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Replace Czech Republic with Czechia #1196

Merged
merged 3 commits into from
Oct 3, 2024
Merged

Replace Czech Republic with Czechia #1196

merged 3 commits into from
Oct 3, 2024

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alexhbnr
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@alexhbnr alexhbnr commented Oct 3, 2024

After the official name of the country "Czech Republic" was changed to Czechia, the website https://unstats.un.org/unsd/methodology/m49/ changed it, too. This PR changes all occurrences of "Czech Republic" to "Czechia" and updates the JSON file with the allowed values.

alexhbnr and others added 2 commits October 3, 2024 12:50
After the official name of the country "Czech Republic" was changed to
Czechia, the website https://unstats.un.org/unsd/methodology/m49/
changed it, too. The commit changes all occurrences of "Czech Republic
to Czechia" and updates the JSON file with the allowed values.
@alexhbnr alexhbnr requested a review from jfy133 October 3, 2024 13:07
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jfy133 commented Oct 3, 2024

I used this: https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/ (as that's what ENA uses) as our source of truth.

I see the change has been made there too - maybe just update the entire JSON with the updated list to see if tehre are any other new names?

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github-actions bot commented Oct 3, 2024

AMDirT, version 1.6.2

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error Source Column Row Message
Schema Validation Error Czechia geo_loc_name 866 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 867 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 869 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error Source Column Row Message
Schema Validation Error Czechia geo_loc_name 9 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 50 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 51 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 111 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 369 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 391 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 442 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 443 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 444 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 445 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 446 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 449 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 459 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 460 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 488 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 489 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 499 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 502 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 503 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 507 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error Czechia geo_loc_name 513 'Czechia' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

@alexhbnr
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alexhbnr commented Oct 3, 2024

Yes, the link that I posted (https://unstats.un.org/unsd/methodology/m49/) is the underlying source for https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/.

I pulled the list and added the additional three changes to the JSON file. However, none of them affected our tables.

@alexhbnr alexhbnr merged commit c1e88b8 into master Oct 3, 2024
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@alexhbnr alexhbnr deleted the czechia branch October 3, 2024 15:22
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2 participants