Compatibility with Clickhouse

jakejh commented 4 years ago

[ ] test parsing functions
[ ] test unark, which is used by getCitation
[x] update connect, making sure to use db = dbname
[x] update deleteOldPmidVersions - Clickhouse doesn't have window functions, so try rowNumberInAllBlocks
[x] update addSourceToTarget - try rowNumberInAllBlocks and change delete statements
[x] 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 4 years ago

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

JSchoenbachler commented 4 years ago

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 4 years ago

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 2 years ago

@JSchoenbachler Can we close this issue for now?

JSchoenbachler commented 2 years ago

Yep, closing!

hugheylab / pmparser