+ {
+ FileOutputStream out = new FileOutputStream(new File(createImageFileName(image)));
+ InputStream in = image.getImage();
+ StreamUtils.copyThenClose(in, out);
+ out.close();
+ in.close();
+ }
+ }
+
+ private static String createImageFileName(PlateSingleImage image)
+ {
+ WellPosition well = image.getWellPosition();
+ return "img_r" + well.getWellRow() + "_c" + well.getWellColumn() + "_ch"
+ + image.getChannel() + "_t" + image.getTile() + ".png";
}
}
--
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