From 33ba40a2521c0af32a4ee0c77a21fd5cf4acf525 Mon Sep 17 00:00:00 2001 From: hyginn Date: Mon, 9 Nov 2020 22:02:27 +1000 Subject: [PATCH] Bugfix in AddProtein - paste() returns deparsed expression for single-column lists... --- scripts/ABC-dbUtilities.R | 48 ++++++++++++++++++++------------------- 1 file changed, 25 insertions(+), 23 deletions(-) diff --git a/scripts/ABC-dbUtilities.R b/scripts/ABC-dbUtilities.R index 7a6bc05..71709c8 100644 --- a/scripts/ABC-dbUtilities.R +++ b/scripts/ABC-dbUtilities.R @@ -2,12 +2,14 @@ # # Purpose: Database utilities for ABC learning units. # -# Version 2.2 +# Version 2.3 # -# Date: 2017-11 - 2020-10 +# Date: 2017-11 - 2020-11 # Author: Boris Steipe (boris.steipe@utoronto.ca) # # Versions: +# 2.3 Bug in treatment of single-column dataframes which returns +# a deparsed expression from paste() # 2.2 Bugfixes # 2.1 Add JSON export functions # 2.0 Test all JSON import and prevent addition of duplicates. This @@ -34,26 +36,26 @@ #TOC> #TOC> Section Title Line #TOC> ------------------------------------------------------- -#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() 227 -#TOC> 3.07 dbAddTaxonomy() 258 -#TOC> 3.08 dbAddAnnotation() 293 -#TOC> 3.09 dbFetchUniProtSeq() 340 -#TOC> 3.10 dbFetchPrositeFeatures() 386 -#TOC> 3.11 node2text() 436 -#TOC> 3.12 dbFetchNCBItaxData() 448 -#TOC> 3.13 UniProtIDmap() 487 -#TOC> 3.14 dbProt2JSON() 526 -#TOC> 3.15 dbSeq2JSON() 611 -#TOC> 3.16 dbRow2JSON() 640 -#TOC> 4 TESTS 660 +#TOC> 1 INITIALISATIONS AND PARAMETERS 63 +#TOC> 2 PACKAGES 68 +#TOC> 3 FUNCTIONS 84 +#TOC> 3.01 dbSanitizeSequence() 87 +#TOC> 3.02 dbConfirmUnique() 122 +#TOC> 3.03 dbInit() 140 +#TOC> 3.04 dbAutoincrement() 180 +#TOC> 3.05 dbAddProtein() 193 +#TOC> 3.06 dbAddFeature() 229 +#TOC> 3.07 dbAddTaxonomy() 260 +#TOC> 3.08 dbAddAnnotation() 295 +#TOC> 3.09 dbFetchUniProtSeq() 342 +#TOC> 3.10 dbFetchPrositeFeatures() 388 +#TOC> 3.11 node2text() 438 +#TOC> 3.12 dbFetchNCBItaxData() 450 +#TOC> 3.13 UniProtIDmap() 489 +#TOC> 3.14 dbProt2JSON() 528 +#TOC> 3.15 dbSeq2JSON() 613 +#TOC> 3.16 dbRow2JSON() 642 +#TOC> 4 TESTS 662 #TOC> #TOC> ========================================================================== @@ -209,7 +211,7 @@ dbAddProtein <- function(db, jsonDF) { if (isValid) { if (length(jsonDF$name) == 1) { # jsonlite:: oversimplifies - jsonDF$sequence <- paste(jsonDF$sequence, collapse = "") + jsonDF$sequence <- paste0(unlist(jsonDF$sequence), collapse = "") } x <- data.frame(ID = dbAutoincrement(db$protein), name = jsonDF$name[i],