diff --git a/R/createMassBank.R b/R/createMassBank.R
index d2aa3a5b77a432b04e776df545868fe1cedb4fcb..020230102957b70de9d8b95179ebb82b6737a754 100755
--- a/R/createMassBank.R
+++ b/R/createMassBank.R
@@ -160,6 +160,8 @@ resetInfolists <- function(mb)
#' @param infolist_path A path where to store newly downloaded compound informations,
#' which should then be manually inspected.
#' @param mb The \code{mbWorkspace} to work in.
+#' @param useCTS A boolean variable denoting whether to retrieve information using CTS or to use babel
+#' to retrieve minimal information.
#' @return The processed \code{mbWorkspace}.
#' @seealso \code{\link{mbWorkspace-class}}
#' @author Michael A. Stravs, Eawag <michael.stravs@@eawag.ch>
@@ -170,22 +172,28 @@ resetInfolists <- function(mb)
#'
#' }
#' @export
-mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.csv")
+mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.csv", useCTS = TRUE)
{
# Step 1: Find which compounds don't have annotation information yet. For these
# compounds, pull information from CTS (using gatherData).
if(1 %in% steps)
{
mbdata_ids <- lapply(mb@aggregatedRcSpecs$specFound, function(spec) spec$id)
-
- message("mbWorkflow: Step 1. Gather info from CTS")
-
+ if(useCTS){
+ message("mbWorkflow: Step 1. Gather info from CTS")
+ } else{
+ message("mbWorkflow: Step 1. Gather info using babel")
+ }
# Which IDs are not in mbdata_archive yet?
new_ids <- setdiff(as.numeric(unlist(mbdata_ids)), mb@mbdata_archive$id)
mb@mbdata <- lapply(new_ids, function(id)
{
#print(id)
- d <- gatherData(id)
+ if(useCTS){
+ d <- gatherData(id)
+ } else{
+ d <- gatherDataBabel(id)
+ }
#print(d$dataused)
message(paste(id, ": ", d$dataused, sep=''))
return(d)
@@ -581,7 +589,107 @@ gatherData <- function(id)
return(mbdata)
} # function gather.mbdata
-
+# Retrieve annotation data for a compound, using only babel
+#' Retrieve annotation data
+#'
+#' Retrieves annotation data for a compound by using babel,
+#' based on the SMILES code and name of the compounds stored in the
+#' compound list.
+#'
+#' Composes the "upper part" of a MassBank record filled with chemical data
+#' about the compound: name, exact mass, structure, CAS no..
+#' The instrument type is also written into this block (even
+#' if not strictly part of the chemical information). Additionally, index
+#' fields are added at the start of the record, which will be removed later:
+#' \code{id, dbcas, dbname} from the compound list.
+#'
+#' Additionally, the fields \code{ACCESSION} and \code{RECORD_TITLE} are
+#' inserted empty and will be filled later on.
+#'
+#' This function is an alternative to gatherData, in case CTS is down or if information
+#' on one or more of the compounds in the compound list are sparse
+#'
+#' @usage gatherDataBabel(id)
+#' @param id The compound ID.
+#' @return Returns a list of type \code{list(id= \var{compoundID}, ...,
+#' 'ACCESSION' = '', 'RECORD_TITLE' = '', )} etc. %% ...
