AttributeError: 'Context' object has no attribute 'gi'

[mpoelchau]

Hi everyone! I need to load annotations to the Apollo2.7 UcA track. I've previously used add_transcripts_from_gff3_to_annotations.pl but it looks like the load_gff3 function from this library is the new way to go. I ran into the following error:

(apollo-arrow-env) ARS5APVN2WD42YY:Downloads mpoelchau$ arrow annotations load_gff3 --source https://apollo2-stage-node1-cbo.nal.usda.gov/apollo Galleria_mellonella test.gff
/Users/mpoelchau/Documents/programs/apollo-arrow-env/lib/python3.9/site-packages/urllib3/__init__.py:34: NotOpenSSLWarning: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
  warnings.warn(
Traceback (most recent call last):
  File "/Users/mpoelchau/Documents/programs/apollo-arrow-env/lib/python3.9/site-packages/arrow/decorators.py", line 16, in custom_exception
    return wrapped(*args, **kwargs)
  File "/Users/mpoelchau/Documents/programs/apollo-arrow-env/lib/python3.9/site-packages/arrow/decorators.py", line 46, in str_output
    print(wrapped(*args, **kwargs))
  File "/Users/mpoelchau/Documents/programs/apollo-arrow-env/lib/python3.9/site-packages/arrow/commands/annotations/load_gff3.py", line 51, in cli
    return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, timing=timing)
AttributeError: 'Context' object has no attribute 'gi'

'Context' object has no attribute 'gi'

I also get the same error when I use show_organism to make sure the library can find Galleria_mellonella.

The gff seems fine - I can load it onto the browser without a problem. I can also find the organism via curl:

(apollo-arrow-env) ARS5APVN2WD42YY:Downloads mpoelchau$ curl -i -X POST -H "Content-Type: application/json" -d '{ "username": "my-username", "password": "my-password", "organism": "Galleria_mellonella", "client_token": "ignore"}' https://apollo2-stage-node1-cbo.nal.usda.gov/apollo/organism/findAllOrganisms
HTTP/1.1 200 
Server: nginx/1.25.1
Date: Fri, 11 Aug 2023 13:33:47 GMT
Content-Type: application/json;charset=UTF-8
Transfer-Encoding: chunked
Connection: keep-alive
Access-Control-Allow-Origin: *
Access-Control-Allow-Credentials: true
Access-Control-Allow-Methods: GET, POST, OPTIONS
Front-End-Https: on

[{"commonName":"Galleria_mellonella","blatdb":"/usr/local/blat/db/galmel/GCF_026898425.1_CSIRO_AGI_GalMel_v1_genomic.fna.2bi","metadata":"{\"creator\":\"1357111\"}","annotationCount":1,"currentOrganism":true,"obsolete":false,"sequences":221,"directory":"/app/data/other_species/galmel/CSIRO_AGI_GalMel_v1/jbrowse/data","publicMode":true,"valid":true,"genomeFastaIndex":null,"genus":"Galleria","species":"mellonella","id":4690912

Could someone point me in the right direction for debugging? Does this have something to do with the NotOpenSSLWarning?

Thanks!

[mpoelchau]

Never mind, thanks to https://github.com/GMOD/Apollo/issues/2641 I realized that I needed to run arrow init first.

[abretaud]

Hi Monica! Yep it's a typical message you get when there's a problem with the arrow config file, glad you found it, the message could be more explicit :thinking: