From 9ffb116072d716ee3bfdc97e4a3e5e42c94f18e7 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 27 Jun 2011 13:11:12 +0000
Subject: [PATCH] LMS-2138 listAnalysisProcedure implemented. MatLab:
listDataSets extended.
SVN: 21847
---
.../api/v1/impl/OpenbisServiceFacade.java | 2 +-
.../api/v1/filter/AndDataSetFilter.java | 64 +++++++++++++++
.../shared/api/v1/filter/IDataSetFilter.java | 33 ++++++++
.../filter/PropertiesBasedDataSetFilter.java | 77 +++++++++++++++++++
.../api/v1/filter/TypeBasedDataSetFilter.java | 55 +++++++++++++
.../shared/api/v1/dto/DataSetBuilder.java | 59 ++++++++++++++
.../PropertiesBasedDataSetFilterTest.java | 55 +++++++++++++
.../v1/filter/TypeBasedDataSetFilterTest.java | 40 ++++++++++
screening/source/java/OpenBISScreeningML.java | 55 ++++++++++++-
.../v1/IScreeningOpenbisServiceFacade.java | 42 +++++++++-
.../api/v1/ScreeningClientApiTester.java | 24 ++++++
.../api/v1/ScreeningOpenbisServiceFacade.java | 63 ++++++++++++---
.../shared/basic/dto/ScreeningConstants.java | 2 +
.../java/OpenBISScreeningMLTest.java | 55 ++++++++++++-
.../v1/ScreeningOpenbisServiceFacadeTest.java | 61 +++++++++++++--
15 files changed, 660 insertions(+), 27 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/AndDataSetFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/IDataSetFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilter.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
index ef575db4f20..a34e70e8c72 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
@@ -93,7 +93,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
/**
* ctor.
*/
- OpenbisServiceFacade(String sessionToken, IGeneralInformationService service,
+ public OpenbisServiceFacade(String sessionToken, IGeneralInformationService service,
IDssComponent dssComponent)
{
this.sessionToken = sessionToken;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/AndDataSetFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/AndDataSetFilter.java
new file mode 100644
index 00000000000..4e34ca0537b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/AndDataSetFilter.java
@@ -0,0 +1,64 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+
+/**
+ * Combining filters by logical AND.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class AndDataSetFilter implements IDataSetFilter
+{
+ private final IDataSetFilter[] dataSetFilters;
+
+ public AndDataSetFilter(IDataSetFilter... dataSetFilters)
+ {
+ this.dataSetFilters = dataSetFilters;
+ }
+
+ public boolean pass(DataSet dataSet)
+ {
+ for (IDataSetFilter filter : dataSetFilters)
+ {
+ if (filter.pass(dataSet) == false)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder builder = new StringBuilder();
+ for (IDataSetFilter filter : dataSetFilters)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(" AND ");
+ }
+ builder.append(filter);
+ }
+ return builder.toString();
+ }
+
+
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/IDataSetFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/IDataSetFilter.java
new file mode 100644
index 00000000000..49a3f931d7b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/IDataSetFilter.java
@@ -0,0 +1,33 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+
+
+/**
+ * Interface filters of {@link DataSet} instances.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IDataSetFilter
+{
+ /**
+ * Returns <code>true</code> if the specified data set passes the filter.
