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 d48f91516d10f12c1d264f39c585c29fb95da9f9..3d2237fb09913899d2fed707e279aae7f33948f9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
@@ -326,13 +326,14 @@ public final class ETLDaemon
final boolean notifySuccessfulRegistration)
{
final File storeRootDir = DssPropertyParametersUtil.getStoreRootDir(properties);
+ File dssInternalTempDir = DssPropertyParametersUtil.getDssInternalTempDir(properties);
migrateStoreRootDir(storeRootDir, openBISService.getHomeDatabaseInstance());
String dssCode = DssPropertyParametersUtil.getDataStoreCode(properties);
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState(dssCode, shareId, storeRootDir,
- openBISService, mailClient, dataSetValidator, dataSourceQueryService,
- new DynamicTransactionQueryFactory(), notifySuccessfulRegistration,
- threadParameters);
+ dssInternalTempDir, openBISService, mailClient, dataSetValidator,
+ dataSourceQueryService, new DynamicTransactionQueryFactory(),
+ notifySuccessfulRegistration, threadParameters);
ITopLevelDataSetRegistrator registrator =
ClassUtils.create(ITopLevelDataSetRegistrator.class, threadParameters
@@ -356,15 +357,16 @@ public final class ETLDaemon
Class<?> defaultTopLevelDataSetRegistratorClass)
{
final File storeRootDir = DssPropertyParametersUtil.getStoreRootDir(properties);
+ File dssInternalTempDir = DssPropertyParametersUtil.getDssInternalTempDir(properties);
migrateStoreRootDir(storeRootDir, openBISService.getHomeDatabaseInstance());
String dssCode = DssPropertyParametersUtil.getDataStoreCode(properties);
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState(dssCode, shareId, storeRootDir,
- openBISService, mailClient, dataSetValidator, dataSourceQueryService,
- new DynamicTransactionQueryFactory(), notifySuccessfulRegistration,
- threadParameters, useIsFinishedMarkerFile, deleteUnidentified,
- preRegistrationScriptOrNull, postRegistrationScriptOrNull,
- validationScriptsOrNull);
+ dssInternalTempDir, openBISService, mailClient, dataSetValidator,
+ dataSourceQueryService, new DynamicTransactionQueryFactory(),
+ notifySuccessfulRegistration, threadParameters, useIsFinishedMarkerFile,
+ deleteUnidentified, preRegistrationScriptOrNull,
+ postRegistrationScriptOrNull, validationScriptsOrNull);
ITopLevelDataSetRegistrator registrator =
ClassUtils
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
index 59c86bd84d9c5e5dc00fa031514fcb71c2ebed7c..4eea2ca41646b2d13712b0edb0fd8f39047c0cc9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
@@ -48,6 +48,8 @@ public class TopLevelDataSetRegistratorGlobalState
private final File storeRootDir;
+ private final File dssInternalTempDir;
+
private final IEncapsulatedOpenBISService openBisService;
private final IMailClient mailClient;
@@ -85,13 +87,14 @@ public class TopLevelDataSetRegistratorGlobalState
* @param threadParameters
*/
public TopLevelDataSetRegistratorGlobalState(String dssCode, String shareId, File storeRootDir,
- IEncapsulatedOpenBISService openBisService, IMailClient mailClient,
- IDataSetValidator dataSetValidator, IDataSourceQueryService dataSourceQueryService,
+ File dssInternalTempDir, IEncapsulatedOpenBISService openBisService,
+ IMailClient mailClient, IDataSetValidator dataSetValidator,
+ IDataSourceQueryService dataSourceQueryService,
DynamicTransactionQueryFactory dynamicTransactionQueryFactory,
boolean notifySuccessfulRegistration, ThreadParameters threadParameters)
{
- this(dssCode, shareId, storeRootDir, openBisService, mailClient, dataSetValidator,
- dataSourceQueryService, dynamicTransactionQueryFactory,
+ this(dssCode, shareId, storeRootDir, dssInternalTempDir, openBisService, mailClient,
+ dataSetValidator, dataSourceQueryService, dynamicTransactionQueryFactory,
notifySuccessfulRegistration, threadParameters, threadParameters
.useIsFinishedMarkerFile(), threadParameters.deleteUnidentified(),
threadParameters.tryGetPreRegistrationScript(), threadParameters
@@ -99,8 +102,9 @@ public class TopLevelDataSetRegistratorGlobalState
}
public TopLevelDataSetRegistratorGlobalState(String dssCode, String shareId, File storeRootDir,
- IEncapsulatedOpenBISService openBisService, IMailClient mailClient,
- IDataSetValidator dataSetValidator, IDataSourceQueryService dataSourceQueryService,
+ File dssInternalTempDir, IEncapsulatedOpenBISService openBisService,
+ IMailClient mailClient, IDataSetValidator dataSetValidator,
+ IDataSourceQueryService dataSourceQueryService,
DynamicTransactionQueryFactory dynamicTransactionQueryFactory,
boolean notifySuccessfulRegistration, ThreadParameters threadParameters,
boolean useIsFinishedMarkerFile, boolean deleteUnidentified,
@@ -111,6 +115,7 @@ public class TopLevelDataSetRegistratorGlobalState
this.dssCode = dssCode;
this.shareId = shareId;
this.storeRootDir = storeRootDir;
+ this.dssInternalTempDir = dssInternalTempDir;
this.openBisService = openBisService;
this.mailClient = mailClient;
this.dataSetValidator = dataSetValidator;
@@ -140,6 +145,14 @@ public class TopLevelDataSetRegistratorGlobalState
return storeRootDir;
}
+ /**
+ * Get a directory that can be used for temporary files, and is local to the server.
