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  1. OMG Specification

Macromolecular Structure — Closed Issues

  • Acronym: MACSTR
  • Issues Count: 2
  • Description: Issues resolved by a task force and approved by Board
Closed All
Issues resolved by a task force and approved by Board

Issues Descriptions

Ambiguity in section 2.3.2 of the specification describing the EntryFactory

  • Key: MACSTR-2
  • Legacy Issue Number: 4737
  • Status: closed  
  • Source: Research Collaboratory Structural Bioinformatics ( Douglas Greer)
  • Summary:

    In section 2.3.2 of the specification describing the EntryFactory
    Interface, there is a subtle ambiguity that if interpreted the
    wrong way would might require indefinite locking of the underlying
    data source. In particular the "get_entry_from_id()" method does
    not specify a behavior if the id given was not in the list of
    ids returned by the method "get_entry_id_list()" or
    "get_entry_modification_dates()".

    I propose that this be resolved by:

    1) adding the following sentence at the end of the first paragraph
    of the subsection labeled "Obtaining an Entry Object".

    "This method may successfully return an Entry object even when
    the id specified was not included in the list returned by
    get_entry_id_list().

    2) In the first two sentences of the subsection labeled "Retrieving
    Lists of Entries" the word "known" be inserted after the word "all"
    So that they read:

    "get_entry_id_list() retrieves a list of all known entries.

    The get_entry_modification_dates() method retrieves a list of all
    known entries along with the date they were last modified.

  • Reported: MACSTR 1.0b1 — Wed, 5 Dec 2001 05:00 GMT
  • Disposition: Resolved — MACSTR 1.0
  • Disposition Summary:

    Make the two changes to the text as described below to remove the ambiguity

  • Updated: Fri, 6 Mar 2015 20:58 GMT

issue: Identifier Strings

  • Key: MACSTR-1
  • Legacy Issue Number: 4550
  • Status: closed  
  • Source: Research Collaboratory Structural Bioinformatics ( Douglas Greer)
  • Summary:

    The definition of "Identifier Strings" in the MMS specification
    is incompatible with other LSR specifications.

    PROPOSED RESOLUTION:

    On page 2-3 of dtc/2001-04-06 change the paragraph that
    reads:

    ---- Old paragraph ----

    The kind-field of a component is used to represent information
    indicating the release, version or mutation of an entry, and can
    be empty. An empty kind-field is synonymous with the 'standard'
    or most widely accepted version. It is up to the implementation
    to document the syntax and semantics of the version information.


    To:

    ---- New paragraph ----

    The kind-field of a component is used to represent information
    indicating the release or version of an entry, and can be empty.
    An empty kind-field is synonymous with the most recent version.
    It is up to the implementation to document the syntax and
    semantics of the version information.


    And also on page 2-3 of dtc/2001-04-06 change the paragraph that
    reads:

    ---- Old paragraph ----

    Except for the assumption that an empty kind-field signifies a
    standardized version, the revised submission on Biomolecular Sequence
    Analysis [BSA99] and the revised submission on Genomic Maps[GM99] use
    the same Identifier type and semantics. In these specifications an
    empty kind-field signifies the most recent version. The default was
    made to signify the standard version based on the general software
    engineering principle that applications (in particular end-user
    demonstrations) rely on fixed names to generate predictable
    results. The potential harm to system reliability caused by the
    substitution of new data is seen to override the potential benefit of
    using the modified data. This is reinforced by the fact that the newer
    data can be accessed from applications by using a non-empty
    kind-field.


    To:

    ---- New paragraph ----

    An empty kind-field signifies the most recent version as specified
    in the revised submission on Biomolecular Sequence Analysis [BSA99].
    However, it is strongly recommended that changes be limited to
    corrections of data that are clearly erroneous. In particular,
    new refinements of existing experimental data should be given
    new identifiers.

  • Reported: MACSTR 1.0b1 — Fri, 31 Aug 2001 04:00 GMT
  • Disposition: Resolved — MACSTR 1.0
  • Disposition Summary:

    Change the two paragraphs defining the Identifier Strings as described below

  • Updated: Fri, 6 Mar 2015 20:58 GMT