You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@uima.apache.org by re...@apache.org on 2021/04/21 19:43:35 UTC
[uima-uimaj] branch
bugfix/UIMA-6352-CAS-reinit-CASCompleteSerializer-does-not-properly-reset-indexes
created (now fd9e01f)
This is an automated email from the ASF dual-hosted git repository.
rec pushed a change to branch bugfix/UIMA-6352-CAS-reinit-CASCompleteSerializer-does-not-properly-reset-indexes
in repository https://gitbox.apache.org/repos/asf/uima-uimaj.git.
at fd9e01f [UIMA-6352] reinit(CASCompleteSerializer) does not properly reset indexes
This branch includes the following new commits:
new fd9e01f [UIMA-6352] reinit(CASCompleteSerializer) does not properly reset indexes
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
[uima-uimaj] 01/01: [UIMA-6352] reinit(CASCompleteSerializer) does
not properly reset indexes
Posted by re...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
rec pushed a commit to branch bugfix/UIMA-6352-CAS-reinit-CASCompleteSerializer-does-not-properly-reset-indexes
in repository https://gitbox.apache.org/repos/asf/uima-uimaj.git
commit fd9e01fe57a30a3d59a842928fe14a3d76f12b58
Author: Richard Eckart de Castilho <re...@apache.org>
AuthorDate: Wed Apr 21 21:43:48 2021 +0200
[UIMA-6352] reinit(CASCompleteSerializer) does not properly reset indexes
- Fixed issue by calling setupCasFromCasMgrSerializer in reinit(CASCompleteSerializer) instead of using incomplete custom code
- Added unit test
---
.../org/apache/uima/cas/impl/BinaryCasSerDes.java | 27 +--
.../uima/cas/test/CompleteSerializationTest.java | 195 ++++++++++-----------
2 files changed, 97 insertions(+), 125 deletions(-)
diff --git a/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes.java b/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes.java
index cd9e19b..620cc1e 100644
--- a/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes.java
+++ b/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes.java
@@ -297,32 +297,7 @@ public class BinaryCasSerDes {
* @param casCompSer -
*/
public void reinit(CASCompleteSerializer casCompSer) {
- TypeSystemImpl ts = casCompSer.getCASMgrSerializer().getTypeSystem();
-
- /*
- * Special clearing:
- * Skips the resetNoQuestions operation of flushing the indexes,
- * since these will be reinitialized with potentially new definitions.
- *
- * Clears additional data related to having the
- * - type system potentially change
- * - the features belonging to indexes change
- */
- baseCas.svd.clear(); // does all clearing except index repositories which will be wiped out
- baseCas.installTypeSystemInAllViews(ts); // the commit (next) re-installs it if it changes
- baseCas.commitTypeSystem();
-
- // reset index repositories -- wipes out Sofa index
- casCompSer.getCASMgrSerializer().getIndexRepository(baseCas); // sets the argument's index repository
- baseCas.indexRepository.commit();
-
- // get handle to existing initial View
- CASImpl initialView = (CASImpl) baseCas.getInitialView();
-
- // freshen the initial view
- initialView.refreshView(baseCas, null); // sets jcas to null for the view, too
- baseCas.svd.setViewForSofaNbr(1, initialView);
- baseCas.svd.viewCount = 1;
+ setupCasFromCasMgrSerializer(casCompSer.getCASMgrSerializer());
// deserialize heap
CASSerializer casSer = casCompSer.getCASSerializer();
diff --git a/uimaj-core/src/test/java/org/apache/uima/cas/test/CompleteSerializationTest.java b/uimaj-core/src/test/java/org/apache/uima/cas/test/CompleteSerializationTest.java
index 7015d0e..dfe150b 100644
--- a/uimaj-core/src/test/java/org/apache/uima/cas/test/CompleteSerializationTest.java
+++ b/uimaj-core/src/test/java/org/apache/uima/cas/test/CompleteSerializationTest.java
@@ -16,156 +16,133 @@
* specific language governing permissions and limitations
* under the License.
