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Bugfix in AddProtein - paste() returns deparsed expression for single-column lists...

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hyginn 2020-11-09 22:02:27 +10:00
parent 39b1da5897
commit 33ba40a252
1 changed files with 25 additions and 23 deletions
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scripts/ABC-dbUtilities.R
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@ -2,12 +2,14 @@
# #
# Purpose: Database utilities for ABC learning units. # 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) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 2.3 Bug in treatment of single-column dataframes which returns
# a deparsed expression from paste()
# 2.2 Bugfixes # 2.2 Bugfixes
# 2.1 Add JSON export functions # 2.1 Add JSON export functions
# 2.0 Test all JSON import and prevent addition of duplicates. This # 2.0 Test all JSON import and prevent addition of duplicates. This
@ -34,26 +36,26 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------------------- #TOC> -------------------------------------------------------
#TOC> 1 INITIALISATIONS AND PARAMETERS 61 #TOC> 1 INITIALISATIONS AND PARAMETERS 63
#TOC> 2 PACKAGES 66 #TOC> 2 PACKAGES 68
#TOC> 3 FUNCTIONS 82 #TOC> 3 FUNCTIONS 84
#TOC> 3.01 dbSanitizeSequence() 85 #TOC> 3.01 dbSanitizeSequence() 87
#TOC> 3.02 dbConfirmUnique() 120 #TOC> 3.02 dbConfirmUnique() 122
#TOC> 3.03 dbInit() 138 #TOC> 3.03 dbInit() 140
#TOC> 3.04 dbAutoincrement() 178 #TOC> 3.04 dbAutoincrement() 180
#TOC> 3.05 dbAddProtein() 191 #TOC> 3.05 dbAddProtein() 193
#TOC> 3.06 dbAddFeature() 227 #TOC> 3.06 dbAddFeature() 229
#TOC> 3.07 dbAddTaxonomy() 258 #TOC> 3.07 dbAddTaxonomy() 260
#TOC> 3.08 dbAddAnnotation() 293 #TOC> 3.08 dbAddAnnotation() 295
#TOC> 3.09 dbFetchUniProtSeq() 340 #TOC> 3.09 dbFetchUniProtSeq() 342
#TOC> 3.10 dbFetchPrositeFeatures() 386 #TOC> 3.10 dbFetchPrositeFeatures() 388
#TOC> 3.11 node2text() 436 #TOC> 3.11 node2text() 438
#TOC> 3.12 dbFetchNCBItaxData() 448 #TOC> 3.12 dbFetchNCBItaxData() 450
#TOC> 3.13 UniProtIDmap() 487 #TOC> 3.13 UniProtIDmap() 489
#TOC> 3.14 dbProt2JSON() 526 #TOC> 3.14 dbProt2JSON() 528
#TOC> 3.15 dbSeq2JSON() 611 #TOC> 3.15 dbSeq2JSON() 613
#TOC> 3.16 dbRow2JSON() 640 #TOC> 3.16 dbRow2JSON() 642
#TOC> 4 TESTS 660 #TOC> 4 TESTS 662
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -209,7 +211,7 @@ dbAddProtein <- function(db, jsonDF) {
if (isValid) { if (isValid) {
if (length(jsonDF$name) == 1) { # jsonlite:: oversimplifies if (length(jsonDF$name) == 1) { # jsonlite:: oversimplifies
jsonDF$sequence <- paste(jsonDF$sequence, collapse = "") jsonDF$sequence <- paste0(unlist(jsonDF$sequence), collapse = "")
} }
x <- data.frame(ID = dbAutoincrement(db$protein), x <- data.frame(ID = dbAutoincrement(db$protein),
name = jsonDF$name[i], name = jsonDF$name[i],