Comments (4)
Actually I didn't know that eido provides positional
--st-index
argument which actually solves the problem (facepalm).
Ok, great.
Another option is to change to:
1. Value specified in Project constructor
2. Value specified in Config
3. Default value (sample_name)
4. If no match, use the first column
The schema specification doesn't make sense, because it would make the peppy Project constructor rely on the schema. You can, of course, get the value from the schema yourself, and then just pass it to the project constructor. But don't make peppy require a schema for creating a Project.
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@nsheff can I have your comment here? Which option looks better for you?
Also @nleroy917 @khoroshevskyi I would love to hear what do you think.
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Actually I didn't know that eido provides positional --st-index
argument which actually solves the problem (facepalm).
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then the only way to specify this and allow correct validation from command line is to have config.yaml defining new sample table index column name.
Not exactly. Another way is to just pass the name of the index column as a command-line argument. Another way is to assume that the first column is the index column.
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Related Issues (20)
- ImportError: cannot import name 'load_yaml' from 'peppy.utils' HOT 1
- Warn if bad filter HOT 2
- list of available output formats HOT 5
- [BREAKING] KeyError: '_samples' Cant validate schema HOT 11
- CSV filter output for multi-value sample attributes HOT 1
- Uniform eido validation behavior for inputs HOT 1
- `convert_project` exits program HOT 1
- Processed PEP filter HOT 10
- CSV filter bug after peppy update HOT 1
- Upgrade the way errors are printed for CLI usage of eido
- Use eido with project modifiers HOT 1
- RemoteYAMLError HOT 6
- Unused parameter in validate_* functions HOT 2
- removelarge historical files HOT 1
- Object type for mutable mapping HOT 1
- Handling errors HOT 1
- Eido should use the same attribute names as pipestat for its schemas
- eido validate is broken in v0.2 HOT 1
- Hitting an `ImportError` through indirect dependency on `eido` on Python 3.10 HOT 5
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