For the previous version of this page dealing with the harvester 1.1.1 and previous versions, see Pubmed _ Example _ Script (1.1.1)

Your first Harvest

Since pubmed is a national data source, much of the work has been already done for your harvest. No translation file needs to be created, nor does the workflow need created as the harvester team has completed these steps for you. However, you will need to do the some configuration so the harvest knows where your vivo data is and the pubmed records you wish to ingest.

• Change directory to example-scripts/bash-scripts/full-harvest-examples/example-pubmed
• Edit the pubmedfetch.config.xml file
  
  • Set the email parameter to your email address
  • Set the termSearch to your search. The search term is the same syntax as found on pubmed.org
  • For more information on these parameters and their use, please see PubmedFetch
• Edit the vivo.model.xml file
  
  • Set the dbURLdbUrl, dbUser, dbPass, and Namespace
  • For more information on these parameters and their use, please see Harvester vivo configuration file 
• Edit changenamespace-authors.config.xml, changenamespace-authorship.config.xml, changenamespace-journal.config.xml, and changenamespace-publication.config.xml files and set the namespace parameters in each one to be your vivo namespace
  
  • For more information on these parameters and their use, please see ChangeNamespace
• Edit the run-pubmed.sh file and set the HARVESTER_INSTALL_DIR= to be the directory you unpacked the harvester in
• Run bash run-pubmed.sh
• Restart tomcat and apache2. You may also need to force the index to rebuild to see the new data. The index can be rebuilt by issuing the following URL in a browser:http://your.vivo.address/vivo/SearchIndex. This will require site admin permission, and prompt you to login if your not already.

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