From 750a907b2441a572f0151cb520dccfadd3a1ad1e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 23 May 2011 18:32:25 +0000
Subject: [PATCH] LMS-2251 adapt MatLab API
SVN: 21447
---
.../dss/client/api/v1/IDataSetDss.java | 3 +-
screening/source/java/OpenBISScreeningML.java | 27 +++-
.../v1/IScreeningOpenbisServiceFacade.java | 26 +--
.../api/v1/ScreeningClientApiTester.java | 2 +-
.../api/v1/ScreeningOpenbisServiceFacade.java | 35 +++--
.../java/BiozentrumMatLabApiTest.java | 78 +++++++++
.../java/OpenBISScreeningMLTest.java | 148 ++++++++++--------
.../v1/ScreeningOpenbisServiceFacadeTest.java | 84 +++++-----
8 files changed, 263 insertions(+), 140 deletions(-)
create mode 100644 screening/sourceTest/java/BiozentrumMatLabApiTest.java
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 00fddc7d947..a6ba5dab6c3 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
@@ -75,8 +75,7 @@ public interface IDataSetDss
* the downloadDir containing the contents of the data set.
*
* @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.
+ * 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.
* @return A File containing the contents of the data set.
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index 70cc12d816a..1d249397653 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
@@ -514,7 +515,8 @@ public class OpenBISScreeningML
*
* @param augmentedPlateCode The augmented plate code.
* @return <code>{ images width, images height, number of tiles in the well,
- * number of tiles rows, number of tiles columns }</code> .
+ * number of tiles rows, number of tiles columns, number of plate rows, number of plate columns }</code>
+ * .
*/
public static Object[][] getImagesMetadata(String augmentedPlateCode)
{
@@ -527,10 +529,13 @@ public class OpenBISScreeningML
for (int i = 0; i < metaList.size(); ++i)
{
ImageDatasetMetadata meta = metaList.get(i);
+ ImageDatasetReference imageDatasetReference = imageDatasets.get(i);
+ Geometry plateGeometry = imageDatasetReference.getPlateGeometry();
result[i] =
new Object[]
{ meta.getWidth(), meta.getHeight(), meta.getNumberOfTiles(),
- meta.getTilesRows(), meta.getTilesCols() };
+ meta.getTilesRows(), meta.getTilesCols(),
+ plateGeometry.getNumberOfRows(), plateGeometry.getNumberOfColumns() };
}
return result;
}
@@ -650,7 +655,9 @@ public class OpenBISScreeningML
/**
* Loads data sets for specified plate code. For each data set the path to the root of the data
* set is returned. 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.
+ * is copied. Otherwise the data is retrieved from the data store server.<br>
+ * If the same dataset is loaded for the second time in one session it will be immediately
+ * returned from the local cache.
* <p>
* Matlab example:
*
@@ -664,16 +671,22 @@ public class OpenBISScreeningML
* </pre>
*
* @param augmentedPlateCode The augmented plate code.
+ * @param datasetTypeCodePattern only datasets of the type which matche 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
+ * system mounts.
* @return Each row contains information about one data set:
* <p>
* <code>{ data set code, data set root path }</code>
*/
- public static Object[][] loadDataSets(String augmentedPlateCode)
+ public static Object[][] loadDataSets(String augmentedPlateCode, String datasetTypeCodePattern,
+ String overrideStoreRootPathOrNull)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
- List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier);
+ List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, datasetTypeCodePattern);
Object[][] result = new Object[dataSets.size()][];
try
{
@@ -684,7 +697,9 @@ public class OpenBISScreeningML
File file = new File(dataSetsDir, code);
if (file.exists() == false)
{
- file = dataSet.getLinkOrCopyOfContents(null, dataSetsDir);
+ file =
+ dataSet.getLinkOrCopyOfContents(overrideStoreRootPathOrNull,
+ dataSetsDir);
}
result[i] = new Object[]
{ code, file.getPath() };
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 130c9cc4e28..1ed3d41ecab 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
@@ -150,12 +150,12 @@ public interface IScreeningOpenbisServiceFacade
* For the given <var>plateIdentifier</var> find all wells that are connected to it.
