From 172b2c19999311a0a57a6ed0ae0ea355b88e74bf Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 12 Jul 2012 09:40:37 +0000
Subject: [PATCH] SP-183, BIS-91: provide correct destination path in e-mail
message
SVN: 26086
---
.../AbstractDropboxProcessingPlugin.java | 4 +-
.../plugins/standard/DataSetCopier.java | 9 ++-
.../standard/DataSetCopierForUsers.java | 61 +++++++++++++------
.../standard/DataSetCopierForUsersTest.java | 47 ++++++++++++--
.../server/plugins/DataSetCopier.java | 5 +-
.../etl/DropboxProcessingPluginYeastX.java | 5 +-
6 files changed, 100 insertions(+), 31 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
index 37b20b2122e..75f1bdcd7a3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
@@ -117,7 +117,7 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
dataSetDescription.getSampleTypeCode());
boolean withSample = sampleOrNull != null;
boolean processingFailed = status.isError();
- String processingDescription = getProcessingDescription();
+ String processingDescription = getProcessingDescription(dataSetDescription, context);
Template template = getEMailMessageTemplate(processingFailed, withSample).createFreshCopy();
String subject;
if (processingFailed)
@@ -159,7 +159,7 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
/**
* Returns a description to be used in e-mails.
*/
- protected abstract String getProcessingDescription();
+ protected abstract String getProcessingDescription(DatasetDescription dataset, DataSetProcessingContext context);
private String render(String entity, String entityType)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopier.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopier.java
index 530eac02899..6ea60a47932 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopier.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopier.java
@@ -22,7 +22,9 @@ import java.util.Properties;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.common.utilities.SystemTimeProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
import ch.systemsx.cisd.openbis.dss.generic.shared.IPostRegistrationDatasetHandler;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
* Processing plugin which copies data sets to a destination folder by using rsync. The destination
@@ -80,13 +82,14 @@ public class DataSetCopier extends AbstractDropboxProcessingPlugin
}
public DataSetCopier(Properties properties, File storeRoot,
- IPostRegistrationDatasetHandler dropboxHandler)
+ IPostRegistrationDatasetHandler dropboxHandler, ITimeProvider timeProvider)
{
- super(properties, storeRoot, dropboxHandler);
+ super(properties, storeRoot, dropboxHandler, timeProvider);
}
@Override
- protected String getProcessingDescription()
+ protected String getProcessingDescription(DatasetDescription dataset,
+ DataSetProcessingContext context)
{
return "Copy to " + properties.getProperty(DESTINATION_KEY);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsers.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsers.java
index 86d3369dd8f..0822e1af601 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsers.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsers.java
@@ -23,6 +23,10 @@ import java.util.Properties;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.ITimeProvider;
+import ch.systemsx.cisd.common.utilities.SystemTimeProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
*
@@ -37,13 +41,15 @@ public class DataSetCopierForUsers extends DataSetCopier
public DataSetCopierForUsers(Properties properties, File storeRoot)
{
- this(properties, storeRoot, new RsyncCopierFactory(), new SshCommandExecutorFactory(), new ImmutableCopierFactory());
+ this(properties, storeRoot, new RsyncCopierFactory(), new SshCommandExecutorFactory(),
+ new ImmutableCopierFactory(), SystemTimeProvider.SYSTEM_TIME_PROVIDER);
}
@Private
DataSetCopierForUsers(Properties properties, File storeRoot,
IPathCopierFactory pathCopierFactory,
- ISshCommandExecutorFactory sshCommandExecutorFactory, IImmutableCopierFactory immutableCopierFactory)
+ ISshCommandExecutorFactory sshCommandExecutorFactory,
+ IImmutableCopierFactory immutableCopierFactory, ITimeProvider timeProvider)
{
super(properties, storeRoot, new Copier(properties, pathCopierFactory,
sshCommandExecutorFactory, immutableCopierFactory)
@@ -54,25 +60,40 @@ public class DataSetCopierForUsers extends DataSetCopier
protected String transformHostFile(String originalHostFile,
Map<String, String> parameterBindings)
{
- int indexOfParameter = originalHostFile.indexOf(USER_PARAMETER_STRING);
- String hostFile = originalHostFile;
- if (indexOfParameter >= 0)
- {
- String user = parameterBindings.get(USER_PARAMETER);
- if (user == null)
- {
- throw new UserFailureException("Missing parameter '" + USER_PARAMETER
- + "'.");
- }
- hostFile =
- originalHostFile.substring(0, indexOfParameter)
- + user
- + originalHostFile.substring(indexOfParameter
- + USER_PARAMETER_STRING.length());
- }
- return hostFile;
+ return createDestinationFileName(originalHostFile, parameterBindings);
}
- });
+ }, timeProvider);
+ }
+
+ private static String createDestinationFileName(String originalHostFile,
+ Map<String, String> parameterBindings)
+ {
+ int indexOfParameter = originalHostFile.indexOf(USER_PARAMETER_STRING);
+ String hostFile = originalHostFile;
+ if (indexOfParameter >= 0)
+ {
+ String user = parameterBindings.get(USER_PARAMETER);
+ if (user == null)
+ {
+ throw new UserFailureException("Missing parameter '" + USER_PARAMETER
+ + "'.");
+ }
+ hostFile =
+ originalHostFile.substring(0, indexOfParameter)
+ + user
+ + originalHostFile.substring(indexOfParameter
+ + USER_PARAMETER_STRING.length());
+ }
+ return hostFile;
+ }
+
+ @Override
+ protected String getProcessingDescription(DatasetDescription dataset,
+ DataSetProcessingContext context)
+ {
+ return "Copy to "
+ + createDestinationFileName(properties.getProperty(DESTINATION_KEY),
+ context.getParameterBindings());
}
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsersTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsersTest.java
index 45929b766e0..b9bff125128 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsersTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetCopierForUsersTest.java
@@ -28,6 +28,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
+import org.hamcrest.core.IsNull;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.annotations.AfterMethod;
@@ -40,6 +41,10 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.filesystem.IPathCopier;
import ch.systemsx.cisd.common.filesystem.ssh.ISshCommandExecutor;
+import ch.systemsx.cisd.common.mail.EMailAddress;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
import ch.systemsx.cisd.openbis.generic.shared.Constants;
@@ -54,6 +59,8 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
{
private static final String USER_ID = "test-user";
+ private static final String USER_EMAIL = "a@bc.de";
+
private static final String DS_LOCATION = "ds";
private Mockery context;
@@ -68,6 +75,10 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
private IImmutableCopierFactory hardLinkMakerFactory;
+ private IMailClient mailClient;
+
+ private ITimeProvider timeProvider;
+
private File storeRoot;
private File sshExecutableDummy;
@@ -86,6 +97,8 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
public void beforeMethod() throws IOException
{
context = new Mockery();
+ timeProvider = context.mock(ITimeProvider.class);
+ mailClient = context.mock(IMailClient.class);
pathFactory = context.mock(IPathCopierFactory.class);
sshFactory = context.mock(ISshCommandExecutorFactory.class);
hardLinkMakerFactory = context.mock(IImmutableCopierFactory.class);
@@ -101,9 +114,11 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
properties.setProperty("ssh-executable", sshExecutableDummy.getPath());
properties.setProperty("rsync-executable", rsyncExecutableDummy.getPath());
DatasetDescriptionBuilder dsb =
- new DatasetDescriptionBuilder("ds1").location(DS_LOCATION).sample("s").space("g")
+ new DatasetDescriptionBuilder("ds1").type("MY-DATA").location(DS_LOCATION).sample("s").space("g")
.project("p").experiment("e").databaseInstance("i");
ds = dsb.getDatasetDescription();
+ ds.setExperimentIdentifier("/g/p/e");
+ ds.setExperimentTypeCode("MY_EXPERIMENT");
File ds1Folder = new File(new File(storeRoot, DEFAULT_SHARE_ID), DS_LOCATION + "/original");
ds1Folder.mkdirs();
dsData = new File(ds1Folder, "data.txt");
@@ -113,7 +128,15 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
MockDataSetDirectoryProvider directoryProvider =
new MockDataSetDirectoryProvider(storeRoot, DEFAULT_SHARE_ID);
