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Bugfix: isa-json not working when tool is not launched in the ENA-upload-cli directory #90

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merged 1 commit into from
Feb 26, 2024

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bedroesb
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This will fix:

Traceback (most recent call last):
  File "/home/bedro/.pyenv/versions/3.11.3/bin/ena-upload-cli", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/bedro/.pyenv/versions/3.11.3/lib/python3.11/site-packages/ena_upload/ena_upload.py", line 889, in main
    submission = EnaSubmission.from_isa_json(isa_json, required_assays)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bedro/.pyenv/versions/3.11.3/lib/python3.11/site-packages/ena_upload/json_parsing/ena_submission.py", line 92, in from_isa_json
    validate_isa_json(isa_json)
  File "/home/bedro/.pyenv/versions/3.11.3/lib/python3.11/site-packages/ena_upload/json_parsing/ena_submission.py", line 49, in validate_isa_json
    IsaBase.validate_json(isa_json, EnaSubmission.investigation_schema)
  File "/home/bedro/.pyenv/versions/3.11.3/lib/python3.11/site-packages/ena_upload/json_parsing/characteristic.py", line 16, in validate_json
    json_file = open(schema_path)
                ^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: './ena_upload/json_parsing/json_schemas/investigation_schema.json'

When the script is launched outside its original repo. Important to get working for the Galaxy tool wrapper.

@bedroesb bedroesb added the bug Something isn't working label Feb 26, 2024
@bedroesb bedroesb requested a review from bgruening February 26, 2024 08:34
@bedroesb bedroesb merged commit b8fcc64 into master Feb 26, 2024
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2 participants