From 0541612e0bec6bc7837be3032456e0d95ce677cd Mon Sep 17 00:00:00 2001 From: hyginn Date: Tue, 13 Oct 2020 20:27:56 +1000 Subject: [PATCH] Bugfixes --- scripts/ABC-dbUtilities.R | 61 ++++++++++++++++++++------------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/scripts/ABC-dbUtilities.R b/scripts/ABC-dbUtilities.R index c5b8a9b..89c4784 100644 --- a/scripts/ABC-dbUtilities.R +++ b/scripts/ABC-dbUtilities.R @@ -2,17 +2,18 @@ # # Purpose: Database utilities for ABC learning units. # -# Version 2.1 +# Version 2.2 # # Date: 2017-11 - 2020-10 # Author: Boris Steipe (boris.steipe@utoronto.ca) # # Versions: -# 2.1 Add JSON export functions -# 2.0 Test all JSON import and prevent addition of duplicates. This +# 2.2 Bugfixes +# 2.1 Add JSON export functions +# 2.0 Test all JSON import and prevent addition of duplicates. This # is necessary for import of data from the public page -# 1.1 2020 Updates -# 1.0 Live version 2017 +# 1.1 2020 Updates +# 1.0 Live version 2017 # # Notes: # There are no functions to modify or delete entries. To do either, @@ -33,26 +34,26 @@ #TOC> #TOC> Section Title Line #TOC> ------------------------------------------------------- -#TOC> 1 INITIALISATIONS AND PARAMETERS 60 -#TOC> 2 PACKAGES 65 -#TOC> 3 FUNCTIONS 81 -#TOC> 3.01 dbSanitizeSequence() 84 -#TOC> 3.02 dbConfirmUnique() 119 -#TOC> 3.03 dbInit() 137 -#TOC> 3.04 dbAutoincrement() 177 -#TOC> 3.05 dbAddProtein() 190 -#TOC> 3.06 dbAddFeature() 222 -#TOC> 3.07 dbAddTaxonomy() 253 -#TOC> 3.08 dbAddAnnotation() 288 -#TOC> 3.09 dbFetchUniProtSeq() 335 -#TOC> 3.10 dbFetchPrositeFeatures() 381 -#TOC> 3.11 node2text() 431 -#TOC> 3.12 dbFetchNCBItaxData() 443 -#TOC> 3.13 UniProtIDmap() 482 -#TOC> 3.14 dbProt2JSON() 521 -#TOC> 3.15 dbSeq2JSON() 606 -#TOC> 3.16 dbRow2JSON() 636 -#TOC> 4 TESTS 656 +#TOC> 1 INITIALISATIONS AND PARAMETERS 61 +#TOC> 2 PACKAGES 66 +#TOC> 3 FUNCTIONS 82 +#TOC> 3.01 dbSanitizeSequence() 85 +#TOC> 3.02 dbConfirmUnique() 120 +#TOC> 3.03 dbInit() 138 +#TOC> 3.04 dbAutoincrement() 178 +#TOC> 3.05 dbAddProtein() 191 +#TOC> 3.06 dbAddFeature() 224 +#TOC> 3.07 dbAddTaxonomy() 255 +#TOC> 3.08 dbAddAnnotation() 290 +#TOC> 3.09 dbFetchUniProtSeq() 337 +#TOC> 3.10 dbFetchPrositeFeatures() 383 +#TOC> 3.11 node2text() 433 +#TOC> 3.12 dbFetchNCBItaxData() 445 +#TOC> 3.13 UniProtIDmap() 484 +#TOC> 3.14 dbProt2JSON() 523 +#TOC> 3.15 dbSeq2JSON() 608 +#TOC> 3.16 dbRow2JSON() 637 +#TOC> 4 TESTS 657 #TOC> #TOC> ========================================================================== @@ -197,6 +198,7 @@ dbAddProtein <- function(db, jsonDF) { # fromJSON() for (i in seq_len(nrow(jsonDF))) { + isValid <- TRUE if (jsonDF$name[i] %in% db$protein$name) { cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n", i, jsonDF$name[i], @@ -237,7 +239,7 @@ dbAddFeature <- function(db, jsonDF) { isValid <- FALSE } - if (isVALID) { + if (isValid) { x <- data.frame(ID = dbAutoincrement(db$feature), name = jsonDF$name[i], description = jsonDF$description[i], @@ -306,11 +308,11 @@ dbAddAnnotation <- function(db, jsonDF) { sel <- db$annotation$proteinID == pID & db$annotation$featureID == fID & - db$annotation$start == as.integer(jsonDF$start[idx]) & - db$annotation$end == as.integer(jsonDF$end[idx]) + db$annotation$start == as.integer(jsonDF$start[i]) & + db$annotation$end == as.integer(jsonDF$end[i]) if (any(sel)) { - cat(sprintf("Note: annotation No. %d in the input has %s%s%\n", + cat(sprintf("Note: annotation No. %d in the input has %s%s\n", i, "the same protein name, feature name, start, and end ", "as one that already exists in the database. ", @@ -630,7 +632,6 @@ dbSeq2JSON <- function(s, nIndents = 4, width = 70) { out <- c(out, sprintf("%s]", ind)) return(paste0(out, collapse = "\n")) } -cat(dbSeq2JSON(myDB$protein$sequence[1])) # == 3.16 dbRow2JSON() =====================================================