From 2d0ff9dde427acad8139667599fb86dc77caea4b Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 27 Jul 2011 13:35:08 +0000
Subject: [PATCH] [LMS-2407] additional methods exposed to Matlab. Data set
properties are now supplied by the loadDataSet***() methods.
SVN: 22269
---
screening/source/java/OpenBISScreeningML.java | 142 +++++++++++++--
.../v1/IScreeningOpenbisServiceFacade.java | 13 ++
.../api/v1/ScreeningOpenbisServiceFacade.java | 30 ++++
.../java/OpenBISScreeningMLTest.java | 169 ++++++++++++++----
4 files changed, 306 insertions(+), 48 deletions(-)
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index 350fdc3dd7c..a787546f3f4 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -33,6 +33,7 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
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;
@@ -462,6 +463,37 @@ public class OpenBISScreeningML
return listPlates(experimentPlates);
}
+ /**
+ * Lists the plates of <var>experiment</var> and analysis procedure. Each returned plate has at
+ * least one data set with the specified analysis procedure.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % Get all plates having data sets with analysis procedure 'PROC' in the experiment MYEXP in project PROJ of space SPACE
+ * plates = OpenBISScreeningML.listPlates('/SPACE/PROJ/MYEXP', 'PROC');
+ * % Get all information about plate 2
+ * plate2 = plates(2,:)
+ * % Get the augmented plate codes for all plates
+ * acodes = plates(:,1)
+ * </pre>
+ *
+ * @param experiment The augmented code of the experiment to list the plates for
+ * @param analysisProcedure The analysis procedure
+ * @return Each row contains information about one plate:
+ * <p>
+ * <code>{ plate augmented code, plate perm id, plate space code, plate code,
+ * experiment augmented code, experiment perm id, experiment space code,
+ * experiment project code, experiment code }</code>
+ */
+ public static Object[][] listPlates(String experiment, String analysisProcedure)
+ {
+ checkLoggedIn();
+ ExperimentIdentifier experimentIdentifier = getExperimentIdentifierOrFail(experiment);
+ List<Plate> resultPlates = openbis.listPlates(experimentIdentifier, analysisProcedure);
+ return listPlates(resultPlates);
+ }
+
private static Object[][] listPlates(final List<Plate> list)
{
final Object[][] result = new Object[list.size()][9];
@@ -481,6 +513,44 @@ public class OpenBISScreeningML
return result;
}
+ /**
+ * Returns an alphabetically sorted list of analysis procedure codes of all data sets of a
+ * specified experiment.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % Get the analysis procedures for experiment MYEXP in project PROJ of space SPACE
+ * analysisProcedures = OpenBISScreeningML.listAnalysisProcedures('/SPACE/PROJ/MYEXP');
+ * % How many analysis procedures do we have?
+ * length(analysisProcedures)
+ * % Get all the analysis procedure codes
+ * acodes = analysisProcedures(:,1)
+ * </pre>
+ *
+ * @param experiment The augmented code of the experiment to list analysis procedures for
+ * @return Each row contains information about one analysis procedure:
+ * <p>
+ * <code>{ analysis procedure code }</code>
+ */
+ public static Object[][] listAnalysisProcedures(String experiment)
+ {
+ checkLoggedIn();
+ ExperimentIdentifier experimentIdentifier = getExperimentIdentifierOrFail(experiment);
+ List<String> proceduresList = openbis.listAnalysisProcedures(experimentIdentifier);
+ return listAnalysisProcedures(proceduresList);
+ }
+
+ private static Object[][] listAnalysisProcedures(final List<String> list)
+ {
+ final Object[][] result = new Object[list.size()][1];
+ for (int i = 0; i < list.size(); ++i)
+ {
+ result[i][0] = list.get(i);
+ }
+ return result;
+ }
+
/**
* Returns the properties of specified well for specified plate.
