Mercurial > repos > prog > lcmsmatching
diff ChemspiderCompound.R @ 1:253d531a0193 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
| author | prog |
|---|---|
| date | Sat, 03 Sep 2016 17:02:01 -0400 |
| parents | e66bb061af06 |
| children |
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--- a/ChemspiderCompound.R Tue Jul 12 12:02:37 2016 -0400 +++ b/ChemspiderCompound.R Sat Sep 03 17:02:01 2016 -0400 @@ -40,14 +40,14 @@ accession <- xpathSApply(xml, "//li[starts-with(., 'ChemSpider ID')]", xmlValue) if (length(accession) > 0) { accession <- sub('^ChemSpider ID([0-9]+)$', '\\1', accession, perl = TRUE) - compound$setField(RBIODB.ACCESSION, accession) + compound$setField(BIODB.ACCESSION, accession) } compounds <- c(compounds, compound) } # Replace elements with no accession id by NULL - compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x) + compounds <- lapply(compounds, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x) # If the input was a single element, then output a single object if (drop && length(contents) == 1)