*/
public List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier);
-
+
/**
* Returns all properties of specified well as a map.
*/
public Map<String, String> getWellProperties(WellIdentifier wellIdentifier);
-
+
/**
* Updates properties of specified well.
*/
@@ -164,12 +164,15 @@ public interface IScreeningOpenbisServiceFacade
/**
* Get proxies to the data sets owned by specified well.
*
+ * @param datasetTypeCodePattern only datasets of the type which matche the specified pattern
+ * will be returned. To fetch all datasets specify ".*".
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier)
- throws IllegalStateException, EnvironmentFailureException;
+ public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
+ String datasetTypeCodePattern) throws IllegalStateException,
+ EnvironmentFailureException;
/**
* Upload a new data set to the DSS for a well.
@@ -189,15 +192,18 @@ public interface IScreeningOpenbisServiceFacade
EnvironmentFailureException, IOException;
/**
- * Get proxies to the data sets owned by specified plate.
+ * Get proxies to the data sets of the specified type owned by specified plate.
*
+ * @param datasetTypeCodePattern only datasets of the type which matche the specified pattern
+ * will be returned. To fetch all datasets specify ".*".
* @throws IllegalStateException Thrown if the user has not yet been authenticated.
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier)
- throws IllegalStateException, EnvironmentFailureException;
-
+ public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
+ String datasetTypeCodePattern) throws IllegalStateException,
+ EnvironmentFailureException;
+
/**
* Upload a new data set to the DSS for a plate.
*
@@ -214,7 +220,7 @@ public interface IScreeningOpenbisServiceFacade
public IDataSetDss putDataSet(PlateIdentifier plateIdentifier, File dataSetFile,
NewDataSetMetadataDTO dataSetMetadataOrNull) throws IllegalStateException,
EnvironmentFailureException, IOException;
-
+
/**
* Converts the given list of {@link PlateWellReferenceWithDatasets} into a list of
* {@link FeatureVectorDatasetWellReference}.
@@ -566,5 +572,5 @@ public interface IScreeningOpenbisServiceFacade
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull);
-
+
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
index a31a35940d0..a04792d5873 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
@@ -246,7 +246,7 @@ public class ScreeningClientApiTester
}
for (WellIdentifier wellIdentifier : listPlateWells)
{
- List<IDataSetDss> dataSets = facade.getDataSets(wellIdentifier);
+ List<IDataSetDss> dataSets = facade.getDataSets(wellIdentifier, ".*");
if (dataSets.isEmpty() == false)
{
JOptionPane.showMessageDialog(TesterFrame.this, "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 069dcc63bca..e818d7c3666 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
@@ -93,7 +93,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
private final IScreeningApiServer openbisScreeningServer;
private final IGeneralInformationService generalInformationService;
-
+
private final IGeneralInformationChangingService generalInformationChangingService;
private final IDssComponent dssComponent;
@@ -190,7 +190,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
IGeneralInformationChangingService.class, serverUrl);
return service;
}
-
+
ScreeningOpenbisServiceFacade(String sessionToken, IScreeningApiServer screeningServer,
int minorVersion, final IDssServiceFactory dssServiceFactory,
IDssComponent dssComponent, IGeneralInformationService generalInformationService,
@@ -383,7 +383,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
checkASMinimalMinorVersion("listPlateWells", PlateIdentifier.class);
return openbisScreeningServer.listPlateWells(sessionToken, plateIdentifier);
}
-
+
public Map<String, String> getWellProperties(WellIdentifier wellIdentifier)
{
Sample wellSample = openbisScreeningServer.getWellSample(sessionToken, wellIdentifier);
@@ -394,7 +394,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
public void updateWellProperties(WellIdentifier wellIdentifier, Map<String, String> properties)
{
Sample wellSample = openbisScreeningServer.getWellSample(sessionToken, wellIdentifier);
- generalInformationChangingService.updateSampleProperties(sessionToken, wellSample.getId(), properties);
+ generalInformationChangingService.updateSampleProperties(sessionToken, wellSample.getId(),
+ properties);
}
/**
@@ -404,11 +405,12 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier)
- throws IllegalStateException, EnvironmentFailureException
+ public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
+ String datasetTypeCodePattern) throws IllegalStateException,
+ EnvironmentFailureException
{
final Sample wellSample = getWellSample(wellIdentifier);
- return getDataSets(wellSample);
+ return getDataSets(wellSample, datasetTypeCodePattern);
}
/**
@@ -418,22 +420,26 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
* @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
* the server.
