diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/EntitiesFinder.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/EntitiesFinder.java
index 93599afa034a8b8e014915160bfbb9b7db76b29e..74cba6fac81838d003bbfd8bde8f6362168b50ea 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/EntitiesFinder.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/EntitiesFinder.java
@@ -214,6 +214,7 @@ class EntitiesFinder
fetchOptions.withRegistrator();
fetchOptions.withModifier();
fetchOptions.withDataSets();
+ fetchOptions.withContainer();
return api.getSamples(sessionToken, samplePermIds, fetchOptions).values();
}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutor.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutor.java
index ab2aff3d40ac306d408c367448c2d987ac62a974..27df4ad8b89c7a71c91b96e27c90a77762d5638b 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutor.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutor.java
@@ -44,6 +44,7 @@ import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
+import java.io.InputStream;
import java.io.OutputStream;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
@@ -131,7 +132,11 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.NotFetchedException;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.DataSetFilePermId;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
@@ -227,8 +232,6 @@ public class ExportExecutor implements IExportExecutor
@Autowired
private ISessionWorkspaceProvider sessionWorkspaceProvider;
-// private IDataStoreServerApi v3Dss = (IDataStoreServerApi) ServiceProvider.getDssServiceV3().getService();
-
@Resource(name = ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME)
private ExposablePropertyPlaceholderConfigurer configurer;
@@ -369,6 +372,7 @@ public class ExportExecutor implements IExportExecutor
for (final Sample sample : samples)
{
final List<DataSet> dataSets = sample.getDataSets();
+ final Sample container = sample.getContainer();
for (final DataSet dataSet : dataSets)
{
@@ -382,18 +386,49 @@ public class ExportExecutor implements IExportExecutor
OPERATION_LOG.info(String.format("Found: %d files", results.getTotalCount()));
- for (final DataSetFile file : results.getObjects())
+ final List<DataSetFile> dataSetFiles = results.getObjects();
+ final List<DataSetFilePermId> fileIds = dataSetFiles.stream().map(DataSetFile::getPermId).collect(Collectors.toList());
+
+ final DataSetFileDownloadOptions options = new DataSetFileDownloadOptions();
+ options.setRecursive(true);
+
+ final InputStream stream = v3Dss.downloadFiles(sessionToken, fileIds, options);
+ final DataSetFileDownloadReader reader = new DataSetFileDownloadReader(stream);
+
+ DataSetFileDownload file;
+ while ((file = reader.read()) != null)
{
- final String filePath = file.getPath();
- final Sample container = sample.getContainer();
- putNextDataZipEntry(existingZipEntries, zos, 'S', getSpaceCode(sample), getProjectCode(SAMPLE),
- container == null ? null : container.getCode(), sample.getCode(), getEntityName(sample), getFileName(filePath));
+ final DataSetFile dataSetFile = file.getDataSetFile();
+ final String filePath = dataSetFile.getPath();
+// putNextDataZipEntry(existingZipEntries, zos, 'O', getSpaceCode(sample), getProjectCode(sample),
+// container == null ? null : container.getCode(), sample.getCode(), getEntityName(sample), getFileName(filePath));
- if (!file.isDirectory())
+ if (!dataSetFile.isDirectory())
{
- // TODO: add content
+ try (final InputStream is = file.getInputStream())
+ {
+ writeInChunks(bos, is);
+ }
}
}
+
+// for (final DataSetFile dataSetFile : dataSetFiles)
+// {
+// final String filePath = dataSetFile.getPath();
+// final Sample container = sample.getContainer();
+// putNextDataZipEntry(existingZipEntries, zos, 'O', getSpaceCode(sample), getProjectCode(sample),
+// container == null ? null : container.getCode(), sample.getCode(), getEntityName(sample), getFileName(filePath));
+//
+// v3Dss.downloadFiles(sessionToken, )
+//
+// if (!dataSetFile.isDirectory())
+// {
+// try (final FileInputStream fis = new FileInputStream(filePath))
+// {
+// writeInChunks(bos, fis);
+// }
+// }
+// }
} else
{
OPERATION_LOG.info(String.format("Omitted data export for link dataset with permId: %s", dataSetPermId));
@@ -824,6 +859,17 @@ public class ExportExecutor implements IExportExecutor
os.flush();
}
+ private static void writeInChunks(final OutputStream os, final InputStream is) throws IOException
+ {
+ final byte[] buffer = new byte[BUFFER_SIZE];
+ int length;
+ while ((length = is.read(buffer)) > 0)
+ {
+ os.write(buffer, 0, length);
+ }
+ os.flush();
+ }
+
/**
* Adds an entry only if it is needed.
