Add tests for sheet2linkml #8
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Might be a good idea to do this for the data in https://harmonization.datacommons.cancer.gov/additional-resources |
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gaurav
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Dec 10, 2021
This PR adds a "dummy sheet test" (#8) -- it runs sheet2linkml with a Google Sheet I've created solely for testing at https://docs.google.com/spreadsheets/d/1HpsF12vl_CeIzV2TEtANeysnh7cy6YOUDdv6fMXT00I/edit#gid=1810442705, and ensures that the output is identical to the schema generated on previous runs, which is included in this PR. In addition to this, this PR also fixes some minor bugs found along with the way: - The CCDH Terminology Service enumeration endpoint changed its format, so we have to modify our API to match it. - The CCDH Terminology Service now returns 404s if the field doesn't exist or is not an enumeration, so we modify our code to catch that possibility. - Fixes #10 by allowing the use of [Google API Service Accounts in an environmental variable](https://pygsheets.readthedocs.io/en/stable/authorization.html#service-account), allowing testing on GitHub Actions. - Added `pytest` to support testing. - Added a command line option to set the Google Sheet ID. - Added checks to ensure that the `logging_config` and `google_sheet_id` command line arguments are set before using them. - Made sheet2linkml explicitly set the error code to `0` in case of successful execution. - Replaced a stray `print()` with `logging.debug()`.
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The easiest way to test this would be to see if it can convert the CRDC-H model in Google Sheets into valid LinkML, but this is a bad idea since the CRDC-H model in Google Sheets will probably be changing soon. Instead, we should probably come up with a dummy spreadsheet whose sole purpose is to test this generator.
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