+ */
+ public boolean pass(DataSet dataSet);
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilter.java
new file mode 100644
index 00000000000..ccceb1521ee
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilter.java
@@ -0,0 +1,77 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+
+
+/**
+ * Filter based on data set properties.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class PropertiesBasedDataSetFilter implements IDataSetFilter
+{
+ private final Map<String, String> map;
+
+ public PropertiesBasedDataSetFilter(Map<String, String> properties)
+ {
+ map = properties;
+ }
+
+ public boolean pass(DataSet dataSet)
+ {
+ HashMap<String, String> properties = dataSet.getProperties();
+ Set<Entry<String, String>> entrySet = map.entrySet();
+ for (Entry<String, String> entry : entrySet)
+ {
+ String key = entry.getKey();
+ String value = entry.getValue();
+ if (value.equals(properties.get(key)) == false)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ @Override
+ public String toString()
+ {
+ Set<Entry<String, String>> entrySet = map.entrySet();
+ List<Entry<String, String>> sortedEntries = new ArrayList<Entry<String, String>>(entrySet);
+ Collections.sort(sortedEntries, new Comparator<Entry<String, String>>()
+ {
+ public int compare(Entry<String, String> o1, Entry<String, String> o2)
+ {
+ return o1.getKey().compareTo(o2.getKey());
+ }
+ });
+ return "Properties:" + sortedEntries;
+ }
+
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilter.java
new file mode 100644
index 00000000000..ecd97dca034
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilter.java
@@ -0,0 +1,55 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+
+
+/**
+ * Filter which will be passed only by data sets with a data set type code matching a certain
+ * regular expression.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TypeBasedDataSetFilter implements IDataSetFilter
+{
+ private final String datasetTypeCodePattern;
+
+ /**
+ * Creates an instance for the specified regular expression.
+ */
+ public TypeBasedDataSetFilter(String datasetTypeCodePattern)
+ {
+ this.datasetTypeCodePattern = datasetTypeCodePattern;
+ }
+
+ /**
+ * Return <code>true</code> if the data set type code of the specified data set matches the
+ * regular expression provided as constructor argument.
+ */
+ public boolean pass(DataSet dataSet)
+ {
+ return dataSet.getDataSetTypeCode().matches(datasetTypeCodePattern);
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Type:" + datasetTypeCodePattern;
+ }
+}
+
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
new file mode 100644
index 00000000000..0882b12f8bf
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
@@ -0,0 +1,59 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
+
+/**
+ * Builder of {@link DataSet} instances.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetBuilder
+{
+ private DataSetInitializer initializer = new DataSetInitializer();
+
+ public DataSet getDataSet()
+ {
+ return new DataSet(initializer);
+ }
+
+ public DataSetBuilder code(String code)
+ {
+ initializer.setCode(code);
+ return this;
+ }
+
+ public DataSetBuilder type(String type)
+ {
+ initializer.setDataSetTypeCode(type);
+ return this;
+ }
+
+ public DataSetBuilder experiment(String experimentIdentifier)
+ {
+ initializer.setExperimentIdentifier(experimentIdentifier);
+ return this;
+ }
+
+ public DataSetBuilder property(String key, String value)
+ {
+ initializer.getProperties().put(key, value);
+ return this;
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
new file mode 100644
index 00000000000..d4a0ee46a4e
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
@@ -0,0 +1,55 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import java.util.HashMap;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetBuilder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class PropertiesBasedDataSetFilterTest extends AssertJUnit
+{
+ @Test
+ public void testNoProperties()
+ {
+ IDataSetFilter filter = new PropertiesBasedDataSetFilter(new HashMap<String, String>());
+
+ DataSetBuilder builder = new DataSetBuilder().code("A").type("A").experiment("E");
+ assertEquals(true, filter.pass(builder.getDataSet()));
+ assertEquals(true, filter.pass(builder.property("a", "alpha").getDataSet()));
+ }
+
+ @Test
+ public void testWithProperties()
+ {
+ HashMap<String, String> properties = new HashMap<String, String>();
+ properties.put("a", "alpha");
+ PropertiesBasedDataSetFilter filter = new PropertiesBasedDataSetFilter(properties);
+
+ DataSetBuilder builder = new DataSetBuilder().code("A").type("A").experiment("E");
+ assertEquals(false, filter.pass(builder.getDataSet()));
