On 03/11/20 11:19, Mario Juric wrote:
Thanks Rafaella.We haven’t had any need for type priorities yet, so we don’t use this feature at all. I am not sure, how the problem I am describing, where these annotations are not included in the selection, can be caused by arbitrary ordering?
Hi, unfortunately I can't try your example at the moment, but if `/JCasUtil.selectCovered/` behavior is similar to `AnnotationIndex.subiterator` behavior, than having an arbitrary ordering between your annotation types could impact the definition of "covered by".
I am referring to this passage in the /subiterator/ JavaDoc:For annotations x, y,|x < y|here is to be interpreted as "x comes before y in the index", according to the rules defined in the description of|this class| <https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/cas/text/AnnotationIndex.html>.
This definition implies that annotations|b|that have the same span as|annot|may or may not be returned by the subiterator. This is determined by the type priorities; the subiterator will only return such an annotation|b|if the type of|annot|precedes the type of|b|in the type priorities definition. If you have not specified the priority, or if|annot|and|b|are of the same type, then the behavior is undefined.
Bye, /Raf/
Cheers MarioOn 3 Nov 2020, at 09.49, Raffaella Ventaglio <raffaella.ventag...@celi.it> wrote: External email – Do not click links or open attachments unless you recognize the sender and know that the content is safe. Hi Mario, Have you defined the TypePriority[0] for your /SubType/ Annotation? As per the /AnnotationIndex/ documentation[1] this property impacts the ordering of different annotation types with an equal span coverage: * Annotations whose start offsets are equal and whose end offsets are equal are sorted based on|TypePriorities| <https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/resource/metadata/TypePriorities.html>if type priorities are specified. Type Priorities specification is an optional element of the component descriptor). When type priorities are in use, if|a.start = b.start|,|a.end = b.end|, and the type of|a|is defined before the type of|b|in the type priorities, then|a < b|. * If none of the above rules apply, then the ordering is arbitrary. This will occur if you have two annotations of the exact same type that also have the same span. It will also occur if you have not defined any type priority between two annotations that have the same span. Hope this helps. Bye, /Raf/ [0] https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/resource/metadata/TypePriorities.html [1] https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/cas/text/AnnotationIndex.html On 02/11/20 22:16, Mario Juric wrote:Hi, I am migrating some code to the new UIMA v3 select API, and I am seeing some odd behaviour. My reference implementation is the good old JCasUtil.selectCovered, which I am trying to replace first, and I thought the following line should do it: jCas.select(annotationType).coveredBy(annotation) This works fine as long annotation is of annotationType, but I am seeing some strange different output when annotation is of a different Annotation subtype. More specifically I have a unit test (see bottom) where annotationType is the Annotation class and annotation is an instance of some direct subtype of Annotation, which was added to the CAS index prior to the call. In this case all annotations that have the exact same bounds as annotation are not selected, only those that are completely enclosed get selected (begin > annotation.getBegin() and end < annotation.getEnd()). The JCasUtil includes the missing annotations. None of the available select configurations seem to address this, and superficially stepping through the code didn’t help me much, since it’s not trivial to get into the details of the underlying API, so I thought that I maybe get a faster answer here. Cheers Mario @Test public void verify_selectCovered() throws CASException, ResourceInitializationException { JCas jCas = JCasFactory.createJCas(); Annotation[] fixture = new Annotation[] { new Annotation(jCas, 5, 10), new Annotation(jCas, 5, 15), new Annotation(jCas, 0, 10), new Annotation(jCas, 0, 15), new Annotation(jCas, 5, 7), new Annotation(jCas, 8, 10), new Annotation(jCas, 6, 9), new Annotation(jCas, 5, 10) }; Stream.of(fixture).forEach(Annotation::addToIndexes); assertEquals(4, JCasUtil.selectCovered(jCas, Annotation.class, fixture[0]).size()); List<Annotation> selection1 = jCas.select(Annotation.class) .coveredBy(fixture[0]) .collect(Collectors.toList()); assertEquals(4, selection1.size()); SubType subType = new SubType(jCas, 5, 10); subType.addToIndexes(); assertEquals(5, JCasUtil.selectCovered(jCas, Annotation.class, subType).size()); List<Annotation> selection2 = jCas.select(Annotation.class) .coveredBy(subType) .collect(Collectors.toList()); assertEquals(5, selection2.size()); // Fails! } ________________________________ Disclaimer: This email and any files transmitted with it are confidential and directed solely for the use of the intended addressee or addressees and may contain information that is legally privileged, confidential, and exempt from disclosure. 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