*
@@ -863,7 +909,8 @@ public class ExportExecutor implements IExportExecutor
entryBuilder.append('/').append(projectCode);
if (experimentCode != null)
{
- addFullEntityName(entryBuilder, experimentCode, experimentName);
+ entryBuilder.append('/');
+ addFullEntityName(entryBuilder, null, experimentCode, experimentName);
if (sampleCode == null && dataSetCode != null)
{
@@ -881,7 +928,8 @@ public class ExportExecutor implements IExportExecutor
if (sampleCode != null)
{
- addFullEntityName(entryBuilder, sampleCode, sampleName);
+ entryBuilder.append('/');
+ addFullEntityName(entryBuilder, containerCode, sampleCode, sampleName);
if (dataSetCode != null)
{
@@ -896,10 +944,11 @@ public class ExportExecutor implements IExportExecutor
private static void putNextDataZipEntry(final Set<String> existingZipEntries, final ZipOutputStream zos, final char prefix,
final String spaceCode, final String projectCode, final String containerCode, final String entityCode, final String entityName,
- final String fileName)
+ final String dataSetTypeCode, final String dataSetCode, final String dataSetName, final String fileName)
throws IOException
{
- final String entry = getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, entityName);
+ final String entry = getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, dataSetTypeCode, dataSetCode,
+ dataSetName, fileName);
if (!existingZipEntries.contains(entry))
{
zos.putNextEntry(new ZipEntry(entry));
@@ -908,11 +957,17 @@ public class ExportExecutor implements IExportExecutor
}
static String getFolderName(final char prefix, final String spaceCode, final String projectCode,
- final String containerCode, final String entityCode, final String entityName)
+ final String containerCode, final String entityCode, final String dataSetTypeCode,
+ final String dataSetCode, final String dataSetName, final String fileName)
{
if (prefix != 'O' && prefix != 'E')
{
- throw new IllegalArgumentException("Only 'O' and 'E' can be used as prefix.");
+ throw new IllegalArgumentException(String.format("Only 'O' and 'E' can be used as prefix got '%c' instead.", prefix));
+ }
+
+ if (containerCode != null && prefix != 'O')
+ {
+ throw new IllegalArgumentException("Only objects can have containers.");
}
final StringBuilder entryBuilder = new StringBuilder(String.valueOf(prefix));
@@ -936,46 +991,64 @@ public class ExportExecutor implements IExportExecutor
throw new IllegalArgumentException("Project code cannot be null for experiments.");
}
- entryBuilder.append('+');
+ if (entityCode != null)
+ {
+ entryBuilder.append('+');
+ addFullEntityCode(entryBuilder, containerCode, entityCode);
+ } else
+ {
+ throw new IllegalArgumentException("Entity code is mandatory");
+ }
- if (containerCode != null)
+ if (dataSetTypeCode != null)
{
- if (prefix == 'O')
- {
- entryBuilder.append(containerCode).append('*');
- } else
- {
- throw new IllegalArgumentException("Only objects can have containers.");
- }
+ entryBuilder.append('+').append(dataSetTypeCode);
+ } else
+ {
+ throw new IllegalArgumentException("Data set type code is mandatory");
}
- if (entityCode != null)
+ if (dataSetCode != null)
{
- entryBuilder.append(entityCode);
+ entryBuilder.append('+');
+ addFullEntityName(entryBuilder, null, dataSetCode, dataSetName);
} else
{
- throw new IllegalArgumentException();
+ throw new IllegalArgumentException("Data set code is mandatory");
}
- if (entityName != null)
+ if (fileName != null)
{
- entryBuilder.append('+').append(entityName);
+ entryBuilder.append('/').append(fileName);
}
return entryBuilder.toString();
}
- private static void addFullEntityName(final StringBuilder entryBuilder, final String entityCode, final String entityName)
+ private static void addFullEntityName(final StringBuilder entryBuilder, final String containerCode, final String entityCode,
+ final String entityName)
{
if (entityName == null || entityName.isEmpty())
{
- entryBuilder.append("/").append(entityCode);
