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Add CI/CD for retrieving and building ontologies into rustyms#53

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douweschulte merged 36 commits intomainfrom
feature-build-cicd
Feb 7, 2025
Merged

Add CI/CD for retrieving and building ontologies into rustyms#53
douweschulte merged 36 commits intomainfrom
feature-build-cicd

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@wfondrie
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@wfondrie wfondrie commented Feb 5, 2025

This PR add a GitHub action to automate the download and serialization of the required ontologies for building rustyms.

@wfondrie wfondrie changed the base branch from release to main February 5, 2025 10:35
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wfondrie commented Feb 6, 2025

Here's the most recent glycan error:

error: Invalid iupac monosaccharide name
    ╷
476 │ G00023PO,"Qui2
    ·              ‾‾‾
    ╵
This name could not be recognised as a standard iupac glycan name
error: Invalid iupac monosaccharide name
    ╷
479 │ G00063TX,"Fuc2
    ·              ‾‾‾
    ╵
This name could not be recognised as a standard iupac glycan name
error: Invalid iupac monosaccharide name
    ╷
538 │ G00006RP,"D-Araf2
    ·                 ‾‾‾
    ╵
This name could not be recognised as a standard iupac glycan name
error: Invalid iupac monosaccharide name
    ╷
539 │ G00028ZX,"Hex2F4
    ·                ‾‾‾
    ╵
This name could not be recognised as a standard iupac glycan name
error: Invalid iupac monosaccharide name
    ╷
541 │ G00053UV,"D-Ara2
    ·                ‾‾‾
    ╵
This name could not be recognised as a standard iupac glycan name
thread 'main' panicked at rustyms-generate-databases/src/../../rustyms/src/shared/glycan.rs:377:24:
index out of bounds: the len is 2 but the index is 2
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

@wfondrie
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wfondrie commented Feb 6, 2025

Alright, I think this is ready to go! Check out #61 just to make sure.

Update external databases and ontologies
@douweschulte douweschulte merged commit ba6dad7 into main Feb 7, 2025
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@douweschulte douweschulte deleted the feature-build-cicd branch June 23, 2025 21:13
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