From 096e3a36b3a99821839c659c4b45d470764219da Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 16 Jun 2011 10:40:36 +0000
Subject: [PATCH] LMS-2294 Extend OpenBISScreeningML with methods to list files
in data sets and to down load files from a data set.
SVN: 21717
---
.../dss/client/api/v1/IDataSetDss.java | 15 ++
.../dss/client/api/v1/impl/DataSetDss.java | 8 +-
.../dss/client/api/v1/impl/DssComponent.java | 36 ++++-
.../server/api/v1/DssServiceRpcGeneric.java | 14 +-
.../api/v1/DssServiceRpcGenericTest.java | 137 ++++++++++++------
screening/source/java/OpenBISScreeningML.java | 88 ++++++++++-
.../v1/IScreeningOpenbisServiceFacade.java | 3 +
.../api/v1/ScreeningOpenbisServiceFacade.java | 8 +
.../java/OpenBISScreeningMLTest.java | 55 +++++++
9 files changed, 304 insertions(+), 60 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/IDataSetDss.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/IDataSetDss.java
index a5402790f83..22543b7d1a8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/IDataSetDss.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/IDataSetDss.java
@@ -84,5 +84,20 @@ public interface IDataSetDss
*/
public File getLinkOrCopyOfContents(String overrideStoreRootPathOrNull, File downloadDir)
throws IllegalArgumentException, InvalidSessionException;
+
+ /**
+ * Returns a {@link File}, if possible, that directly references some specified content of a data set in
+ * the data store server. If not possible, downloads that content and returns a File in
+ * the downloadDir containing that content.
+ *
+ * @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
+ * the DSS' store root. If null, datasets are copied to the downloadDir folder.
+ * @param downloadDir The directory in which to place the contents of the data set if they must
+ * be downloaded.
+ * @param pathInDataSet Path of requested content inside the data set.
+ * @return A File containing the requested content.
+ */
+ public File getLinkOrCopyOfContent(String overrideStoreRootPathOrNull, File downloadDir,
+ String pathInDataSet) throws IllegalArgumentException, InvalidSessionException;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
index 05f6dea8522..d9603fa4ad9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
@@ -71,7 +71,13 @@ public class DataSetDss implements IDataSetDss
public File getLinkOrCopyOfContents(String overrideStoreRootPathOrNull, File downloadDir)
throws IllegalArgumentException, InvalidSessionException
{
- return parent.getLinkOrCopyOfContents(this, overrideStoreRootPathOrNull, downloadDir);
+ return parent.getLinkOrCopyOfContents(this, overrideStoreRootPathOrNull, downloadDir, null);
+ }
+
+ public File getLinkOrCopyOfContent(String overrideStoreRootPathOrNull, File downloadDir,
+ String pathInDataSet) throws IllegalArgumentException, InvalidSessionException
+ {
+ return parent.getLinkOrCopyOfContents(this, overrideStoreRootPathOrNull, downloadDir, pathInDataSet);
}
public AuthenticatedState getParent()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
index 7fd14d1456d..37a8ce28241 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
@@ -479,6 +479,41 @@ class AuthenticatedState extends AbstractDssComponentState
* otherwise copy the contents locally.
*/
File getLinkOrCopyOfContents(DataSetDss dataSetDss, String overrideStoreRootPathOrNull,
+ File downloadDir, String pathInDataSetOrNull) throws InvalidSessionException
+ {
+ if (pathInDataSetOrNull == null)
+ {
+ return getLinkOrCopyOfContents(dataSetDss, overrideStoreRootPathOrNull, downloadDir);
+ }
+ File link = tryLinkToContents(dataSetDss, overrideStoreRootPathOrNull);
+ if (null != link)
+ {
+ File file = new File(link, pathInDataSetOrNull);
+ if (file.exists() == false)
+ {
+ throw new IllegalArgumentException("Data set " + dataSetDss.getCode()
+ + " has no file/folder with path '" + pathInDataSetOrNull + "'.");
+ }
+ return file;
+ }
+
+ FileInfoDssDTO[] fileInfos =
+ dataSetDss.getService().listFilesForDataSet(getSessionToken(),
+ dataSetDss.getCode(), pathInDataSetOrNull, true);
+ File result = new File(new File(downloadDir, dataSetDss.getCode()), pathInDataSetOrNull);
+ File outputDir = result;
+ if (fileInfos.length == 1 && fileInfos[0].isDirectory() == false)
+ {
+ outputDir = result.getParentFile();
+ }
+ outputDir.mkdirs();
+ FileInfoDssDownloader downloader =
+ new FileInfoDssDownloader(dataSetDss, fileInfos, outputDir);
+ downloader.downloadFiles();
+ return result;
+ }
+
+ private File getLinkOrCopyOfContents(DataSetDss dataSetDss, String overrideStoreRootPathOrNull,
File downloadDir) throws InvalidSessionException
{
File link = tryLinkToContents(dataSetDss, overrideStoreRootPathOrNull);
@@ -500,7 +535,6 @@ class AuthenticatedState extends AbstractDssComponentState
return outputDir;
}
-
/**
* Create a connection to the DSS server referenced by url
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
index 5337f54edee..4e0553ff8d6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
@@ -88,13 +88,15 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
{
content = getHierarchicalContent(dataSetCode);
IHierarchicalContentNode startPathNode = getContentNode(content, startPath);
-
- IHierarchicalContentNode listingRootNode =
- (startPathNode.isDirectory()) ? startPathNode : content.getNode(startPathNode
- .getParentRelativePath());
-
ArrayList<FileInfoDssDTO> list = new ArrayList<FileInfoDssDTO>();
- appendFileInfosForFile(listingRootNode, list, isRecursive);
+ if (startPathNode.isDirectory())
+ {
+ appendFileInfosForFile(startPathNode, list, isRecursive);
+ } else
+ {
+ list.add(new FileInfoDssDTO(startPathNode.getRelativePath(), startPathNode
+ .getName(), false, startPathNode.getFileLength()));
+ }
FileInfoDssDTO[] fileInfos = new FileInfoDssDTO[list.size()];
return list.toArray(fileInfos);
} catch (IOException ex)
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
index 3c1cf8167b2..e596c75ee46 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
@@ -90,7 +90,7 @@ public class DssServiceRpcGenericTest extends AssertJUnit
}
@Test
- public void testFilesForData()
+ public void testListSingleFileForData()
{
final String dataSetCode = "ds-1";
final String path = "abc/de";
@@ -100,61 +100,102 @@ public class DssServiceRpcGenericTest extends AssertJUnit
context.checking(new Expectations()
{
{
- IHierarchicalContentNode mainNode = createNodeMock("mainNode");
one(content).getNode(path);
+ IHierarchicalContentNode mainNode = context.mock(IHierarchicalContentNode.class, "mainNode");
will(returnValue(mainNode));
-
- IHierarchicalContentNode childNode1 = createNodeMock("childNode1");
- IHierarchicalContentNode childNode1Child1 = createNodeMock("childNode1Child1");
- IHierarchicalContentNode childNode1Child2 = createNodeMock("childNode1Child2");
- IHierarchicalContentNode childNode2 = createNodeMock("childNode2");
- IHierarchicalContentNode childNode2Child1 = createNodeMock("childNode2Child1");
- IHierarchicalContentNode childNode3 = createNodeMock("childNode3");
-
- prepareDirectoryNode(mainNode, path, childNode1, childNode2, childNode3);
- // child1
- prepareDirectoryNode(childNode1, path + "/child1", childNode1Child1,
- childNode1Child2);
- prepareFileNode(childNode1Child1, path + "/child1/child1", 11);
- prepareFileNode(childNode1Child2, path + "/child1/child2", 12);
- // child2
- prepareDirectoryNode(childNode2, path + "/child2", childNode2Child1);
- prepareFileNode(childNode2Child1, path + "/child2/child1", 21);
- // child3