+ assertEquals(true, filter.pass(builder.property("a", "alpha").getDataSet()));
+ assertEquals(false, filter.pass(builder.property("a", "beta").getDataSet()));
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
new file mode 100644
index 00000000000..6013c718040
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
@@ -0,0 +1,40 @@
+/*
+ * 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.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetBuilder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TypeBasedDataSetFilterTest extends AssertJUnit
+{
+ @Test
+ public void test()
+ {
+ IDataSetFilter filter = new TypeBasedDataSetFilter(".*ANA");
+ DataSetBuilder builder = new DataSetBuilder().code("ds1").experiment("/S/P/E");
+ assertEquals(true, filter.pass(builder.type("MY-ANA").getDataSet()));
+ assertEquals(false, filter.pass(builder.type("MY-ANA2").getDataSet()));
+ assertEquals(false, filter.pass(builder.type("HELLO").getDataSet()));
+ }
+}
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index d0857889e8c..ebce71368e0 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -37,6 +37,9 @@ 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.filter.AndDataSetFilter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.PropertiesBasedDataSetFilter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacadeFactory;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
@@ -685,7 +688,7 @@ 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
@@ -716,11 +719,53 @@ public class OpenBISScreeningML
*/
public static Object[][] loadDataSets(String augmentedPlateCode, String dataSetTypeCodePattern,
String overrideStoreRootPathOrNull)
+ {
+ return loadDataSets(augmentedPlateCode, dataSetTypeCodePattern, new Object[0][],
+ overrideStoreRootPathOrNull);
+ }
+
+ /**
+ * 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.<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:
+ *
+ * <pre>
+ * % Load all data sets of plate P005 in space SPACE
+ * properties = {'ANALYSIS_PROCEDURE' AX87}
+ * dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', properties, '/mount/openbis-store')
+ * % Get the data set codes
+ * dsinfo(:,1)
+ * % Get root path of first data set (assuming there is at least one)
+ * dsginfo(1,2)
+ * </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 ".*".
+ * @param properties Only data set with specified property values will be returned. This is a
+ * two dimensional array where the first column contains the property codes and the
+ * second column the corresponding property values.
+ * @return Each row contains information about one 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.
+ * <p>
+ * <code>{ data set code, data set root path }</code>
+ */
+ public static Object[][] loadDataSets(String augmentedPlateCode,
+ final String dataSetTypeCodePattern, final Object[][] properties,
+ String overrideStoreRootPathOrNull)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
-
- List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, dataSetTypeCodePattern);
+ List<IDataSetDss> dataSets =
+ openbis.getDataSets(plateIdentifier, new AndDataSetFilter(new TypeBasedDataSetFilter(
+ dataSetTypeCodePattern), new PropertiesBasedDataSetFilter(
+ createMap(properties))));
Object[][] result = new Object[dataSets.size()][];
try
{
@@ -805,7 +850,9 @@ public class OpenBISScreeningML
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
- List<IDataSetDss> dataSets = openbis.getDataSets(plateIdentifier, dataSetTypeCodePattern);
+ List<IDataSetDss> dataSets =
+ openbis.getDataSets(plateIdentifier, new TypeBasedDataSetFilter(
+ dataSetTypeCodePattern));
Object[][][] result = new Object[dataSets.size()][][];
for (int i = 0; i < dataSets.size(); i++)
{
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 40e9a0c8b98..c8749648af5 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
@@ -25,6 +25,8 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
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.generic.shared.api.v1.filter.IDataSetFilter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
@@ -62,7 +64,7 @@ public interface IScreeningOpenbisServiceFacade
/** Closes connection with the server. After calling this method this facade cannot be used. */
public void logout();
-
+
/**
* Removes all images loaded by {@link #loadImageWellCaching(PlateImageReference, ImageSize)}
* and {@link #loadThumbnailImageWellCaching(PlateImageReference)} from the image cache, thus
@@ -162,18 +164,32 @@ public interface IScreeningOpenbisServiceFacade
public void updateWellProperties(WellIdentifier wellIdentifier, Map<String, String> properties);
/**
- * Get proxies to the data sets owned by specified well.
+ * Gets proxies to the data sets owned by specified well.
*
+ * @deprecated use {@link #getDataSets(WellIdentifier, IDataSetFilter)} with
+ * {@link TypeBasedDataSetFilter}.
* @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.
*/
+ @Deprecated
public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException;
+ /**
+ * Gets proxies to the data sets owned by specified well and passing specified filter..
+ *
+ * @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,
+ IDataSetFilter dataSetFilter) throws IllegalStateException,
+ EnvironmentFailureException;
+
public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
EnvironmentFailureException;
@@ -195,18 +211,32 @@ public interface IScreeningOpenbisServiceFacade
EnvironmentFailureException, IOException;
/**
- * Get proxies to the data sets of the specified type owned by specified plate.
+ * Gets proxies to the data sets of the specified type owned by specified plate.
*
+ * @deprecated use {@link #getDataSets(PlateIdentifier, IDataSetFilter)} with
+ * {@link TypeBasedDataSetFilter}.
* @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.
*/
+ @Deprecated
public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException;
+ /**
+ * Gets proxies to the data sets owned by specified plate and passing specified filter.
+ *
+ * @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,
+ IDataSetFilter dataSetFilter) throws IllegalStateException,
+ EnvironmentFailureException;
+
/**
* Upload a new data set to the DSS for a plate.
*
@@ -575,5 +605,11 @@ public interface IScreeningOpenbisServiceFacade
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull);
+
+ /**
+ * Returns an alphabetically sorted list of analysis procedure codes of all data sets of the
+ * specified experiment.
+ */
+ public List<String> listAnalysisProcedures(ExperimentIdentifier experimentIdentifier);
}
\ 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 a04792d5873..1f6e8468f1d 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
@@ -54,6 +54,7 @@ import org.apache.log4j.PropertyConfigurator;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
@@ -163,6 +164,15 @@ public class ScreeningClientApiTester
loadOverlays();
}
});
+ JMenuItem listAnalysisProceduresMenuItem = new JMenuItem("List Analysis Procedures...");
+ callApiMenu.add(listAnalysisProceduresMenuItem);
+ listAnalysisProceduresMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ listAnalysisProcedures();
+ }
+ });
}
void setUp(String[] args)
@@ -261,6 +271,20 @@ public class ScreeningClientApiTester
validate(panel);
}
+ private void listAnalysisProcedures()
+ {
+ Form form = new Form(this, "Analysis Procedures for an Experiment");
+ List<ExperimentIdentifier> experiments = facade.listExperiments();
+ JComboBox experimentComboBox =
+ new JComboBox(experiments.toArray(new ExperimentIdentifier[0]));
+ form.addField("Experiment", experimentComboBox);
+ form.showForm();
+ List<String> analysisProcedures =
+ facade.listAnalysisProcedures((ExperimentIdentifier) experimentComboBox
+ .getSelectedItem());
+ JOptionPane.showMessageDialog(this, "Analysis Procedures: " + analysisProcedures);
+ }
+
private void loadImagesByDataSetCode()
{
Form form = new Form(this, "Parameters for Loading Images by Data Set");
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 54f661b6076..76b665ad1ef 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
@@ -39,6 +39,12 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangin
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.WellImageCache.CachedImage;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.WellImageCache.WellImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
@@ -63,6 +69,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMate
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
* A client side facade of openBIS and Datastore Server API.
@@ -89,7 +96,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return new DssServiceRpcScreeningHolder(serverUrl);
}
};
-
+
private final IScreeningApiServer openbisScreeningServer;
private final IGeneralInformationService generalInformationService;
@@ -119,6 +126,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
private IDssServiceFactory dssServiceCache;
+
/**
* Creates a service facade which communicates with the openBIS server at the specified URL.
* Authenticates the user.
@@ -243,7 +251,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
checkASMinimalMinorVersion("logoutScreening");
openbisScreeningServer.logoutScreening(sessionToken);
}
-
+
public void clearWellImageCache()
{
imageCache.clear();
@@ -408,12 +416,16 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException
+ {
+ return getDataSets(wellIdentifier, new TypeBasedDataSetFilter(datasetTypeCodePattern));
+ }
+
+ public List<IDataSetDss> getDataSets(WellIdentifier wellIdentifier, IDataSetFilter dataSetFilter)
+ throws IllegalStateException, EnvironmentFailureException
{
final Sample wellSample = getWellSample(wellIdentifier);
- return getDataSets(wellSample, datasetTypeCodePattern);
+ return getDataSets(wellSample, dataSetFilter);
}
-
-
public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
EnvironmentFailureException
@@ -429,22 +441,28 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
* the server.
*/
public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
- String datasetTypeCodePattern) throws IllegalStateException,
+ final String datasetTypeCodePattern) throws IllegalStateException,
EnvironmentFailureException
+ {
+ return getDataSets(plateIdentifier, new TypeBasedDataSetFilter(datasetTypeCodePattern));
+ }
+
+ public List<IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
+ IDataSetFilter dataSetFilter) throws IllegalStateException, EnvironmentFailureException
{
checkASMinimalMinorVersion("getPlateSample", PlateIdentifier.class);
Sample sample = openbisScreeningServer.getPlateSample(sessionToken, plateIdentifier);
- return getDataSets(sample, datasetTypeCodePattern);
+ return getDataSets(sample, dataSetFilter);
}
- private List<IDataSetDss> getDataSets(final Sample sample, final String datasetTypeCodePattern)
+ private List<IDataSetDss> getDataSets(final Sample sample, IDataSetFilter filter)
{
final List<DataSet> dataSets =
generalInformationService.listDataSetsForSample(sessionToken, sample, true);
final List<IDataSetDss> result = new ArrayList<IDataSetDss>();
for (DataSet dataSet : dataSets)
{
- if (dataSet.getDataSetTypeCode().matches(datasetTypeCodePattern))
+ if (filter.pass(dataSet))
{
result.add(dssComponent.getDataSet(dataSet.getCode()));
}
@@ -1378,6 +1396,33 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
materialTypeIdentifierOrNull);
}
+ public List<String> listAnalysisProcedures(ExperimentIdentifier experimentIdentifier)
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria experimentCriteria = new SearchCriteria();
+ experimentCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, experimentIdentifier.getExperimentCode()));
+ experimentCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.PROJECT, experimentIdentifier.getProjectCode()));
+ experimentCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.SPACE, experimentIdentifier.getSpaceCode()));
+ searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(experimentCriteria));
+ List<DataSet> dataSets = generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ Set<String> procedures = new HashSet<String>();
+ for (DataSet dataSet : dataSets)
+ {
+ HashMap<String, String> properties = dataSet.getProperties();
+ String analysisProcedure = properties.get(ScreeningConstants.ANALYSIS_PROCEDURE);
+ if (analysisProcedure != null)
+ {
+ procedures.add(analysisProcedure);
+ }
+ }
+ ArrayList<String> result = new ArrayList<String>(procedures);
+ Collections.sort(result);
+ return result;
+ }
+
// --------- helpers -----------
private static final class WrappedIOException extends RuntimeException
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index 14accb1d7b2..492c3c19f02 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -130,6 +130,8 @@ public class ScreeningConstants
/** Used to import Qiagen siRNA libraries. */
public static final String LIBRARY_PLUGIN_TYPE_CODE = "LIBRARY";
+
+ public static final String ANALYSIS_PROCEDURE = "ANALYSIS_PROCEDURE";
// --- !!!!!! It's discouraged to use this constant, try hard not to do that !!!!!!!! ---
diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
index 45961ee6522..9bcc84c3e41 100644
--- a/screening/sourceTest/java/OpenBISScreeningMLTest.java
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -44,6 +44,7 @@ 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.filter.IDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacadeFactory;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
@@ -539,10 +540,11 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
@Test
public void testListDataSetsFiles()
{
+ final RecordingMatcher<IDataSetFilter> filterMatcher = new RecordingMatcher<IDataSetFilter>();
context.checking(new Expectations()
{
{
- one(openbis).getDataSets(p1, ".*");
+ one(openbis).getDataSets(with(p1), with(filterMatcher));
will(returnValue(Arrays.asList(ds1, ds2)));
one(ds1).listFiles("/", true);
@@ -561,7 +563,8 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
});
Object[][][] files = OpenBISScreeningML.listDataSetsFiles(p1.getAugmentedCode(), ".*");
-
+
+ assertEquals("Type:.*", filterMatcher.recordedObject().toString());
assertEquals("ds1", files[0][0][0]);
assertEquals("[a, a/b]", Arrays.asList(files[0][1]).toString());
assertEquals("ds2", files[1][0][0]);
@@ -600,11 +603,12 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
ds2Folder.mkdirs();
final String datasetTypePattern = "blablaCode";
final String mountPoint = "/mount/openbis/store";
+ final RecordingMatcher<IDataSetFilter> filterMatcher = new RecordingMatcher<IDataSetFilter>();
context.checking(new Expectations()
{
{
- one(openbis).getDataSets(new Plate("PLATE-1", "S", "s-1", eId1),
- datasetTypePattern);
+ one(openbis).getDataSets(with(new Plate("PLATE-1", "S", "s-1", eId1)),
+ with(filterMatcher));
will(returnValue(Arrays.asList(ds1, ds2)));
one(ds1).getCode();
@@ -621,6 +625,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Object[][] result =
OpenBISScreeningML.loadDataSets("/S/PLATE-1", datasetTypePattern, mountPoint);
+ assertEquals("Type:blablaCode AND Properties:[]", filterMatcher.recordedObject().toString());
assertEquals("ds-1", result[0][0]);
assertEquals(ds1Folder.getPath(), result[0][1]);
assertEquals("ds-2", result[1][0]);
@@ -629,6 +634,48 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+ @Test
+ public void testLoadDataSetsFilteredOnProperties()
+ {
+ 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";
+ final RecordingMatcher<IDataSetFilter> filterMatcher = new RecordingMatcher<IDataSetFilter>();
+ 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"}};
+ Object[][] result =
+ 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]);
+ assertEquals("ds-2", result[1][0]);
+ assertEquals(ds2Folder.getPath(), result[1][1]);
+ assertEquals(2, result.length);
+ context.assertIsSatisfied();
+ }
+
@Test
public void testUpdateDataSet()
{
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 e2b1b00da0b..c0d4c2fb367 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
@@ -54,6 +54,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.server.ScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
@@ -74,6 +76,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageRef
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
* @author Franz-Josef Elmer
@@ -120,7 +123,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
private IDssServiceFactory dssServiceFactory;
- private ScreeningOpenbisServiceFacade facade;
+ private IScreeningOpenbisServiceFacade facade;
private ImageDatasetReference i1id;
@@ -142,6 +145,8 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
private IDataSetDss ds1Proxy;
+ private IDataSetFilter filter;
+
@BeforeMethod