dataSetProcessingContext =
- new DataSetProcessingContext(null, directoryProvider, parameterBindings, null, null);
+ new DataSetProcessingContext(null, directoryProvider, parameterBindings,
+ mailClient, USER_EMAIL);
+ context.checking(new Expectations()
+ {
+ {
+ allowing(timeProvider).getTimeInMilliseconds();
+ will(returnValue(42L));
+ }
+ });
}
@AfterMethod
@@ -128,23 +151,39 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
public void testCopyWithDestinationTemplate()
{
properties.setProperty(DESTINATION_KEY, "tmp/${" + Constants.USER_PARAMETER + "}");
+ properties.setProperty(AbstractDropboxProcessingPlugin.SEND_DETAILED_EMAIL_KEY, "true");
prepareCreateAndCheckCopier();
+ final RecordingMatcher<String> subjectRecorder = new RecordingMatcher<String>();
+ final RecordingMatcher<String> contentRecorder = new RecordingMatcher<String>();
+ final RecordingMatcher<EMailAddress[]> recipientsRecorder =
+ new RecordingMatcher<EMailAddress[]>();
context.checking(new Expectations()
{
{
File canonicalFile = getCanonicalFile("tmp/" + USER_ID);
one(copier).copyToRemote(dsData, canonicalFile, null, null, null);
will(returnValue(Status.OK));
+
+ one(mailClient).sendEmailMessage(with(subjectRecorder), with(contentRecorder),
+ with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
+ with(recipientsRecorder));
}
});
DataSetCopier dataSetCopier =
new DataSetCopierForUsers(properties, storeRoot, pathFactory, sshFactory,
- hardLinkMakerFactory);
+ hardLinkMakerFactory, timeProvider);
ProcessingStatus processingStatus =
dataSetCopier.process(Arrays.asList(ds), dataSetProcessingContext);
assertNoErrors(processingStatus);
assertSuccessful(processingStatus, ds);
+ assertEquals(USER_EMAIL, recipientsRecorder.recordedObject()[0].tryGetEmailAddress());
+ assertEquals("Data set ds1 [MY-DATA] successfully processed",
+ subjectRecorder.recordedObject());
+ assertEquals("Successfully processed data set ds1 [MY-DATA].\n\n" + "Processing details:\n"
+ + "Description: Copy to tmp/test-user\n" + "Experiment: /g/p/e [MY_EXPERIMENT]\n"
+ + "Started: 1970-01-01 01:00:00 +0100.\n" + "Finished: 1970-01-01 01:00:00 +0100.",
+ contentRecorder.recordedObject());
context.assertIsSatisfied();
}
@@ -164,7 +203,7 @@ public class DataSetCopierForUsersTest extends AbstractFileSystemTestCase
});
DataSetCopier dataSetCopier =
new DataSetCopierForUsers(properties, storeRoot, pathFactory, sshFactory,
- hardLinkMakerFactory);
+ hardLinkMakerFactory, timeProvider);
ProcessingStatus processingStatus =
dataSetCopier.process(Arrays.asList(ds), dataSetProcessingContext);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
index 07b85da7ba1..72e0c5de15e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
@@ -27,6 +27,8 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierF
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.RsyncCopierFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.SshCommandExecutorFactory;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
*
@@ -50,7 +52,8 @@ public class DataSetCopier extends AbstractDropboxProcessingPlugin
}
@Override
- protected String getProcessingDescription()
+ protected String getProcessingDescription(DatasetDescription dataset,
+ DataSetProcessingContext context)
{
return "Copy to " + properties.getProperty(DESTINATION_KEY);
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DropboxProcessingPluginYeastX.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DropboxProcessingPluginYeastX.java
index 41ab3e190c3..eb01f10a959 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DropboxProcessingPluginYeastX.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DropboxProcessingPluginYeastX.java
@@ -21,7 +21,9 @@ import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDropboxProcessingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
* A dropbox processing plugin that gets its dropbox directory from properties.
@@ -75,7 +77,8 @@ public class DropboxProcessingPluginYeastX extends AbstractDropboxProcessingPlug
}
@Override
- protected String getProcessingDescription()
+ protected String getProcessingDescription(DatasetDescription dataset,
+ DataSetProcessingContext context)
{
return "Copy to " + properties.getProperty(DROPBOX_INCOMING_DIRECTORY_PROPERTY);
}
--
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