*/
- public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier)
- throws IllegalStateException, EnvironmentFailureException
+ public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
+ String datasetTypeCodePattern) throws IllegalStateException,
+ EnvironmentFailureException
{
checkASMinimalMinorVersion("getPlateSample", PlateIdentifier.class);
Sample sample = openbisScreeningServer.getPlateSample(sessionToken, plateIdentifier);
- return getDataSets(sample);
+ return getDataSets(sample, datasetTypeCodePattern);
}
- private List<IDataSetDss> getDataSets(final Sample sample)
+ private List<IDataSetDss> getDataSets(final Sample sample, final String datasetTypeCodePattern)
{
final List<DataSet> dataSets =
generalInformationService.listDataSetsForSample(sessionToken, sample, true);
final List<IDataSetDss> result = new ArrayList<IDataSetDss>();
for (DataSet dataSet : dataSets)
{
- result.add(dssComponent.getDataSet(dataSet.getCode()));
+ if (dataSet.getDataSetTypeCode().matches(datasetTypeCodePattern))
+ {
+ result.add(dssComponent.getDataSet(dataSet.getCode()));
+ }
}
return result;
}
@@ -490,7 +496,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
NewDataSetMetadataDTO dataSetMetadataOrNull, File dataSetFile) throws IOException
{
final NewDataSetMetadataDTO dataSetMetadata =
- (dataSetMetadataOrNull == null) ? new NewDataSetMetadataDTO() : dataSetMetadataOrNull;
+ (dataSetMetadataOrNull == null) ? new NewDataSetMetadataDTO()
+ : dataSetMetadataOrNull;
final DataSetOwner dataSetOwner =
new DataSetOwner(DataSetOwnerType.SAMPLE, sample.getIdentifier());
final String dataSetFolderNameOrNull = null;
@@ -499,7 +506,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
new NewDataSetDTO(dataSetMetadata, dataSetOwner, dataSetFolderNameOrNull, fileInfos);
return dssComponent.putDataSet(newDataSet, dataSetFile);
}
-
+
private List<FileInfoDssDTO> getFileInfosForPath(File file) throws IOException
{
ArrayList<FileInfoDssDTO> fileInfos = new ArrayList<FileInfoDssDTO>();
diff --git a/screening/sourceTest/java/BiozentrumMatLabApiTest.java b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
new file mode 100644
index 00000000000..14e109d8d25
--- /dev/null
+++ b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright 2011 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.
+ */
+
+/**
+ * Integration tests of MatLab API on Biozentrum server.
+ *
+ * @author Tomasz Pylak
+ */
+public class BiozentrumMatLabApiTest
+{
+ public static void main(String[] args)
+ {
+ if (args.length == 0)
+ {
+ System.err
+ .println("Specify the password and optionally the plate identifier, mount point and dataset type pattern!");
+ }
+ String passwd = args[0];
+ String chosenPlate = "/TEST/KB01";
+ String mountPoint = null;
+ String datasetTypePattern = "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT";
+ if (args.length > 1)
+ {
+ chosenPlate = args[1];
+ }
+ if (args.length > 2)
+ {
+ mountPoint = args[2];
+ }
+
+ OpenBISScreeningML.login("admin", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
+
+ Object[][] meta = OpenBISScreeningML.getImagesMetadata(chosenPlate);
+ System.out.println(String.format("Number of tiles: %s. Plate geometry %sx%s", meta[1][3],
+ meta[1][6], meta[1][7]));
+
+ // fetch 3ed tile of well (1,1). The second call to fetch this image will return it from the
+ // local cache.
