From f8ffa7c3fd5f766320f972caf726f8fa462cace5 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 26 Feb 2013 09:45:05 +0000
Subject: [PATCH] SP-351, BIS-235:
IMasterDataRegistrationTransaction.addVocabularyTermTo() removed. Logic of
implementation is moved to VocabularyWrapper.addTerm(). Example term added to
vocabulary TREATMENT_TYPE in core plugin 'proteomics-optional'.
SVN: 28445
---
.../IMasterDataRegistrationTransaction.java | 5 -----
.../MasterDataRegistrationTransaction.java | 20 +------------------
.../jython/api/v1/impl/VocabularyWrapper.java | 18 ++++++++++++++++-
...MasterDataRegistrationTransactionTest.java | 9 +++++----
.../1/as/initialize-master-data.py | 8 ++++++++
5 files changed, 31 insertions(+), 29 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
index ad5f6b7151a..3b0900916bb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
@@ -265,11 +265,6 @@ public interface IMasterDataRegistrationTransaction
*/
IVocabularyTerm createNewVocabularyTerm(String code);
- /**
- * Adds the specified vocabulary term to the specified vocabulary.
- */
- void addVocabularyTermTo(IVocabularyImmutable vocabulary, IVocabularyTerm term);
-
/**
* Returns the vocabulary term with specified code from the specified vocabulary.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransaction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransaction.java
index ee7c0dcf27a..c1dfe413f8c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransaction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransaction.java
@@ -418,24 +418,6 @@ public class MasterDataRegistrationTransaction implements IMasterDataRegistratio
return vocabulary;
}
- @Override
- public void addVocabularyTermTo(IVocabularyImmutable vocabulary, IVocabularyTerm term)
- {
- if (vocabulary instanceof Vocabulary)
- {
- ((Vocabulary) vocabulary).addTerm(term);
- return;
- }
- Long id = ((VocabularyImmutable) vocabulary).getVocabulary().getId();
- List<VocabularyTerm> terms = createdVocabularyTerms.get(id);
- if (terms == null)
- {
- terms = new ArrayList<VocabularyTerm>();
- createdVocabularyTerms.put(id, terms);
- }
- terms.add((VocabularyTerm) term);
- }
-
@Override
public IVocabularyTerm getVocabularyTerm(IVocabularyImmutable vocabulary,
String vocabularyTermCode)
@@ -474,7 +456,7 @@ public class MasterDataRegistrationTransaction implements IMasterDataRegistratio
IVocabularyImmutable vocabulary = getVocabulary(code);
if (vocabulary != null)
{
- return new VocabularyWrapper((VocabularyImmutable) vocabulary);
+ return new VocabularyWrapper((VocabularyImmutable) vocabulary, createdVocabularyTerms);
}
return createNewVocabulary(code);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/VocabularyWrapper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/VocabularyWrapper.java
index c1220575a76..7bc2c8ed5b3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/VocabularyWrapper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/VocabularyWrapper.java
@@ -16,6 +16,10 @@
package ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabulary;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyTerm;
@@ -26,9 +30,13 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyTerm;
*/
class VocabularyWrapper extends VocabularyImmutable implements IVocabulary
{
- VocabularyWrapper(VocabularyImmutable vocabulary)
+ private final Map<Long, List<VocabularyTerm>> createdVocabularyTerms;
+
+ VocabularyWrapper(VocabularyImmutable vocabulary,
+ Map<Long, List<VocabularyTerm>> createdVocabularyTerms)
{
super(vocabulary.getVocabulary());
+ this.createdVocabularyTerms = createdVocabularyTerms;
}
@Override
@@ -59,5 +67,13 @@ class VocabularyWrapper extends VocabularyImmutable implements IVocabulary
@Override
public void addTerm(IVocabularyTerm term)
{
+ Long id = getVocabulary().getId();
+ List<VocabularyTerm> terms = createdVocabularyTerms.get(id);
+ if (terms == null)
+ {
+ terms = new ArrayList<VocabularyTerm>();
+ createdVocabularyTerms.put(id, terms);
+ }
+ terms.add((VocabularyTerm) term);
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransactionTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransactionTest.java
index 2b20741e3f6..be5bcac1c64 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransactionTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationTransactionTest.java
@@ -502,7 +502,7 @@ public class MasterDataRegistrationTransactionTest extends AssertJUnit
IVocabularyTerm term = transaction.createNewVocabularyTerm("ABC");
term.setLabel("abc");
term.setDescription("Hello abc");
- transaction.addVocabularyTermTo(voca, term);
+ voca.addTerm(term);
transaction.commit();
assertEquals("[abc [ABC]]", newTermsMatcher.recordedObject().toString());
@@ -585,7 +585,7 @@ public class MasterDataRegistrationTransactionTest extends AssertJUnit
term2.setLabel("Beta");
term2.setDescription("Hello B");
term2.setOrdinal(1L);
- transaction.addVocabularyTermTo(voca, term2);
+ voca.addTerm(term2);
transaction.commit();
NewVocabulary newVoca = newVocaMatcher.recordedObject();
@@ -652,6 +652,7 @@ public class MasterDataRegistrationTransactionTest extends AssertJUnit
context.assertIsSatisfied();
}
+ @SuppressWarnings("unchecked")
@Test
public void testAddVocabularyTermsFailed()
{
@@ -667,8 +668,8 @@ public class MasterDataRegistrationTransactionTest extends AssertJUnit
});
IVocabulary voca = transaction.getOrCreateNewVocabulary(KNOWN);
- transaction.addVocabularyTermTo(voca, transaction.createNewVocabularyTerm("ABC"));
- transaction.addVocabularyTermTo(voca, transaction.createNewVocabularyTerm("Delta"));
+ voca.addTerm(transaction.createNewVocabularyTerm("ABC"));
+ voca.addTerm(transaction.createNewVocabularyTerm("Delta"));
transaction.commit();
assertEquals("Failed to register new terms [ABC, DELTA]: Oohps!", transaction
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py b/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
index 43f0b50e81c..143643faf00 100644
--- a/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
+++ b/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
@@ -30,6 +30,14 @@ file_type_ZIP.setDescription('A zipped package')
vocabulary_TREATMENT_TYPE = tr.getVocabulary('TREATMENT_TYPE')
+vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
+vocabulary_term_TREATMENT_TYPE_PH = tr.createNewVocabularyTerm('PH')
+vocabulary_term_TREATMENT_TYPE_PH.setDescription(None)
+vocabulary_term_TREATMENT_TYPE_PH.setUrl(None)
+vocabulary_term_TREATMENT_TYPE_PH.setLabel('ph')
+vocabulary_term_TREATMENT_TYPE_PH.setOrdinal(1)
+vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
+
exp_type_BIOLOGICAL_EXPERIMENT = tr.getOrCreateNewExperimentType('BIOLOGICAL_EXPERIMENT')
exp_type_BIOLOGICAL_EXPERIMENT.setDescription('A biological experiment')
--
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