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Make eluent_introduction_category & has_mass_spectrometry_configuration slots on MassSpectrometry required and implement migrator #2461

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Merged
merged 11 commits into from
May 28, 2025
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Make eluent_introduction_category & has_mass_spectrometry_configuration slots on MassSpectrometry required and implement migrator #2461

merged 11 commits into from
May 28, 2025

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hesspnnl
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@hesspnnl hesspnnl commented May 22, 2025 •
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  • Make MassSpectromery's slots eluent_introduction_category, has_mass_spectrometry_configuration required
  • create a migrator to that will raise an error if the slots do not exist. Data for these slots has already been back filled.
  • Tested the migrators locally against mongo db data

This MR will close #2455

@hesspnnl hesspnnl self-assigned this May 22, 2025
@hesspnnl hesspnnl linked an issue May 22, 2025 that may be closed by this pull request
Make modifications to MassSpectromery's eluent_introduction_category #2455
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@hesspnnl hesspnnl marked this pull request as draft May 22, 2025 15:15
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github-actions bot commented May 22, 2025 •
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PR Preview Action v1.6.1

🚀 View preview at
https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-2461/

Built to branch gh-pages at 2025-05-28 13:22 UTC.
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@hesspnnl hesspnnl requested a review from kheal May 22, 2025 18:01
@hesspnnl hesspnnl marked this pull request as ready for review May 22, 2025 18:01
@hesspnnl hesspnnl requested review from eecavanna and turbomam May 22, 2025 18:01
@hesspnnl hesspnnl marked this pull request as draft May 22, 2025 18:08
kheal
kheal approved these changes May 22, 2025
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@kheal kheal changed the title Make eluent_introduction_category & has_mass_spectrometry_configuration slots on MassSpectrometry objects required and implement migrator Make eluent_introduction_category & has_mass_spectrometry_configuration slots on MassSpectrometry required and implement migrator May 22, 2025
@hesspnnl hesspnnl marked this pull request as ready for review May 23, 2025 14:28
eecavanna
eecavanna approved these changes May 24, 2025
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The migrator looks good to me. I left one PR comment about checking whether a key exists versus checking whether it exists and the value of its item is not None.

@hesspnnl hesspnnl mentioned this pull request May 27, 2025
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@hesspnnl @eecavanna
Update nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/…
8f3cfd3 
…migrator_from_11_7_0_to_11_8_0_part_3.py

Co-authored-by: eecavanna <[email protected]>
turbomam
turbomam reviewed May 28, 2025
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Wow, you have been prolific recently

I have the same questions here that I had about invalid examples files in the following PR. You don't need to address that in both places.

@hesspnnl hesspnnl merged commit 74681d8 into main May 28, 2025
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@hesspnnl hesspnnl deleted the 2455-make-modifications-to-massspectromery branch May 28, 2025 20:50
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@kheal kheal kheal approved these changes

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Make modifications to MassSpectromery's eluent_introduction_category
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