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National Cancer Institute Center for Bioinformatics
Protege 1.4.3 Release Notes
26 January 2011


Product Changes


The objective of this release of Protege 1.4.3 is to provide the remaining bugs fixes found in previous Protege releases that have been determined to be a priority for the final release of Protege.  Currently, there is no development planned after the 1.4.3 release.

Behavior To Be Aware Of

A number of GForge items were created that need additional comment.

  • GF#22104 - search string appears empty when invoked from restriction dialog box*
    • When searching for filler values when creating Restrictions, a secondary search box occasionally shows up empty and the search parameters need to be entered again.  When creating a restriction, the first, second and third dialog boxes appear normally. The trouble occurs randomly and with a low frequency: when one gets to the 'Select a named Class' dialog, fills in a search term, then hits the search button, the 'Search for Class' dialog opens. This dialog box ordinarily has the selected string and Search Results filled in. On occasions, this dialog box appears without either the selected string or the search results.  The Search for Class dialog box must then be directly edited to initiate the search brand new.
  • GF#23565 & 29720- refactoring namespaces
    • Refactoring namespaces and class names works correctly; however, when followed by a complex operation such as split or merge in the same editing session, the refactored class is not identified properly by the GUI.  This behavior persists until the protege server is restarted.  This functionality is intended to support BGT and other vocabularies such as NPO that reference multiple namespaces, this functionality is not intended for NCIt editing.
  • GF#24510 - Need a fail-safe for creating codes for properties
    • As this operation is not done frequently, a workaround, consisting of selecting the "code" as the display slot for properties followed by an examination of the sorted list, was deemed acceptable for production.
  • GF#26667 - Robustness/QC
    • If the network goes down or is disconnected during a batch edit, the log will indicate more concepts created than were actual created.  Because of this, a user will need to re-run any batch edits once the protégé server is available again.
  • GF#28509 - Edit tab does not handle & or < properly
    • The & and < characters are handled differently when using Edit tab or batch load.  For edit tab you do NOT need to escape & or <, in a batch load file & needs to be & and < needs to be <
  • GF#28710 - The rejection of the modification failed in Prompt.
    • The "Reject Diff" in the "Tree View tab" of Prompt works, but "Reject Diff" in the "Table View tab" doesn't work.  This has been left as is because of the redundancy in functionality.
  • GF#29143 - role groups not handled when toggling prim/defined
    • Editing a legacy role group is problematic as the GUI enforces the class expressions we have defined for role groups.  A concept can be edited without problems as long as the role group itself is not edited.
  • GF#29347 - Cannot complete SMW roundtrip with Protege / NPO SMW
  • GF#29358 - (NPO) Association Edit/Delete failed
    • Relations using the built-in owl elements can only be constructed with the owl:disjointWith element, other elements do not work.
  • GF#29513 - Improved formatting of batch load with error
  • GF#29517 - When invalid format is provided on a clone it doesn't retain previously entered Definition
    • The definition must be corrected prior to another copy/clone attempt.  Will be considered for a fix in a future release.
  • GF#29665 - "Create Workflow Task" doesn't work" in 1.4.2.223 ByCode.
    • Creating workflow tasks work in a "by name" vocabulary.  Will be considered for a fix in a future release.
  • GF#29752 - Generate Reports shows undesirable internal values

List of Bug Fixes


GForge number
(hyperlinked)

Brief description of item

29517

When invalid format is provided on a clone it doesn't retain previously entered Definition

29752

Generate Reports shows undesirable internal values

29753

Extra box character shows in generated report

29758

Duplicate restrictions are found in the class BRCA1_wt_Allele.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


Other Items Closed


The defects in the following list were not reproducible, or were fixed as a by-product of refactoring, or were related to configuration setup.

GForge number
(hyperlinked)

Brief description of item

 

 

 

 

 

 

 

 

 

 

 

 

 

 


 

 

 


Remaining Issues

The defects in the following list were not reproducible, or were fixed as a by-product of refactoring, or were related to configuration setup.

GForge number
(hyperlinked)

Brief description of item

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


CORE Product Dependencies

No caCORE dependencies. This software is used for editing and maintaining NCI Thesaurus and BiomedGT

Release History

Release

Date

1.0

Jun 07

1.1

Sept 07

1.2.0

Dec 07

1.2.1

Feb 08

1.2.2

May 08

1.2.3

Jul 08

1.2.3 Patch

Aug 08

1.3.0

Mar 09

1.4.0

Sep 09

1.4.1

Jan 10

1.4.2

Sep 10



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