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NCI Protégé 1.4.2 Release Notes

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

Product Changes

The objective of this release of Protégé 1.4.2 is to provide the remaining feature requests and bugs fixes found in previous Protégé 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#26667 - Robustness/QC
    • Validation on batch loads, better error reporting in batch edit/loads, null exceptions
  • GF#26668 - wiki collaboration
    • Performed testing on the Wiki/Protege workflow roundtrip.
  • GF#26634 - "by code" (rdf:ID is meaningless)
  • GF#26669 - Runtime Classifcation
  • GF#26633 - Internationalization
  • GF#26666 - Configurability
  • GF#24359 - Batch job robustness performance

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 Protégé / 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 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

 

28860 

:NAME needs to be added to pull down list of Attributes w/ID in Report Writer

 

29103

Prevent save of a class that has less than 2 N&S conditions.

 

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

28127

AQP export needs to escape comma everywhere

28265

rename a class and rename it back leads to loss of type information.

28284

Tabs in Edit Tab Preferences can't be removed. (Tabs in Edit Tab Preferences can't be added).

28312

"Delete FULL_SYN" in batch processing doesn't work

28335

Batch delete of Semantic_Type fails

28364

Need to be able to configure Property Value Query in the LQP

28400

Performance Issues

28416

New concept with existing rdf:ID fails to be created, insufficient error message.

28417

Can only shutdown protege server through the Administer Server GUI

28532

There is error message when batch processing special characters "& and <" fails.

28553 

Classification Optimization

28586 

Reasoner Error While Classifying in Standalone Mode

28589

New scenarios that have strange behavior on PT change

29097

Performance testing

29102

Preretire causes multiplication of OLD_SOURCE_ROLEs from referencing classes

29145

Figure out if LQP result display timing is okay for a number of search scenarios.

29147 

LastUsageInvocationHandler being called with a high frequency

29193

Restrictions drop off when toggling from primitive to defined related to concurrency

29236 

Split and Copy don't work in protege ByCode 1.4.2.174.

29258

Typo in Batch Load parent causes infinitely repeating exception

29286 

Qualifiers of Complex Properties don't display (ByCode)

29289

Legacy_Concept_Name ReadOnly works but it is passed to new concepts

29290

Retired concept is not listed under Retired Concepts

29342

Changing Preferred name makes 2nd rdfs:label be added. (NCIt - ByCode)

29344

There is no check-box next to Retire in the "Edit Tab Preferences"

29346

Cannot Edit Concept assigned in NCI Workflow (NPO)

29357

java.lang.NullPointerException is displayed in console windows after check /uncheck Copy, Split, Merge, or Retire  in Preference.

29358

Association Edit/Delete failed.

29383

Does not retain assignment of workflow task from creation dialog

29445

report writer fails to produce correct output for no attributes

29463

The record number in the batch log may not match with the "line number" of the input file.

29464

An invalid value is able to be added into the protperty Contributing_Source by the batch processing

29550

Need to use Display slot in Explanation tab panel

29552

After merge, redirected filler values are not updated by the Explanation Server

29565 

A user was able to premerge two classes into a third class during concurrent editing

29569

Duplicate restrictions after merge with restriction pointing to surviving concept

29571

Invalid messagebox/warning to user when modify a concept with N&S restrictions

29646

Review panel from LQT pane displays class name as "foo"

29707

Exceptions are thrown when closing "Select a property" dialog-box nested in "Edit an Object-Valued Property" dialog-box.

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.

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

22104

search string appears empty when invoked from restriction dialog box

23565

refactoring namespaces

24510

Need a fail-safe for creating codes for properties

28509

Edit tab does not handle & or < properly

29143

role groups not handled when toggling prim/defined

29358

(NPO) Association Edit/Delete failed.

29513

Improved formatting of batch load with error

29517

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

29665

"Create Workflow Task" doesn't work" in 1.4.2.223 ByCode.

29720

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

29752

Generate Reports shows undesirable internal values

29753

Extra box character shows in generated report

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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