From a4e74705dcab3a5737361742dc9680856542dff7 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 9 Apr 2009 14:20:07 +0000
Subject: [PATCH] LMS-809 Communication between DSS and openBIS server changed,
new service properties for DSS code and download URL introduced
SVN: 10662
---
datastore_server/dist/etc/service.properties | 6 ++
datastore_server/etc/service.properties | 6 ++
.../source/java/applicationContext.xml | 8 ++-
.../ch/systemsx/cisd/etlserver/ETLDaemon.java | 8 ++-
.../etlserver/TransferredDataSetHandler.java | 13 +++--
.../server/DataStoreServiceLogger.java | 2 +-
.../server/EncapsulatedOpenBISService.java | 57 ++++++++++++++-----
.../TransferredDataSetHandlerTest.java | 12 ++--
.../EncapsulatedOpenBISServiceTest.java | 47 +++++++++++----
9 files changed, 121 insertions(+), 38 deletions(-)
diff --git a/datastore_server/dist/etc/service.properties b/datastore_server/dist/etc/service.properties
index 3255029161d..487dfa5de25 100644
--- a/datastore_server/dist/etc/service.properties
+++ b/datastore_server/dist/etc/service.properties
@@ -1,3 +1,6 @@
+# Unique code of this Data Store Server. Not more than 40 characters.
+data-store-server-code = DSS1
+
# The root directory of the data store
storeroot-dir = data/store
@@ -45,6 +48,9 @@ username = etlserver
# The password to use when contacting the openBIS server
password = etlserver
+# The base URL for Web client access.
+download-url = https://localhost:8889
+
# SMTP properties (must start with 'mail' to be considered).
# mail.smtp.host = localhost
# mail.from = datastore_server@localhost
diff --git a/datastore_server/etc/service.properties b/datastore_server/etc/service.properties
index 3fe083d39a8..8e890e0101c 100644
--- a/datastore_server/etc/service.properties
+++ b/datastore_server/etc/service.properties
@@ -1,3 +1,6 @@
+# Unique code of this Data Store Server. Not more than 40 characters.
+data-store-server-code = my-dss
+
# The root directory of the data store
storeroot-dir = targets/store
@@ -43,6 +46,9 @@ username = etlserver
# The password to use when contacting the openBIS server
password = doesnotmatter
+# The base URL for Web client access.
+download-url = https://localhost:8889
+
# SMTP properties (must start with 'mail' to be considered).
# mail.smtp.host = localhost
# mail.from = datastore_server@localhost
diff --git a/datastore_server/source/java/applicationContext.xml b/datastore_server/source/java/applicationContext.xml
index 39f4e82c0da..20b51472da4 100644
--- a/datastore_server/source/java/applicationContext.xml
+++ b/datastore_server/source/java/applicationContext.xml
@@ -22,9 +22,11 @@
<bean id="openBIS-service" class="ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService">
<constructor-arg ref="session-token-manager"/>
<constructor-arg value="${server-url}"/>
- <constructor-arg value="${port}"/>
- <constructor-arg value="${username}"/>
- <constructor-arg value="${password}"/>
+ <property name="username" value="${username}"/>
+ <property name="password" value="${password}"/>
+ <property name="port" value="${port}"/>
+ <property name="downloadUrl" value="${download-url}"/>
+ <property name="dataStoreCode" value="${data-store-server-code}"/>
</bean>
<bean id="data-store-server"
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
index 23ebd9bfcb5..822547f4c8d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
@@ -75,6 +75,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
public final class ETLDaemon
{
static final String STOREROOT_DIR_KEY = "storeroot-dir";
+ static final String DSS_CODE_KEY = "data-store-server-code";
static final String NOTIFY_SUCCESSFUL_REGISTRATION = "notify-successful-registration";
@@ -343,8 +344,13 @@ public final class ETLDaemon
migrateDataStoreByRenamingObservableTypeToDataSetType(storeRootDir);
plugin.getStorageProcessor().setStoreRootDirectory(storeRootDir);
final Properties mailProperties = parameters.getMailProperties();
+ String dssCode = parameters.getProperties().getProperty(DSS_CODE_KEY);
+ if (dssCode == null)
+ {
+ throw new ConfigurationFailureException("Missing service property '" + DSS_CODE_KEY + "'");
+ }
final TransferredDataSetHandler pathHandler =
- new TransferredDataSetHandler(threadParameters.tryGetGroupCode(), plugin,
+ new TransferredDataSetHandler(threadParameters.tryGetGroupCode(), dssCode, plugin,
authorizedLimsService, mailProperties, highwaterMarkWatcher,
notifySuccessfulRegistration, threadParameters.useIsFinishedMarkerFile());
pathHandler.setProcessorFactories(processorFactories);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index f0cb6579050..bf62cdf2cdf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -119,6 +119,8 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
private final String groupCode;
+ private final String dssCode;
+
private final boolean notifySuccessfulRegistration;
private final boolean useIsFinishedMarkerFile;
@@ -130,33 +132,35 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
private DatabaseInstancePE homeDatabaseInstance;
- /**
+ /**
* @param useIsFinishedMarkerFile if true, file/directory is processed when a marker file for it
* appears. Otherwise processing starts if the file/directory is not modified for a
* certain amount of time (so called "quiet period").