+ // The last optional parameter can specify a list of channels to load (otherwise all
+ // channels are loaded).
+ Object[][][] images = OpenBISScreeningML.loadImages(chosenPlate, 1, 1, 3);
+ System.out.println("Image path: " + images[1][1]);
+
+ // properties of well (2,4)
+ Object[][] props = OpenBISScreeningML.getWellProperties(chosenPlate, 2, 4);
+ for (int i = 0; i < props.length; i++)
+ {
+ System.out.println(String.format("Property %s = %s ", props[i][0], props[i][1]));
+ }
+
+ // save description of the well (2,4)
+ props = new Object[][]
+ {
+ { "DESCRIPTION", "hello example" } };
+ OpenBISScreeningML.updateWellProperties(chosenPlate, 2, 4, props);
+
+ // Loads dataset with classification results.
+ // OpenBIS store diretcory is mounted locally in "/mount/openbis/store", so no data are
+ // copied and just a path to the appropriate location
+ // is returned.
+ Object[][] datasets =
+ OpenBISScreeningML.loadDataSets(chosenPlate, datasetTypePattern, mountPoint);
+ System.out.println("Path to the first downloaded dataset: " + datasets[0][1]);
+ }
+}
diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
index e8337604633..28d212ad45a 100644
--- a/screening/sourceTest/java/OpenBISScreeningMLTest.java
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -14,8 +14,6 @@
* limitations under the License.
*/
-
-
import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
@@ -55,8 +53,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifie
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
@@ -70,7 +66,8 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
}
};
- private Mockery context;
+ private Mockery context;
+
private IScreeningOpenbisServiceFacade openbis;
private File tempDir;
@@ -80,11 +77,11 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
private ExperimentIdentifier eId2;
private IDataSetDss ds1;
-
+
private IDataSetDss ds2;
private IScreeningOpenbisServiceFacadeFactory facadeFactory;
-
+
@BeforeMethod
public void beforeMethod()
{
@@ -103,10 +100,10 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
one(facadeFactory).tryToCreate("user", "password", "url");
will(returnValue(openbis));
-
+
one(openbis).listExperiments();
will(returnValue(Arrays.asList(eId1, eId2)));
-
+
one(openbis).listPlates();
Plate p1 = new Plate("PLATE-1", "S", "s-1", eId1);
Plate p2 = new Plate("PLATE-2", "S", "s-2", eId2);
@@ -117,13 +114,13 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
OpenBISScreeningML.login("user", "password", "url");
tempDir = OpenBISScreeningML.tempDir.listFiles(FILTER_TEMP_DIR)[0];
}
-
+
@AfterMethod
public void afterMethod()
{
context.assertIsSatisfied();
}
-
+
@Test
public void testLogout()
{
@@ -137,13 +134,13 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
a.mkdirs();
FileUtilities.writeToFile(new File(a, "1.txt"), "one");
FileUtilities.writeToFile(new File(tempDir, "2.txt"), "two");
-
+
OpenBISScreeningML.logout();
-
+
assertEquals(false, tempDir.exists());
context.assertIsSatisfied();
}
-
+
@Test
public void testCheckLoggedInFailsBecauseOfMissingSessionTokenFile()
{
@@ -154,7 +151,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
}
});
OpenBISScreeningML.logout();
-
+
try
{
OpenBISScreeningML.listExperiments();
@@ -163,10 +160,10 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
assertEquals("Not logged in.", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testCheckLoggedInFailsBecauseOfInvalidSession()
{
@@ -182,7 +179,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Login.OPENBIS_USER_FILE.getParentFile().mkdirs();
FileUtilities.writeToFile(Login.OPENBIS_TOKEN_FILE, "session-token-1");
FileUtilities.writeToFile(Login.OPENBIS_SERVER_URL_FILE, "url");
-
+
try
{
OpenBISScreeningML.listExperiments();