- prepareFileNode(childNode3, path + "/child3", 3);
- }
-
- private IHierarchicalContentNode createNodeMock(String mockName)
- {
- return context.mock(IHierarchicalContentNode.class, mockName);
- }
-
- private void prepareFileNode(IHierarchicalContentNode node,
- final String relativePath, long length)
- {
- allowing(node).isDirectory();
+
+ allowing(mainNode).getName();
+ will(returnValue("main-node"));
+
+ allowing(mainNode).isDirectory();
will(returnValue(false));
- allowing(node).getRelativePath();
- will(returnValue(relativePath));
- one(node).getFileLength();
- will(returnValue(length));
+
+ allowing(mainNode).getRelativePath();
+ will(returnValue(path));
+
+ one(mainNode).getFileLength();
+ will(returnValue(42L));
}
- private void prepareDirectoryNode(IHierarchicalContentNode node,
- final String relativePath, IHierarchicalContentNode... childNodes)
- {
- allowing(node).isDirectory();
- will(returnValue(true));
- allowing(node).getRelativePath();
- will(returnValue(relativePath));
- one(node).getChildNodes();
- will(returnValue(Arrays.asList(childNodes)));
- }
});
- FileInfoDssDTO[] dataSets =
+ FileInfoDssDTO[] files =
dssService.listFilesForDataSet(SESSION_TOKEN, dataSetCode, path, true);
+ assertEquals(path, files[0].getPathInDataSet());
+ assertEquals("main-node", files[0].getPathInListing());
+ assertEquals(42L, files[0].getFileSize());
+ assertEquals(1, files.length);
+ context.assertIsSatisfied();
+ }
+
+
+ @Test
+ public void testFilesForData()
+ {
+ final String dataSetCode = "ds-1";
+ final String path = "abc/de";
+ prepareLockDataSet(dataSetCode);
+ prepareAuthorizationCheck(dataSetCode);
+ prepareGetContent(dataSetCode);
+ context.checking(new Expectations()
+ {
+ {
+ IHierarchicalContentNode mainNode = createNodeMock("mainNode");
+ one(content).getNode(path);
+ will(returnValue(mainNode));
+
+ IHierarchicalContentNode childNode1 = createNodeMock("childNode1");
+ IHierarchicalContentNode childNode1Child1 = createNodeMock("childNode1Child1");
+ IHierarchicalContentNode childNode1Child2 = createNodeMock("childNode1Child2");
+ IHierarchicalContentNode childNode2 = createNodeMock("childNode2");
+ IHierarchicalContentNode childNode2Child1 = createNodeMock("childNode2Child1");
+ IHierarchicalContentNode childNode3 = createNodeMock("childNode3");
+
+ prepareDirectoryNode(mainNode, path, childNode1, childNode2, childNode3);
+ // child1
+ prepareDirectoryNode(childNode1, path + "/child1", childNode1Child1,
+ childNode1Child2);
+ prepareFileNode(childNode1Child1, path + "/child1/child1", 11);
+ prepareFileNode(childNode1Child2, path + "/child1/child2", 12);
+ // child2
+ prepareDirectoryNode(childNode2, path + "/child2", childNode2Child1);
+ prepareFileNode(childNode2Child1, path + "/child2/child1", 21);
+ // child3
+ prepareFileNode(childNode3, path + "/child3", 3);
+ }
+
+ private IHierarchicalContentNode createNodeMock(String mockName)
+ {
+ return context.mock(IHierarchicalContentNode.class, mockName);
+ }
+
+ private void prepareFileNode(IHierarchicalContentNode node,
+ final String relativePath, long length)
+ {
+ allowing(node).isDirectory();
+ will(returnValue(false));
+ allowing(node).getRelativePath();
+ will(returnValue(relativePath));
+ one(node).getFileLength();
+ will(returnValue(length));
+ }
+
+ private void prepareDirectoryNode(IHierarchicalContentNode node,
+ final String relativePath, IHierarchicalContentNode... childNodes)
+ {
+ allowing(node).isDirectory();
+ will(returnValue(true));
+ allowing(node).getRelativePath();
+ will(returnValue(relativePath));
+ one(node).getChildNodes();
+ will(returnValue(Arrays.asList(childNodes)));
+ }
+ });
+
+ FileInfoDssDTO[] dataSets =
+ dssService.listFilesForDataSet(SESSION_TOKEN, dataSetCode, path, true);
+
assertEquals(6, dataSets.length);
assertEquals(fileInfoString(path, "child1", -1), dataSets[0].toString());
assertEquals(fileInfoString(path, "child1/child1", 11), dataSets[1].toString());
@@ -164,7 +205,7 @@ public class DssServiceRpcGenericTest extends AssertJUnit
assertEquals(fileInfoString(path, "child3", 3), dataSets[5].toString());
context.assertIsSatisfied();
}
-
+
private static String fileInfoString(String startPath, String pathInListing, long length)
{
