From 061bab1bd8d24230177fa577bb640b4193e3f19f Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 4 Jun 2013 10:53:23 +0000
Subject: [PATCH] SP-668, BIS-428: handle checksum in case of uncompressed zip
file. ZipDataSetpackagerTest added.
SVN: 29280
---
.../server/AbstractDataSetPackager.java | 38 ++-
.../dss/generic/server/MetaDataBuilder.java | 11 +-
.../generic/server/ZipDataSetPackager.java | 23 +-
.../plugins/standard/DistributedArchiver.java | 164 ----------
.../server/ZipDataSetPackagerTest.java | 285 ++++++++++++++++++
5 files changed, 346 insertions(+), 175 deletions(-)
delete mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DistributedArchiver.java
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackagerTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetPackager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetPackager.java
index 27fa640ee66..81700116234 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetPackager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetPackager.java
@@ -19,7 +19,9 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.List;
+import java.util.zip.CRC32;
+import ch.systemsx.cisd.common.io.IOUtilities;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
@@ -49,8 +51,16 @@ public abstract class AbstractDataSetPackager
/**
* Adds an entry with specified entry path and last modification date filled with data from
* specified input stream.
+ *
+ * @param size Number of bytes.
+ * @param checksum Checksum. Can be 0 if {@link #isChecksumNeeded()} return <code>false</code>.
*/
- public abstract void addEntry(String entryPath, long lastModified, InputStream in);
+ public abstract void addEntry(String entryPath, long lastModified, long size, long checksum, InputStream in);
+
+ /**
+ * Returns <code>true</code> if the checksum is needed.
+ */
+ protected abstract boolean isChecksumNeeded();
/**
* Closes the package.
@@ -61,8 +71,15 @@ public abstract class AbstractDataSetPackager
{
try
{
- addEntry(rootPath + META_DATA_FILE_NAME, System.currentTimeMillis(),
- new ByteArrayInputStream(MetaDataBuilder.createMetaData(externalData).getBytes()));
+ byte[] bytes = MetaDataBuilder.createMetaData(externalData).getBytes();
+ CRC32 checksumCalculator = new CRC32();
+ for (byte b : bytes)
+ {
+ checksumCalculator.update(0xff & b);
+ }
+ Long checksum = checksumCalculator.getValue();
+ addEntry(rootPath + META_DATA_FILE_NAME, System.currentTimeMillis(), new Long(bytes.length), checksum,
+ new ByteArrayInputStream(bytes));
} catch (Exception ex)
{
throw new RuntimeException(
@@ -111,7 +128,20 @@ public abstract class AbstractDataSetPackager
}
} else
{
- addEntry(newRootPath + node.getRelativePath(), node.getLastModified(),
+ long size = node.getFileLength();
+ long checksum = 0;
+ if (isChecksumNeeded())
+ {
+ boolean checksumCRC32Precalculated = node.isChecksumCRC32Precalculated();
+ if (checksumCRC32Precalculated)
+ {
+ checksum = node.getChecksumCRC32();
+ } else
+ {
+ checksum = IOUtilities.getChecksumCRC32(node.getInputStream());
+ }
+ }
+ addEntry(newRootPath + node.getRelativePath(), node.getLastModified(), size, checksum,
node.getInputStream());
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
index adb91cd1ccb..04d2ebbde41 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
@@ -86,10 +87,10 @@ public class MetaDataBuilder
builder.dataSetProperties(dataSet.getProperties());
StringBuilder stringBuilder = new StringBuilder();
- List<AbstractExternalData> parents = new ArrayList<AbstractExternalData>(dataSet.getParents());
- Collections.sort(parents, DATA_SET_COMPARATOR);
+ List<AbstractExternalData> parents = getParents(dataSet);
if (parents.isEmpty() == false)
{
+ Collections.sort(parents, DATA_SET_COMPARATOR);
for (AbstractExternalData parent : parents)
{
if (stringBuilder.length() > 0)
@@ -123,6 +124,12 @@ public class MetaDataBuilder
return builder.getRenderedMetaData();
}
+ private static List<AbstractExternalData> getParents(AbstractExternalData dataSet)
