Feat/use rust for datacollect - #588
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Oct 20, 2025
| # https://www.alliancegenome.org/downloads#gene-descriptions | ||
| # https://download.alliancegenome.org/8.1.0/GENE-DESCRIPTION-JSON/SGD/GENE-DESCRIPTION-JSON_SGD_9.json.gz | ||
| # origname = pull_via_urllib('https://fms.alliancegenome.org/download/',f'GENE-DESCRIPTION-JSON_{mod}.json.gz',subpath=subp) | ||
| origname = pull_via_urllib(f'https://download.alliancegenome.org/8.1.0/GENE-DESCRIPTION-JSON/{mod}/',f'GENE-DESCRIPTION-JSON_{mod}_9.json.gz', subpath=subp) |
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@jdr0887 The previous URL (https://fms.alliancegenome.org/...) still works for me and is referenced from https://www.alliancegenome.org/downloads#gene-descriptions, and I'm not sure why you added the _9 here. Is there something we need to change in Babel?
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Oct 20, 2025
This PR upgrades [pyoxigraph v0.2.5 to v0.4.11](https://pyoxigraph.readthedocs.io/en/stable/migration.html#from-0-2-to-0-3), which requires the interface to be updated. It also replaces the dodgy/outdated [python-Levenshtein-wheels](https://pypi.org/project/python-Levenshtein-wheels/) with the up-to-date [python-Levenshtein](https://pypi.org/project/python-Levenshtein/). Adapted from PR #588.
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Mar 27, 2026
apybiomart's pre-flight check GETs https://example.org/ to verify internet access, but SSL certificate verification fails in some environments, causing a misleading "No internet connection available!" error before any BioMart query is attempted. Patch _Server._check_connection (the base class shared by all apybiomart server classes) to always return True. The check is redundant — a real connectivity failure will surface as a BioMart-level error instead. See robertopreste/apybiomart#131 for the upstream issue. The patch is temporary until apybiomart is replaced (#588). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Stale-branch sweep note: this draft has no description, has been idle since September, and is 700+ commits behind main. A Rust rewrite of |
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