search

legumeinfo / LIS-autocontent

Scrapes the LIS datastore and populates various configs and databases for deployment
Apache License 2.0
0 stars 1 forks source link

Develop #8

Closed ctcncgr closed 1 year ago

ctcncgr commented 1 year ago

1) python package lis-autocontent. 2) lint on push. 3) Encapsulation of taxon/genus/species/infraspecies resources and collections. 4) code blackened (I'll add this to an action of some kind soon). 5) updated readme. 6) updated examples.

nathanweeks commented 1 year ago

A couple minor suggestions relevant to installation:

  1. Suggest usingvenv from the Python Standard Library (e.g., python3 -m venv) instead of the virtualenvpackage, as virtualenv doesn't exist by default on macOS
  2. It would be convenient for automated installations if this were pip-installable (e.g., python3 -mpip install 'lis-autocontent @ git+https://github.com/legumeinfo/LIS-autocontent@0924204a41ae1db3dcbb616f9847f411c090a0be'); however, for reasons that aren't clear to me (due to my lack of experience creating pip-installable Python packages), the scripts/lis-autocontent.py doesn't get "processed" (e.g., the docstring remains in the first line).
nathanweeks commented 1 year ago

Runtime issue with the develop branch:

$ cat _data/taxon_list.yml 
--- 
- description: "Soybean"
  genus: Glycine
  category: main
$ lis-autocontent.py populate-jbrowse2 --taxa_list ./_data/taxon_list.yml --jbrowse_url /
...
02-06 12:26|populate-jbrowse2|[INFO]: Searching https://data.legumeinfo.org for: Glycine D3-tomentella
02-06 12:26|populate-jbrowse2|[ERROR]: No fai file for: https://data.legumeinfo.org/Glycine/D3-tomentella/genomes/G1403.gnm1.CL6K/glyD3.G1403.gnm1.CL6K.genome_main.fna.gz

I haven't attempted to debug this at the source-code level, but LIS-autocontent is using an upper-case "D" in glyD3.* instead of the actual lower-case glyd3.G1403.gnm1.CL6K.genome_main.fna.gz.fai

ctcncgr commented 1 year ago

merging. going to redo docs next