+ */
+ public File getDssInternalTempDir()
+ {
+ return dssInternalTempDir;
+ }
+
public IEncapsulatedOpenBISService getOpenBisService()
{
return openBisService;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
index 1760346d142f3bad2f518e317b5dc8404d90b9d5..3ba071c406db252ebe4a15159a1ece949ed9f15b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
@@ -236,7 +236,8 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
new ReentrantLock(), FileOperations.getMonitoredInstanceForCurrentThread(),
onErrorDecision);
- DataSetRegistrationTransaction.rollbackDeadTransactions(globalState.getStoreRootDir());
+ DataSetRegistrationTransaction.rollbackDeadTransactions(globalState
+ .getDssInternalTempDir());
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
index c32f960d40c8aa8f1fe59bbc3860258595d199ba..ab8862d86ab842a31f3c7a7ec53c20c449661088 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
@@ -147,7 +147,7 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
// Clone this service for the transaction to keep them independent
DataSetRegistrationTransaction<T> transaction =
new DataSetRegistrationTransaction<T>(registrator.getGlobalState()
- .getStoreRootDir(), workingDirectory, stagingDirectory, this,
+ .getDssInternalTempDir(), workingDirectory, stagingDirectory, this,
detailsFactory);
transactions.add(transaction);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
index 63f06d1e1a42be45305dfa5e6784212ce241b899..d568b8039e33ef6c3485999a037ea10dc03c1eb0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.common.utilities.PropertyParametersUtil;
import ch.systemsx.cisd.common.utilities.PropertyParametersUtil.SectionProperties;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
/**
* Configuration parameters for the Data Set Download Server.
@@ -97,6 +98,8 @@ public final class ConfigParameters implements IServletPropertiesManager
private final File storePath;
+ private final File dssInternalTempDir;
+
private final File rpcIncomingDirectory;
private final int port;
@@ -136,6 +139,7 @@ public final class ConfigParameters implements IServletPropertiesManager
{
this.properties = properties;
storePath = new File(PropertyUtils.getMandatoryProperty(properties, STOREROOT_DIR_KEY));
+ dssInternalTempDir = getInternalTempDirectory(properties);
rpcIncomingDirectory = getRpcIncomingDirectory(properties);
port = getMandatoryIntegerProperty(properties, PORT_KEY);
serverURL = PropertyUtils.getMandatoryProperty(properties, SERVER_URL_KEY);
@@ -162,14 +166,19 @@ public final class ConfigParameters implements IServletPropertiesManager
DEFAULT_AUTH_CACHE_CLEANUP_TIMER_PERIOD_MINS);
pluginServlets = new LinkedHashMap<String, PluginServletConfig>();
SectionProperties[] pluginServicesProperties =
- PropertyParametersUtil.extractSectionProperties(properties,
- PLUGIN_SERVICES_LIST_KEY, false);
+ PropertyParametersUtil.extractSectionProperties(properties,
+ PLUGIN_SERVICES_LIST_KEY, false);
addServletsProperties("", pluginServicesProperties);
webstartJarPath =
PropertyUtils.getProperty(properties, WEBSTART_JAR_PATH, WEBSTART_JAR_PATH_DEFAULT);
}
+ private File getInternalTempDirectory(Properties properties)
+ {
+ return DssPropertyParametersUtil.getDssInternalTempDir(properties);
+ }
+
private static File getRpcIncomingDirectory(final Properties properties)
{
String incomingDirPath = PropertyUtils.getProperty(properties, RPC_INCOMING_DIR);
@@ -233,6 +242,11 @@ public final class ConfigParameters implements IServletPropertiesManager
return rpcIncomingDirectory;
}
+ public File getDssInternalTempDir()
+ {
+ return dssInternalTempDir;
+ }
+
public final int getPort()
{
return port;
@@ -308,6 +322,7 @@ public final class ConfigParameters implements IServletPropertiesManager
if (operationLog.isInfoEnabled())
{
operationLog.info(String.format("Store root directory: '%s'.", storePath));
+ operationLog.info(String.format("Temp file directory: '%s'.", dssInternalTempDir));
operationLog.info(String.format("RPC incoming directory: '%s'.", rpcIncomingDirectory));
operationLog.info(String.format("Port number: %d.", port));
operationLog.info(String.format("URL of openBIS server: '%s'.", serverURL));
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DssPropertyParametersUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DssPropertyParametersUtil.java
index eb0b16594c5e65603d0ed7cd9541f51f701f2f71..5f5640d3c1ab62b0806517ab2146c89cea0dd62a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DssPropertyParametersUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DssPropertyParametersUtil.java
@@ -21,6 +21,7 @@ import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
@@ -43,6 +44,11 @@ public class DssPropertyParametersUtil
public static final String SERVER_URL_KEY = "server-url";
+ /**
+ * Temp directory for dss usage.
