search

DominikBuchner / BOLDigger-commandline

BOLDigger as a commandline tool
MIT License
8 stars 0 forks source link

Running boldigger-cline -h produces error: cannot import name 'requests' #4

Closed aminards closed 2 years ago

aminards commented 2 years ago

Today I installed boldigger and boldigger-cline in Ubuntu on Windows 10. Both seemed to install correctly. Running boldigger-cline -h gives this error:

Traceback (most recent call last): File "/home/smith/.local/bin/boldigger-cline", line 5, in from boldigger_cline.main import main File "/home/smith/.local/lib/python3.8/site-packages/boldigger_cline/main.py", line 2, in from boldigger_cline import boldblast_coi, boldblast_its, boldblast_rbcl, additional_data, first_hit, jamp_hit, digger_sort File "/home/smith/.local/lib/python3.8/site-packages/boldigger_cline/boldblast_its.py", line 8, in from boldigger.boldblast_coi import slices, fasta_to_string, requests, fasta_rewrite ImportError: cannot import name 'requests' from 'boldigger.boldblast_coi' (/home/smith/.local/lib/python3.8/site-packages/boldigger/boldblast_coi.py)

I am not sure how to fix this.

01Andrea01 commented 2 years ago

Same problem here. I just updated the GUI and the command line version. The GUI works, but the command line does not.

Traceback (most recent call last): File "/home/andrea/.local/bin/boldigger-cline", line 5, in from boldigger_cline.main import main File "/home/andrea/.local/lib/python3.8/site-packages/boldigger_cline/main.py", line 2, in from boldigger_cline import boldblast_coi, boldblast_its, boldblast_rbcl, additional_data, first_hit, jamp_hit, digger_sort File "/home/andrea/.local/lib/python3.8/site-packages/boldigger_cline/boldblast_its.py", line 8, in from boldigger.boldblast_coi import slices, fasta_to_string, requests, fasta_rewrite ImportError: cannot import name 'requests' from 'boldigger.boldblast_coi' (/home/andrea/.local/lib/python3.8/site-packages/boldigger/boldblast_coi.py)

pascalhabluetzel commented 2 years ago

I had the same problem. It has to do with how the 'request' package is imported in the python scripts. Try modifying the boldblast_its.py and boldbalst_rbcl.py as follows:

change

from boldigger.boldblast_coi import slices, fasta_to_string, requests, fasta_rewrite

to

from boldigger.boldblast_coi import slices, fasta_to_string, fasta_rewrite
import requests
naurasd commented 2 years ago

Same problem, changing the scripts as described by @pascalhabluetzel did not work for me.

DominikBuchner commented 2 years ago

Will work on these issues once I have time. Fully booked at the moment.

DominikBuchner commented 2 years ago

This is a namespace problem. Old versions of BOLDigger defined a function called request, which are removed in the newer versions. This can be fixed temporarily by downgrading the BOLDigger GUI version. I will update boldigger-cline now to support the new functions.