*/
- public TransferredDataSetHandler(final String groupCode, final IETLServerPlugin plugin,
+ public TransferredDataSetHandler(final String groupCode, String dssCode, final IETLServerPlugin plugin,
final IEncapsulatedOpenBISService limsService, final Properties mailProperties,
final HighwaterMarkWatcher highwaterMarkWatcher,
final boolean notifySuccessfulRegistration, boolean useIsFinishedMarkerFile)
{
- this(groupCode, plugin.getStorageProcessor(), plugin, limsService, new MailClient(
+ this(groupCode, dssCode, plugin.getStorageProcessor(), plugin, limsService, new MailClient(
mailProperties), notifySuccessfulRegistration, useIsFinishedMarkerFile);
}
- TransferredDataSetHandler(final String groupCode,
+ TransferredDataSetHandler(final String groupCode, String dssCode,
final IStoreRootDirectoryHolder storeRootDirectoryHolder,
final IETLServerPlugin plugin, final IEncapsulatedOpenBISService limsService,
final IMailClient mailClient, final boolean notifySuccessfulRegistration,
boolean useIsFinishedMarkerFile)
{
+ assert dssCode != null : "Unspecified data store code";
assert storeRootDirectoryHolder != null : "Given store root directory holder can not be null.";
assert plugin != null : "IETLServerPlugin implementation can not be null.";
assert limsService != null : "IEncapsulatedLimsService implementation can not be null.";
assert mailClient != null : "IMailClient implementation can not be null.";
+ this.dssCode = dssCode;
this.groupCode = groupCode;
this.storeRootDirectoryHolder = storeRootDirectoryHolder;
this.dataSetInfoExtractor = plugin.getDataSetInfoExtractor();
@@ -765,6 +769,7 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
data.setMeasured(typeExtractor.isMeasuredData(incomingDataSetFile));
data.setStorageFormat(storageFormat);
data.setComplete(isCompleteFlag);
+ data.setDataStoreCode(dssCode);
return data;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 7d66b7886b1..10c1f70c0ff 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -92,7 +92,7 @@ class DataStoreServiceLogger implements IDataStoreService
{
builder.append(' ').append(externalDataPE.getCode());
}
- log("upload_data_sets", "USER(%s) LOCATIONS(%s)", context.getUserID(), builder.toString().trim());
+ log("upload_data_sets", "USER(%s) DATASETS(%s)", context.getUserID(), builder.toString().trim());
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index d8c48f7c2f1..7b19b094a61 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
@@ -51,44 +52,67 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, EncapsulatedOpenBISService.class);
- private final int port;
-
- private final String username;
-
- private final String password;
-
private final IETLLIMSService service;
private final SessionTokenManager sessionTokenManager;
+ private int port;
+
+ private String username;
+
+ private String password;
+
+ private String downloadUrl;
+
+ private String dataStoreCode;
+
private String sessionToken; // NOTE: can be changed in parallel by different threads
private Integer version;
private DatabaseInstancePE homeDatabaseInstance;
- public EncapsulatedOpenBISService(SessionTokenManager sessionTokenManager, String serverURL,
- int port, String username, String password)
+ public EncapsulatedOpenBISService(SessionTokenManager sessionTokenManager, String serverURL)
{
this(sessionTokenManager, HttpInvokerUtils.createServiceStub(IETLLIMSService.class,
- serverURL + "/rmi-etl", 5), port, username, password);
+ serverURL + "/rmi-etl", 5));
}
public EncapsulatedOpenBISService(SessionTokenManager sessionTokenManager,
- IETLLIMSService service, int port, String username, String password)
+ IETLLIMSService service)
{
assert sessionTokenManager != null : "Unspecified session token manager.";
assert service != null : "Given IETLLIMSService implementation can not be null.";
- assert username != null : "Given username can not be null.";
- assert password != null : "Given password can not be null.";
this.sessionTokenManager = sessionTokenManager;
this.service = service;
+ }
+
+ public final void setPort(int port)
+ {
this.port = port;
+ }
+
+ public final void setUsername(String username)
+ {
this.username = username;
+ }
+
+ public final void setPassword(String password)
+ {
this.password = password;
}
-
+
+ public final void setDownloadUrl(String downloadUrl)
+ {
+ this.downloadUrl = downloadUrl;
+ }
+
+ public final void setDataStoreCode(String dataStoreCode)
+ {
+ this.dataStoreCode = dataStoreCode;
+ }
+
public Object getObject() throws Exception
{
return this;
@@ -118,7 +142,12 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
"Authentication failure to openBIS server. Most probable cause: user or password are invalid.";
throw new ConfigurationFailureException(msg);
}
- service.registerDataStoreServer(sessionToken, port, sessionTokenManager.drawSessionToken());
+ DataStoreServerInfo dataStoreServerInfo = new DataStoreServerInfo();
