**National Cancer Institute Center for Bioinformatics**

**NCI Protege 1.2.3.25 Patch Release Notes (Draft)**

28 08 2008

This document also available at:
<https://wiki.nci.nih.gov/display/caCORE/NCI+Protege+1.2.3+Patch+Release>

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 Patch                      Aug 08                             |
|                                                                       |
|                                                                       |
|                                                                       |
|                                                                       |
|   -------------------------------- ---------------------------------  |
+-----------------------------------------------------------------------+

**[New Features and Updates]{.smallcaps}**

Highlights of this patch release are:

\- Concurrency management in Run Time Classification

\- Increased Performance of the Prompt User tab

\* This patch release for version 1.2.3 of the Protege NICEditTab plugin
was targeted towards increasing the performance of the Run Time
Classification (RTC). The change is entirely in the infrastructure. The
RTC in the current release synchronizes its data against the Protege
server rather than the Protege client, thereby eliminating network
latency issues affecting all users (but with a larger impact on remote
users).

\* Also, a performance enhancement has been done in Prompt: an
inefficient lookup algorithm has been replaced with a solution that
involves caching of data instead.

\* In addition to the patch release of the software, a Citrix server has
been set up and already deployed to reduce connectivity issues affecting
remote users. The Citrix server is currently supporting NCIT editing,
but it will be expanded to support BGT editing in the future.

**[Bugs Fixed Since Last Release]{.smallcaps}**

List of bug fixes in 1.2.3.25 (Patch release)

\* 9295 Ability to remove menu options by configuration

\* 11119 PROMPT- Exception when navigating from Table View to Tree view

\* 12025 Incorrect behavior while splitting, creating new classes

\* 12342 PROMPT - Exception when selecting \'changed by\' panel in
\'table view\'

\* 12353 OK button off screen with long winded invalid property.

\* 12574 Edit Class and View Instance buttons are broken - dup of 12365

\* 12932 Unmarshal Exception

\* 4057 no copy-and-paste capability in collaboration panel

\* 14290 Problem tracking changes of defining relations if more than one
restriction is present

\* 14507 Prompt reports all concepts changed - concepts get new
properties added

\* 15185 No date on ALT_DEFINITION for NCIt

\* 15228 Exception when edit and classify at same time

\* 15395 NCIt Protege is SLOW

\* 15592 Frame caching on Protege server

\* 15594 :ROLE concrete - Prompt bug fix

**[Known Issues]{.smallcaps}**

NOTE: A number of bug reports involved irreproducible items that have
now been identified as originating in the software components that deal
with database transactions. Because of the amount of work involved to
correct this, this patch release does not include fixes for these bugs,
they have been scoped for version 1.3 of the software. To minimize the
likelihood of these transaction issues occurring:

\(1\) When saving a concept, users need to click OK on the notification
dialog that is displayed when the Save is successful when it first pops
up, e.g. try not to take a break from editing until the OK dialog has
been clicked.

\(2\) If a \"create class\" action fails, do not attempt to execute it
again right away, you can attempt it on your next login.

GForge Open Items (Deferred to 1.3 release or unresolved)

\* 11115 PROMPT- \'Table View\' crashes after visting \'Show sources\'
window

\* 11894 When a class defaults to owl:thing as a parent it disappears

\* 13884 Create a Protege nightly build script

\* 15944 PROMPT: namespaces in Table view

\* 16248 PROMPT extra classes added (Axiom)

\* 11553 Apparent Failure to log out.

\* 11614 Prompt - When accepting changes in all children in branch,
children disappear fm tree

\* 3537 Synchronization of rdfs:label and Preferred_Name

\* 8682 Merged and Retired concepts are not properly tagged with
Retired_Concept

\* 9298 Prompt - accept and reject icons in \'changed by\' panel of
\'table\' view don\'t work

\* 10185 Prompt: Parent concept flagged as changed when a child is added

\* 10186 Prompt: Concept flagged as changed when it is copied

\* 12358 PROMPT- Reject button in Tree view produces error message to
the console

\* 12935 text is not trimmed

\* 14056 Permission allows delete of definition (see comments)

\* 14939 Copy pane Preferred_Name issues after a modeling error

\* 14973 class disappears after editing (winds up under Thing ?)

\* 15230 Error when Retiring a class with existing Editor_Note or
DesignNote

\* 15247 Failure to cross check Preferred Term in Protege 1.2.3 release

\* 15788 Save Confirmation Popup Dialog blocks other editors

\* 16058 Class Creation Problems

\* 16076 Transaction didn\'t close in a class copy operation from the
Copy panel

**CORE Product Dependencies**

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