From f82edcedb72679473c9d7d1d29d8b9f86a7a4e81 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 22 Oct 2012 10:01:58 +0000
Subject: [PATCH] fixing some proteomics tests
SVN: 27291
---
.../server/plugins/APMSReportTest.java | 2 +-
.../plugins/LocalAndRemoteCopierTest.java | 113 +++++++++++++++++-
rtd_phosphonetx/sourceTest/java/tests.xml | 1 +
3 files changed, 113 insertions(+), 3 deletions(-)
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java
index 126bdb80703..daadd3c0eab 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java
@@ -169,7 +169,7 @@ public class APMSReportTest extends AbstractFileSystemTestCase
fileLines.get(0));
assertEquals(4, fileLines.size());
assertEquals("[ERROR: \"Exception occured: "
- + "ch.systemsx.cisd.common.exceptions.UserFailureException: File "
+ + "ch.systemsx.cisd.common.exception.UserFailureException: File "
+ APMSReport.PROTEIN_FILE_NAME + " missing.\"]", status.getErrorStatuses()
.toString());
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java
index 6c43c6b0274..6e4af2d4897 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java
@@ -19,11 +19,13 @@ package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier.SSH_TIMEOUT_MILLIS;
import java.io.File;
+import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Properties;
+import org.apache.commons.io.FileUtils;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.annotations.AfterMethod;
@@ -31,8 +33,11 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.concurrent.ExecutionResult;
+import ch.systemsx.cisd.common.exception.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exception.EnvironmentFailureException;
import ch.systemsx.cisd.common.exception.Status;
import ch.systemsx.cisd.common.filesystem.BooleanStatus;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
@@ -43,7 +48,6 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopie
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.dss.proteomics.server.plugins.LocalAndRemoteCopier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
/**
@@ -117,6 +121,7 @@ public class LocalAndRemoteCopierTest extends AbstractFileSystemTestCase
public void testLocalWithKnownSample()
{
Properties properties = new Properties();
+ prepareCopier(properties);
properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
LocalAndRemoteCopier msInjectionCopier =
new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
@@ -138,11 +143,12 @@ public class LocalAndRemoteCopierTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
-
+
@Test
public void testLocalWithUnknownSample()
{
Properties properties = new Properties();
+ prepareCopier(properties);
properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
LocalAndRemoteCopier msInjectionCopier =
new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
@@ -164,6 +170,7 @@ public class LocalAndRemoteCopierTest extends AbstractFileSystemTestCase
public void testLocalWithAlreadyExistingDestination()
{
Properties properties = new Properties();
+ prepareCopier(properties);
properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
LocalAndRemoteCopier msInjectionCopier =
new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
@@ -257,4 +264,106 @@ public class LocalAndRemoteCopierTest extends AbstractFileSystemTestCase
// ignored
}
}
+
+ private void prepareCopier(Properties properties)
+ {
+ properties.setProperty(DataSetCopier.RSYNC_EXEC + "-executable", rsyncExec.getPath());
+ context.checking(new Expectations()
+ {
+ {
+ one(copierFactory).create(rsyncExec, null, DataSetCopier.SSH_TIMEOUT_MILLIS);
+ will(returnValue(new MockCopier()));
+ }
+ });
+ }
+
+ private final class MockCopier implements IPathCopier
+ {
+
+ @Override
+ public boolean terminate()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean isRemote()
+ {
+ return false;
+ }
+
+ @Override
+ public void check() throws EnvironmentFailureException, ConfigurationFailureException
+ {
+ }
+
+ @Override
+ public Status copy(File sourcePath, File destinationDirectory)
+ {
+ return null;
+ }
+
+ @Override
+ public Status copyContent(File sourcePath, File destinationDirectory)
+ {
+ return null;
+ }
+
+ @Override
+ public Status copyToRemote(File sourcePath, String destinationDirectory,
+ String destinationHostOrNull, String rsyncModuleNameOrNull,
+ String rsyncPasswordFileOrNull)
+ {
+ try
+ {
+ FileUtils.copyDirectoryToDirectory(dataSet, new File(destinationDirectory));
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ File file = new File(destinationDirectory, dataSet.getName());
+ file.setLastModified(dataSet.lastModified());
+ return Status.OK;
+ }
+
+ @Override
+ public Status copyContentToRemote(File sourcePath, String destinationDirectory,
+ String destinationHostOrNull, String rsyncModuleNameOrNull,
+ String rsyncPasswordFileOrNull)
+ {
+ return null;
+ }
+
+ @Override
+ public Status copyFromRemote(String sourcePath, String sourceHost,
+ File destinationDirectory, String rsyncModuleNameOrNull,
+ String rsyncPasswordFileOrNull)
+ {
+ return null;
+ }
+
+ @Override
+ public Status copyContentFromRemote(String sourcePath, String sourceHost,
+ File destinationDirectory, String rsyncModuleNameOrNull,
+ String rsyncPasswordFileOrNull)
+ {
+ return null;
+ }
+
+ @Override
+ public boolean checkRsyncConnectionViaSsh(String host, String rsyncExecutableOnHostOrNull,
+ long millisToWaitForCompletion)
+ {
+ return false;
+ }
+
+ @Override
+ public boolean checkRsyncConnectionViaRsyncServer(String host, String rsyncModule,
+ String rsyncPassworFileOrNull, long millisToWaitForCompletion)
+ {
+ return false;
+ }
+
+ }
+
}
diff --git a/rtd_phosphonetx/sourceTest/java/tests.xml b/rtd_phosphonetx/sourceTest/java/tests.xml
index 64e80ad2542..34383147e47 100644
--- a/rtd_phosphonetx/sourceTest/java/tests.xml
+++ b/rtd_phosphonetx/sourceTest/java/tests.xml
@@ -7,6 +7,7 @@
</groups>
<packages>
<package name="ch.systemsx.cisd.openbis.etlserver.proteomics.*" />
+ <package name="ch.systemsx.cisd.openbis.dss.proteomics.*" />
<package name="ch.systemsx.cisd.openbis.plugin.proteomics.*" />
</packages>
</test>
--
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