From 0ae37e281d0ff82b9f9cd318b8a6a48d1caeef3d Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Mon, 29 Oct 2012 14:27:46 +0000
Subject: [PATCH] BIS-226 SP-327 readonly access to vocabularies from search
service
SVN: 27404
---
.../api/v1/impl/SearchService.java | 8 ++
.../api/v1/impl/VocabularyImmutable.java | 90 +++++++++++++++++++
.../api/v1/impl/VocabularyTermImmutable.java | 63 +++++++++++++
.../server/EncapsulatedOpenBISService.java | 7 ++
.../shared/IEncapsulatedOpenBISService.java | 7 ++
.../api/internal/v1/ISearchService.java | 5 ++
.../api/internal/v1/IVocabularyImmutable.java | 62 +++++++++++++
.../internal/v1/IVocabularyTermImmutable.java | 52 +++++++++++
.../rich-test/rich-data-set-handler.py | 12 ++-
.../FeatureRichDataSetImportSystemTest.java | 44 +++++++++
10 files changed, 349 insertions(+), 1 deletion(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyImmutable.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyTermImmutable.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyImmutable.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyTermImmutable.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
index 072b3a065ea..2a7a0e28072 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentIm
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IMaterialImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IVocabularyImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.MaterialIdentifierCollection;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -42,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
@@ -206,4 +208,10 @@ public class SearchService implements ISearchService
return result;
}
+ @Override
+ public IVocabularyImmutable searchForVocabulary(String code)
+ {
+ Vocabulary vocabulary = openBisService.tryGetVocabulary(code);
+ return new VocabularyImmutable(vocabulary);
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyImmutable.java
new file mode 100644
index 00000000000..9bbe360039b
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyImmutable.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2012 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.etlserver.registrator.api.v1.impl;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IVocabularyImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IVocabularyTermImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+
+/**
+ *
+ *
+ * @author Jakub Straszewski
+ */
+public class VocabularyImmutable implements IVocabularyImmutable
+{
+ private final Vocabulary vocabulary;
+
+ public VocabularyImmutable(Vocabulary vocabulary)
+ {
+ this.vocabulary = vocabulary;
+ }
+
+ @Override
+ public String getCode()
+ {
+ return vocabulary.getCode();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return vocabulary.getDescription();
+ }
+
+ @Override
+ public boolean isManagedInternally()
+ {
+ return vocabulary.isManagedInternally();
+ }
+
+ @Override
+ public boolean isInternalNamespace()
+ {
+ return vocabulary.isInternalNamespace();
+ }
+
+ @Override
+ public boolean isChosenFromList()
+ {
+ return vocabulary.isChosenFromList();
+ }
+
+ @Override
+ public String getUrlTemplate()
+ {
+ return vocabulary.getURLTemplate();
+ }
+
+ @Override
+ public List<IVocabularyTermImmutable> getTerms()
+ {
+ List<IVocabularyTermImmutable> results = new LinkedList<IVocabularyTermImmutable>();
+
+ for (VocabularyTerm term : vocabulary.getTerms())
+ {
+ results.add(new VocabularyTermImmutable(term));
+ }
+
+ return results;
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyTermImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyTermImmutable.java
new file mode 100644
index 00000000000..112b5a087a4
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/VocabularyTermImmutable.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2012 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.etlserver.registrator.api.v1.impl;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IVocabularyTermImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+
+/**
+ * @author Jakub Straszewski
+ */
+public class VocabularyTermImmutable implements IVocabularyTermImmutable
+{
+ private final VocabularyTerm vocabularyTerm;
+
+ public VocabularyTermImmutable(VocabularyTerm vocabularyTerm)
+ {
+ this.vocabularyTerm = vocabularyTerm;
+ }
+
+ @Override
+ public String getCode()
+ {
+ return vocabularyTerm.getCode();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return vocabularyTerm.getDescription();
+ }
+
+ @Override
+ public String getLabel()
+ {
+ return vocabularyTerm.getLabel();
+ }
+
+ @Override
+ public String getUrl()
+ {
+ return vocabularyTerm.getUrl();
+ }
+
+ @Override
+ public Long getOrdinal()
+ {
+ return vocabularyTerm.getOrdinal();
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index aaa4440c848..2ff59c99040 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -64,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
@@ -240,6 +241,12 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.listVocabularyTerms(session.getSessionToken(), vocabularyCode);
}
+ @Override
+ public Vocabulary tryGetVocabulary(String code)
+ {
+ return service.tryGetVocabulary(session.getSessionToken(), code);
+ }
+
@Override
public SampleType getSampleType(String sampleTypeCode) throws UserFailureException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index 3278b66ecd2..798cd88f6a2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -51,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
@@ -193,6 +194,12 @@ public interface IEncapsulatedOpenBISService
public Collection<VocabularyTerm> listVocabularyTerms(String vocabularyCode)
throws UserFailureException;
+ /**
+ * Returns a vocabulary with given code
+ */
+ @ManagedAuthentication
+ public Vocabulary tryGetVocabulary(String code);
+
/**
* Gets the experiment type with assigned property types for the specified experiment type code.
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISearchService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISearchService.java
index 4689d760a22..bf9d7dc41b9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISearchService.java
@@ -102,4 +102,9 @@ public interface ISearchService
* @return a list of materials matching the specified collection.
*/
public List<IMaterialImmutable> listMaterials(MaterialIdentifierCollection identifierCollection);
+
+ /**
+ * @return a controlled vocabulary with the given code.
+ */
+ public IVocabularyImmutable searchForVocabulary(String code);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyImmutable.java
new file mode 100644
index 00000000000..a0aa73c9d23
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyImmutable.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright 2012 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.dss.generic.shared.api.internal.v1;
+
+import java.util.List;
+
+/**
+ * Read-only interface to a vocabulary.
+ *
+ * @author Jakub Straszewski
+ */
+public interface IVocabularyImmutable
+{
+
+ /**
+ * Returns the vocabulary code.
+ */
+ public String getCode();
+
+ /**
+ * Returns the vocabulary description.
+ */
+ public String getDescription();
+
+ /**
+ * Return <code>true</code> if the vocabulary is managed internally in openBIS.
+ */
+ boolean isManagedInternally();
+
+ /**
+ * Return <code>true</code> if the vocabulary is in the internal openBIS namespace.
+ */
+ boolean isInternalNamespace();
+
+ boolean isChosenFromList();
+
+ /**
+ * Returns a URL template (e.g a search query) that can display additional information for the
+ * concrete vocabulary terms. Can return null.
+ */
+ String getUrlTemplate();
+
+ /**
+ * Return a list with all terms within the vocabulary.
+ */
+ List<IVocabularyTermImmutable> getTerms();
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyTermImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyTermImmutable.java
new file mode 100644
index 00000000000..a7aff48fbd3
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IVocabularyTermImmutable.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright 2012 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.dss.generic.shared.api.internal.v1;
+
+/**
+ * Read-only interface to an existing vocabulary term.
+ *
+ * @author Jakub Straszewski
+ */
+public interface IVocabularyTermImmutable
+{
+ /**
+ * Return the term's code.
+ */
+ String getCode();
+
+ /**
+ * Return the term's description.
+ */
+ String getDescription();
+
+ /**
+ * Return the term's label.
+ */
+ String getLabel();
+
+ /**
+ * Return an associated URL specifying additional information for the vocabulary term.
+ */
+ String getUrl();
+
+ /**
+ * Return the position of the term in the context of a vocabulary.
+ */
+ Long getOrdinal();
+
+}
+
diff --git a/datastore_server/sourceTest/core-plugins/generic-test/1/dss/drop-boxes/rich-test/rich-data-set-handler.py b/datastore_server/sourceTest/core-plugins/generic-test/1/dss/drop-boxes/rich-test/rich-data-set-handler.py
index 2bdfdd46e3b..e2260858653 100644
--- a/datastore_server/sourceTest/core-plugins/generic-test/1/dss/drop-boxes/rich-test/rich-data-set-handler.py
+++ b/datastore_server/sourceTest/core-plugins/generic-test/1/dss/drop-boxes/rich-test/rich-data-set-handler.py
@@ -55,6 +55,13 @@ def updateExperiment(transaction):
ex = transaction.getExperimentForUpdate("/CISD/NEMO/EXP1")
ex.setPropertyValue("DESCRIPTION", "modified experiment description")
+def createBacterias(transaction):
+ vocabulary = transaction.getSearchService().searchForVocabulary("ORGANISM")
+ for term in vocabulary.getTerms():
+ mat = transaction.createNewMaterial("BC_%s" % term.getCode(), "BACTERIUM")
+ mat.setPropertyValue("DESCRIPTION", term.getDescription())
+ mat.setPropertyValue("ORGANISM", term.getCode())
+
def process(transaction):
# create experiment
experiment = create_experiment_if_needed(transaction)
@@ -76,5 +83,8 @@ def process(transaction):
# register samples
createSamples(transaction)
-
+
+ # read controlled vocabularies and create materials
+ createBacterias(transaction)
+
transaction.getRegistrationContext().getPersistentMap().put("email_text", "rich_email_text")
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/FeatureRichDataSetImportSystemTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/FeatureRichDataSetImportSystemTest.java
index 3929acb2a5d..9b067dd7b46 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/FeatureRichDataSetImportSystemTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/FeatureRichDataSetImportSystemTest.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.datastoreserver.systemtests;
import java.io.File;
+import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
@@ -80,6 +81,8 @@ public class FeatureRichDataSetImportSystemTest extends SystemTestCase
assertMaterialUpdated(openBISService);
assertExperimentUpdated(openBISService);
+
+ assertVocabularyMaterialsCreated(openBISService);
}
private void assertExperimentUpdated(IEncapsulatedOpenBISService openBISService)
@@ -164,6 +167,47 @@ public class FeatureRichDataSetImportSystemTest extends SystemTestCase
}
+ private void assertVocabularyMaterialsCreated(IEncapsulatedOpenBISService openBISService)
+ {
+ String[] items = new String[]
+ { "RAT", "DOG", "HUMAN", "GORILLA", "FLY" };
+
+ LinkedList<MaterialIdentifier> ids = new LinkedList<MaterialIdentifier>();
+
+ for (String item : items)
+ {
+ MaterialIdentifier ident = new MaterialIdentifier("BC_" + item, "BACTERIUM");
+ ids.add(ident);
+ }
+
+ ListMaterialCriteria criteria = ListMaterialCriteria.createFromMaterialIdentifiers(ids);
+ List<Material> materials = openBISService.listMaterials(criteria, true);
+
+ assertEquals(items.length, materials.size());
+
+ for (Material m : materials)
+ {
+ String code = m.getCode();
+
+ HashMap<String , IEntityProperty> properties = new HashMap<String , IEntityProperty>();
+
+ for (IEntityProperty property : m.getProperties())
+ {
+ properties.put(property.getPropertyType().getCode(), property);
+ }
+
+ IEntityProperty descriptionProperty = properties.get("DESCRIPTION");
+ IEntityProperty organismProperty = properties.get("ORGANISM");
+
+ assertNotNull(descriptionProperty);
+ assertEquals(code.substring(3), organismProperty.getVocabularyTerm().getCode());
+
+ assertEquals(descriptionProperty.getValue(), organismProperty.getVocabularyTerm()
+ .getDescription());
+
+ }
+ }
+
private void assertMaterialUpdated(IEncapsulatedOpenBISService openBISService)
{
LinkedList<MaterialIdentifier> ids = new LinkedList<MaterialIdentifier>();
--
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