names2taxid issue with catalogue of life

[aguilart]

Hi I am trying to use names2taxid and using catalogue of life as the database, but I get as error "Error: no such table: taxa". I get this for even simple queries likes this one

name2taxid("Bombus",db="col")

Any ideas?

• Session info -------------------------------------------------------------------------
  setting value
  version R version 4.0.2 (2020-06-22)
  os Windows 10 x64
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate English_Germany.1252
  ctype English_Germany.1252
  tz Europe/Berlin
  date 2021-03-18

[sckott]

The COL database preparation has run into a problem

[sckott]

follow sckott/col-sql#1 for updates

my repo https://github.com/sckott/col-sql/ where I make a SQLite version of the COL database ran into issues as COL has changed how they provide the database dump.

for now I've uploaded an old version that works but it is from August 2020, so a bit older than the most recent dump they have (Dec 2020).

try again and it should work, let me know

[aguilart]

Thanks! So, does that mean that I have clone the repo and then work from there? Because trying to use the functions from taxizedb do not work still. Also in your repo you state that the download should be done as:
git clone https://github.com/ropensci/col-sql.git
but it should be, right:
git clone https://github.com/sckott/col-sql.git

I am still learning about how to use this, thanks for the patience!

[sckott]

Thanks for the correction, yes, sckott not ropensci on that other repo. I'll fix that.

Perhaps taxizedb is trying to use a bad/corrupted download of the Col database. In R, run tdb_cache, then go to that path that's in "cache path" and delete the file col.sqlite . Then run your example above again and you should get a new download with a COL database file that should work. let me know

[aguilart]

Thanks again! But I have to say I am still a bit lost, so I cloned the repo, then I locate the file col-sql. But I cannot make to work the commands bundle install and rake all. When I run them in git I get for both "command not found". Do I need to install sth else to get those commands to work. I really appreciate the help!

[sckott]

Sorry for late reply, i'm moving on to a new job, so won't be maintaining this any longer.

No, you didn't need to download the col-sql repo. You can download the COL dump from this link https://s3-us-west-2.amazonaws.com/taxize-dbs/col.zip and then connect to it with dplyr via dbplyr https://cloud.r-project.org/web/packages/dbplyr/vignettes/dbplyr.html

[aguilart]

Again thanks a lot for putting the time. Huge fan of all the work you put in all this! Hope the best in the new job!

[sckott]

of course, and thx for the well wishes. You might want to try https://cloud.r-project.org/web/packages/taxadb/ as a somewhat similar approach to this pkg

[maelle]

This repository is about to be archived.

[maelle]

unarchiving it thanks to @stitam 😸