Improve Error-Messages

[KuechlerO]

Hi guys,

thx for your tool! Your concept is really cool and a handy feature :)

I have decided to integrate this tool in my Snakemake-Pipeline.
However, I now already stumbled multiple times over the issue of having metadata-files that fail the eido evaluation, but the Error messages which are returned by the tool are not helping at all.
Thus, every time when I face such an error I have to invest a lot of time to finally figure out what's the reason for the failing validation.

Here is a minimal reproducible example:

1. pep_schemal.yaml

description: Minimal example

imports:
   - http://schema.databio.org/pep/2.1.0.yaml

properties:
  samples:
    type: array
    items:
      type: object
      properties:
        sample_directory:
          type: string
          pattern: "^/\\S+$|None"

2. input_no_error.csv

sample_name,sample_directory
test,/testung

3. input_error.csv

sample_name,sample_directory
test,testung

Then the output:

# No error
$ eido validate input_no_error.csv -s pep_schema.yaml
Validation successful

# Error
$ eido validate input_error.csv -s pep_schema.yaml
Traceback (most recent call last):
  File "/Users/oliverkuchler/miniforge3/envs/snakemake7/bin/eido", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/oliverkuchler/miniforge3/envs/snakemake7/lib/python3.12/site-packages/eido/cli.py", line 159, in main
    validator(*arguments)
  File "/Users/oliverkuchler/miniforge3/envs/snakemake7/lib/python3.12/site-packages/eido/validation.py", line 73, in validate_project
    _validate_object(
  File "/Users/oliverkuchler/miniforge3/envs/snakemake7/lib/python3.12/site-packages/eido/validation.py", line 45, in _validate_object
    instance_name = error.instance[sample_name_colname]
                    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^

Is there any plans for the future to improve the output?
It would be very cool if one could at least see, because of which input the validation fails.

[donaldcampbelljr]

Can this be closed @ClaudeHu ?

[ClaudeHu]

Can this be closed @ClaudeHu ?

I believe so. After eido is merged into peppy I ran it and the error message is very neat:

$ peppy validate input_error.csv -s pep_schema.yaml
Found 1 types of error:
  - 'testung' is not valid under any of the given schemas: (1 samples) test
Validation unsuccessful. 1 error type found.