+ {
+ Collection<AbstractExternalData> parents = dataSet.getParents();
+ return parents == null ? new ArrayList<AbstractExternalData>() : new ArrayList<AbstractExternalData>(parents);
+ }
+
private final StringBuilder builder = new StringBuilder();
private void dataSetProperties(List<IEntityProperty> properties)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackager.java
index a9088d310f0..5fff70928f5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackager.java
@@ -51,29 +51,42 @@ public class ZipDataSetPackager extends AbstractDataSetPackager
}
@Override
- public void addEntry(String entryPath, long lastModified, InputStream in)
+ protected boolean isChecksumNeeded()
{
+ return compress == false;
+ }
+
+ @Override
+ public void addEntry(String entryPath, long lastModified, long size, long checksum, InputStream in)
+ {
+ ZipOutputStream zos = getZipOutputStream();
try
{
ZipEntry zipEntry = new ZipEntry(entryPath.replace('\\', '/'));
zipEntry.setTime(lastModified);
zipEntry.setMethod(compress ? ZipEntry.DEFLATED : ZipEntry.STORED);
- getZipOutputStream().putNextEntry(zipEntry);
+ if (compress == false)
+ {
+ zipEntry.setSize(size);
+ zipEntry.setCompressedSize(size);
+ zipEntry.setCrc(0xffffffffL & checksum);
+ }
+ zos.putNextEntry(zipEntry);
int len;
byte[] buffer = new byte[1024];
while ((len = in.read(buffer)) > 0)
{
- getZipOutputStream().write(buffer, 0, len);
+ zos.write(buffer, 0, len);
}
} catch (IOException ex)
{
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ throw new RuntimeException("Error while adding entry " + entryPath, ex);
} finally
{
IOUtils.closeQuietly(in);
try
{
- getZipOutputStream().closeEntry();
+ zos.closeEntry();
} catch (IOException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DistributedArchiver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DistributedArchiver.java
deleted file mode 100644
index 55d3b57d228..00000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DistributedArchiver.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Copyright 2013 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.generic.server.plugins.standard;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.filesystem.BooleanStatus;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.common.time.TimingParameters;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.server.ZipDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ArchiverTaskContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocation;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class DistributedArchiver extends AbstractArchiverProcessingPlugin
-{
- private static final long serialVersionUID = 1L;
-
- private final boolean compress;
-
- private File destination;
-
- public DistributedArchiver(Properties properties, File storeRoot)
- {
- super(properties, storeRoot, null, null);
- destination = new File(properties.getProperty("destination"));
- compress = PropertyUtils.getBoolean(properties, "compress", true);
- destination.mkdirs();
- }
-
- @Override
- protected DatasetProcessingStatuses doArchive(List<DatasetDescription> datasets, ArchiverTaskContext context)
- {
- List<AbstractExternalData> dataSets = getDataSetMetaData(datasets);
- IHierarchicalContentProvider contentProvider = context.getHierarchicalContentProvider();
- IDataSetDirectoryProvider directoryProvider = context.getDirectoryProvider();
- IShareIdManager shareIdManager = directoryProvider.getShareIdManager();
- DataSetExistenceChecker dataSetExistenceChecker =
- new DataSetExistenceChecker(directoryProvider, TimingParameters.create(new Properties()));
- DatasetProcessingStatuses statuses = new DatasetProcessingStatuses();
- for (AbstractExternalData dataSet : dataSets)
- {
- Status status = Status.OK;
- String dataSetCode = dataSet.getCode();
- File file = new File(getArchive(dataSet), dataSetCode + ".zip");
- shareIdManager.lock(dataSetCode);
- AbstractDataSetPackager dataSetPackager = null;
- try
- {
- dataSetPackager = createPackager(file, contentProvider, dataSetExistenceChecker);
- dataSetPackager.addDataSetTo("", dataSet);
- } catch (Exception ex)
- {
- status = Status.createError(ex.toString());
- operationLog.error("Couldn't create package file: " + file, ex);
- } finally
- {
- if (dataSetPackager != null)
- {
- try
- {
- dataSetPackager.close();
- } catch (Exception ex)
- {
- status = Status.createError("Couldn't close package file: " + file + ": " + ex);
- }
- }
- shareIdManager.releaseLock(dataSetCode);
- operationLog.info("Data set " + dataSetCode + " archived: " + file);
- }
- statuses.addResult(dataSetCode, status, Operation.ARCHIVE);
- }
- return statuses;
- }
-
- private AbstractDataSetPackager createPackager(File file, IHierarchicalContentProvider contentProvider,
- DataSetExistenceChecker dataSetExistenceChecker)
- {
- return new ZipDataSetPackager(file, compress, contentProvider, dataSetExistenceChecker);
- }
-
- private List<AbstractExternalData> getDataSetMetaData(List<DatasetDescription> datasets)
- {
- IEncapsulatedOpenBISService service = getService();
- List<AbstractExternalData> dataSets = new ArrayList<AbstractExternalData>();
- for (DatasetDescription datasetDescription : datasets)
- {
- AbstractExternalData dataSet = service.tryGetDataSet(datasetDescription.getDataSetCode());
- String experimentIdentifier = datasetDescription.getExperimentIdentifier();
- dataSet.setExperiment(service.tryGetExperiment(ExperimentIdentifierFactory.parse(experimentIdentifier)));
- String sampleIdentifier = datasetDescription.getSampleIdentifier();
- if (sampleIdentifier != null)
- {
- dataSet.setSample(service.tryGetSampleWithExperiment(SampleIdentifierFactory.parse(sampleIdentifier)));
- }
- dataSets.add(dataSet);
- }
- return dataSets;
- }
-
- private File getArchive(AbstractExternalData dataSet)
- {
- return destination;
- }
-
- @Override
- protected DatasetProcessingStatuses doUnarchive(List<DatasetDescription> datasets, ArchiverTaskContext context)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected DatasetProcessingStatuses doDeleteFromArchive(List<? extends IDatasetLocation> datasets)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected BooleanStatus isDataSetSynchronizedWithArchive(DatasetDescription dataset, ArchiverTaskContext context)
- {
- return BooleanStatus.createFalse();
- }
-
- @Override
- protected BooleanStatus isDataSetPresentInArchive(DatasetDescription dataset)
- {
- return BooleanStatus.createFalse();
- }
-
-}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackagerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackagerTest.java
new file mode 100644
index 00000000000..beb0763844a
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ZipDataSetPackagerTest.java
@@ -0,0 +1,285 @@
+/*
+ * Copyright 2013 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.generic.server;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.InputStream;
+import java.util.Collections;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.IOUtils;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.io.IOUtilities;
+import ch.systemsx.cisd.common.server.ISessionTokenProvider;
+import ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer;
+import ch.systemsx.cisd.common.time.TimingParameters;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.DefaultFileBasedHierarchicalContentFactory;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.IHierarchicalContentFactory;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetDirectoryProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.HierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
+import ch.systemsx.cisd.openbis.dss.generic.shared.content.DssServiceRpcGenericFactory;
+import ch.systemsx.cisd.openbis.dss.generic.shared.content.IContentCache;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatasetLocationNode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataStoreBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
