PubMed XML in eXist on OS X

This assumes Tomcat is already installed and controlled by launchd. An alternative would be to launch eXist as a standalone service using Jetty (bin/startup.sh)

1. Fetch and build eXist:

   svn co https://exist.svn.sourceforge.net/svnroot/exist/trunk/eXist
   cd eXist
   ./build.sh

2. Install into Tomcat:

   ant dist-war
   sudo cp dist/exist*.war /usr/local/tomcat/webapps/exist.war
   sudo launchctl stop org.apache.tomcat.tomcat6
   sudo launchctl start org.apache.tomcat.tomcat6

3. Fetch XML from PubMed using PHP: include my PHP function for downloading XML from PubMed, and call it with a query for the data required, eg pubmed_fetch('Review[PTYP]');
4. Create a new collection, using the graphical eXist admin client (bin/client.sh):

   'Create new collection' button [call the collection 'pubmed']
   'Store' button [select your PubMed XML file and wait for it to be imported]

5. Connect to the WebDAV service: Finder > Go > Connect to Server: http://localhost:8080/exist/webdav/db
6. Create a configuration file for the new collection: /db/system/config/db/pubmed/collection.xconf
7. Set up some indexes, then reindex the collection (File > Reindex Collection in the admin client).