Project: EVS API s4

Terminology Browser Applications Weekly Status Report (02/21/2009-02/27/2009) NCI Center for Bioinformatics and Information Technology

1. Key Accomplishments For each Subproject list all accomplishments with associated GForge Reference

1.1. NCI Thesaurus Browser . [GF#19255] User Interface - Quick Links o Designed and implemented quicklLink.xhtml. o Performing trouble-shooting on a formatting issue.

. [GF#19244] Concept details page - Terms & Properties o Implemented a toggle/navigation bar to include Terms and Properties, Relationships, Synonym Details, View All, View in Hierarchy, and View History. o Incorporated the hierarchy and history icon files provided by the web team into the navigation bar above. o Read page formatting data from a property file, NCItBrowserProperties.xml. The file contains information about each display item, including property name, display label, URL and hyperlink text if applicable, and variable indicating whether the item is an external code. The file also contains other configurable items, such as MAXIMUM_RETURN. o Implemented property.xhtml.

. [GF#19242] User Interface - Search results page – pagination. o Implemented. The default (i.e., initial) value for the number of matches per page is set to 50.

. [GF#19240] User Interface – Search UI component. o Implemented.

. [GF#19241] User Interface – Search results page. o Implemented.

. [GF#19237] User Interface - Implement property file to hold links for property and terms page o Implemented. Refer to GF#19244 above.

. [GF#19236] User Interface – Site framework (banner, footer navigation). o Implemented.

. [GF#19235] Server-side interface – Pagination functionality. o Implemented through the use of session variables.

. [GF#19232] Server-side interface – Concept Details. o Implemented code to retrieve terms and properties data from LexBIG database. (Refer to GF#19244)

. [GF#19229] Server-side interface – Implemented concept search results. o Implemented.

. [GF#19234] Server-side interface - Caching of objects for performance (e.g., tree roots) Terminology Browser Applications Weekly Status Report (02/21/2009-02/27/2009) NCI Center for Bioinformatics and Information Technology

o Incorporate Apache Java Caching System (JCS) library files into the browser framework. o Constructed the cache configuration file, cache.ccf. o Designed and implemented a CacheManager class for managing root concepts and subconcepts. (See also GF#19231)

. [GF#19243] Concept details page – View in Hierarchy. o Implemented. (See GF#19244, Item 1)

. [GF#19231] Server side interface - View Hierarchy & View in Hierarchy (tree implementation). o Incorporated Yahoo User Interface (YUI) library into the browser framework. o Designed and implemented a TreeUtils class based on the inputs provided by the Mayo team. o Designed and implemented an AjaxServlet class for retrieving root concepts and subconceps from LexBIG database through CacheManager. (See also GF#19234). o Designed and implemented hierarchy.jsp to retrieve tree data from AjaxServlet through Asynchronous JavaScript And XML (AJAX). o Designed and implemented Javascript for refreshing the concept details page when a tree node is selected by the user. (See also GF#19244)

. [GF#19238] User Interface - Create style sheet (.CSS), formatting of UI pages. o Continue to refine the CSS pages as the development progresses. (See also GF#19231, Item 1)

. [#19382] Establish Software Architecture o Build / deployment scripts - Completed  Continuous integration environment setup has been completed. . Hudson CI web application installed and configured

. [#19227] Performance Testing - Run performance tests o Tested the latest SearchUtil class to verify if the search results are correct. o Failed to load ThesaurusInf-ForPublication-byCode-08.12d.owl with the latest LexBIG 5.0.0a loader onto my Windows desktop machine. Continue to have memory limitation issues. Currently, 2GB is not enough. Continue to report problems to Mayo. o Gathered performance results for locally mapped drive containing both LexBIG and Thesaurus data onto my Windows desktop machine. Still need to gather results for a local install of both. Attempted to gather data on server machine instead. o Failed to gather local performance data on cbvapp-d1007 server. NCIt Browser failed to deploy correctly using the current install of JBoss. myfaces-impl.jar and myfaces-api.jar are causing a conflict when the browser is loading. o Tried to install LexBIG 5.0.0a version onto ncias-d171-v server. Linux installation failed. Problems with mayo’s installer. In addition, requested and are waiting for mysql account to load the Thesaurus. Will try to use 4.2.1 LexBIG installer instead.

. [#19226] Performance Tests - Create test framework o Created initial test framework project. Terminology Browser Applications Weekly Status Report (02/21/2009-02/27/2009) NCI Center for Bioinformatics and Information Technology

. [#19295] Server side – Performance tuning cycle o Weekly meeting with Mayo to discuss performance – Every Thursday - In progress.

. [#19228] Create Web Framework o Modified the JSF framework to fit the BDA file layout, tested and checked in to SVN. Added to CI and created a nightly build / deployment. See: http://ncias- d171-v.nci.nih.gov:19280/ncitbrowser/

2. Production Support For each Subproject list ANY Production support and along with the associated GForge Reference . None

3. Meetings List ALL Meeting attended in support of all associated Subprojects . 02/24/2009 – Report Writer/NCI Browser Status Meeting

4. Planned Activities: For each Subproject list the activities/tasks (with associated GForge Trackers where appropriate) planned for the upcoming weeks. . Finish Performance testing using local LexEVS. . Continue development of the NCItBrowser 1.0 release. . Continue BDA process and Dev environment setup.

5. Issues and Recommended Resolutions: List general issues/concerns/risks associated this project team. Items could cross all subprojects or may specific to an individual subproject. Proposed recommendation should be described when available. . None.