@@ -191,10 +188,10 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
assertEquals("Login failed.", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testCheckLoggedInSucceed()
{
@@ -202,10 +199,10 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
{
exactly(2).of(openbis).logout();
-
+
one(facadeFactory).tryToCreate("session-token-1", "url");
will(returnValue(openbis));
-
+
one(openbis).listExperiments();
one(openbis).listPlates();
}
@@ -214,14 +211,14 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Login.OPENBIS_USER_FILE.getParentFile().mkdirs();
FileUtilities.writeToFile(Login.OPENBIS_TOKEN_FILE, "session-token-1");
FileUtilities.writeToFile(Login.OPENBIS_SERVER_URL_FILE, "url");
-
+
OpenBISScreeningML.listExperiments();
OpenBISScreeningML.logout();
-
+
assertEquals(false, Login.OPENBIS_TOKEN_FILE.exists());
context.assertIsSatisfied();
}
-
+
@Test
public void testListExperiments()
{
@@ -241,12 +238,12 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals(2, experiments.length);
context.assertIsSatisfied();
}
-
+
@Test
public void testListPlates()
{
Object[][] plates = OpenBISScreeningML.listPlates();
-
+
sort(plates);
assertEquals("/S/PLATE-1", plates[0][0]);
assertEquals("s-1", plates[0][1]);
@@ -269,7 +266,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals(2, plates.length);
context.assertIsSatisfied();
}
-
+
@Test
public void testListPlatesByExperiment()
{
@@ -281,9 +278,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
assertEquals("No experiment with that code found.", ex.getMessage());
}
-
+
Object[][] plates = OpenBISScreeningML.listPlates("/S/P/E1");
-
+
sort(plates);
assertEquals("/S/PLATE-1", plates[0][0]);
assertEquals("s-1", plates[0][1]);
@@ -297,7 +294,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals(1, plates.length);
context.assertIsSatisfied();
}
-
+
@Test
public void testGetWellProperties()
{
@@ -310,7 +307,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
WellIdentifier w2 = new WellIdentifier(plate1, new WellPosition(1, 2), "w2");
WellIdentifier w3 = new WellIdentifier(plate1, new WellPosition(2, 1), "w3");
will(returnValue(Arrays.asList(w1, w2, w3)));
-
+
one(openbis).getWellProperties(w2);
Map<String, String> properties = new LinkedHashMap<String, String>();
properties.put("answer", "42");
@@ -318,9 +315,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
will(returnValue(properties));
}
});
-
+
Object[][] wellProperties = OpenBISScreeningML.getWellProperties("/S/PLATE-1", 1, 2);
-
+
assertEquals("answer", wellProperties[0][0]);
assertEquals("42", wellProperties[0][1]);
assertEquals("name", wellProperties[1][0]);
@@ -328,7 +325,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals(2, wellProperties.length);
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateWellProperties()
{
@@ -348,38 +345,46 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
one(openbis).updateWellProperties(w2, properties);
}
});
-
- OpenBISScreeningML.updateWellProperties("/S/PLATE-1", 1, 2, new Object[][] {{"A", "42"}, {"B", "43"}});
-
+
+ OpenBISScreeningML.updateWellProperties("/S/PLATE-1", 1, 2, new Object[][]
+ {
+ { "A", "42" },
+ { "B", "43" } });
+
context.assertIsSatisfied();
}
-
+
@Test
public void testLoadDataSets()
{
- final File dataSetFolder = new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ final File dataSetFolder =
+ new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
File ds2Folder = new File(dataSetFolder, "ds-2");
ds2Folder.mkdirs();
+ final String datasetTypePattern = "blablaCode";
+ final String mountPoint = "/mount/openbis/store";
context.checking(new Expectations()
{
{
- one(openbis).getDataSets(new Plate("PLATE-1", "S", "s-1", eId1));
+ one(openbis).getDataSets(new Plate("PLATE-1", "S", "s-1", eId1),
+ datasetTypePattern);
