Feature/ensembl ref db#18
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adamjohnwright
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Feb 11, 2026
…/release-orthoinference into feature/ensembl-ref-db
adamjohnwright
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"The new code adds imports for FileNotFoundException and JSONParser/ParseException. I'd want to verify that failures in fetchSchema or
fetchOrCreateEnsemblDbInstance (e.g., missing refdb.json, malformed JSON, DB query returning unexpected results) produces clear error messages rather than opaque stack traces." Claude.
I agree that, when possible, we should add proper error messages. If this is easy to do please do.
adamjohnwright
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Mar 25, 2026
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This PR updates Species.json and the inference code so it no longer creates reference databases for EnsEMBL.
Instead it pulls the EnsEMBL reference databases that already exist in the MySQL release database (derived from gk_central). There are 3 EnsEMBL reference databases that are needed for inference -- main, protist, and fungi.
It also pulls "alternative" reference databases from the release database if it already exists and only creates it if it doesn't exist.