+ */
+ static final String DSS_TEMP_DIR_PATH = "dss-temp-dir";
+
/** Location of service properties file. */
public static final String SERVICE_PROPERTIES_FILE = "etc/service.properties";
@@ -57,7 +63,8 @@ public class DssPropertyParametersUtil
Properties properties = PropertyUtils.loadProperties(filePath);
Properties systemProperties = System.getProperties();
ExtendedProperties dssSystemProperties =
- ExtendedProperties.getSubset(systemProperties, OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX, true);
+ ExtendedProperties.getSubset(systemProperties,
+ OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX, true);
Set<Entry<Object, Object>> entrySet = dssSystemProperties.entrySet();
for (Entry<Object, Object> entry : entrySet)
{
@@ -81,4 +88,23 @@ public class DssPropertyParametersUtil
{
return PropertyUtils.getMandatoryProperty(serviceProperties, SERVER_URL_KEY);
}
+
+ public static File getDssInternalTempDir(final Properties properties)
+ {
+ String defaultTempDirPath =
+ new File(System.getProperty("user.dir"), "dss-tmp").getAbsolutePath();
+ String tempDirPath =
+ PropertyUtils.getProperty(properties, DSS_TEMP_DIR_PATH, defaultTempDirPath);
+ File tempDir = new File(tempDirPath);
+ tempDir.mkdirs();
+ if (false == tempDir.exists())
+ {
+ throw new ConfigurationFailureException(
+ "Could not create an internal temp directory for the data store server at path: "
+ + tempDir.getPath()
+ + ". Please make sure this directory exists and is writable by the data store server or provide an alternate using directory for the "
+ + DSS_TEMP_DIR_PATH + " configuration setting");
+ }
+ return tempDir;
+ }
}
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 826dcb9c39fdbb894cd7c9d55edb0e9c46389596..b7caa65e228dde94cc3b62f8e24c15e293e6c9fa 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -287,8 +287,9 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, authorizedLimsService, mailClient, dataSetValidator,
- null, new DynamicTransactionQueryFactory(), true, threadParameters);
+ workingDirectory, workingDirectory, authorizedLimsService, mailClient,
+ dataSetValidator, null, new DynamicTransactionQueryFactory(), true,
+ threadParameters);
context.checking(new Expectations()
{
@@ -806,8 +807,9 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, authorizedLimsService, mailClient, dataSetValidator,
- null, new DynamicTransactionQueryFactory(), true, threadParameters);
+ workingDirectory, workingDirectory, authorizedLimsService, mailClient,
+ dataSetValidator, null, new DynamicTransactionQueryFactory(), true,
+ threadParameters);
context.checking(new Expectations()
{
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
index 440479560246ce91a8549ae5b223fcab0845136d..6034333437fcdc976c24b79c2b89145d770ff371 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
@@ -173,8 +173,8 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator,
- dataSourceQueryService, myFactory, true, threadParameters);
+ workingDirectory, workingDirectory, openBisService, mailClient,
+ dataSetValidator, dataSourceQueryService, myFactory, true, threadParameters);
return globalState;
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
index f3e1832298bc12d5c00488e8dc91e8cb0345a30f..43dffe1af828eea4968617300c1eed0473edc46c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
@@ -111,8 +111,9 @@ public class DataSetStorageRollbackerTest extends AbstractFileSystemTestCase
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator, null,
- new DynamicTransactionQueryFactory(), true, threadParameters);
+ workingDirectory, workingDirectory, openBisService, mailClient,
+ dataSetValidator, null, new DynamicTransactionQueryFactory(), true,
+ threadParameters);
return globalState;
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
index 4df92f78de45aebd653c9f4f5dffc867cca82ff9..130a17d29ba9a873c338562708d82729ad313baf 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
@@ -421,8 +421,9 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator, null,
- new DynamicTransactionQueryFactory(), true, threadParameters);
+ workingDirectory, workingDirectory, openBisService, mailClient,
+ dataSetValidator, null, new DynamicTransactionQueryFactory(), true,
+ threadParameters);
return globalState;
}