will(returnValue(Arrays.asList(ds1, ds2)));
-
+
one(ds1).getCode();
will(returnValue("ds-1"));
-
- one(ds1).getLinkOrCopyOfContents(null, dataSetFolder);
+
+ one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
will(returnValue(ds1Folder));
-
+
one(ds2).getCode();
will(returnValue("ds-2"));
}
});
-
- Object[][] result = OpenBISScreeningML.loadDataSets("/S/PLATE-1");
-
+
+ Object[][] result =
+ OpenBISScreeningML.loadDataSets("/S/PLATE-1", datasetTypePattern, mountPoint);
+
assertEquals("ds-1", result[0][0]);
assertEquals(ds1Folder.getPath(), result[0][1]);
assertEquals("ds-2", result[1][0]);
@@ -387,14 +392,16 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals(2, result.length);
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateDataSet()
{
- final File dataSetFolder = new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ final File dataSetFolder =
+ new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
ds1Folder.mkdirs();
- final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher = new RecordingMatcher<NewDataSetMetadataDTO>();
+ final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher =
+ new RecordingMatcher<NewDataSetMetadataDTO>();
context.checking(new Expectations()
{
{
@@ -410,29 +417,32 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
-
+
one(ds1).getCode();
will(returnValue("DS-1"));
}
});
-
+
Object code =
OpenBISScreeningML.uploadDataSet("/S/PLATE-1", ds1Folder.getPath(), "my-type",
- new Object[][] {{"A", "42"}, {"B", "43"}});
-
+ new Object[][]
+ {
+ { "A", "42" },
+ { "B", "43" } });
+
assertEquals("DS-1", code);
assertEquals("my-type", metaDataMatcher.recordedObject().tryDataSetType());
assertEquals("{A=42, B=43}", metaDataMatcher.recordedObject().getProperties().toString());
context.assertIsSatisfied();
}
-
+
@Test
public void testLoadImages()
{
final RecordingMatcher<List<PlateImageReference>> imgRefsMatcher1 =
new RecordingMatcher<List<PlateImageReference>>();
final RecordingMatcher<List<PlateImageReference>> imgRefsMatcher2 =
- new RecordingMatcher<List<PlateImageReference>>();
+ new RecordingMatcher<List<PlateImageReference>>();
final Sequence sequence = context.sequence("load");
context.checking(new Expectations()
{
@@ -531,8 +541,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
}
}
});
-
- Object[][][] result1 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2, 1, new String[] {"G"});
+
+ Object[][][] result1 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2, 1, new String[]
+ { "G" });
List<PlateImageReference> imgRefs1 = imgRefsMatcher1.recordedObject();
for (PlateImageReference plateImageReference : imgRefs1)
{
@@ -552,7 +563,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
"[G, 1, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
Arrays.asList(result1[1][0]).toString());
assertEquals(1, result1[1].length);
-
+
Object[][][] result2 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2);
List<PlateImageReference> imgRefs2 = imgRefsMatcher2.recordedObject();
for (PlateImageReference plateImageReference : imgRefs2)
@@ -568,7 +579,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals("G", imgRefs2.get(2).getChannel());
assertEquals(0, imgRefs2.get(2).getTile());
assertEquals(3, imgRefs2.size());
-
+
assertEquals(2, result2.length);
assertEquals("/images/img_PLATE-1_ds1_row1_col2_R_tile0.tiff", getImagePath(result2, 0));
assertEquals("Image for [dataset ds1, well [1, 2], channel R, tile 0] (2)", FileUtilities
@@ -601,19 +612,18 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
private String getImagePath(Object[][][] result, int i)
{
- return result[0][i][0].toString()
- .substring(tempDir.getPath().length());
+ return result[0][i][0].toString().substring(tempDir.getPath().length());
}
-
+
private void sort(Object[][] entities)
