LMS-1505 Created an interface for the Screening Service Facade.

SVN: 15888

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java

+/*
+ * 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.client.api.v1;
+
+import java.io.IOException;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
+
+/**
+ * 
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface IScreeningOpenbisServiceFacade
+{
+
+    /**
+     * Return the session token for this authenticated user.
+     */
+    public abstract String getSessionToken();
+
+    /** Closes connection with the server. After calling this method this facade cannot be used. */
+    public abstract void logout();
+
+    /**
+     * Return the list of all visible plates assigned to any experiment, along with their
+     * hierarchical context (space, project, experiment).
+     */
+    public abstract List<Plate> listPlates();
+
+    /**
+     * For a given set of plates provides the list of all connected data sets containing feature
+     * vectors.
+     */
+    public abstract List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
+            List<? extends PlateIdentifier> plates);
+
+    /**
+     * For a given set of plates provides the list of all connected data sets containing images.
+     */
+    public abstract List<ImageDatasetReference> listImageDatasets(
+            List<? extends PlateIdentifier> plates);
+
+    /**
+     * Converts a given list of dataset codes to dataset identifiers which can be used in other API
+     * calls.
+     */
+    public abstract List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes);
+
+    /**
+     * For a given set of feature vector data sets provides 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, provides the union of the feature names of all data sets.
+     */
+    public abstract List<String> listAvailableFeatureNames(
+            List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+
+    /**
+     * For a given set of data sets and a set of features (given by their name), provide all the
+     * feature vectors.
+     */
+    public abstract List<FeatureVectorDataset> loadFeatures(
+            List<? extends IFeatureVectorDatasetIdentifier> featureDatasets,
+            List<String> featureNames);
+
+    /**
+     * Saves images for a given list of image references (given by data set code, well position,
+     * channel and tile) in the provided output streams. Output streams will not be closed
+     * automatically.<br>
+     * The number of image references has to be the same as the number of files.
+     * 
+     * @throws IOException when reading images from the server or writing them to the output streams
+     *             fails
+     */
+    public abstract void loadImages(List<PlateImageReference> imageReferences,
+            IImageOutputStreamProvider outputStreamProvider) throws IOException;
+
+    /**
+     * For a given set of image data sets, provide all image channels that have been acquired and
+     * the available (natural) image size(s).
+     */
+    public abstract List<ImageDatasetMetadata> listImageMetadata(
+            List<? extends IImageDatasetIdentifier> imageDatasets);
+
+}
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java

@@ -66,7 +66,7 @@ public class ScreeningClientApiTest
 
         System.out.println(String.format("Connecting to the server '%s' as a user '%s.", serverUrl,
                 userId));
-        ScreeningOpenbisServiceFacade facade =
+        IScreeningOpenbisServiceFacade facade =
                 ScreeningOpenbisServiceFacade.tryCreate(userId, userPassword, serverUrl);
         if (facade == null)
         {
@@ -104,7 +104,7 @@ public class ScreeningClientApiTest
         facade.logout();
     }
 
-    private static IDatasetIdentifier getDatasetIdentifier(ScreeningOpenbisServiceFacade facade,
+    private static IDatasetIdentifier getDatasetIdentifier(IScreeningOpenbisServiceFacade facade,
             String datasetCode)
     {
         IDatasetIdentifier datasetIdentifier =
@@ -112,7 +112,7 @@ public class ScreeningClientApiTest
         return datasetIdentifier;
     }
 
-    private static void loadImages(ScreeningOpenbisServiceFacade facade,
+    private static void loadImages(IScreeningOpenbisServiceFacade facade,
             IDatasetIdentifier datasetIdentifier) throws FileNotFoundException, IOException
     {
         File dir = new File(datasetIdentifier.getDatasetCode());
@@ -148,7 +148,7 @@ public class ScreeningClientApiTest
      * 
      * @throws IOException when reading images from the server or writing them to the files fails
      */
-    private static void loadImages(ScreeningOpenbisServiceFacade facade,
+    private static void loadImages(IScreeningOpenbisServiceFacade facade,
             List<PlateImageReference> imageReferences, List<File> imageOutputFiles)
             throws IOException
     {

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java

@@ -28,7 +28,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageRef
  * 
  * @author Tomasz Pylak
  */
-public class ScreeningOpenbisServiceFacade
+public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFacade
 {
     private static final String DSS_SCREENING_API = "/rmi-datastore-server-screening-api-v1/";
 
@@ -48,7 +48,7 @@ public class ScreeningOpenbisServiceFacade
      * 
      * @return null if the user could not be authenticated.
      */
-    public static ScreeningOpenbisServiceFacade tryCreate(String userId, String userPassword,
+    public static IScreeningOpenbisServiceFacade tryCreate(String userId, String userPassword,
             String serverUrl)
     {
         IScreeningApiServer openbisServer = createScreeningOpenbisServer(serverUrl);
@@ -60,6 +60,19 @@ public class ScreeningOpenbisServiceFacade
         return new ScreeningOpenbisServiceFacade(openbisServer, sessionToken);
     }
 
+    /**
+     * Creates a service facade which communicates with the openBIS server at the specified URL for
+     * an authenticated user.
+     * 
+     * @param sessionToken The session token for the authenticated user
+     * @param serverUrl The URL for the openBIS application server
+     */
+    public static IScreeningOpenbisServiceFacade tryCreate(String sessionToken, String serverUrl)
+    {
+        IScreeningApiServer openbisServer = createScreeningOpenbisServer(serverUrl);
+        return new ScreeningOpenbisServiceFacade(openbisServer, sessionToken);
+    }
+
     private static IScreeningApiServer createScreeningOpenbisServer(String serverUrl)
     {
         return HttpInvokerUtils.createServiceStub(IScreeningApiServer.class, serverUrl
@@ -79,6 +92,14 @@ public class ScreeningOpenbisServiceFacade
         this.sessionToken = sessionToken;
     }
 
+    /**
+     * Return the session token for this authenticated user.
+     */
+    public String getSessionToken()
+    {
+        return sessionToken;
+    }
+
     /** Closes connection with the server. After calling this method this facade cannot be used. */
     public void logout()
     {
@@ -192,7 +213,8 @@ public class ScreeningOpenbisServiceFacade
         InputStream stream = dssServer.loadImages(sessionToken, imageReferences);
         try
         {
-            ConcatenatedFileOutputStreamWriter imagesWriter = new ConcatenatedFileOutputStreamWriter(stream);
+            ConcatenatedFileOutputStreamWriter imagesWriter =
+                    new ConcatenatedFileOutputStreamWriter(stream);
             for (PlateImageReference imageRef : imageReferences)
             {
                 OutputStream output = outputStreamProvider.getOutputStream(imageRef);