Code

Refactor cli#32

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bedroesb merged 45 commits intomainelixir-europe/MARS:mainfrom refactor_clielixir-europe/MARS:refactor_cliCopy head branch name to clipboardMay 7, 2024

+2,677-1,729

Commits

Commits on Apr 15, 2024

• add click arguments and options to main function

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• Generate settings file on install

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• Move external references logic to separate file

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• change entry point to cli

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• Don't overwrite config file by default when reinstalling

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• Add logging

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• Add constraints on the size of the files and the number of older log files.

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• Add logging documentation

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• Add ISA JSON models for validation

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• Add validator for assay comments

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• Exclude all __init__.py files from coverage

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• Add log files

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• Make model validation more strict

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• Remove unused variables

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• linting

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• Use pydantic classes instead of dictionaries

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• Migrate from @validator to @field_validator

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• Move TargetRepository and TARGET_REPO_KEY to shared file

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• Add EVA to TargetRepository

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• Remove empty unused validation.py

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Commits on Apr 16, 2024

• update target repo validator

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• add validator tests

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• linting

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• Modify function to write different levels

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• Fix import statements

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• Add context to CLI

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• Add URLs to the config file

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Commits on Apr 19, 2024

• Change settings dir dependend of environmental variable.

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• Print to std err when error is logged

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• Add health check command

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• Add IsaJson wrapper around Investigation

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• Formatting

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• Invalid material type according to the specs:

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• Formatting

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• move model to mars_lib

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• Add validation command to CLI

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• Remove phone nr validator

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• Fix for ARC

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Commits on Apr 22, 2024

• Add option for ISA JSON's when investigation is root

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• Update tests

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• Update README

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• Fix failing tests

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• Add pydantic to requirements

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Commits on Apr 24, 2024

• Fix typo

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Commits on May 7, 2024

• add l click

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