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National Cancer Institute Center for Bioinformatics
Protege 1.4.3 Release Notes

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07 February 2011

Product Changes

The objective of this release of

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Protégé 1.4.3 is

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to provide the remaining bugs fixes found in

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previous Protégé releases that have been determined to be a priority for the final release of

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Protégé Currently, there is no development planned after the 1.4.3 release.

Behavior

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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.

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GForge number

Brief description of item

Workaround

GF#30038

Change of Semantic_Type value after changing PTs.

GF#30265

Possible bug in LQT

If user encounters this issue and wants to continue to proceed with the clone immediately, they must resolve the invalid class name and delete and re-type the definition in the "Clone" dialog box. Then click OK to save

GF#30338

If only 2 N&S restriction and one is removed through merge of filler values - shows as defined

Users should probably manually check known referencing classes before or after the merge. User is able to correct the issue by either indicating that the concept is no longer fully defined or adding a condition that makes it fully defined.

GF#30352

Changing Concept Name in namespace and refreshing causes blank preferred name

The workaround is to re-start the client.

GF#30375

After resolving referencing class in PreRetire, does not refresh referencing classes list

If the user is aware of the refresh issue, they can continue editing without concequence. If they want to visually confirm that all referencing classes have been resolved, they can clear the PreRetire pane and re-drag in the class and examine the referencing classes sub-tab.

GF#30376

If rename class_name two classes, can never PreMerge them.

The workaround is to toggle around in the OWLClasses panel until the classes appear with their full uris. It is then safe to use the renamed classes in merges/splits

GF#30378

Null pointer if renamespace while class is loaded in Merge tab.

The workaround is toggle around in the OWLClasses panel until the classes appear with their full uris.  It is then safe to use the renames classes in merges/splits

GF#30401

Inability to export data from DB to OWL file, and inability to class

Cleanup scripts are available that server as the workaround

GF#30516

Language on Definition not displayed in Edit Tab

The workaround is to restart the Protege server.

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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.

29770

Concept History Plugin - OLD_PARENT is deleted during save of concept history

29923

Unalble to search from box by hitting return key

30082

Explanation Server Does Not Properly Startup for NPO Vocabulary

30111

Modeler can't create workflow tasks

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30414

Can edit a parent to a retired class.

30416

Workflow modeler cannot edit assignment

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.

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29720

PreMerge "two concepts" after renaming them is not allowed.

30265

Possible bug in LQT

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
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Brief description of item

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30038

Change of Semantic_Type value after changing PTs

30305

When cloning, not escaping definition if invalid class name

30338

If only 2 N&S restriction and one is removed through merge of filler values - shows as defined

30352

Changing Concept Name in namespace and refreshing causes blank preferred name

30375

After resolving referencing class in PreRetire, does not refresh referencing classes list

30376

If rename class_name two classes, can never PreMerge them

30378

Null pointer if rename namespace while class is loaded in Merge tab

30401

Inability to export data from DB to OWL file, and inability to classify

30516

Language on Definition not displayed in Edit Tab

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

1.4.3

Feb 11