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https://issues.apache.org/jira/browse/UIMA-4049?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14170890#comment-14170890
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Peter Klügl commented on UIMA-4049:
-----------------------------------
I do not know if this is a good idea. I often work transformation-based with
Ruta meaning that I change the offsets of a given annotation dependent on
occuring patterns. If the setter methods should not be used, then you need to
create new annotations. The old ones remain in the CAS filling it up.
> The curious case of the zombie annotation
> -----------------------------------------
>
> Key: UIMA-4049
> URL: https://issues.apache.org/jira/browse/UIMA-4049
> Project: UIMA
> Issue Type: Bug
> Components: Core Java Framework
> Reporter: Richard Eckart de Castilho
> Assignee: Marshall Schor
> Attachments: CuriousTestCase.java
>
>
> When annotations are removed from indexes, sometimes they come back... the
> following test case shows how an annotation is removed but still present when
> iterating over the index later.
> {code}
> @Test
> public void testForZombies() throws Exception
> {
> // No zombie here
> int[] offsets1 = { 0, 4, 5, 11, 12, 21, 22, 25, 26, 29, 30, 35, 36,
> 40, 41, 50, 51, 60, 61,
> 64, 64, 65 };
> testForZombies("Dies flößte Friedrich II. für seine neue Eroberung
> Besorgnis ein.", offsets1);
>
> // Zombie hiding in here
> int[] offsets2 = { 0, 3, 4, 7, 8, 13, 14, 18, 19, 22, 23, 33, 34, 35
> };
> testForZombies("Ich bin Franz III. von Hammerfels !", offsets2);
> }
> public void testForZombies(String aText, int[] aOffsets) throws Exception
> {
> // Init some dictionaries we ues
> Set<String> names = new HashSet<String>();
> names.add("Friedrich");
> names.add("Franz");
> Set<String> suffix = new HashSet<String>();
> suffix.add("II.");
> suffix.add("III.");
> // Set up type system
> TypeSystemDescription tsd = new TypeSystemDescription_impl();
> tsd.addType("Token", "", CAS.TYPE_NAME_ANNOTATION);
>
> // Create CAS
> CAS jcas = CasCreationUtils.createCas(tsd, null, null);
> jcas.setDocumentText(aText);
>
> Type tokenType = jcas.getTypeSystem().getType("Token");
> Feature beginFeature = tokenType.getFeatureByBaseName("begin");
>
> // Create tokens in CAS
> for (int i = 0; i < aOffsets.length; i += 2) {
> jcas.addFsToIndexes(jcas.createAnnotation(tokenType, aOffsets[i],
> aOffsets[i+1]));
> }
>
> // List the tokens in the CAS
> for (AnnotationFS token : jcas.getAnnotationIndex(tokenType)) {
> System.out.printf("Starting with %s%n", token.getCoveredText());
> }
> // Merge some tokens, in particular "Franz" "III." -> "Franz III."
> and "Friedrich" "II."
> // into "Friedrich II."
> AnnotationFS previous = null;
> List<AnnotationFS> toDelete = new ArrayList<>();
> for (AnnotationFS token : jcas.getAnnotationIndex(tokenType)) {
> if (previous != null && names.contains(previous.getCoveredText())
> && suffix.contains(token.getCoveredText())) {
> token.setIntValue(beginFeature, previous.getBegin());
> toDelete.add(previous);
> }
> previous = token;
> }
> // Remove the no longer necessary tokens ("Friedrich" and "Franz"),
> since we expanded the
> // following tokens "III." and "II." to include their text
> Set<String> removedWords = new HashSet<String>();
> for (AnnotationFS token : toDelete) {
> System.out.printf("Removing %s%n", token.getCoveredText());
> removedWords.add(token.getCoveredText());
> jcas.removeFsFromIndexes(token);
> }
> // Check if the tokens that we wanted to remove are really gone
> for (AnnotationFS token : jcas.getAnnotationIndex(tokenType)) {
> System.out.printf("Remaining %s%n", token.getCoveredText());
> if (removedWords.contains(token.getCoveredText())) {
> org.junit.Assert.fail("I saw a zombie!!!");
> }
> }
> }
> {code}
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