hugheylab/pmparser

Compatibility with Clickhouse

Closed this issue · 5 comments

jakejh commented
  • test parsing functions
  • test unark, which is used by getCitation
  • update connect, making sure to use db = dbname
  • update deleteOldPmidVersions - Clickhouse doesn't have window functions, so try rowNumberInAllBlocks
  • update addSourceToTarget - try rowNumberInAllBlocks and change delete statements
  • update runStatement for Clickhouse delete statements
  • test speed of various queries on database
  • test clickhouse backup and restore
  • update documentation
  • update pkgdown site
  • possibly add clickhouse dump to Zenodo repo along with instructions for restoring it
jakejh commented

Soon we'll be able to use dbname instead of db.

IMSMWU/RClickhouse#69

JSchoenbachler commented

I have pushed many of my updates and merged with some of the pull requests this morning. Going to be testing to make sure it is working properly.

dwinkler1 commented

We have merged the parameter name change. Could you test with our master branch and let us know if something is not working?

jakejh commented

@JSchoenbachler Can we close this issue for now?

JSchoenbachler commented

Yep, closing!