+ dataStoreServerInfo.setPort(port);
+ dataStoreServerInfo.setDataStoreCode(dataStoreCode);
+ dataStoreServerInfo.setDownloadUrl(downloadUrl);
+ dataStoreServerInfo.setSessionToken(sessionTokenManager.drawSessionToken());
+ service.registerDataStoreServer(sessionToken, dataStoreServerInfo);
}
private final void checkSessionToken()
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
index f5ca427307c..0fc18e3f573 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -57,10 +57,10 @@ import ch.systemsx.cisd.common.mail.JavaMailProperties;
import ch.systemsx.cisd.common.test.LogMonitoringAppender;
import ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.server.SessionTokenManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
@@ -267,10 +267,12 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
final IETLServerPlugin plugin =
new ETLServerPlugin(new MockDataSetInfoExtractor(dataSetInfoExtractor),
typeExtractor, storageProcessor);
- final IEncapsulatedOpenBISService authorizedLimsService =
- new EncapsulatedOpenBISService(new SessionTokenManager(), limsService, 0, "u", "p");
+ final EncapsulatedOpenBISService authorizedLimsService =
+ new EncapsulatedOpenBISService(new SessionTokenManager(), limsService);
+ authorizedLimsService.setUsername("u");
+ authorizedLimsService.setPassword("p");
handler =
- new TransferredDataSetHandler(null, storageProcessor, plugin,
+ new TransferredDataSetHandler(null, "dss", storageProcessor, plugin,
authorizedLimsService, mailClient, true, true);
handler.setProcessorFactories(map);
@@ -389,7 +391,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
will(returnValue(SESSION_TOKEN));
one(limsService).registerDataStoreServer(with(equal(SESSION_TOKEN)),
- with(equal(0)), with(any(String.class)));
+ with(any(DataStoreServerInfo.class)));
atLeast(1).of(limsService).tryToGetBaseExperiment(SESSION_TOKEN,
dataSetInformation.getSampleIdentifier());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
index 08e63deba5d..bfd00bdfc25 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.annotations.AfterMethod;
@@ -23,14 +25,11 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
-import ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.server.SessionTokenManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
/**
* Test cases for corresponding {@link EncapsulatedOpenBISService} class.
@@ -39,11 +38,17 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
*/
public class EncapsulatedOpenBISServiceTest
{
+ private static final int PORT = 4711;
+
+ private static final String DOWNLOAD_URL = "download-url";
+
+ private static final String DATA_STORE_CODE = "data-store1";
+
private Mockery context;
private IETLLIMSService limsService;
- private IEncapsulatedOpenBISService encapsulatedLimsService;
+ private EncapsulatedOpenBISService encapsulatedLimsService;
private static final String LIMS_USER = "testuser";
@@ -61,7 +66,7 @@ public class EncapsulatedOpenBISServiceTest
{
exp.one(limsService).authenticate(LIMS_USER, LIMS_PASSWORD);
exp.one(limsService).registerDataStoreServer(exp.with(Expectations.equal("")),
- exp.with(Expectations.equal(0)), exp.with(Expectations.any(String.class)));
+ exp.with(Expectations.any(DataStoreServerInfo.class)));
exp.one(limsService).tryToGetBaseExperiment("", dataSetInformation.getSampleIdentifier());
}
@@ -76,12 +81,35 @@ public class EncapsulatedOpenBISServiceTest
one(limsService).authenticate(LIMS_USER, LIMS_PASSWORD);
one(limsService).registerDataStoreServer(
- with(equal("")), with(equal(0)), with(any(String.class)));
+ with(equal("")), with(new BaseMatcher<DataStoreServerInfo>()
+ {
+
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataStoreServerInfo)
+ {
+ DataStoreServerInfo info = (DataStoreServerInfo) item;
+ return DATA_STORE_CODE.equals(info.getDataStoreCode())
+ && DOWNLOAD_URL.equals(info.getDownloadUrl())
+ && PORT == info.getPort();
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ }
+
+ }));
}
});
encapsulatedLimsService =
- new EncapsulatedOpenBISService(new SessionTokenManager(), limsService, 0,
- LIMS_USER, LIMS_PASSWORD);
+ new EncapsulatedOpenBISService(new SessionTokenManager(), limsService);
+ encapsulatedLimsService.setUsername(LIMS_USER);
+ encapsulatedLimsService.setPassword(LIMS_PASSWORD);
+ encapsulatedLimsService.setDataStoreCode(DATA_STORE_CODE);
+ encapsulatedLimsService.setDownloadUrl(DOWNLOAD_URL);
+ encapsulatedLimsService.setPort(PORT);
}
@AfterMethod
@@ -126,7 +154,6 @@ public class EncapsulatedOpenBISServiceTest
public final void testRegisterDataSet()
{
final DataSetInformation dataSetInfo = createDataSetInformation();
- final ProcedureTypeCode procedureTypeCode = ProcedureTypeCode.DATA_ACQUISITION;
final ExternalData data = new ExternalData();
context.checking(new Expectations()
{
--
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