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patch a problem where jsonlite:: oversimplifies from single entries to array, rather than list.

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This commit is contained in:
hyginn 2020-10-13 22:38:47 +10:00
parent d2fffdf0b8
commit 55a0d18a66
1 changed files with 15 additions and 12 deletions
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27
scripts/ABC-dbUtilities.R
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@ -42,18 +42,18 @@
#TOC> 3.03 dbInit() 138 #TOC> 3.03 dbInit() 138
#TOC> 3.04 dbAutoincrement() 178 #TOC> 3.04 dbAutoincrement() 178
#TOC> 3.05 dbAddProtein() 191 #TOC> 3.05 dbAddProtein() 191
#TOC> 3.06 dbAddFeature() 224 #TOC> 3.06 dbAddFeature() 227
#TOC> 3.07 dbAddTaxonomy() 255 #TOC> 3.07 dbAddTaxonomy() 258
#TOC> 3.08 dbAddAnnotation() 290 #TOC> 3.08 dbAddAnnotation() 293
#TOC> 3.09 dbFetchUniProtSeq() 337 #TOC> 3.09 dbFetchUniProtSeq() 340
#TOC> 3.10 dbFetchPrositeFeatures() 383 #TOC> 3.10 dbFetchPrositeFeatures() 386
#TOC> 3.11 node2text() 433 #TOC> 3.11 node2text() 436
#TOC> 3.12 dbFetchNCBItaxData() 445 #TOC> 3.12 dbFetchNCBItaxData() 448
#TOC> 3.13 UniProtIDmap() 484 #TOC> 3.13 UniProtIDmap() 487
#TOC> 3.14 dbProt2JSON() 523 #TOC> 3.14 dbProt2JSON() 526
#TOC> 3.15 dbSeq2JSON() 608 #TOC> 3.15 dbSeq2JSON() 611
#TOC> 3.16 dbRow2JSON() 637 #TOC> 3.16 dbRow2JSON() 640
#TOC> 4 TESTS 657 #TOC> 4 TESTS 660
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -208,6 +208,9 @@ dbAddProtein <- function(db, jsonDF) {
} }
if (isValid) { if (isValid) {
if (length(jsonDF$name) == 1) { # jsonlite:: oversimplifies
jsonDF$sequence <- paste(jsonDF$sequence, collapse = "")
}
x <- data.frame(ID = dbAutoincrement(db$protein), x <- data.frame(ID = dbAutoincrement(db$protein),
name = jsonDF$name[i], name = jsonDF$name[i],
RefSeqID = jsonDF$RefSeqID[i], RefSeqID = jsonDF$RefSeqID[i],