From 23d37eb55d7f03a380878ce5631e8ecea07e930f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 7 Jul 2011 11:55:24 +0000
Subject: [PATCH] MINOR: Added a test for the analysis procedure stuff.
SVN: 22043
---
.../client/api/v1/AnalysisProcedureTest.java | 162 ++++++++++++++++++
1 file changed, 162 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/AnalysisProcedureTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/AnalysisProcedureTest.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/AnalysisProcedureTest.java
new file mode 100644
index 00000000000..6c6d8a8691f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/AnalysisProcedureTest.java
@@ -0,0 +1,162 @@
+/*
+ * 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.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.PropertyConfigurator;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
+
+/**
+ * A test class for the methods that take an analysis procedure.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class AnalysisProcedureTest
+{
+ public static void main(String[] args) throws IOException
+ {
+ if (args.length != 3)
+ {
+ System.err.println("Usage: <user> <password> <openbis-server-url>");
+ System.err.println("Example parameters: test-user my-password http://localhost:8888");
+ System.exit(1);
+ return;
+ }
+
+ configureLogging();
+
+ String userId = args[0];
+ String userPassword = args[1];
+ String serverUrl = args[2];
+
+ print(String.format("Connecting to the server '%s' as a user '%s.", serverUrl, userId));
+ IScreeningOpenbisServiceFacade facade =
+ ScreeningOpenbisServiceFacadeFactory.tryCreate(userId, userPassword, serverUrl);
+ if (facade == null)
+ {
+ System.err.println("Authentication failed: check the user name and password.");
+ System.exit(1);
+ return;
+ }
+
+ // Specify the permId of the plate we want to download images for.
+ AnalysisProcedureTest newMe =
+ new AnalysisProcedureTest(facade, "20110203094807621-79771", "proc1");
+
+ newMe.runTest();
+
+ newMe.logout();
+ }
+
+ private final IScreeningOpenbisServiceFacade facade;
+
+ private final String permIdOfPlateInterest;
+
+ private final String analysisProcedure;
+
+ private AnalysisProcedureTest(IScreeningOpenbisServiceFacade facade, String permIdOfInterest,
+ String analysisProcedure)
+ {
+ this.facade = facade;
+ this.permIdOfPlateInterest = permIdOfInterest;
+ this.analysisProcedure = analysisProcedure;
+ }
+
+ public void runTest() throws IOException
+ {
+
+ print("Listing all analysis procedures...");
+ List<String> allAnalysisProcedures = listAllAnalysisProcedures();
+ print("\t" + allAnalysisProcedures);
+ print("Done.");
+
+ List<Plate> plates = findPlates();
+ List<FeatureVectorDatasetReference> allFeatureVectorsForPlate =
+ facade.listFeatureVectorDatasets(plates);
+ List<FeatureVectorDatasetReference> featureVectorMatchingAnalysisProcedure =
+ facade.listFeatureVectorDatasets(plates, analysisProcedure);
+ print("Out of " + allFeatureVectorsForPlate.size() + " feature vector data sets found "
+ + featureVectorMatchingAnalysisProcedure.size()
+ + " data set(s) matching the procedure \"" + analysisProcedure + "\"");
+ for (FeatureVectorDatasetReference dataSet : featureVectorMatchingAnalysisProcedure)
+ {
+ print("\t" + dataSet.getDatasetCode());
+ }
+
+ print("Finished.");
+
+ }
+
+ private List<String> listAllAnalysisProcedures()
+ {
+ ArrayList<String> allAnalysisProcedures = new ArrayList<String>();
+ for (ExperimentIdentifier experimentIdentifier : facade.listExperiments())
+ {
+ allAnalysisProcedures.addAll(facade.listAnalysisProcedures(experimentIdentifier));
+ }
+ return allAnalysisProcedures;
+ }
+
+ private List<Plate> findPlates()
+ {
+ print("Looking for plates...");
+
+ List<Plate> plates = facade.listPlates();
+ List<Plate> platesOfInterest = new ArrayList<Plate>();
+
+ // We are interested in just one plate
+ for (Plate plate : plates)
+ {
+ if (plate.getPermId().equals(permIdOfPlateInterest))
+ {
+ platesOfInterest.add(plate);
+ break;
+ }
+ }
+
+ print("...found " + platesOfInterest.size() + " plate(s).");
+ return platesOfInterest;
+ }
+
+ public void logout()
+ {
+ facade.logout();
+ }
+
+ private static void print(String msg)
+ {
+ System.out.println(new Date() + "\t" + msg);
+ }
+
+ private static void configureLogging()
+ {
+ Properties props = new Properties();
+ props.put("log4j.appender.STDOUT", "org.apache.log4j.ConsoleAppender");
+ props.put("log4j.appender.STDOUT.layout", "org.apache.log4j.PatternLayout");
+ props.put("log4j.appender.STDOUT.layout.ConversionPattern", "%d %-5p [%t] %c - %m%n");
+ props.put("log4j.rootLogger", "INFO, STDOUT");
+ PropertyConfigurator.configure(props);
+ }
+}
--
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