AllenNeuralDynamics / AllenNeuralDynamics/aind-ephys-pipeline

Add `logging` section to the parameters

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#123 1 則留言 0 個 reaction 已指派 2 人 已被 @arjunsridhar12345 認領 在 GitHub 檢視
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Nextflow
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25 分鐘
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2

描述

To customize logging, we could add a `logging` section to the params.

This would allow both to custmize the default logging and to optionally use the AIND-specific `log-schema`.

For example, the logging section could look like this:
```
"logging": {
"package": "logging" / "log_schema",
"logging_cgf": {
...
}
}
```

The `main.nf` can take care of appending the `logging` section (if available) to the params of every process. Individual processes can then dispatch and setup the logging. For the AIND `log-schema`, the `main.nf` could also add the `acquisition_name` and `pipeline_name` because they are shared across processes. The individual processes will then append the `process_name`.

Note: we need to update the containers to install `log-schema`

FYI: @dyf @arielleleon @dougollerenshaw

貢獻指南

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研究方向

Start with main.nf and the process definitions that consume pipeline parameters, then inspect the container definitions to see where logging dependencies are installed. Compare the proposed logging parameter shape with current parameter handling and verify that shared logging values reach each process and that the containers support the selected logging package.

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評估

領域
data-engineering
Issue 類型
功能
難度
4/5
預估耗時
3-5 天
活躍度
活躍
描述清晰度
基本清楚
新手友好度
42/100

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