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Introduction

The purpose of this document is to detail the Installation Steps and Site Configuration Options for the caDSR UmlModelBrowser Tool Version 4.0.1. The UmlModelBrowser Tool source and all related documentation are on the GForge project archive. All caCORE companion projects can be found from the the caCORE GForge Archive page.

Pre-requisites

The caDSR UmlModelBrowser Tool project is a Manual deployment. The steps are noted below

Installation Steps

Download the project package from the NCICB Download Site.

Extract all project files into the desired location. For the purpose of this document, /umlmodelbrowser-401/ is assumed to be the project root folder. File references beginning with "./" can be found in the project path from this root.

Building the Application

A war file need to be build before the application can be installed, follow the steps below to build a war file. A war file is not provided with the download because the database connection information and environment properties could be different for each deployment.

  1. Update umlbrowser.properties located in directory <root>/config/properties/
    • Update value for property CDEBROWSER_URL to point to the CDE browser URL that provides access to your caDSR database, e.g.

      CDEBROWSER_URL=https://cdebrowser.nci.nih.gov/CDEBrowser/
    • Update value for property CADSR_URL to point to the caCore API remote service URL, e.g.

      CADSR_URL=http://cadsrapi-dev.nci.nih.gov/cadsrapi40/
    • Update the URLs for other caDSR tools, e.g.

      CURATION_TOOL_URL=https://cdecurate-dev.nci.nih.gov
      NCI_METATHESAURUS_URL=http://bioportal.nci.nih.gov/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=NCI%20MetaThesaurus
      NCI_TERMINOLOGY_SERVER_URL=http://bioportal.nci.nih.gov/ncbo/faces/pages/ontology_list.xhtml
      SENTINEL_TOOL_URL=https://cadsrsentinel.nci.nih.gov/cadsrsentinel/do/logon
      CDEBROWSER_TOOL_URL=https://cdebrowser.nci.nih.gov/CDEBrowser/
  2. Update Ant properties file, named build.properties, using the ./build.properties
    • Update the database host properties so that it could be used to connect to correct caDSR repository.
    • Please also update the values for user and password with the username/password to be used to connect to caDSR repository.
  3. Run the build script (build.xml) from directory src/java with target "dist_dev" for DEV, "dist_qa" for QA, "dist_stage" for stage, "dist_umlstage" for Sandbox, "dist_prod" for Prod e.g. ant -f build.xml dist_dev
  4. umlmodelbrowser.war will be created under directory <root>/dist

Deploying Application

  1. Shutdown Jboss instance
  2. Copy file umlmodelbrowser.war from <root>/dist to <JBOSS_HOME>/server/default/deploy
  3. Copy files umlmodelbrowser-log4j-appender.xml and umlmodelbrowse-log4j-category.xml from <root>/dist/ to <JBOSS_HOME>/server/default/conf/log4j/
  4. Startup the Jboss instance
  5. Access the application using url http://<HOST>:<POST>/umlmodelbrowser/
    eg. http://localhost:8080/umlmodelbrowser/

    The user must have access to the server and in some environments this may require running a Virtual Private Network (VPN) connection.

Runtime Options

Some of the UMLModelBrowser Tool logic are controlled by configuration options stored in a table within the caDSR database. These options are set via the sql script umlbrowseroptions.sql located at <root>/src/sql/. Save and modify the sql script to specify tier where " (TIER)" can be stage, prod etc. The options contained in this script allow for dynamic changes without the need to build or deploy a umlmodelbrowser.war file.
The options are identified by the tool name and a property. For the UMLModelBrowser Tool the tool name in the script is always 'UMLModelBrowser'. Details of the property and values of the configuration options follow. Each is identified by the property name followed by a description of its use. In addition to the information provided here there are extensive comments in the load_tool_options.sql file concerning valid values for each property.

  1. URL
    The URL to access the UMLModelBrowser, should be stored in the format - "https//<UMLModelBrowser Tool Alias>". E.g. NCICB production is https://umlmodelbrowser.nci.nih.gov. If <UMLModelBrowser Tool Alias> does not exist it should follow this format: "http//<server_name>:<port>/umlmodelbrowser".

Required Technology

The product versions which follow were used during the development and system testing of the caDSR UMLModelBrowser Tool. Although new versions of the products have been released they have not yet been certified with the UMLModelBrowser Version 4.0.1.

Deviating in any way from the products and versions listed below may cause errors. When attempting to deploy the CDEBrowser Tool to a different technology stack, please first deploy as documented in this Installation Guide and then begin the migration.

Product

Version

Web Site and Notes

JBoss

4.0.5

http://www.jboss.org/downloads/index

JDK

1.5.0_10

http://java.sun.com/j2se/1.5.0/

Recommend downloading the J2EE 1.5 SDK.

ANT

1.6.5

http://ant.apache.org/

Eclipse

Current

http://www.eclipse.org/platform/

This is a development environment only and provides no runtime or build components.

IE

7.0+

http://www.microsoft.com/windows/ie/downloads

This is the latest Internet Explorer from Microsoft.

FireFox

3.0+

http://www.mozilla.com/products/download.html?product=firefox-3.0.10&os=win&lang=en-US

This is the latest FireFox version from Mozilla.

Troubleshooting

Following is a list of known errors and resolutions that may occur during the build and deployment process. If you have a question or situation not covered in this document please contact Application Support by email.

  1. Error page with the message "Unexpected System Error has Occurred"
    • Verify the cadsrApi url is working and a valid url is stored in tool options table
  2. java.net.bind.exception JVM_8080 port not available.
    • Correct the JBoss installation.
  3. Data Element public id or Class Details links display page cannot be found or display error.
    • Make sure that CDE Browser is working and URL in the tool options is valid.

 

 

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