+ addFullEntityCode(entryBuilder, containerCode, entityCode);
} else
{
- entryBuilder.append("/").append(entityName).append(" (").append(entityCode).append(")");
+ entryBuilder.append(entityName).append(" (");
+ addFullEntityCode(entryBuilder, containerCode, entityCode);
+ entryBuilder.append(")");
}
}
+ private static void addFullEntityCode(final StringBuilder entryBuilder, final String containerCode, final String entityCode)
+ {
+ if (containerCode != null)
+ {
+ entryBuilder.append(containerCode).append('*');
+ }
+
+ entryBuilder.append(entityCode);
+ }
+
private static String getEntityName(final IPropertiesHolder entity)
{
try
@@ -989,7 +1062,7 @@ public class ExportExecutor implements IExportExecutor
static String escapeUnsafeCharacters(final String name)
{
- return name.replaceAll(UNSAFE_CHARACTERS_REGEXP, "_");
+ return name != null ? name.replaceAll(UNSAFE_CHARACTERS_REGEXP, "_") : null;
}
private static void exportXls(final ZipOutputStream zos, final BufferedOutputStream bos, final XLSExport.PrepareWorkbookResult xlsExportResult,
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServiceProvider.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServiceProvider.java
index 95ec68f22ddd29091379c8fb9ade5ea05dc73421..4dbede8a54b57d1100ceb7168c5568883b593c1c 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServiceProvider.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServiceProvider.java
@@ -55,7 +55,14 @@ public class CommonServiceProvider
public static void setDataStoreServerApi(final String dssURL, final int timeoutInMinutes)
{
- dataStoreServerApi = HttpInvokerUtils.createServiceStub(IDataStoreServerApi.class, dssURL + IDataStoreServerApi.SERVICE_URL, timeoutInMinutes * 60 * 1000);
+ dataStoreServerApi = HttpInvokerUtils.createServiceStub(IDataStoreServerApi.class, dssURL +
+ "/datastore_server" + IDataStoreServerApi.SERVICE_URL,
+ timeoutInMinutes * 60 * 1000);
+ }
+
+ public static void setDataStoreServerApi(final IDataStoreServerApi dataStoreServerApi)
+ {
+ CommonServiceProvider.dataStoreServerApi = dataStoreServerApi;
}
public static ICommonServerForInternalUse getCommonServer()
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutorTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutorTest.java
index e47d75c2c7974416cb4fd25d00a44bf2c9b7fc27..3d11d380a7dea5fe49f31760e46d43428b0cbd41 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutorTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/exporter/ExportExecutorTest.java
@@ -237,57 +237,80 @@ public class ExportExecutorTest
private static final Object[][] FOLDER_NAME_DATA = {
{
- 'O', "SPACE", "PROJECT", null, "CODE_A", "NAME_A", "O+SPACE+PROJECT+CODE_A+NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", null,
+ "O+DEFAULT_LAB_NOTEBOOK+DEFAULT_PROJECT+OBJ1+ANALYZED_DATA+my dataset (AD_1)"
},
{
- 'O', "SPACE", null, null, "CODE_A", "NAME_A", "O+SPACE+CODE_A+NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file",
+ "O+DEFAULT_LAB_NOTEBOOK+DEFAULT_PROJECT+OBJ1+ANALYZED_DATA+my dataset (AD_1)/file"
},
{
- 'O', null, null, null, "CODE_A", "NAME_A", "O+CODE_A+NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", "AD_1", null, "file",
+ "O+DEFAULT_LAB_NOTEBOOK+DEFAULT_PROJECT+OBJ1+ANALYZED_DATA+AD_1/file"
},
{
- 'E', "SPACE", "PROJECT", null, "CODE_A", null, "E+SPACE+PROJECT+CODE_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", null, null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file",
+ "O+DEFAULT_LAB_NOTEBOOK+OBJ1+ANALYZED_DATA+my dataset (AD_1)/file"
},
{
- 'O', "SPACE", "PROJECT", "CODE_B", "CODE_A", "NAME_A", "O+SPACE+PROJECT+CODE_B*CODE_A+NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", null, null, "OBJ1", "ANALYZED_DATA", "AD_1", null, "file",
+ "O+DEFAULT_LAB_NOTEBOOK+OBJ1+ANALYZED_DATA+AD_1/file"
+ },
+ {
+ 'O', null, null, null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file",
