PASS Journal Loader

Parses the PMC type A journal .csv file, and/or the medline database .txt file, and syncs with the repository:

* Adds journals if they do not already exist
* Updates PMC method A participation if it differs from the corresponding resource in the repository

Usage

Using java system properties to launch the journal:

java -Dpmc=/path/to/pmc.csv -Dmedline=/path/to/medline.txt -Dpass.fedore.baseurl=http://localhost:8080/fcrepo/rest/ -jar pass-journal-loader-nih-0.1.0-exe.jar

Properties or Environment Variables

The following may be provided as system properties on the command line -Dprop-value, or as environment variables PROP=value:

The first four are needed by the PASS java client.

pass.fedora.url BaseURL of Fedora. Must end in trailing slash e.g. http://localhost:8080/fcrepo/rest/

pass.fedora.user The username for the Fedora user.

pass.fedora.password The Fedora user's password

pass.elasticsearch.url The url for the PASS elasticsearch service.

dryRun Do not add or update resources in the repository, just give statistics of resources that would be added or updated

pmc Location of the PMC "type A" journal .csv file, as retrieved from http://www.ncbi.nlm.nih.gov/pmc/front-page/NIH_PA_journal_list.csv

medline Location of the Medline journal file, as retrieved from ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt

LOG.* Adjust the logging level of a particular component, e.g. LOG.org.dataconservancy.pass.client=WARN