public void beforeMethod()
{
@@ -152,6 +157,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
dssComponent = context.mock(IDssComponent.class);
ds1Proxy = context.mock(IDataSetDss.class);
dssServiceFactory = context.mock(IDssServiceFactory.class);
+ filter = context.mock(IDataSetFilter.class);
i1id = new ImageDatasetReference(DATA_SET1, null, URL1, null, null, null, null, null, null);
i2id = new ImageDatasetReference(DATA_SET2, null, URL2, null, null, null, null, null, null);
f1id = context.mock(IFeatureVectorDatasetIdentifier.class, "f1id");
@@ -508,6 +514,42 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
context.assertIsSatisfied();
}
+
+ @Test
+ public void testListAnalysisProcedures()
+ {
+ final ExperimentIdentifier experimentIdentifier = ExperimentIdentifier.createFromAugmentedCode("/S/P/E");
+ final RecordingMatcher<SearchCriteria> searchCriteriaMatcher = new RecordingMatcher<SearchCriteria>();
+ context.checking(new Expectations()
+ {
+ {
+ one(generalInformationService).searchForDataSets(with(SESSION_TOKEN),
+ with(searchCriteriaMatcher));
+ DataSetInitializer ds1 = new DataSetInitializer();
+ ds1.setCode("ds1");
+ ds1.getProperties().put(ScreeningConstants.ANALYSIS_PROCEDURE, "FZ-87");
+ ds1.setExperimentIdentifier(experimentIdentifier.toString());
+ ds1.setDataSetTypeCode("my-type");
+ DataSetInitializer ds2 = new DataSetInitializer();
+ ds2.setCode("ds2");
+ ds2.getProperties().put(ScreeningConstants.ANALYSIS_PROCEDURE, "ALPHA-42");
+ ds2.setExperimentIdentifier(experimentIdentifier.toString());
+ ds2.setDataSetTypeCode("my-type");
+ will(returnValue(Arrays.asList(new DataSet(ds1), new DataSet(ds2))));
+ }
+ });
+
+ List<String> procedures = facade.listAnalysisProcedures(experimentIdentifier);
+
+ assertEquals("[ALPHA-42, FZ-87]", procedures.toString());
+ assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],"
+ + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
+ + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,CODE,E], "
+ + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,PROJECT,P], "
+ + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,SPACE,S]],[]]]]]",
+ searchCriteriaMatcher.recordedObject().toString());
+ context.assertIsSatisfied();
+ }
@Test
public void testGetDataSetsOfAWell()
@@ -523,15 +565,18 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
one(generalInformationService).listDataSetsForSample(SESSION_TOKEN, sample,
true);
DataSetInitializer initializer1 = dataSetInitializer(DATA_SET1);
- will(returnValue(Arrays.asList(new DataSet(initializer1))));
+ DataSet dataSet = new DataSet(initializer1);
+ will(returnValue(Arrays.asList(dataSet)));
one(dssComponent).getDataSet(DATA_SET1);
will(returnValue(ds1Proxy));
+
+ one(filter).pass(dataSet);
+ will(returnValue(true));
}
});
- List<IDataSetDss> dataSets =
- facade.getDataSets(wellIdentifier, ".*" + MY_DATA_SET_TYPE + ".*");
+ List<IDataSetDss> dataSets = facade.getDataSets(wellIdentifier, filter);
assertSame(ds1Proxy, dataSets.get(0));
assertEquals(1, dataSets.size());
@@ -552,14 +597,18 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
one(generalInformationService).listDataSetsForSample(SESSION_TOKEN, sample,
true);
DataSetInitializer initializer1 = dataSetInitializer(DATA_SET1);
- will(returnValue(Arrays.asList(new DataSet(initializer1))));
+ DataSet dataSet = new DataSet(initializer1);
+ will(returnValue(Arrays.asList(dataSet)));
one(dssComponent).getDataSet(DATA_SET1);
will(returnValue(ds1Proxy));
+
+ one(filter).pass(dataSet);
+ will(returnValue(true));
}
});
- List<IDataSetDss> dataSets = facade.getDataSets(plateIdentifier, MY_DATA_SET_TYPE);
+ List<IDataSetDss> dataSets = facade.getDataSets(plateIdentifier, filter);
assertSame(ds1Proxy, dataSets.get(0));
assertEquals(1, dataSets.size());
--
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