Pre Cassette save

This is just a save before we move to cassettes where we will have the code generate cassette data and reduce allele sets. This will be used until the Alliance is ready for the cassettes. Note v2.13.0 schema was used for this. We might need a separate branch if this needs updating at all.

v8.2.0

Code used to generate data for the Alliance 8.2.0 public release, using v2.10.0 LinkML.
Note that the generate_aggregated_allele_mutation_descriptions() method was added as a hotfix 250724.

What's Changed

• Refactor gene by @gildossantos in #12
• Refactor gene by @gildossantos in #13
• Split out code into smaller files; 1st draft of gene and gene-allele export. by @gildossantos in #14
• Update linkml - v2.2.3 by @gildossantos in #15
• Refactor disease by @gildossantos in #17
• Fix feature lookup by @gildossantos in #18
• Suppress synonym pubs until LinkML loads get faster by @gildossantos in #19
• rename mod_entity_id to primary_external_id" by @gildossantos in #20
• Refactor export code by @gildossantos in #21
• FTA-4: Minimal genotype submission. by @gildossantos in #22
• Minimal submission for genotype (FTA-12), aberrations (FTA-9) and insertions (FTA-2). by @gildossantos in #23
• FTA-32: Generate incremental export files based on comparison of production to explore_chado_last_week by @gildossantos in #25
• FTA-32: Mark new entities in production_chado as internal = True for incremental Alliance persistent store loads. by @gildossantos in #26
• FTA-33: Update export data to comply with LinkML v2.9.0. by @gildossantos in #27

Full Changelog: v1.7.3...v8.2.0

v1.7.3

Export FlyBase genes, alleles, strains and allele-level disease annotations to Alliance LinkML v1.7.3 JSON files.

v1.6.0

Export FlyBase genes, alleles and disease annotations into v1.6.0 LinkML.

v1.5.0

Gene, allele and disease annotations conforming to Alliance LinkML v1.5.0.