{
Arrays.sort(entities, new Comparator<Object[]>()
- {
- public int compare(Object[] o1, Object[] o2)
{
- return o1[0].toString().compareTo(o2[0].toString());
- }
- });
+ public int compare(Object[] o1, Object[] o2)
+ {
+ return o1[0].toString().compareTo(o2[0].toString());
+ }
+ });
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index dfb6d44e181..614686926e0 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -81,6 +81,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
@Friend(toClasses = DssServiceRpcScreeningHolder.class)
public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCase
{
+ private static final String MY_DATA_SET_TYPE = "my-data-set";
+
private static final class MockPlateImageHandler implements IPlateImageHandler
{
private final StringBuilder recorder = new StringBuilder();
@@ -465,7 +467,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
context.assertIsSatisfied();
}
-
+
@Test
public void testGetWellProperties()
{
@@ -479,13 +481,13 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
will(returnValue(new Sample(initializer)));
}
});
-
+
Map<String, String> wellProperties = facade.getWellProperties(wellIdentifier);
-
+
assertEquals("{a=alpha}", wellProperties.toString());
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateWellProperties()
{
@@ -496,16 +498,17 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
{
one(screeningService).getWellSample(SESSION_TOKEN, wellIdentifier);
will(returnValue(new Sample(sampleInitializer())));
-
- one(generalInformationChangingService).updateSampleProperties(SESSION_TOKEN, 42L, properties);
+
+ one(generalInformationChangingService).updateSampleProperties(SESSION_TOKEN,
+ 42L, properties);
}
});
facade.updateWellProperties(wellIdentifier, properties);
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testGetDataSetsOfAWell()
{
@@ -516,23 +519,25 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
one(screeningService).getWellSample(SESSION_TOKEN, wellIdentifier);
Sample sample = new Sample(sampleInitializer());
will(returnValue(sample));
-
- one(generalInformationService).listDataSetsForSample(SESSION_TOKEN, sample, true);
+
+ one(generalInformationService).listDataSetsForSample(SESSION_TOKEN, sample,
+ true);
DataSetInitializer initializer1 = dataSetInitializer(DATA_SET1);
will(returnValue(Arrays.asList(new DataSet(initializer1))));
-
+
one(dssComponent).getDataSet(DATA_SET1);
will(returnValue(ds1Proxy));
}
});
-
- List<IDataSetDss> dataSets = facade.getDataSets(wellIdentifier);
-
+
+ List<IDataSetDss> dataSets =
+ facade.getDataSets(wellIdentifier, ".*" + MY_DATA_SET_TYPE + ".*");
+
assertSame(ds1Proxy, dataSets.get(0));
assertEquals(1, dataSets.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testGetDataSetsOfAPlate()
{
@@ -554,13 +559,13 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
}
});
- List<IDataSetDss> dataSets = facade.getDataSets(plateIdentifier);
-
+ List<IDataSetDss> dataSets = facade.getDataSets(plateIdentifier, MY_DATA_SET_TYPE);
+
assertSame(ds1Proxy, dataSets.get(0));
assertEquals(1, dataSets.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testPutDataSetForWell() throws IOException
{
@@ -571,14 +576,15 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
File dir = new File(dataSetRoot, "dir");
dir.mkdir();
FileUtilities.writeToFile(new File(dir, "hello.txt"), "hello world");
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
+ final RecordingMatcher<NewDataSetDTO> dataSetMatcher =
+ new RecordingMatcher<NewDataSetDTO>();
context.checking(new Expectations()
{
{
one(screeningService).getWellSample(SESSION_TOKEN, wellIdentifier);
Sample sample = new Sample(sampleInitializer());
will(returnValue(sample));
-
+
one(dssComponent).putDataSet(with(dataSetMatcher), with(dataSetRoot));
