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Confirmed issues in the Hierarchical Model Composition package specification

This page lists all issues officially noted for any release of the the SBML Level 3 Hierarchical Model Composition package specification.

Release 3

Release 3 was released 14 November, 2013. It incorporates all the fixes to Releases 2 and 1, below.

In the following table, the ID# of each issue refers to the reference number automatically assigned to the issue in the SBML issue tracking system. The gaps in this numbering are not consequential for SBML and do not signify deleted or unresolved issues. Issues with no ID# were issues corrected by the Hierarchical Model Composition package working group, but never entered into the sourceforge tracker.

The page/line numbers of each issues refer to Release 3 of the specification, where the issue was found.

ID# Description Page and line number(s) Date added
253 Should be validation rule 21011 that restricts the use of the 'deletion' and 'conversion factor' attributes in the same ReplacedElement. p. 51 05 Apr.'14

Release 2

The following issues were discovered and fixed in Release 3. For historical purposes, Release 2 (released 15 February 2013) can still be downloaded but should be considered superseded by Release 3, above.

The page/line numbers of each issues refer to Release 2 of the specification, where the issue was found.

ID# Description Page and line number(s) Date added
(no id) Text should say that the 'required' flag should always be 'true'. p. 11 line 13 31 May '13
(no id) Validation rule 20204 should be removed. p. 43 line 38 31 May '13
(no id) Validation rule 20203 should be removed. p. 43 line 33 01 July '13
(no id) Validation rule 20212 should be added, and say that the 'required' flag should always be 'true'. p. 44 line 24 01 July '13
(no id) Need new validation rule 20712 saying that an SBaseRef element must point to an object. p. 47 line 10 16 July '13
(no id) Need new validation rule 20713 saying that only one of its object-pointing attributes must be set. p. 47 line 10 16 July '13
(no id) Need new validation rule 21201 saying that replaced classes must match (with Parameter exception). p. 50 line 10 24 July '13
(no id) Need new validation rule 21202 saying that replacements should have id if replaced had an id. p. 50 line 10 24 July '13
(no id) Need new validation rule 21203 saying that replacements should have metaid if replaced had a metaid. p. 50 line 10 24 July '13
(no id) Need new validation rule 21204 saying that replacements should have a package id if replaced had a package id. p. 50 line 10 24 July '13
(no id) Need new validation rule 10501 saying that units of replacements should match, caveat conversion factors. p. 50 line 10 24 July '13
(no id) Need better explanation of replacements and deletions of nested objects: replacing or deleting an element whose parent has been replaced or deleted is legal, and does not imply any new relationship with the replaced or deleted parent. Section 3.6.5 in particular needs to be updated. p. 24 line 20+ 20 Oct '13

Release 1

The following issues were discovered and fixed in Release 2. For historical purposes, Release 1 (released 30 November 2012) can still be downloaded but should be considered superseded by Release 2 and 3, above.

In the following table, the ID# of each issue refers to the reference number automatically assigned to the issue in the SBML issue tracking system. The gaps in this numbering are not consequential for SBML and do not signify deleted or unresolved issues. Issues with no ID# were issues corrected by the Hierarchical Model Composition package working group, but never entered into the sourceforge tracker.

The page/line numbers of each issues refer to Release 2 of the specification, where the issue was fixed.

ID# Description Page and line number(s) Date added
3596852 The UML box for ExternalModelDefinition should include the md5 attribute. p. 13 Fig. 2 15 Feb.'13
3594223 The UML diagram claimed the spelling of a child SBaseRef object was 'sbaseRef', while the text claimed the spelling was 'sBaseRef'. After a vote from the Hierarchical Model Composition package working group, 'sBaseRef' was declared canonical, and 'sbaseRef' was declared legal but deprecated. p. 25 Fig. 7 and
p. 28 line 22-26
15 Feb.'13
(no id) Validation rule 10301 should not mention ExternalModelDefinitions. p. 42 line 20 15 Feb.'13
(no id) Validation rule 10301 should mention the SId namespace from other packages. p. 42 line 26 15 Feb.'13
(no id) No validation rule present (now 10311) describing the syntax of the comp:name attribute. p. 43 lines 4–5 15 Feb.'13
3599004 Validation rule 20201 should reference the core specification as defining the need for the comp:required attribute, not the 'comp' specification. p. 43 lines 29–30 15 Feb.'13
3599001 Validation rule 20205 was misnumbered as 20211. p. 44 line 1 15 Feb.'13
(no id) Validation rule 20210 should formally define the "Hierarchical Model Composition" namespace. p. 44 lines 22–23 15 Feb.'13
(no id) Validation rule 20302 also applies to the Hierarchical Model Composition namespace. p. 44 lines 34–35 15 Feb.'13
3599096 Validation rule 20303 should mention the optional comp:name, comp:modelRef and comp:md5 attributes. p. 44 lines 38–39 15 Feb.'13
3599432 Validation rule 20304 should state that the target of an ExternalModelDefinition must be an SBML Level 3 Version 1 document: the version must be specified. p. 44 line 43 15 Feb.'13
(no id) Validation rule 20305 should mention that ExternalModelDefinition objects are legal targets of the comp:modelRef attribute. p. 45 line 2 15 Feb.'13
(no id) No validation rule present (now 20710) to state that an SBaseRef object may have an SBaseRef child. p. 48 lines 7–9 15 Feb.'13
3594223 No validation rule present (now 20711) to clarify the 'sbaseRef' vs. 'sBaseRef' spelling. p. 48 lines 10–12 15 Feb.'13
3598853 Validation rule 20803 should mention the optional comp:name attribute on Port objects. p. 48 lines 23–24 15 Feb.'13
(no id) Validation rule 20903 should state that the comp:id attribute is optional, not required, and should mention the optional comp:name attribute for Deletion objects. p. 48 lines 39–41 15 Feb.'13
3599456 Validation rules 21007, 21008, and 21009 were duplicates of validation rules 10308, 10309, and 10310, respectively. p. 49 lines 28–30 15 Feb.'13
3599480 Validation rule 21010 should read 'the same object' instead of 'the object'. p. 49 line 31 15 Feb.'13
3599587 Validation rule 21105 was a duplicate of validation rule 10308. p. 50 line 9 15 Feb.'13


Please use our issue tracking system for any questions or suggestions about this website. This page was last modified 05:24, 5 April 2014.