fix: improve error handling and fix minor bugs - #2
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- utilities.R: geneset_download now calls stop() when download fails and no local cache exists, instead of returning FALSE and letting callers crash with a cryptic fst::read.fst error - getEnrichrdb.R, getHgDisease.R, getMsigdb.R: geneset_name now returns an empty data.frame instead of logical NA, keeping the return type consistent with other get*() functions - getKEGG.R: fix typo 'categoty' -> 'category' and grammar 'support' -> 'supports' - getKEGG.R: include category in local cache filename to avoid collisions between pathway/module/enzyme caches for the same organism
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Hi @liuyunze, thank you for maintaining this useful package!
This PR addresses a few bugs and improvements I noticed while reviewing the code. All changes are backward-compatible from the user's perspective.
1. Download failure now throws a clear error (
utilities.R)Before: When
geneset_download()failed and no local cache existed, it returnedFALSEsilently. None of the callers (getGO,getKEGG, etc.) checked the return value, so the next line —fst::read.fst(destfile)— crashed with a cryptic file-not-found error from thefstpackage.After: When download fails and no local cache is available,
geneset_download()now callsstop()directly with the helpful message that was already being printed (including the download URL and manual instructions).2.
geneset_namereturns an empty data.frame instead of logicalNA(getEnrichrdb.R,getHgDisease.R,getMsigdb.R)Before: For data sources that don't have a separate name table, the code set
res[['geneset_name']] <- NA, returning a logicalNA. This is inconsistent with otherget*functions that always return adata.frame, and breaks downstream code that callshead(),colnames(), ornrow()on the result.After: Now returns
data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE), which is type-compatible with the rest of the API.3. Fixed typo in
getKEGG.RCorrected
categotytocategoryandsupporttosupportsin the error message for non-human KEGG categories.Please feel free to let me know if you'd like any adjustments!