+ "O+OBJ1+ANALYZED_DATA+my dataset (AD_1)/file"
+ },
+ {
+ 'O', null, null, null, "OBJ1", "ANALYZED_DATA", "AD_1", null, "file",
+ "O+OBJ1+ANALYZED_DATA+AD_1/file"
+ },
+ {
+ 'E', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "EXP1", "ANALYZED_DATA", "AD_1", "my dataset", "file",
+ "E+DEFAULT_LAB_NOTEBOOK+DEFAULT_PROJECT+EXP1+ANALYZED_DATA+my dataset (AD_1)/file"
+ },
+ {
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", "OBJ_CONTAINER", "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file",
+ "O+DEFAULT_LAB_NOTEBOOK+DEFAULT_PROJECT+OBJ_CONTAINER*OBJ1+ANALYZED_DATA+my dataset (AD_1)/file"
},
};
private static final Object[][] ERRONEOUS_FOLDER_NAME_DATA = {
{
- 'P', "SPACE", "PROJECT", null, "CODE_A", "NAME_A"
+ 'P', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
- 'O', null, "PROJECT", null, "CODE_A", "NAME_A"
+ 'O', null, "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
- 'O', "SPACE", "PROJECT", null, null, "NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, null, "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
- 'O', "SPACE", "PROJECT", null, null, null
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", "OBJ_CONTAINER", null, "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
- 'O', "SPACE", "PROJECT", "CODE_B", null, "NAME_A"
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", null, "AD_1", "my dataset", "file"
},
{
- 'O', "SPACE", "PROJECT", "CODE_B", null, null
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", null, "my dataset", "file"
},
-
{
- // Experiments cannot have containers
- 'E', "SPACE", "PROJECT", "CODE_B", "CODE_A", null
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", null, null, "file"
},
+ {
+ 'O', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", null, "OBJ1", "ANALYZED_DATA", null, null, null
+ },
+
{
// Experiments cannot have containers
- 'E', "SPACE", "PROJECT", "CODE_B", "CODE_A", "NAME_A"
+ 'E', "DEFAULT_LAB_NOTEBOOK", "DEFAULT_PROJECT", "EXP_CONTAINER", "EXP1", "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
// Experiments cannot be on the space level
- 'E', "SPACE", null, null, "CODE_A", "NAME_A"
+ 'E', "DEFAULT_LAB_NOTEBOOK", null, null, "EXP1", "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
{
- // Experiments cannot be standalone
- 'E', null, null, null, "CODE_A", "NAME_A"
+ // Experiments cannot be shared (w/o space)
+ 'E', null, null, null, "EXP1", "ANALYZED_DATA", "AD_1", "my dataset", "file"
},
};
@@ -334,17 +357,19 @@ public class ExportExecutorTest
@Test(dataProvider = FOLDER_NAME_DATA_PROVIDER)
public void testGetFolderName(final char prefix, final String spaceCode, final String projectCode,
- final String containerCode, final String entityCode, final String entityName, final String expectedResult)
+ final String containerCode, final String entityCode, final String dataSetTypeCode, final String dataSetCode,
+ final String dataSetName, final String fileName, final String expectedResult)
{
- assertEquals(ExportExecutor.getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, entityName),
- expectedResult);
+ assertEquals(ExportExecutor.getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, dataSetTypeCode, dataSetCode,
+ dataSetName, fileName), expectedResult);
}
@Test(dataProvider = ERRONEOUS_FOLDER_NAME_DATA_PROVIDER, expectedExceptions = IllegalArgumentException.class)
public void testGetFolderNameError(final char prefix, final String spaceCode, final String projectCode,
- final String containerCode, final String entityCode, final String entityName)
+ final String containerCode, final String entityCode, final String dataSetTypeCode, final String dataSetCode,
+ final String dataSetName, final String fileName)
{
- ExportExecutor.getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, entityName);
+ ExportExecutor.getFolderName(prefix, spaceCode, projectCode, containerCode, entityCode, dataSetTypeCode, dataSetCode, dataSetName, fileName);
}
@Test()