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This page describes additional UIMA Version 3 iterator support for accessing Feature Structures.  It draws on the uimaFIT design, with these goals:

  • uniformity (ease of learning)
  • conciseness (in expression)
  • alignment with / exploitation of Java 8 styles, including streams
  • hiding implementation internals

PDF of chapter on select documentation for review

This is the version 2 after incorporating most of Richard's suggestions on version 1, uploaded Monday 17 Oct at 3:45 EDT.

Here: 

View file
nameuima_v3_users_guide.pdf
height250

Conceptual overview MS

Gliffy Diagram
nameuv3 fs iteration design

Translations of uimaFIT select methods to the new API

Format: the samples not in a box are uimaFIT styles; in the boxes are possible new API styles (sometimes multiples), with some commentary.

select

Convenience method to iterator over all features structures of a given type.

select(JCas, Class<T>)
Code Block
languagejava
jcas.select() // selects an implicit index,
              // starts with top level default bag index
              // switches to AnnotationIndex if any subsequent build operations imply needing this
              // switches to explicitly specified index if subsequently specified
              // can subsequently specify a top-level type (must be the type or a subtype of the type defined in the index)
 
jcas.select(Token.class)  // note: in UV3, these should also work with cas (not just with jcas)? 
                          //       We're trying to reduce the distinction between these because it's less needed in UV3.
jcas.select(Token.type)
jcas.select("my.package.Token") 
 
for (Token.class : jcas.select(Token.class)) {
  ...
}
 
jcas.select(Token.class).forEach( t -> System.out.println(t) );
jcas.select(Token.class).forEach(System.out::println);      
select(FSArray, Class<T>)
select(FSList, Class<T>
Code Block
languagejava
myArray.select(Token.class)  // select also on arrays and fslists
myList.select(Token.class)  
myIndex.select(FSList, Class<T>
Code Block
languagejava
myIndex.select(Token.class)  // select also works on uima indexes
selectAll

Convenience method to iterate over all features structures indexed in a particular index in a particular view. 
(.allViews()) not part of uimaFIT). 

selectAll(JCas)
Code Block
languagejava
jcas.select() // leave off type specification
selectAt

Get all annotations of the given type at the specified offsets, i.e. all annotations with exactly the given start and end offset.

MS: Does this mean covered-by (limit the FSs returned) or startAt - no limit?

REC: It does not mean covered-by because only annotations at the exact specified offset are returned. If there are multiple annotations at the given offset, then all of the specified type are returned.

selectAt(JCas, Class<T>, int, int)
Code Block
languagejava
jcas.select(Token.class).at(1, 3)
selectBetween

Get a list of annotations of the given annotation type located between two annotations. Does not use subiterators and does not respect type priorities. Zero-width annotations what lie on the borders are included in the result, e.g. if the boundary annotations are [1..2] and [2..3] then an annotation [2..2] is returned. If there is a non-zero overlap between the boundary annotations, the result is empty. The method properly handles cases where the second boundary annotations occurs before the first boundary annotation by switching their roles.

selectBetween(Class<T>, AnnotationFS, AnnotationFS)

Example same as selectBetween(JCas, Class<T>, AnnotationFS, AnnotationFS) below unless we introduce a static method.

selectBetween(JCas, Class<T>, AnnotationFS, AnnotationFS)
Code Block
languagejava
jcas.select(Token.class).between(fs1, fs2) // might make more sense because we are using offsets, not index positions
jcas.select(Token.class).startAt(fs1).endAt(fs2) // this looks more like index positions... 
selectByIndex
selectByIndex(JCas, Class<T>, int)
Code Block
languagejava
jcas.select(Token.class).skip(indexPosition)  // skip is standard stream operator
selectCovered

Get a list of annotations of the given annotation type constrained by a 'covering' annotation. Iterates over all annotations of the given type to find the covered annotations. Does not use subiterators.

The covering annotation is never returned itself, even if it is of the queried-for type or a subtype of that type.
 

MS: Not sure why this is special-cased?

REC: Because the covering annotation itself would always be included in the result and it is almost never needed. So handling it specifically (since we already know it) is easier than tediously filtering it out from the result in 99.9% of the cases.

