diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java
new file mode 100644
index 0000000000000000000000000000000000000000..425327175037945004da898ac644e8e34e508da4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java
@@ -0,0 +1,281 @@
+/*
+ * 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.dss.phosphonetx.server.plugins;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.filesystem.BooleanStatus;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.filesystem.IPathCopier;
+import ch.systemsx.cisd.common.filesystem.ssh.ISshCommandExecutor;
+import ch.systemsx.cisd.common.highwatermark.HostAwareFile;
+import ch.systemsx.cisd.common.highwatermark.HostAwareFileWithHighwaterMark;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.process.ProcessResult;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.common.utilities.StringUtilities;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.Copier;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier;
+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.IPostRegistrationDatasetHandler;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class MsInjectionCopier implements Serializable, IPostRegistrationDatasetHandler
+{
+
+ private static final class ExceptionWithStatus extends RuntimeException
+ {
+ private static final long serialVersionUID = 1L;
+ private final Status status;
+
+ ExceptionWithStatus(Status status)
+ {
+ this.status = status;
+ }
+
+ public Status getStatus()
+ {
+ return status;
+ }
+ }
+
+ private static interface IExecutor
+ {
+ BooleanStatus exists(File file);
+ void deleteFolder(File folder);
+ void copyDataSet(File dataSet, File destination);
+ void renameTo(File newFile, File oldFile);
+ }
+
+ private static final class LocalExcecutor implements IExecutor
+ {
+ public BooleanStatus exists(File file)
+ {
+ return BooleanStatus.createFromBoolean(file.exists());
+ }
+
+ public void deleteFolder(File folder)
+ {
+ boolean successful = folder.delete();
+ if (successful == false)
+ {
+ operationLog.error("Deletion of '" + folder + "' failed for some unknown reason.");
+ throw new ExceptionWithStatus(Status.createError("couldn't delete"));
+ }
+ }
+
+ public void copyDataSet(File dataSet, File destination)
+ {
+ try
+ {
+ FileUtilities.copyFileTo(dataSet, destination, true);
+ } catch (Exception ex)
+ {
+ operationLog.error("Couldn't copy '" + dataSet + "' to '" + destination + "'.");
+ throw new ExceptionWithStatus(Status.createError("copy failed"));
+ }
+ }
+
+ public void renameTo(File newFile, File oldFile)
+ {
+ boolean result = oldFile.renameTo(newFile);
+ if (result == false)
+ {
+ operationLog.error("Couldn't rename '" + oldFile + "' to '" + newFile + "'.");
+ throw new ExceptionWithStatus(Status.createError("rename failed"));
+ }
+ }
+
+ }
+
+ private static final class RemoteExecutor implements IExecutor
+ {
+ private final ISshCommandExecutor executor;
+ private final IPathCopier copier;
+ private final String host;
+ private final String rsyncModuleNameOrNull;
+ private final String rsyncPasswordFileOrNull;
+
+ public RemoteExecutor(ISshCommandExecutor executor, IPathCopier copier, String host,
+ String rsyncModuleNameOrNull, String rsyncPasswordFileOrNull)
+ {
+ this.executor = executor;
+ this.copier = copier;
+ this.host = host;
+ this.rsyncModuleNameOrNull = rsyncModuleNameOrNull;
+ this.rsyncPasswordFileOrNull = rsyncPasswordFileOrNull;
+ }
+
+ public BooleanStatus exists(File file)
+ {
+ return executor.exists(file, DataSetCopier.SSH_TIMEOUT_MILLIS);
+ }
+
+ public void deleteFolder(File folder)
+ {
+ ProcessResult result =
+ executor.tryExecuteCommandRemotely("delete " + folder.getPath(),
+ DataSetCopier.SSH_TIMEOUT_MILLIS);
+ if (result.isOK() == false)
+ {
+ operationLog.error("Remote deletion of '" + folder
+ + "' failed with exit value: " + result.getExitValue());
+ throw new ExceptionWithStatus(Status.createError("couldn't delete"));
+ }
+ List<String> output = result.getOutput();
+ if (output.isEmpty() == false)
+ {
+ operationLog.error("Remote deletion of '" + folder
+ + "' seemed to be successful but produced following output:\n"
+ + StringUtilities.concatenateWithNewLine(output));
+ throw new ExceptionWithStatus(Status.createError("deletion leads to a problem"));
+ }
+ }
+
+ public void copyDataSet(File dataSet, File destination)
+ {
+ Status result =
+ copier.copyToRemote(dataSet, destination, host, rsyncModuleNameOrNull,
+ rsyncPasswordFileOrNull);
+ if (result.isError())
+ {
+ throw new ExceptionWithStatus(result);
+ }
+ }
+
+ public void renameTo(File newFile, File oldFile)
+ {
+ ProcessResult result =
+ executor.tryExecuteCommandRemotely("mv " + oldFile.getPath() + " "
+ + newFile.getPath(), DataSetCopier.SSH_TIMEOUT_MILLIS);
+ if (result.isOK() == false)
+ {
+ operationLog.error("Remote move of '" + oldFile
+ + "' to '" + newFile + "' failed with exit value: " + result.getExitValue());
+ throw new ExceptionWithStatus(Status.createError("couldn't move"));
+ }
+ List<String> output = result.getOutput();
+ if (output.isEmpty() == false)
+ {
+ operationLog.error("Remote move of '" + oldFile
+ + "' to '" + newFile
+ + "' seemed to be successful but produced following output:\n"
+ + StringUtilities.concatenateWithNewLine(output));
+ throw new ExceptionWithStatus(Status.createError("moving leads to a problem"));
