Added script relevant for the pseudo-bulk expression and UMAP coordinates rendering - #327
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StevenQiaoUT wants to merge 4 commits into
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Added script relevant for the pseudo-bulk expression and UMAP coordinates rendering#327StevenQiaoUT wants to merge 4 commits into
StevenQiaoUT wants to merge 4 commits into
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rmobmina
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Aug 10, 2026
Integrates the UMAP coordinate/expression endpoint and per-tissue pseudobulk gene expression endpoint (originally PR BioAnalyticResource#327) onto the current combined_master.json-driven schema catalog, since the old pre-refactor helpers that PR was written against no longer exist. Adds 7 new pseudobulk databases to the schema catalog (species + gene_id_class sourced from combined_master.json, hand-added pending the real XML scrape/verify pass once that metadata is available) and wires their MySQL binds into CI config. The pseudobulk sample_data tables carry one extra data_signal_std column beyond the standard 3-column schema; query_efp_database_dynamic only selects columns by name so this needed no schema changes. UMAP databases are queried directly via raw SQL and are intentionally left out of the schema catalog since they use a different table shape.
rmobmina
added a commit
to rmobmina/BAR_API
that referenced
this pull request
Aug 10, 2026
Integrates the UMAP coordinate/expression endpoint and per-tissue pseudobulk gene expression endpoint (originally PR BioAnalyticResource#327) onto the current combined_master.json-driven schema catalog, since the old pre-refactor helpers that PR was written against no longer exist. Adds 7 new pseudobulk databases to the schema catalog (species + gene_id_class sourced from combined_master.json, hand-added pending the real XML scrape/verify pass once that metadata is available) and wires their MySQL binds into CI config. The pseudobulk sample_data tables carry one extra data_signal_std column beyond the standard 3-column schema; query_efp_database_dynamic only selects columns by name so this needed no schema changes. UMAP databases are queried directly via raw SQL and are intentionally left out of the schema catalog since they use a different table shape.
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