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National Cancer Institute Center for Bioinformatics
Protege 1.4.2 Release Notes
24 September 2010

Product Changes

The objective of this release of Protege 1.4.2 is to provide the remaining feature requests and 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 1.4.2 release.

New Feature Highlights
* GF#:  Text

* GF#:  Text  

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.
  • 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
    • Losing a connection between a client and the server in the middle of an batch job results in misleading log.  Information is output to the logs stating that an operation was completed when it actually wasn't.  This scenario does not occur if the server is shut down programmatically, the logs record accurately the state of a batch job at the time of the interruption.
  • 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.

This is deemed an inconsistency in behavior and is slated for a fix in 1.4.1. For now, editors need to be aware that deleting associations in batch requires that the association's rdf:ID be entered in its entirety.

List of New Features

GForge number
(hyperlinked)

Brief description of item

16191

Export of inferred Ontology - Tweaks to output file

18998

Load explanation server from the Protege KB using the OWL API converter in Protege 3.4

18999

Serialize state at explanation server shut-down so start-up can be incremental since previous run

22785

Only exports the first page of results in LQT search

23385

update protege/workflow and SWM to handle new XML Literal complex properties

24359

Batch jobs performance improvements

24360

Batch jobs robustness

24461

Allow multiple domains and ranges

26328

Report Writer outputs extra instances in 'Property value present' query

26416

Unable to get filler values from roles in query export


26548

A button to refresh the class hierarchy tree in the class browser pane.

 

26567

Disable Tooltips for NCI ontologies.

 

26568

Add a Complete button to workflow subtab

 

26569

Remove Unnecessary scripts from Protege Server / Explanation Server Folder

 

26570

Lucene query tab default setting will not search PATO

 

26571

Export of Annotations are viewed by OWLAPI as ObjectProperties

 

26573

Start or restart of the Explanation server has lost the time/date reference

 

26605

In all NCI Editor Tabs except the Edit tab concept name property is not displayed properly

 

26606

Edit set as default instead of Load Please

 

26634

“by code” (rdf:ID is meaningless)

 

26666

Configurability

 

26668

wiki collaboration

 

26669

Runtime classification

 

27029

Results panel callable from the explanation tab

 

 

 

 

List of Bug Fixes


GForge number
(hyperlinked)

Brief description of item

7679

(make configurable) Default search parameters for Advanced Search are not default for search w/in search

9298

Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work

11082

Change of Focus after Retire

20906

Protege incorrectly exporting names with quotes

21549

Single quote mark around multi-word parents

21738

Hierarchy is not refreshing the D when retire concept

21946

Incorrect unretire functionality

22090

Tool Tab compression and disappearance

22104

search string appears empty when invoked from restriction dialog box

22181

Convert project to format seems to run twice

22902

Create a restriction with retired individual in premerge only

23457

lucene search option falls off pull down list not sure of the trigger

23527

Explanation server syncronization issue with retire action

23564

protege:readOnly=true behavior is unexpected

23581

Inconsistant reject button availablility

23582

PROMPT Tree View reject gave null pointer exception

23710

Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions

23795

Legacy_Concept_Name should not transfer during merge

23874

User's Guide goes to Protege 2000 page

23876

Cannot change case of PT and PN

24274

inheritance of role restrictions is no longer working correctly

24432

Strange behavior on Preferred Name change

24445

Failure of Lucene to index at runtime

24503

LQT nested query causes error dialog

24803

Edit of Preferred_Name does not always sync the NCI PT

24837

Search using contains is very slow

24955

Rejection of changes to Retired Concept branch caused deletion of newly retired classes

25019

Selection of display slot for individuals is not scrollable

25464

Properties that have spaces cannot be edited in the Edit tab

25645

identificable?

25646

SPCA contrib source

25769

Error Message displays association error, yet performs edit

25840

Strange output during Explanation Server restart

26169

Duplicate Full Syn atom could not be deleted via NCI Editor Tab

26432

unable to find concept

26463

Remove hard-coding of LONG_DEFINITION and other deprecated complex properties

26478

Cannot add role after editing a parent due to loss of focus in class browser

26512

"Increase or Decrease Font Size" causes Edit Tab increment

26540

extra prefix string when exporting ALT-DEFINITION and DEFINITION

26682

report writer fails to produce output

26715

EditTab not persisting complex properties correctly

26759

GO_Annotation props not showing in correct panel

27037

Allows duplicated roles to be added with batch processing

27038

Different “Reviewer Name” is displayed

27041

"Delete Parent" is allowed to delete last parent when batch processing.

27043

OLD_PARENTS and OLD_ROLEs ought to be added simultaneously

27076

batch delete definitions fails

27078

“Required field” for FULL_SYN is not enforced when doing Batch Processing.

27079

“Required field” for DEFINITION or ALT_DEFINITION is not enforced when doing Batch Processing.

27248

deleting a role takes rdfs:label (preferred name) and should take rdfs:ID

27755

Trouble with usage of datatype properties

27757

Spotty Synchronization of NCIEditor Hierarchy with Explanation and OWLClasses Tabs

27855

Enable the use of rdfs:comment

27969

New strange behavior on PT change

28088

Preretire fails if redirect or remove two of the same restrictions pointing to the preretiree

28123

Generate Report with attributes does not display Definition or FULL_SYN

 

 

 

 

 

 

 

 


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

23917

IndexOutOfBoundsException in Mac OS X

24813

Red Widget Appears after Loading Thesaurus OWL File to Protege Database

26195

Variability in Batch Loading Times

26256

Notes on behavior of logins to the Annotation project

26730

Hierarchy scrolls out of control

26744

embedded XML is converting XMLLiterals to strings

27677

Changing the value of property "protege:readOnly" doesn't work.


https://gforge.nci.nih.gov/tracker/?group_id=174&atid=822&func=detail&aid=27755

 

 


 

 


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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