return String.format("FileInfoDssDTO[%s/%s,%s,%d]", startPath, pathInListing,
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index ebc52ae0d4f..ae2418811fc 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -34,6 +34,7 @@ import java.util.Set;
import java.util.TreeSet;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.generic.client.cli.Login;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
@@ -290,6 +291,7 @@ public class OpenBISScreeningML
{
throw new RuntimeException("Couldn't create a temporary directory.");
}
+ temporarySessionDir.deleteOnExit();
loadedImages = new HashMap<PlateImageReference, File>();
experiments = openbis.listExperiments();
experimentCodeToExperimentMap.clear();
@@ -695,7 +697,7 @@ public class OpenBISScreeningML
*
* <pre>
* % Load all data sets of plate P005 in space SPACE
- * dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005')
+ * dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', '.*', '')
* % Get the data set codes
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
@@ -703,7 +705,7 @@ public class OpenBISScreeningML
* </pre>
*
* @param augmentedPlateCode The augmented plate code.
- * @param datasetTypeCodePattern only datasets of the type which matche the specified pattern
+ * @param dataSetTypeCodePattern only datasets of the type which matches the specified pattern
* will be returned. To fetch all datasets specify ".*".
* @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
* the DSS' store root. If null, paths are returned in the context of the DSS' file
@@ -712,13 +714,13 @@ public class OpenBISScreeningML
* <p>
* <code>{ data set code, data set root path }</code>
*/
- public static Object[][] loadDataSets(String augmentedPlateCode, String datasetTypeCodePattern,
+ public static Object[][] loadDataSets(String augmentedPlateCode, String dataSetTypeCodePattern,
String overrideStoreRootPathOrNull)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
- List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, datasetTypeCodePattern);
+ List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, dataSetTypeCodePattern);
Object[][] result = new Object[dataSets.size()][];
try
{
@@ -743,6 +745,84 @@ public class OpenBISScreeningML
+ "' failed: " + ex, ex);
}
}
+
+ /**
+ * Loads file/folder of specified data set and specified file/folder path inside the data set.
+ * If it is possible the path points directly into the data set store. No data is copied.
+ * Otherwise the data is retrieved from the data store server.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
+ * % of a type starting with HCS_IMAGE
+ * files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
+ * % Load from the first data set (assuming at least one data set found) the third file/folder
+ * % (assuming at least three files/folders)
+ * file = OpenBISScreeningML.loadDataSetFile(files(1,1), files(1,2,3), '')
+ * </pre>
+ *
+ * @param dataSetCode The code of the data set.
+ * @param pathInDataSet Path inside the data set pointing to the file/folder which should be
+ * down loaded. Use '/' if all files are requested.
+ * @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
+ * the DSS' store root. If null, paths are returned in the context of the DSS' file
+ * system mounts.
+ * @return path to the down loaded file/folder.
+ */
+ public static Object loadDataSetFile(String dataSetCode, String pathInDataSet, String overrideStoreRootPathOrNull)
+ {
+ checkLoggedIn();
+ IDataSetDss dataSet = openbis.getDataSet(dataSetCode);
+ return dataSet.getLinkOrCopyOfContent(overrideStoreRootPathOrNull, temporarySessionDir, pathInDataSet).toString();
+ }
+
+ /**
+ * Lists all files of all data sets for specifies plate and data set type code matching
+ * specified regular expression pattern.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
+ * % of a type starting with HCS_IMAGE
+ * files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
+ * % Codes of all found data sets
+ * files(:,1)
+ * % Code of third data set (assuming at least three data sets found)
+ * files(3,1)
+ * % Files of third data set (assuming at least three data sets found)
+ * files(3,2,:)
+ * </pre>
+ *
+ * @param augmentedPlateCode The augmented plate code.
+ * @param dataSetTypeCodePattern only data sets of the type which matches the specified pattern
+ * will be returned. To fetch all data sets specify ".*".
+ * @return <code>{data set code, file/folder paths}</code>
+ */
+ public static Object[][][] listDataSetsFiles(String augmentedPlateCode, String dataSetTypeCodePattern)
+ {
+ checkLoggedIn();
+ Plate plateIdentifier = getPlate(augmentedPlateCode);
+
+ List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, dataSetTypeCodePattern);
+ Object[][][] result = new Object[dataSets.size()][][];
+ for (int i = 0; i < dataSets.size(); i++)
+ {
+ IDataSetDss dataSet = dataSets.get(i);
+ FileInfoDssDTO[] fileInfos = dataSet.listFiles("/", true);
+ String code = dataSet.getCode();
+ result[i] = new Object[2][];
+ result[i][0] = new Object[] {code};
+ result[i][1] = new Object[fileInfos.length];
+ for (int j = 0; j < fileInfos.length; j++)
+ {
+ FileInfoDssDTO fileInfo = fileInfos[j];
+ result[i][1][j] = fileInfo.getPathInDataSet();
+ }
+ }
+ return result;
+ }
/**
* Uploads specified data set for specified plate. The data set code will be returned.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 1ed3d41ecab..40e9a0c8b98 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -173,6 +173,9 @@ public interface IScreeningOpenbisServiceFacade
public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException;
+
+ public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+ EnvironmentFailureException;
/**
* Upload a new data set to the DSS for a well.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index a2934019b4e..09f410524bb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -412,6 +412,14 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
final Sample wellSample = getWellSample(wellIdentifier);
return getDataSets(wellSample, datasetTypeCodePattern);
}
+
+
+
+ public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+ EnvironmentFailureException
+ {
+ return dssComponent.getDataSet(dataSetCode);
+ }
/**
* Get proxies to the data sets owned by specified plate.
diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
index 651a5074fc2..45961ee6522 100644
--- a/screening/sourceTest/java/OpenBISScreeningMLTest.java
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.test.RecordingMatcher;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.generic.client.cli.Login;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
@@ -535,6 +536,60 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+ @Test
+ public void testListDataSetsFiles()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).getDataSets(p1, ".*");
+ will(returnValue(Arrays.asList(ds1, ds2)));
+
+ one(ds1).listFiles("/", true);
+ will(returnValue(new FileInfoDssDTO[]
+ { new FileInfoDssDTO("a", "a", true, -1),
+ new FileInfoDssDTO("a/b", "a/b", false, 42) }));
+ one(ds1).getCode();
+ will(returnValue("ds1"));
+
+ one(ds2).listFiles("/", true);
+ will(returnValue(new FileInfoDssDTO[]
+ { new FileInfoDssDTO("c", "c", false, 137) }));
+ one(ds2).getCode();
+ will(returnValue("ds2"));
+ }
+ });
+
+ Object[][][] files = OpenBISScreeningML.listDataSetsFiles(p1.getAugmentedCode(), ".*");
+
+ assertEquals("ds1", files[0][0][0]);
+ assertEquals("[a, a/b]", Arrays.asList(files[0][1]).toString());
+ assertEquals("ds2", files[1][0][0]);
+ assertEquals("[c]", Arrays.asList(files[1][1]).toString());
+ assertEquals(2, files.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadDataSetFile()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).getDataSet("ds1");
+ will(returnValue(ds1));
+
+ one(ds1).getLinkOrCopyOfContent("root", tempDir, "a/b/c");
+ will(returnValue(new File("data")));
+ }
+ });
+
+ Object file = OpenBISScreeningML.loadDataSetFile("ds1", "a/b/c", "root");
+
+ assertEquals("data", file);
+ context.assertIsSatisfied();
+ }
+
@Test
public void testLoadDataSets()
{
--
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