* <p>
@@ -506,16 +576,8 @@ public class OpenBISScreeningML
checkLoggedIn();
WellPosition wellPosition = new WellPosition(row, column);
WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
- List<Map.Entry<String, String>> list =
- new ArrayList<Map.Entry<String, String>>(openbis.getWellProperties(wellIdentifier)
- .entrySet());
- Object[][] result = new Object[list.size()][2];
- for (int i = 0; i < list.size(); i++)
- {
- result[i] = new Object[]
- { list.get(i).getKey(), list.get(i).getValue() };
- }
- return result;
+ Map<String, String> wellProperties = openbis.getWellProperties(wellIdentifier);
+ return listProperties(wellProperties);
}
/**
@@ -696,7 +758,7 @@ public class OpenBISScreeningML
}
return result;
}
-
+
/**
* 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
@@ -713,6 +775,12 @@ public class OpenBISScreeningML
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
* dsginfo(1,2)
+ * % Get the properties for the first data set
+ * props = dsginfo(1,3)
+ * % Get property key of first property
+ * props(1,1)
+ * % Get property value of first property
+ * props(1,2)
* </pre>
*
* @param augmentedPlateCode The augmented plate code.
@@ -723,7 +791,7 @@ public class OpenBISScreeningML
* system mounts.
* @return Each row contains information about one data set:
* <p>
- * <code>{ data set code, data set root path }</code>
+ * <code>{ data set code, data set root path, { {key1, value1}, {key2, value2} ...} }</code>
*/
public static Object[][] loadDataSets(String augmentedPlateCode, String dataSetTypeCodePattern,
String overrideStoreRootPathOrNull)
@@ -749,6 +817,12 @@ public class OpenBISScreeningML
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
* dsginfo(1,2)
+ * % Get the properties for the first data set
+ * props = dsginfo(1,3)
+ * % Get property key of first property
+ * props(1,1)
+ * % Get property value of first property
+ * props(1,2)
* </pre>
*
* @param augmentedPlateCode The augmented plate code.
@@ -761,8 +835,8 @@ public class OpenBISScreeningML
* @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.
- * <p>
- * <code>{ data set code, data set root path }</code>
+ * <p>
+ * <code>{ data set code, data set root path, { {key1, value1}, {key2, value2} ...} }</code>
*/
public static Object[][] loadDataSets(String augmentedPlateCode,
final String dataSetTypeCodePattern, final Object[][] properties,
@@ -770,8 +844,9 @@ public class OpenBISScreeningML
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
- List<IDataSetDss> dataSets =
- openbis.getDataSets(plateIdentifier, new AndDataSetFilter(new TypeBasedDataSetFilter(
+ List<DataSet> dataSets =
+ openbis.getFullDataSets(plateIdentifier, new AndDataSetFilter(
+ new TypeBasedDataSetFilter(
dataSetTypeCodePattern), new PropertiesBasedDataSetFilter(
createMap(properties))));
Object[][] result = new Object[dataSets.size()][];
@@ -779,7 +854,7 @@ public class OpenBISScreeningML
{
for (int i = 0; i < dataSets.size(); i++)
{
- IDataSetDss dataSet = dataSets.get(i);
+ DataSet dataSet = dataSets.get(i);
String code = dataSet.getCode();
File file = new File(dataSetsDir, code);
if (file.exists() == false)
@@ -788,8 +863,9 @@ public class OpenBISScreeningML
dataSet.getLinkOrCopyOfContents(overrideStoreRootPathOrNull,
dataSetsDir);
}
+ Object[][] dataSetProperties = listProperties(dataSet.getProperties());
result[i] = new Object[]
- { code, file.getPath() };
+ { code, file.getPath(), dataSetProperties };
}
return result;
} catch (Exception ex)
@@ -1870,6 +1946,24 @@ public class OpenBISScreeningML
return result;
}
+ private static Object[][] listProperties(Map<String, String> properties)
