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LexWiki Links

Known Issues

The templates do not import correctly so there will be some broken (red) links on the concept pages.

Installation Process

The installation will take place in four separate steps.

  1. Use a bat file to extract the metadata about the concepts and write them as files into a directory.
  2. Run a php file to read the files and publish them to the Wiki.
  3. Edit the Main page to show the ontology hierarchy
  4. Import the templates into the Wiki

Installation Instructions

Setup and configuration

  1. Download and unzip the VKC:LexWikiPublisher 1.0 zip file.
  2. Open the lexWikiPublisher.prop file and enter the configuration information

    The following are the configuration variables along with an example for each.

    Required configuration information

    logfile - location to store the published concepts
    C:/Temp/publishbatch-local

    configpath - the path to the configuration file in the LexEVS installation
    X:\\services\\lexevs\\resources\\config
    lbconfig.props
    csn -the code system name to be published
    NPO
    ccd - the concept code at the root of the hierarchy
    Entity
    wiki - the name of the wiki
    LexWiki test
    template - SMW template name
    LexWiki
    formname - the name of the semantic mediawiki form

    LexWiki_NPO_Form

    Optional configuration information

    republishexistingpages - Republish existing pages?
    yes
    propertiesonly - If you want to get properties and associations published only
    no
    vsformname - the name of the semantic mediawiki form for value sets

user - Wiki user name
Wiki user name
pwd - Wiki user password
Wiki user password
self - is the selected node to be published?
yes
batch - will all the children of the selected node be published?
yes
server - the server where the wiki is located
informatics.mayo.edu
port - the port number where the wiki is setup
8080
batchsize - number of concepts to process in each batch
50
namespace - the over riding namespace to use for pages
LexWiki master
startPage - the starting page where index.php is the default
index.php

Extracting concepts from LexEVS

  1. Be sure the directory configured for the logfile variable exists and is write enabled.
  2. Run the lexWikiPublisher file useing the bat file or shell script.

Publishing to the Wiki

  1. Open a command prompt in the lexwiki's maintenance directory
  2. Run the publish php using the directory location of the files created during the lexEVS as the only argument
    php publish.php /home/myhomedir/tobepublishedpages

Displaying the category tree

  1. Log in to the Wiki and display the Main Page.
  2. Click on the Edit tab at the top of the page.
  3. Update the information between the cateegorytree tags to match your onotology information
    BGT Gene Kind(B179)
    BGT - the coding scheme name
    Gene Kind - the root node for the Ontology
    (B179) - short name for the root node
    NPO_Entity(Entity)

Importing the templates

  1. From the wiki, select SpecialPages.
  2. On the SpecialPages, select import file.
  3. Import the templates which correspond to the ontology you created.
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