will(returnValue(ds1Proxy));
}
@@ -588,14 +594,15 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
HashMap<String, String> props = new HashMap<String, String>();
props.put("a", "b");
metaData.setProperties(props);
-
+
IDataSetDss dataSet = facade.putDataSet(wellIdentifier, dataSetRoot, metaData);
assertSame(ds1Proxy, dataSet);
assertEquals("MY-TYPE", dataSetMatcher.recordedObject().tryDataSetType());
assertEquals(NewDataSetDTO.DEFAULT_DATA_SET_FOLDER_NAME, dataSetMatcher.recordedObject()
.getDataSetFolderName());
- assertEquals(DataSetOwnerType.SAMPLE, dataSetMatcher.recordedObject().getDataSetOwner().getType());
+ assertEquals(DataSetOwnerType.SAMPLE, dataSetMatcher.recordedObject().getDataSetOwner()
+ .getType());
assertEquals("/S/abc", dataSetMatcher.recordedObject().getDataSetOwner().getIdentifier());
assertEquals("{a=b}", dataSetMatcher.recordedObject().getProperties().toString());
List<FileInfoDssDTO> fileInfos = dataSetMatcher.recordedObject().getFileInfos();
@@ -609,7 +616,6 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
context.assertIsSatisfied();
}
-
@Test
public void testPutDataSetForPlate() throws IOException
{
@@ -620,31 +626,33 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
File dir = new File(dataSetRoot, "dir");
dir.mkdir();
FileUtilities.writeToFile(new File(dir, "hello.txt"), "hello world");
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
+ final RecordingMatcher<NewDataSetDTO> dataSetMatcher =
+ new RecordingMatcher<NewDataSetDTO>();
context.checking(new Expectations()
- {
{
- one(screeningService).getPlateSample(SESSION_TOKEN, plateIdentifier);
- Sample sample = new Sample(sampleInitializer());
- will(returnValue(sample));
-
- one(dssComponent).putDataSet(with(dataSetMatcher), with(dataSetRoot));
- will(returnValue(ds1Proxy));
- }
- });
+ {
+ one(screeningService).getPlateSample(SESSION_TOKEN, plateIdentifier);
+ Sample sample = new Sample(sampleInitializer());
+ will(returnValue(sample));
+
+ one(dssComponent).putDataSet(with(dataSetMatcher), with(dataSetRoot));
+ will(returnValue(ds1Proxy));
+ }
+ });
NewDataSetMetadataDTO metaData = new NewDataSetMetadataDTO();
metaData.setDataSetTypeOrNull("my-type");
HashMap<String, String> props = new HashMap<String, String>();
props.put("a", "b");
metaData.setProperties(props);
-
+
IDataSetDss dataSet = facade.putDataSet(plateIdentifier, dataSetRoot, metaData);
-
+
assertSame(ds1Proxy, dataSet);
assertEquals("MY-TYPE", dataSetMatcher.recordedObject().tryDataSetType());
assertEquals(NewDataSetDTO.DEFAULT_DATA_SET_FOLDER_NAME, dataSetMatcher.recordedObject()
.getDataSetFolderName());
- assertEquals(DataSetOwnerType.SAMPLE, dataSetMatcher.recordedObject().getDataSetOwner().getType());
+ assertEquals(DataSetOwnerType.SAMPLE, dataSetMatcher.recordedObject().getDataSetOwner()
+ .getType());
assertEquals("/S/abc", dataSetMatcher.recordedObject().getDataSetOwner().getIdentifier());
assertEquals("{a=b}", dataSetMatcher.recordedObject().getProperties().toString());
List<FileInfoDssDTO> fileInfos = dataSetMatcher.recordedObject().getFileInfos();
@@ -657,7 +665,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
assertEquals("[/dir, /dir/hello.txt, /readme]", paths.toString());
context.assertIsSatisfied();
}
-
+
private SampleInitializer sampleInitializer()
{
SampleInitializer initializer = new SampleInitializer();
@@ -673,7 +681,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
private DataSetInitializer dataSetInitializer(String code)
{
DataSetInitializer initializer = new DataSetInitializer();
- initializer.setDataSetTypeCode("my-data-set");
+ initializer.setDataSetTypeCode(MY_DATA_SET_TYPE);
initializer.setExperimentIdentifier("/S/P/E");
initializer.setCode(code);
return initializer;
--
GitLab