+ {
+ if (properties == null || properties.isEmpty())
+ {
+ return new Object[0][];
+ }
+
+ List<Map.Entry<String, String>> list =
+ new ArrayList<Map.Entry<String, String>>(properties.entrySet());
+ Object[][] result = new Object[list.size()][2];
+ for (int i = 0; i < list.size(); i++)
+ {
+ result[i] = new Object[]
+ { list.get(i).getKey(), list.get(i).getValue() };
+ }
+ return result;
+ }
+
private static Plate getPlate(String augmentedPlateCode)
{
Plate plateIdentifier = plateCodeToPlateMap.get(augmentedPlateCode);
@@ -1881,6 +1975,17 @@ public class OpenBISScreeningML
return plateIdentifier;
}
+ private static ExperimentIdentifier getExperimentIdentifierOrFail(String experiment)
+ {
+ ExperimentIdentifier experimentIdentifier = experimentCodeToExperimentMap.get(experiment);
+ if (experimentIdentifier == null)
+ {
+ String errorMessage = String.format("No experiment with code '%s' found.", experiment);
+ throw new RuntimeException(errorMessage);
+ }
+ return experimentIdentifier;
+ }
+
private static String createPlateWellDescription(PlateIdentifier p, FeatureVector f)
{
return createPlateWellDescription(p, f.getWellPosition().getWellRow(), f.getWellPosition()
@@ -1957,4 +2062,5 @@ public class OpenBISScreeningML
}
}
}
+
}
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 5565eb0ba56..b029222220d 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
@@ -23,6 +23,7 @@ import java.util.Map;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
@@ -261,6 +262,18 @@ public interface IScreeningOpenbisServiceFacade
public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
IDataSetFilter dataSetFilter) throws IllegalStateException, EnvironmentFailureException;
+ /**
+ * A list of data sets owned by specified plate and passing specified filter. The data set
+ * objects provide metadata (e.g. code, properties etc. from the openBIS AS) as well as data
+ * (e.g. files from from openBIS DSS).
+ *
+ * @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<DataSet> getFullDataSets(PlateIdentifier plateIdentifier,
+ IDataSetFilter dataSetFilter) throws IllegalStateException, EnvironmentFailureException;
+
/**
* Upload a new data set to the DSS for a plate.
*
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 04c5c2f8958..6e5f803c6d0 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
@@ -558,6 +558,36 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return result;
}
+ public List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getFullDataSets(
+ PlateIdentifier plateIdentifier,
+ IDataSetFilter dataSetFilter) throws IllegalStateException, EnvironmentFailureException
+ {
+ checkASMinimalMinorVersion("getPlateSample", PlateIdentifier.class);
+ Sample sample = openbisScreeningServer.getPlateSample(sessionToken, plateIdentifier);
+ return getFullDataSets(sample, dataSetFilter);
+ }
+
+ private List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getFullDataSets(
+ final Sample sample, IDataSetFilter filter)
+ {
+ final List<DataSet> dataSets =
+ generalInformationService.listDataSetsForSample(sessionToken, sample, true);
+ final List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> result =
+ new ArrayList<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet>();
+ for (DataSet dataSet : dataSets)
+ {
+ if (filter.pass(dataSet))
+ {
+ ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet fullDataset =
+ new ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet(
+ openbisServiceFacade, dssComponent, dataSet, null);
+
+ result.add(fullDataset);
+ }
+ }
+ return result;
+ }
+
/**
* Upload a new data set to the DSS for a well.