*/
-
package org.apache.uima.cas.test;
+import static org.apache.uima.cas.impl.Serialization.deserializeCASComplete;
+import static org.apache.uima.cas.impl.Serialization.serializeCASComplete;
+import static org.apache.uima.cas.impl.Serialization.serializeWithCompression;
+import static org.apache.uima.util.CasCreationUtils.createCas;
+import static org.apache.uima.util.CasIOUtils.load;
+import static org.assertj.core.api.Assertions.assertThatExceptionOfType;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.Feature;
import org.apache.uima.cas.FeatureStructure;
import org.apache.uima.cas.Type;
+import org.apache.uima.cas.TypeSystem;
import org.apache.uima.cas.admin.CASMgr;
import org.apache.uima.cas.impl.CASCompleteSerializer;
import org.apache.uima.cas.impl.CASImpl;
import org.apache.uima.cas.impl.CasCompare;
import org.apache.uima.cas.impl.LowLevelCAS;
-import org.apache.uima.cas.impl.LowLevelException;
import org.apache.uima.cas.impl.Serialization;
-import org.apache.uima.internal.util.Int2ObjHashMap;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
-import org.apache.uima.jcas.cas.TOP;
import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl;
-import org.apache.uima.test.junit_extension.JUnitExtension;
import org.apache.uima.util.AutoCloseableNoException;
import org.apache.uima.util.CasCreationUtils;
-
-import junit.framework.TestCase;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
/**
* CAS complete serialization test class
- *
*/
-public class CompleteSerializationTest extends TestCase {
-
- /**
- * Constructor for CASTest.
- *
- * @param arg0
- */
- public CompleteSerializationTest(String arg0) {
- super(arg0);
+public class CompleteSerializationTest {
+
+ @BeforeClass
+ public static void setupClass() {
+ System.setProperty("uima.enable_strict_type_source_check", "true");
}
+ @AfterClass
+ public static void tearDownClass() {
+ System.getProperties().remove("uima.enable_strict_type_source_check");
+ }
+
+ @Test
public void testSerialization() throws Exception {
- try {
- CASMgr cas = null;
- try {
- cas = (CASMgr) CASInitializer.initCas(new CASTestSetup(), null);
- } catch (Exception e) {
- assertTrue(false);
- }
- ((CAS) cas).setDocumentText("Create the sofa for the inital view");
- assertTrue(((CASImpl) cas).isBackwardCompatibleCas());
- CASCompleteSerializer ser = Serialization.serializeCASComplete(cas);
+ CASMgr cas = (CASMgr) CASInitializer.initCas(new CASTestSetup(), null);
- // deserialize into a new CAS with a type system that only contains the builtins
- CAS newCas = CasCreationUtils.createCas(new TypeSystemDescription_impl(), null, null);
+ ((CAS) cas).setDocumentText("Create the sofa for the inital view");
+ assertTrue(((CASImpl) cas).isBackwardCompatibleCas());
+ CASCompleteSerializer ser = Serialization.serializeCASComplete(cas);
- try {
- Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
- } catch (Exception e) {
- assertTrue(false);
- }
- assertTrue(((CASImpl) newCas).getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
- assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
- assertEquals("Create the sofa for the inital view", newCas.getDocumentText());
+ // deserialize into a new CAS with a type system that only contains the builtins
+ CAS newCas = CasCreationUtils.createCas(new TypeSystemDescription_impl(), null, null);
- // make sure JCas can be created
- newCas.getJCas();
+ Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
- // deserialize into newCas a second time (OF bug found 7/7/2006)
- try {
- Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
- } catch (Exception e) {
- assertTrue(false);
- }
- assertTrue(cas.getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
- assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
- boolean caught = false;
- try {
- ((LowLevelCAS)newCas).ll_enableV2IdRefs();
- } catch (IllegalStateException e) {
- caught = true;
- }
- assertTrue(caught);
- } catch (Exception e) {
- JUnitExtension.handleException(e);
- }
-
+ assertTrue(((CASImpl) newCas).getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
+ assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
+ assertEquals("Create the sofa for the inital view", newCas.getDocumentText());
+
+ // make sure JCas can be created
+ newCas.getJCas();
+ // deserialize into newCas a second time (OF bug found 7/7/2006)
+ Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
+
+ assertTrue(cas.getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
+ assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
+
+ assertThatExceptionOfType(IllegalStateException.class)
+ .isThrownBy(() -> ((LowLevelCAS) newCas).ll_enableV2IdRefs());
}
+ @Test
public void testSerializationV2IdRefs() throws Exception {
- try (AutoCloseableNoException a = LowLevelCAS.ll_defaultV2IdRefs()){
- CAS cas = null;
- JCas jcas = null;
-
- try {
- cas = CASInitializer.initCas(new CASTestSetup(), null);
- jcas = cas.getJCas();
- } catch (Exception e) {
- assertTrue(false);
- }
+ try (AutoCloseableNoException a = LowLevelCAS.ll_defaultV2IdRefs()) {
+ CAS cas = CASInitializer.initCas(new CASTestSetup(), null);
+ JCas jcas = cas.getJCas();
+
cas.setDocumentText("Create the sofa for the inital view");
assertTrue(((CASImpl) cas).isBackwardCompatibleCas());
-
+
Type t1 = cas.getTypeSystem().getType(CASTestSetup.ARRAYFSWITHSUBTYPE_TYPE);
Feature feat1 = t1.getFeatureByBaseName(CASTestSetup.ARRAYFSWITHSUBTYPE_TYPE_FEAT);
-
FSArray<FeatureStructure> fsa1 = new FSArray<>(jcas, 1);
FeatureStructure f1 = cas.createFS(t1);
f1.setFeatureValue(feat1, fsa1);
Annotation myAnnot = new Annotation(jcas);
-
+
fsa1.set(0, myAnnot);
myAnnot = new Annotation(jcas);
int id = myAnnot._id();
myAnnot = new Annotation(jcas);
int id2 = myAnnot._id();
- assertEquals(4, id2 - id); // type code, sofa, begin, end
-
- CASCompleteSerializer ser = Serialization.serializeCASComplete((CASMgr)cas);
+ assertEquals(4, id2 - id); // type code, sofa, begin, end
+
+ CASCompleteSerializer ser = Serialization.serializeCASComplete((CASMgr) cas);
// deserialize into a new CAS with a type system that only contains the builtins
CAS newCas = CasCreationUtils.createCas(new TypeSystemDescription_impl(), null, null);
- try {
Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
- } catch (Exception e) {
- assertTrue(false);
- }
+
LowLevelCAS ll = newCas.getLowLevelCAS();
- boolean caught = false;
- try {
+
assertEquals(id, ll.ll_getFSForRef(id)._id());
- } catch (LowLevelException e ) {
- caught = true;
- }
- assertFalse(caught);
- CasCompare cc = new CasCompare((CASImpl)cas, (CASImpl)newCas);
+ CasCompare cc = new CasCompare((CASImpl) cas, (CASImpl) newCas);
cc.compareIds(true);
assertTrue(cc.compareCASes());
-
- Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
+
+ Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
assertEquals(id, ll.ll_getFSForRef(id)._id());
- assertEquals(id2, ll.ll_getFSForRef(id2)._id());
-
- assertEquals(id2, ll.ll_getFSForRef(id2)._id());
+ assertEquals(id2, ll.ll_getFSForRef(id2)._id());
+
+ assertEquals(id2, ll.ll_getFSForRef(id2)._id());
assertTrue(((CASImpl) newCas).getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
assertEquals("Create the sofa for the inital view", newCas.getDocumentText());
@@ -174,16 +151,36 @@ public class CompleteSerializationTest extends TestCase {
newCas.getJCas();
// deserialize into newCas a second time (OF bug found 7/7/2006)
- try {
- Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
- } catch (Exception e) {
- assertTrue(false);
- }
- assertTrue(((CASMgr)cas).getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
+ Serialization.deserializeCASComplete(ser, (CASImpl) newCas);
+
+ assertTrue(((CASMgr) cas).getTypeSystemMgr().getType(CASTestSetup.GROUP_1) != null);
assertTrue(((CASImpl) newCas).isBackwardCompatibleCas());
- } catch (Exception e) {
- JUnitExtension.handleException(e);
}
}
-
+
+ @Test
+ public void thatReplacingTypeSystemInCasWorks() throws Exception {
+ // Construct a CAS with two views
+ CAS cas = CasCreationUtils.createCas();
+ cas.setDocumentText("First view text");
+ cas.createView("secondView").setDocumentText("Second view text");
+
+ // Save the CAS data to a buffer
+ TypeSystem originalTypeSystem = cas.getTypeSystem();
+ ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+ serializeWithCompression(cas, buffer, originalTypeSystem);
+
+ // Create a new type system
+ TypeSystemDescription newTSD = new TypeSystemDescription_impl();
+ newTSD.addType("my.Type", "", CAS.TYPE_NAME_ANNOTATION);
+
+ // Replace the type system in the CAS with the new type system
+ CAS tempCas = createCas(newTSD, null, null, null);
+ CASCompleteSerializer serializer = serializeCASComplete((CASImpl) tempCas);
+ deserializeCASComplete(serializer, (CASImpl) cas);
+
+ // Write the CAS data from the buffer back into the CAS - this throws an exception if the
+ // FSIndexRepositories are not properly reset (cf. UIMA-6352)
+ load(new ByteArrayInputStream(buffer.toByteArray()), cas, originalTypeSystem);
+ }
}