fix!: use more precise name for CLI source option #204
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korikuzma
reviewed
May 9, 2023
README.md
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| @@ -73,15 +73,15 @@ Use the `gene_update` command in a shell to update the database. | |||
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| The normalizer currently pulls data from [HGNC](https://www.genenames.org/), [Ensembl](https://useast.ensembl.org/index.html), and [NCBI](https://www.ncbi.nlm.nih.gov/gene/). | |||
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| To update one source, simply set `--normalizer` to the source you wish to update. The normalizer will check to see if local source data is up-to-date, acquire the most recent data if not, and use it to populate the database. | |||
| To update one source, simply set `--source` to the source you wish to update. The normalizer will check to see if local source data is up-to-date, acquire the most recent data if not, and use it to populate the database. | |||
korikuzma
previously approved these changes
May 9, 2023
| To update specific sources, use the ``--normalizer`` option along with source name(s), quoted and separated by spaces. While it is possible to update individual source data without updating the normalized record data with ``--update_merged``, the normalization query endpoints may not function properly until normalized data is refreshed again. :: | ||
| To update specific sources, use the ``--source`` option along with source name(s), quoted and separated by spaces. While it is possible to update individual source data without updating the normalized record data with ``--update_merged``, the normalization query endpoints may not function properly until normalized data is refreshed again. :: | ||
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| gene_norm_update --source="HGNC NCBI" --update_merged |
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Should we consider using plural?
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Yeah I think plural makes sense
korikuzma
previously approved these changes
May 9, 2023
korikuzma
requested changes
May 9, 2023
korikuzma
reviewed
May 9, 2023
gene/cli.py
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| ) -> None: | ||
| """Update selected normalizer sources. | ||
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| :param normalizers: names of sources to update | ||
| :param source: names of sources to update |
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sorry i missed this one
Suggested change
| :param source: names of sources to update | |
| :param sources: names of sources to update |
korikuzma
approved these changes
May 9, 2023
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close #179