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- 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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