MS: Good point.  Just for completeness, I'll point out a somewhat surprising fact that the covering annotation is not always included; it is only returned if

  • it is in the index 
  • it's type is the index's type or subtype.
  • You can make annotations that don't fit these criteria, and use them as "covering" spec.
selectCovered(Class<T>, AnnotationFS)

Same as selectCovered(JCas, Class<T>, AnnotationFS) below unless we introduce a static method.

selectCovered(JCas, Class<T>, AnnotationFS)
Code Block
languagejava
jcas.select(Token.class).within(contextAnnotation) // within is variant of coveredby
selectCovered(JCas, Class<T>, int, int)
Code Block
languagejava
jcas.select(Token.class).within(1,3)
selectCovering

Get a list of annotations of the given annotation type constraint by a certain annotation. Iterates over all annotations to find the covering annotations.

selectCovering(Class<T>, AnnotationFS)

Same as selectCovering(JCas, Class<T>, AnnotationFS) below unless we introduce a static method.

selectCovering(JCas, Class<T>, AnnotationFS)
Code Block
languagejava
 jcas.select(Token.class).containing(contextAnnotation) // containing is variant of covering
selectCovering(JCas, Class<T>, int, int)
Code Block
languagejava
 jcas.select(Token.class).containing(1,3) 
selectFollowing

Returns the n annotations following the given annotation.

selectFollowing(Class<T>, AnnotationFS, int)

Same as selectFollowing(JCas, Class<T>, AnnotationFS, int) below unless we introduce a static method.

selectFollowing(JCas, Class<T>, AnnotationFS, int)
Code Block
languagejava
// Initial brainstorming
jcas.select(Token.class).startAt(contextAnnotation).limit(10) // it is IMHO not entirely clear here that contextAnnotation is not included in the result...
jcas.select(Token.class).seek(contextAnnotation).skip(1).limit(10) // somehow too complex...
jcas.select(Token.class).following(contextAnnotation).limit(10)
 
// Suggestion MS - deleted - I like REC's better with the fs first.

 
// Suggestion REC 1
jcas.select().following(fs, 10)  // the 10 FSs >= fs
jcas.select().following(fs, 10, -3) // the 10 FSs >= { fs , after a -3 offset }
jcas.select().following(2, 20, 10, -3) // the 10 FSs >= { a bounding FS with begin=10, end=100, offset by -3}
jcas.select().preceding(10, 100, 3)  // the 3 FSs < a bounding FS with begin=10, end=100, in reverse order(?)
// Suggestion REC 2
jcas.at(fs).select(Token.class).following(10)  // the 10 FSs >= fs
jcas.at(fs).select(Token.class).skip(-3).following(10) // the 10 FSs >= { fs , after a -3 offset }
jcas.at(10, 100).select(Token.class).preceding(3)  // the 3 FSs < a bounding FS with begin=10, end=100, in reverse order(?)
// MS: following(10) is the same as the standard stream method limit(10), I think. 
// Suggestion REC 3
jcas.select(Token.class, fs).following(10)  // the 10 FSs >= fs
jcas.select(Token.class, fs).skip(-3).following(10) // the 10 FSs >= { fs , after a -3 offset }
jcas.select(Token.class, 10, 100).preceding(3)  // the 3 FSs < a bounding FS with begin=10, end=100, in reverse order(?)
// MS: basic idea: extend select syntax, with 2nd positional argument, representing a position or a bound

REC: I would put the context to the front and the conditions to the back...

selectPreceding

Returns the n annotations preceding the given annotation.

selectPreceding(Class<T>, AnnotationFS, int)

Same as selectPreceding(JCas, Class<T>, AnnotationFS, int) below unless we introduce a static method.

selectPreceding(JCas, Class<T>, AnnotationFS, int)
Code Block
languagejava
jcas.select(Token.class).startAt(contextAnnotation).reverse().limit(10)
jcas.select(Token.class).startAt(contextAnnotation).limit(-10) // probably not because limit is standard stream method
                                                               // throws exception on negative arg
selectSingle

Get the single instance of the specified type from the JCas.

selectSingle(JCas, Class<T>)
Code Block
languagejava
jcas.select(DocumentMetaData.class).single()
jcas.select(DocumentMetaData.class).single().getDocumentUri()
jcas.select(DocumentMetaData.type).get()  // alternative name
jcas.select(DocumentMetaData.type).get(1) // arg is offset
selectSingleAt

Get a single annotations of the given type at the specified offsets.

selectSingleAt(JCas, Class<T>, int, int)
Code Block
languagejava
 jcas.select(Token.class).at(begin, end).single()
 jcas.select(Token.class).at(begin, end).get()
selectSingleRelative

Return an annotation preceding or following of a given reference annotation.

selectSingleRelative(Class<T>, AnnotationFS, int)

Same as selectSingleRelative(JCas, Class<T>, AnnotationFS, int) below unless we introduce a static method.

selectSingleRelative(JCas, Class<T>, AnnotationFS, int)
Code Block
languagejava
jcas.select(Token.class).startAt(contextAnnotation).skip(10).single()
jcas.select(Token.class).startAt(contextAnnotation).reverse().skip(10).single()
jcas.select(Token.class).startAt(contextAnnotation).skip(-10).single()
jcas.select(Token.type).at(contextAnnotation, -10),get();