+
+import de.schlichtherle.io.FileInputStream;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ZipDataSetPackagerTest extends AbstractFileSystemTestCase
+{
+ private static final String DATA_SET_CODE = "ds1";
+ private static final String DSS_CODE = "DSS";
+ private static final String SHARE_ID = "1";
+ private Mockery context;
+ private IEncapsulatedOpenBISService openbisService;
+ private IShareIdManager shareIdManager;
+ private IConfigProvider configProvider;
+ private HierarchicalContentProvider contentProvider;
+ private DataSetExistenceChecker existenceChecker;
+ private IHierarchicalContentFactory contentProviderFactory;
+ private File rootFolder;
+
+ @BeforeMethod
+ public void prepareTestFixture()
+ {
+ context = new Mockery();
+ openbisService = context.mock(IEncapsulatedOpenBISService.class);
+ shareIdManager = context.mock(IShareIdManager.class);
+ configProvider = context.mock(IConfigProvider.class);
+ context.checking(new Expectations()
+ {
+ {
+ allowing(configProvider).getStoreRoot();
+ will(returnValue(workingDirectory));
+
+ allowing(configProvider).getDataStoreCode();
+ will(returnValue(DSS_CODE));
+ }
+ });
+ IContentCache contentCache = null;
+ ISessionTokenProvider sessionTokenProvider = null;
+ ExposablePropertyPlaceholderConfigurer infoProvider = null;
+ IDataSetDirectoryProvider dataSetDirectoryProvider = new DataSetDirectoryProvider(workingDirectory, shareIdManager);
+ contentProviderFactory = new DefaultFileBasedHierarchicalContentFactory();
+ contentProvider = new HierarchicalContentProvider(openbisService, dataSetDirectoryProvider, contentProviderFactory,
+ new DssServiceRpcGenericFactory(), contentCache, sessionTokenProvider, DSS_CODE, infoProvider);
+ existenceChecker = new DataSetExistenceChecker(dataSetDirectoryProvider, TimingParameters.getDefaultParameters());
+ File share = new File(workingDirectory, SHARE_ID);
+ share.mkdirs();
+ rootFolder = new File(share, DATA_SET_CODE);
+ File subFolder = new File(rootFolder, "subfolder");
+ subFolder.mkdirs();
+ FileUtilities.writeToFile(new File(rootFolder, "read.me"), "Don't read me!");
+ FileUtilities.writeToFile(new File(subFolder, "change-log.txt"), "nothing changed");
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one does not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCreateCompressed() throws Exception
+ {
+ PhysicalDataSet dataSet = new DataSetBuilder().store(new DataStoreBuilder(DSS_CODE).getStore())
+ .code(DATA_SET_CODE).type("MY-DATASET").fileFormat("XML").location(DATA_SET_CODE).property("AGE", "42")
+ .experiment(new ExperimentBuilder().identifier("/S/P/E1").type("MY-EXPERIMENT").property("GREETINGS", "Hello").getExperiment())
+ .getDataSet();
+ prepareShareIdManager(DATA_SET_CODE);
+ prepareGetDataSetLocation(dataSet);
+ File zipFile = new File(workingDirectory, "archived1.zip");
+ ZipDataSetPackager packager = new ZipDataSetPackager(zipFile, true, contentProvider, existenceChecker);
+
+ packager.addDataSetTo("", dataSet);
+ packager.close();
+
+ checkZipFileContent(zipFile, dataSet, "data_set\tcode\tds1\n" +
+ "data_set\tproduction_timestamp\t\n" +
+ "data_set\tproducer_code\t\n" +
+ "data_set\tdata_set_type\tMY-DATASET\n" +
+ "data_set\tis_measured\tTRUE\n" +
+ "data_set\tis_complete\tFALSE\n" +
+ "data_set\tAGE\t42\n" +
+ "data_set\tparent_codes\t\n" +
+ "experiment\tspace_code\tS\n" +
+ "experiment\tproject_code\tP\n" +
+ "experiment\texperiment_code\tE1\n" +
+ "experiment\texperiment_type_code\tMY-EXPERIMENT\n" +
+ "experiment\tregistration_timestamp\t\n" +
+ "experiment\tregistrator\t\n" +
+ "experiment\tGREETINGS\tHello\n");
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCreateUncompressed() throws Exception
+ {
+ PhysicalDataSet dataSet = new DataSetBuilder().store(new DataStoreBuilder(DSS_CODE).getStore())
+ .code(DATA_SET_CODE).type("MY-DATASET").fileFormat("XML").location(DATA_SET_CODE).property("AGE", "24")
