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Workflow.md

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Workflow

This is a working document describing the process of updating the website. It is not a perfect process, and requires more manual scripting than I would like.

(1) Download data to local repository

  1. Download most recent references from PubMed as an XML to data/pubmed_output.xml (note: the PubMed interface has changed, no longer allowing more than 10,000 references to be downloaded. Working on a workaround.) [as often as desired]
  2. Download most recent included references from DistillerSR site to data/FILENAME.csv [as often as desired]

(2) Data processing

  1. If you have updated the included list from DistillerSR,
    • Add "current_" prefix to the DistillerSR .csv located in data/
    • Remove "current_" prefix from the old csv, and keep as many versions as you want for backup.
  2. If you have updated the reference list from PubMed, run processing.R which does the following (requires a file called data/pubmed_output.xml which depends on the old PubMed... fix coming):
    • Parses pubmed date; the date of publication is very inconsistently included and we needed a consistent solution.
    • Parses ISO abbreviations of journal names
    • Parse full journal names
    • Writes these data to data/metadata.csv

(3) Test locally

shiny::runApp()

(4) Deployment

  1. Transfer changes to your live environment however you want. I push to a remote dev branch of the repo, merge the changes to the master branch, and then pull these changes into the server.
  2. Restart shinyserver: sudo systemctl restart shiny-server
  3. Check that it's live and working.