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Commit 2d0ff9dd authored by kaloyane's avatar kaloyane
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[LMS-2407] additional methods exposed to Matlab. Data set properties are now... 

[LMS-2407] additional methods exposed to Matlab. Data set properties are now supplied by the loadDataSet***() methods.

SVN: 22269
parent a6cd4d38
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screening/source/java/OpenBISScreeningML.java
+ 124
− 18
View file @ 2d0ff9dd
......@@ -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
}
}
}
}
screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+ 13
− 0
View file @ 2d0ff9dd
......@@ -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.
*
......
screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+ 30
− 0
View file @ 2d0ff9dd
......@@ -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.
*
......
screening/sourceTest/java/OpenBISScreeningMLTest.java
+ 139
− 30
View file @ 2d0ff9dd
......@@ -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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