+ .experiment(new ExperimentBuilder().identifier("/S/P/E1").type("MY-EXPERIMENT").getExperiment())
+ .sample(new SampleBuilder().identifier("/S/S1").type("MY-SAMPLE").property("GREETINGS", "Hi").getSample())
+ .parent(new DataSetBuilder().code("P1").getDataSet())
+ .getDataSet();
+ prepareShareIdManager(DATA_SET_CODE);
+ prepareGetDataSetLocation(dataSet);
+ File zipFile = new File(workingDirectory, "archived2.zip");
+ ZipDataSetPackager packager = new ZipDataSetPackager(zipFile, false, contentProvider, existenceChecker);
+
+ packager.addDataSetTo("", dataSet);
+ packager.close();
+
+ checkZipFileContent(zipFile, dataSet, "data_set\tcode\tds1\n" +
+ "data_set\tproduction_timestamp\t\n" +
+ "data_set\tproducer_code\t\n" +
+ "data_set\tdata_set_type\tMY-DATASET\n" +
+ "data_set\tis_measured\tTRUE\n" +
+ "data_set\tis_complete\tFALSE\n" +
+ "data_set\tAGE\t24\n" +
+ "data_set\tparent_codes\tP1\n" +
+ "sample\ttype_code\tMY-SAMPLE\n" +
+ "sample\tcode\tS1\n" +
+ "sample\tspace_code\tS\n" +
+ "sample\tregistration_timestamp\t\n" +
+ "sample\tregistrator\t\n" +
+ "sample\tGREETINGS\tHi\n" +
+ "experiment\tspace_code\tS\n" +
+ "experiment\tproject_code\tP\n" +
+ "experiment\texperiment_code\tE1\n" +
+ "experiment\texperiment_type_code\tMY-EXPERIMENT\n" +
+ "experiment\tregistration_timestamp\t\n" +
+ "experiment\tregistrator\t\n");
+ context.assertIsSatisfied();
+ }
+
+ private void checkZipFileContent(File zipFile, PhysicalDataSet dataSet, String metaData) throws Exception
+ {
+ assertEquals(true, zipFile.exists());
+ ZipFile zFile = new ZipFile(zipFile);
+ for (ZipEntry zipEntry : Collections.list(zFile.entries()))
+ {
+ String relativePath = zipEntry.getName();
+ if (relativePath.equals(AbstractDataSetPackager.META_DATA_FILE_NAME))
+ {
+ checkContent(zFile, zipEntry, new ByteArrayInputStream(metaData.getBytes()));
+ } else
+ {
+ checkZipEntry(zFile, zipEntry);
+ }
+ }
+ }
+
+ private void checkZipEntry(ZipFile zf, ZipEntry entry) throws Exception
+ {
+ String relativePath = entry.getName();
+ File file = new File(rootFolder, relativePath);
+ assertEquals(relativePath + " exists", true, file.exists());
+ assertEquals(relativePath + " folder or file", file.isDirectory(), entry.isDirectory());
+ if (entry.isDirectory())
+ {
+ return;
+ }
+ assertEquals(relativePath + " size", file.length(), entry.getSize());
+ assertEquals(relativePath + " checksum", calculateChecksum(file), (int) entry.getCrc());
+ checkContent(zf, entry, new FileInputStream(file));
+ }
+
+ private void checkContent(ZipFile zf, ZipEntry entry, InputStream inputStream) throws Exception
+ {
+ String expectedContent = getContentAndClose(inputStream);
+ String actualContent = getContentAndClose(zf.getInputStream(entry));
+ assertEquals(entry.getName() + " content", expectedContent, actualContent);
+ }
+
+ private String getContentAndClose(InputStream inputStream) throws Exception
+ {
+ try
+ {
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ IOUtils.copy(inputStream, output);
+ return output.toString();
+ } finally
+ {
+ IOUtils.closeQuietly(inputStream);
+ }
+ }
+
+ private int calculateChecksum(File file) throws Exception
+ {
+ InputStream inputStream = null;
+ try
+ {
+ inputStream = new FileInputStream(file);
+ return IOUtilities.getChecksumCRC32(inputStream);
+ } finally
+ {
+ IOUtils.closeQuietly(inputStream);
+ }
+ }
+
+ private void prepareGetDataSetLocation(final PhysicalDataSet dataSet)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).tryGetDataSetLocation(dataSet.getCode());
+ will(returnValue(new DatasetLocationNode(dataSet)));
+ }
+ });
+ }
+
+ private void prepareShareIdManager(final String dataSetCode)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ exactly(2).of(shareIdManager).getShareId(dataSetCode);
+ will(returnValue(SHARE_ID));
+
+ one(shareIdManager).lock(dataSetCode);
+
+ one(shareIdManager).releaseLock(dataSetCode);
+ }
+ });
+ }
+
+}
--
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