I’m seeing a reproducible failure in PerformGeneMapping() when using org_code="bsu".
Running mSet <- PerformGeneMapping(mSet, geneList, org_code="bsu", gene_id_type=...) prints DEBUG: Attempting to connect to SQLite database at: bsu_genes.sqlite, followed by File exists: TRUE and File size: 0 bytes, and mapping then fails because the sqlite file is empty.
I tried to manually download the expected DB via GitHub raw URLs for bsu_genes.sqlite, but they return 404 (and I get 0-byte/invalid downloads). It looks like the code either points at an outdated DB location or doesn’t validate download success before proceeding.
Could you confirm the intended current source/location for the gene-mapping sqlite DBs (or whether bsu is supported for this module)? A small robustness improvement would be to check that the DB is non-zero and has a valid SQLite header (“SQLite format 3”) before connecting, and throw a clear error if not.
I’m seeing a reproducible failure in PerformGeneMapping() when using org_code="bsu".
Running mSet <- PerformGeneMapping(mSet, geneList, org_code="bsu", gene_id_type=...) prints DEBUG: Attempting to connect to SQLite database at: bsu_genes.sqlite, followed by File exists: TRUE and File size: 0 bytes, and mapping then fails because the sqlite file is empty.
I tried to manually download the expected DB via GitHub raw URLs for bsu_genes.sqlite, but they return 404 (and I get 0-byte/invalid downloads). It looks like the code either points at an outdated DB location or doesn’t validate download success before proceeding.
Could you confirm the intended current source/location for the gene-mapping sqlite DBs (or whether bsu is supported for this module)? A small robustness improvement would be to check that the DB is non-zero and has a valid SQLite header (“SQLite format 3”) before connecting, and throw a clear error if not.