From 33dcd744579ca99b11c540bcb69fb3270d86d6b0 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 19 Apr 2010 11:55:40 +0000
Subject: [PATCH] LMS-1491 screening API: client facade (not finished)
SVN: 15509
---
.../client/ScreeningOpenbisServiceFacade.java | 135 ++++++++++++++++++
1 file changed, 135 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/ScreeningOpenbisServiceFacade.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/ScreeningOpenbisServiceFacade.java
new file mode 100644
index 00000000000..9093d01a769
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/ScreeningOpenbisServiceFacade.java
@@ -0,0 +1,135 @@
+package ch.systemsx.cisd.openbis.plugin.screening.client;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.IScreeningOpenbisServer;
+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.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.IPlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.dto.Plate;
+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 API for Genedata Screener integration.
+ *
+ * @author Tomasz Pylak
+ */
+public class ScreeningOpenbisServiceFacade
+{
+ private static final int SERVER_TIMEOUT_MIN = 5;
+
+ private final IScreeningOpenbisServer screeningServer;
+
+ private final String sessionToken;
+
+ /**
+ * Creates a service facade which communicates with the openBIS server at the specified URL.
+ * Authenticates the user.
+ */
+ public static ScreeningOpenbisServiceFacade create(String userId, String userPassword,
+ String serverUrl)
+ {
+ IScreeningOpenbisServer server = createScreeningServer(serverUrl);
+ String sessionToken = server.tryLoginScreening(userId, userPassword);
+ if (sessionToken == null)
+ {
+ return null;
+ }
+ return new ScreeningOpenbisServiceFacade(server, sessionToken);
+ }
+
+ private static IScreeningOpenbisServer createScreeningServer(String serverUrl)
+ {
+ return HttpInvokerUtils.createServiceStub(IScreeningOpenbisServer.class, serverUrl
+ + "/rmi-screening", SERVER_TIMEOUT_MIN);
+ }
+
+ private ScreeningOpenbisServiceFacade(IScreeningOpenbisServer screeningServer,
+ String sessionToken)
+ {
+ this.screeningServer = screeningServer;
+ this.sessionToken = sessionToken;
+ }
+
+ /** Closes connection with the server. After calling this method this facade cannot be used. */
+ public void logout()
+ {
+ screeningServer.logoutScreening(sessionToken);
+ }
+
+ /**
+ * Return the list of all visible plates, along with their hierarchical context (space, project,
+ * experiment).
+ */
+ public List<Plate> listPlates()
+ {
+ return screeningServer.listPlates(sessionToken);
+ }
+
+ /**
+ * For a given set of plates provides the list of all connected data sets containing feature
+ * vectors.
+ */
+ public List<Dataset> listFeatureVectorDatasets(List<IPlateIdentifier> plates)
+ {
+ return screeningServer.listFeatureVectorDatasets(sessionToken, plates);
+ }
+
+ /**
+ * For a given set of plates provides the list of all connected data sets containing images.
+ */
+ public List<Dataset> listImageDatasets(List<IPlateIdentifier> plates)
+ {
+ return screeningServer.listImageDatasets(sessionToken, plates);
+ }
+
+ /**
+ * 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 List<String> listAvailableFeatureNames(List<IDatasetIdentifier> featureDatasets)
+ {
+ // TODO 2010-04-16, Tomasz Pylak:
+ return null;
+ }
+
+ /**
+ * 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<IDatasetIdentifier> featureDatasets,
+ List<String> featureNames)
+ {
+ // TODO 2010-04-16, Tomasz Pylak:
+ return null;
+ }
+
+ /**
+ * For a given set of wells (given by feature vector data set code and well position), provide
+ * all images for all channels and tiles.
+ */
+ public List<PlateSingleImage> loadWellImages(List<WellFeaturesReference> wells)
+ {
+ // TODO 2010-04-16, Tomasz Pylak:
+ return null;
+ }
+
+ /**
+ * For a given set of image data sets, provide all image channels that have been acquired and
+ * the available (natural) image size(s).
+ */
+ public List<ImageDatasetMetadata> listImageMetadata(List<IDatasetIdentifier> imageDatasets)
+ {
+ // TODO 2010-04-16, Tomasz Pylak:
+ return null;
+ }
+
+}
--
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