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Update Counts in DO Website HTML

update_website_count_tables.Rd

Directly updates counts listed in the tables on the disease-ontology.org "DO Imports" and "DO Slims" pages using data from a specified release. Changes to these html files should be reviewed and, if correct, committed to the svn repo for deployment.

Usage

update_website_count_tables(DO_repo, tag, svn_repo)

Arguments

DO_repo

A pyDOID.repo.DOrepo object (see DOrepo()).

tag

The repo tag to extract data from, as a string.

svn_repo

The local path to the DO website svn directory, as a string. The correct directory will include a Dockerfile and the 'disease_ontology' directory.

Value

Updated counts directly in the html of the svn repo for each page, as well as, the old and new counts for comparison as a list of tibbles (invisibly).

Speed Note

Expect this function to make more than a minute. The majority of the time is consumed loading the doid-merged.owl file and cannot be sped up without a faster RDF/OWL parser. This is currently handled via DO.utils' dependency on the python package pyDOID with RDF handled by the RDFLib python package.