Issues for Genomic Maps FTF discussion list

List of issues (green=resolved, yellow=pending Board vote, red=unresolved)

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Issue 4234: vocabulary names issue
Issue 4235: VocabularyEntryIterator issue
Issue 4495: Request for Conformance Points

Issue 4234: vocabulary names issue (genomic_map-ftf)

1) The spec should say that the vocabulary names presented by the
vocabulary finder are usually equivalent to the names available from the
Vocabulary interface, but not necessarily always. This is because the
finder should provide _unique_ names, but names provided by individual
vocabularies cannot guarantee such uniqueness.

Resolution:
To the penultimate paragraph of section 2.3 (Controlled Vocabularies) (the sentence "The VocabularyEntrys are served by Vocabulary objects, which can in turn be obtained from VocabularyFinder objects."), add the following

2) The VocabularyEntryIterator could be described as behaving similarly
(or even equally) to the iterators in BSA. Which would mean to add to the
spec documentation that reset() can raise CORBA.NO_IMPLEMENT if the
underlying implementation does not allow resetting (and what minor code to
be used here),

Issue: Some aspects of the Genomic Maps Specification are not required for a functional implementation. Specifically, support for map correlations was an optional requirement in the Genomic Maps RFP and support for nested maps can be provided in several ways in addition to the one specified in the Genomic Maps Adopted Specification (e.g., the maps in the underlying map database could be preprocessed to integrate nested maps into unified maps, while, if necessary, keeping the original map fragments as individually available maps). Therefore, an adequately functional Genomic Maps service can be implemented that does not support map correlations or nested maps. This "Base Maps" service would be much simpler to implement, maintain, and use. 

Proposed Resolution: Add the following Conformance Points to the Genomic Maps Specification: (1) Base Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: (a) Base Maps implementations ignore the recursion_depth parameter for query operations (implicitly setting it to 0). (b) Base Maps implementations support only the MappableAssignment subtype of Assignment. (c) Base Maps implementations support Mappable as the type of left_flanking_entity and right_flanking_entity in the interface RelativePosition. They are not required to support Map as a type for left_flanking_entity and right_flanking_entity. (d) the additional exceptions listed under the Nested Maps conformance point below. This is a mandatory conformance point. 

(2) Nested Maps. Implements all modules and interfaces as described in Chapter 3, with the following exceptions: (a) the interface MapCorrelation and its factory MapCorrelationFactory (b) the interface AssignmentPairIterator and the data types AssignmentPair and MapPair. This is an optional conformance point. 

(3) Correlated Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: exceptions (a), (b), and (c) listed under Base Maps above. This is an optional conformance point. 

Therefore a Genomic Maps implementation must satisfy conformance point (1) Base Maps and may optionally satisfy either or both of conformance points (2) Nested Maps and (3) Correlated Maps.

Resolution:
Replace the last paragraph of 1.1 ("To be complian ... DsLSRLQSLink is optional") with the following, as a separate new section, 1.2: