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.
$ 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
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.
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:
pep_schemal.yaml
imports:
properties: samples: type: array items: type: object properties: sample_directory: type: string pattern: "^/\S+$|None"
sample_name,sample_directory test,/testung
sample_name,sample_directory test,testung
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
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]