*
diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
index d0b2daea5b5..11df591f5b2 100644
--- a/screening/sourceTest/java/OpenBISScreeningMLTest.java
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -23,9 +23,11 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.Date;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.TreeMap;
import org.hamcrest.BaseMatcher;
import org.hamcrest.Description;
@@ -40,10 +42,14 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
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.DataSet;
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.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacadeFactory;
@@ -300,7 +306,6 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Object[][] plates = OpenBISScreeningML.listPlates("/S/P/E1");
- sort(plates);
assertEquals("/S/PLATE-1", plates[0][0]);
assertEquals("s-1", plates[0][1]);
assertEquals("S", plates[0][2]);
@@ -314,6 +319,35 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+ @Test
+ public void testListPlatesByExperimentAndAnalysisProcedure()
+ {
+
+ final String analysisProcedure = "PROCEDURE";
+
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).listPlates(eId1, analysisProcedure);
+ will(returnValue(Arrays.asList(p1)));
+ }
+ });
+
+ Object[][] plates = OpenBISScreeningML.listPlates("/S/P/E1", analysisProcedure);
+
+ assertEquals("/S/PLATE-1", plates[0][0]);
+ assertEquals("s-1", plates[0][1]);
+ assertEquals("S", plates[0][2]);
+ assertEquals("PLATE-1", plates[0][3]);
+ assertEquals("/S/P/E1", plates[0][4]);
+ assertEquals("e-1", plates[0][5]);
+ assertEquals("S", plates[0][6]);
+ assertEquals("P", plates[0][7]);
+ assertEquals("E1", plates[0][8]);
+ assertEquals(1, plates.length);
+ context.assertIsSatisfied();
+ }
+
@Test
public void testListFeatures()
{
@@ -607,21 +641,20 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
final String datasetTypePattern = "blablaCode";
final String mountPoint = "/mount/openbis/store";
final RecordingMatcher<IDataSetFilter> filterMatcher = new RecordingMatcher<IDataSetFilter>();
+
+ final DataSet dataSet1 = createDataSet("ds-1", ds1);
+ final DataSet dataSet2 = createDataSet("ds-2", ds2);
+
context.checking(new Expectations()
{
{
- one(openbis).getDataSets(with(new Plate("PLATE-1", "S", "s-1", eId1)),
+ one(openbis).getFullDataSets(with(new Plate("PLATE-1", "S", "s-1", eId1)),
with(filterMatcher));
- will(returnValue(Arrays.asList(ds1, ds2)));
-
- one(ds1).getCode();
- will(returnValue("ds-1"));
+ will(returnValue(Arrays.asList(dataSet1, dataSet2)));
one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
will(returnValue(ds1Folder));
- one(ds2).getCode();
- will(returnValue("ds-2"));
}
});
@@ -631,8 +664,10 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
assertEquals("Type:blablaCode AND Properties:[]", filterMatcher.recordedObject().toString());
assertEquals("ds-1", result[0][0]);
assertEquals(ds1Folder.getPath(), result[0][1]);
+ assertEqualProperties(dataSet1.getProperties(), (Object[][]) result[0][2]);
assertEquals("ds-2", result[1][0]);
assertEquals(ds2Folder.getPath(), result[1][1]);
+ assertEqualProperties(dataSet2.getProperties(), (Object[][]) result[1][2]);
assertEquals(2, result.length);
context.assertIsSatisfied();
}
@@ -641,40 +676,46 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testLoadDataSetsFilteredOnProperties()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ 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";
- final RecordingMatcher<IDataSetFilter> filterMatcher = new RecordingMatcher<IDataSetFilter>();
+ final RecordingMatcher<IDataSetFilter> filterMatcher =
+ new RecordingMatcher<IDataSetFilter>();
+
+ final DataSet dataSet1 = createDataSet("ds-1", ds1);
+ final DataSet dataSet2 = createDataSet("ds-2", ds2);
+
context.checking(new Expectations()
- {
{
- one(openbis).getDataSets(with(new Plate("PLATE-1", "S", "s-1", eId1)),
- with(filterMatcher));
- will(returnValue(Arrays.asList(ds1, ds2)));
-
- one(ds1).getCode();
- will(returnValue("ds-1"));
-
- one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
- will(returnValue(ds1Folder));
-
- one(ds2).getCode();
- will(returnValue("ds-2"));
- }
- });
-
- Object[][] properties = new Object[][] {new Object[] {"a", "alpha"}, new Object[] {"b", "beta"}};
+ {
+ one(openbis).getFullDataSets(with(new Plate("PLATE-1", "S", "s-1", eId1)),
+ with(filterMatcher));
+ will(returnValue(Arrays.asList(dataSet1, dataSet2)));
+
+ one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
+ will(returnValue(ds1Folder));
+ }
+ });
+
+ Object[][] properties = new Object[][]
+ { new Object[]
+ { "a", "alpha" }, new Object[]
+ { "b", "beta" } };
Object[][] result =
- OpenBISScreeningML.loadDataSets("/S/PLATE-1", datasetTypePattern, properties, mountPoint);
-
- assertEquals("Type:blablaCode AND Properties:[a=alpha, b=beta]", filterMatcher.recordedObject().toString());
+ OpenBISScreeningML.loadDataSets("/S/PLATE-1", datasetTypePattern, properties,
+ mountPoint);
+
+ assertEquals("Type:blablaCode AND Properties:[a=alpha, b=beta]", filterMatcher
+ .recordedObject().toString());
assertEquals("ds-1", result[0][0]);
assertEquals(ds1Folder.getPath(), result[0][1]);
+ assertEqualProperties(dataSet1.getProperties(), (Object[][]) result[0][2]);
assertEquals("ds-2", result[1][0]);
assertEquals(ds2Folder.getPath(), result[1][1]);
+ assertEqualProperties(dataSet2.getProperties(), (Object[][]) result[1][2]);
assertEquals(2, result.length);
context.assertIsSatisfied();
}
@@ -896,6 +937,44 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+ @Test
+ public void testListAnalysisProcedures()
+ {
+
+ final String[] analysisProcedures = new String[]
+ { "PROC-1", "PROC-2", "PROC-3" };
+
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).listAnalysisProcedures(eId1);
+ will(returnValue(Arrays.asList(analysisProcedures)));
+ }
+ });
+
+ Object[][] result = OpenBISScreeningML.listAnalysisProcedures("/S/P/E1");
+ String[] returnedAnalysisProcedures = new String[result.length];
+ for (int i = 0; i < result.length; i++)
+ {
+ returnedAnalysisProcedures[i] = (String) result[i][0];
+ }
+
+ assertEquals(Arrays.toString(analysisProcedures),
+ Arrays.toString(returnedAnalysisProcedures));
+ context.assertIsSatisfied();
+ }
+
+ private void assertEqualProperties(Map<String, String> properties, Object[][] matlabProps)
+ {
+ TreeMap<String, String> expected = new TreeMap<String, String>(properties);
+ TreeMap<String, String> actual = new TreeMap<String, String>();
+ for (Object[] prop : matlabProps)
+ {
+ actual.put((String) prop[0], (String) prop[1]);
+ }
+ assertEquals(expected.toString(), actual.toString());
+ }
+
private String getImagePath(Object[][][] result, int i)
{
return result[0][i][0].toString().substring(tempDir.getPath().length());
@@ -912,4 +991,34 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
});
}
+ private DataSet createDataSet(String code, IDataSetDss dataSetDss)
+ {
+ EntityRegistrationDetailsInitializer entityRegInitializer =
+ new EntityRegistrationDetailsInitializer();
+ EntityRegistrationDetails regDetails = new EntityRegistrationDetails(entityRegInitializer);
+
+ DataSetInitializer dsInitializer = new DataSetInitializer();
+ dsInitializer.setRegistrationDetails(regDetails);
+ dsInitializer.setCode(code);
+ dsInitializer.setExperimentIdentifier("EXPERIMENT");
+ dsInitializer.setDataSetTypeCode("ds-type");
+
+ Map<String, String> properties = createProperties(code);
+ for (String propKey : properties.keySet())
+ {
+ dsInitializer.putProperty(propKey, properties.get(propKey));
+ }
+
+ ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet metadata =
+ new ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet(dsInitializer);
+ return new DataSet(null, null, metadata, dataSetDss);
+ }
+
+ private Map<String, String> createProperties(String dataSetCode)
+ {
+ Map<String, String> properties = new HashMap<String, String>();
+ properties.put(dataSetCode + "-key1", dataSetCode + "value1");
+ properties.put(dataSetCode + "-key2", dataSetCode + "value2");
+ return properties;
+ }
}
--
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