+ }
+ }
+ }
+
+ private static final long serialVersionUID = 1L;
+
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, MsInjectionCopier.class);
+
+ private final IExecutor executor;
+
+ private final File destination;
+
+ MsInjectionCopier(Properties properties, IPathCopierFactory pathCopierFactory,
+ ISshCommandExecutorFactory sshCommandExecutorFactory)
+ {
+ String hostFile =
+ PropertyUtils.getMandatoryProperty(properties, DataSetCopier.DESTINATION_KEY);
+ HostAwareFile hostAwareFile = HostAwareFileWithHighwaterMark.create(hostFile, -1);
+ String hostOrNull = hostAwareFile.tryGetHost();
+ destination = hostAwareFile.getFile();
+ if (hostOrNull == null)
+ {
+ executor = new LocalExcecutor();
+ } else
+ {
+ File sshExecutable = Copier.getExecutable(properties, DataSetCopier.SSH_EXEC);
+ File rsyncExecutable = Copier.getExecutable(properties, DataSetCopier.RSYNC_EXEC);
+ IPathCopier copier = pathCopierFactory.create(rsyncExecutable, sshExecutable);
+ copier.check();
+ String rsyncModule = hostAwareFile.tryGetRsyncModule();
+ String rsyncPasswordFile =
+ properties.getProperty(DataSetCopier.RSYNC_PASSWORD_FILE_KEY);
+ FileUtilities.checkPathCopier(copier, hostOrNull, null, rsyncModule, rsyncPasswordFile);
+ ISshCommandExecutor sshCommandExecutor =
+ sshCommandExecutorFactory.create(sshExecutable, hostOrNull);
+ executor =
+ new RemoteExecutor(sshCommandExecutor, copier, hostOrNull, rsyncModule,
+ rsyncPasswordFile);
+ }
+ }
+
+ public void undoLastOperation()
+ {
+ }
+
+ public Status handle(File originalData, DataSetInformation dataSetInformation,
+ Map<String, String> parameterBindings)
+ {
+ try
+ {
+ String target = createTargetFolderName(dataSetInformation, parameterBindings);
+ File targetFolder = new File(destination, target);
+ deleteTargetFolder(targetFolder);
+ executor.copyDataSet(originalData, destination);
+ executor.renameTo(targetFolder, new File(destination, originalData.getName()));
+ return null;
+
+ } catch (ExceptionWithStatus ex)
+ {
+ return ex.getStatus();
+ }
+ }
+
+ private String createTargetFolderName(DataSetInformation dataSetInformation,
+ Map<String, String> parameterBindings)
+ {
+ String dataSetTypeCode = dataSetInformation.getDataSetType().getCode();
+ String sampleCode = parameterBindings.get(dataSetInformation.getDataSetCode());
+ return (sampleCode == null ? "sample-unknown" : sampleCode) + "_" + dataSetTypeCode;
+ }
+
+ private void deleteTargetFolder(File targetFolder)
+ {
+ BooleanStatus targetExists = executor.exists(targetFolder);
+ if (targetExists.isError())
+ {
+ operationLog.error("Could not check existence of '" + targetFolder + "': "
+ + targetExists.tryGetMessage());
+ throw new ExceptionWithStatus(Status.createError("couldn't check existence"));
+ }
+ if (targetExists.isSuccess())
+ {
+ executor.deleteFolder(targetFolder);
+ }
+ }
+
+}
+
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionDataSetCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionDataSetCopier.java
new file mode 100644
index 0000000000000000000000000000000000000000..b89716caebfb8ae76582f848c7d4ea06a98a5fe6
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionDataSetCopier.java
@@ -0,0 +1,49 @@
+/*
+ * 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.dss.phosphonetx.server.plugins;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDropboxProcessingPlugin;
+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.server.plugins.standard.RsyncCopierFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.SshCommandExecutorFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class MsInjectionDataSetCopier extends AbstractDropboxProcessingPlugin
+{
+ private static final long serialVersionUID = 1L;
+
+ public MsInjectionDataSetCopier(Properties properties, File storeRoot)
+ {
+ this(properties, storeRoot, new RsyncCopierFactory(), new SshCommandExecutorFactory());
+ }
+
+ @Private MsInjectionDataSetCopier(Properties properties, File storeRoot, IPathCopierFactory pathCopierFactory,
+ ISshCommandExecutorFactory sshCommandExecutorFactory)
+ {
+ super(properties, storeRoot, new MsInjectionCopier(properties, pathCopierFactory,
+ sshCommandExecutorFactory));
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
index c56856f69e52feaba2a14742d556ebf4c9d1f090..b98389ce70508e1832eef1b14f27e5304ca34f8a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -102,6 +102,7 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
List<MsInjectionSample> samples = loadAllRawDataSamples(session);
Set<Long> sampleIDs = new HashSet<Long>();
List<String> dataSetCodes = new ArrayList<String>();
+ Map<String, String> parameterBindings = new HashMap<String, String>();
for (MsInjectionSample sample : samples)
{
if (RAW_DATA_SAMPLE_VALIDATOR.isValid(person, sample))
@@ -111,7 +112,9 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
ExternalData latestDataSet = latestDataSets.get(dataSetType);
if (latestDataSet != null)
{
- dataSetCodes.add(latestDataSet.getCode());
+ String code = latestDataSet.getCode();
+ dataSetCodes.add(code);
+ parameterBindings.put(code, sample.getSample().getCode());
}
}
}
@@ -119,7 +122,6 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
- Map<String, String> parameterBindings = new HashMap<String, String>();
externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
parameterBindings);
}