+#' @author Michael Stravs, Erik Mueller
+#' @seealso \code{\link{mbWorkflow}}
+#' @references MassBank record format:
+#' \url{http://www.massbank.jp/manuals/MassBankRecord_en.pdf}
+#' @examples
+#'
+#' # Gather data for compound ID 131
+#' \dontrun{gatherDataBabel(131)}
+#'
+#' @export
+gatherDataBabel <- function(id){
+ #.checkMbSettings()
+ babeldir <- getOption("RMassBank")$babeldir
+ smiles <- findSmiles(id)
+
+
+ # if no babeldir was set, throw an error that says that either CTS or babel have to be used
+ if(is.na(babeldir))
+ {
+ stop("No babeldir supplied; It is currently not possible to convert the information without either babel or CTS")
+ } else {
+ ###Babel conversion
+ cmdinchikey <- paste0(babeldir, 'obabel -:"',smiles,'" ', '-oinchikey')
+ inchikey <- system(cmdinchikey, intern=TRUE, input=smiles, ignore.stderr=TRUE)
+ cmdinchi <- paste0(babeldir, 'obabel -:"',smiles,'" ', '-oinchi')
+ inchi <- system(cmdinchi, intern=TRUE, input=smiles, ignore.stderr=TRUE)
+
+ ##Read from Compoundlist
+ smiles <- findSmiles(id)
+ mass <- findMass(smiles)
+ dbcas <- findCAS(id)
+ dbname <- findName(id)
+ if(is.na(dbname)) dbname <- ""
+ if(is.na(dbcas)) dbcas <- ""
+ formula <- findFormula(id)
+
+ ##Create
+ mbdata <- list()
+ mbdata[['id']] <- id
+ mbdata[['dbcas']] <- dbcas
+ mbdata[['dbname']] <- dbname
+ mbdata[['dataused']] <- "smiles"
+ mbdata[['ACCESSION']] <- ""
+ mbdata[['RECORD_TITLE']] <- ""
+ mbdata[['DATE']] <- format(Sys.Date(), "%Y.%m.%d")
+ mbdata[['AUTHORS']] <- getOption("RMassBank")$annotations$authors
+ mbdata[['LICENSE']] <- getOption("RMassBank")$annotations$license
+ mbdata[['COPYRIGHT']] <- getOption("RMassBank")$annotations$copyright
+ # Confidence annotation and internal ID annotation.
+ # The ID of the compound will be written like:
+ # COMMENT: EAWAG_UCHEM_ID 1234
+ # if annotations$internal_id_fieldname is set to "EAWAG_UCHEM_ID"
+ mbdata[["COMMENT"]] <- list()
+ mbdata[["COMMENT"]][["CONFIDENCE"]] <- getOption("RMassBank")$annotations$confidence_comment
+ mbdata[["COMMENT"]][["ID"]] <- id
+ # here compound info starts
+ mbdata[['CH$NAME']] <- as.list(dbname)
+
+ # Currently we use a fixed value for Compound Class, since there is no useful
+ # convention of what should go there and what shouldn't, and the field is not used
+ # in search queries.
+ mbdata[['CH$COMPOUND_CLASS']] <- getOption("RMassBank")$annotations$compound_class
+ mbdata[['CH$FORMULA']] <- formula
+ mbdata[['CH$EXACT_MASS']] <- mass
+ mbdata[['CH$SMILES']] <- smiles
+ mbdata[['CH$IUPAC']] <- inchi
+
+ link <- list()
+ if(dbcas != "")
+ link[["CAS"]] <- dbcas
+ link[["INCHIKEY"]] <- inchikey
+ mbdata[['CH$LINK']] <- link
+ mbdata[['AC$INSTRUMENT']] <- getOption("RMassBank")$annotations$instrument
+ mbdata[['AC$INSTRUMENT_TYPE']] <- getOption("RMassBank")$annotations$instrument_type
+ }
+ return(mbdata)
+}
# Flatten the internal tree-like representation of MassBank data to a flat table.
diff --git a/R/leMsmsRaw.R b/R/leMsmsRaw.R
index e1953debea46b7069928b5dd52c5c058c178d867..98a0ba1d77b768317758afd5970af0ec06207000 100755
--- a/R/leMsmsRaw.R
+++ b/R/leMsmsRaw.R
@@ -719,30 +719,43 @@ c.msmsWSspecs <- function(w1 = NA, w2 = NA){
cpdIDsw1 <- sapply(w1@specs, function(x) x$id)
cpdIDsw2 <- sapply(w2@specs, function(x) x$id)
+ if(length(cpdIDsw2) == 0){
+ stop("w2 can't be empty.")
+ }
+
+ if(length(cpdIDsw1) == 0){
+ w1@specs <- w2@specs
+ w1@files <- w2@files
+ return(w1)
+ }
+
for(i in 1:length(cpdIDsw2)){
if(any(cpdIDsw2[i] == cpdIDsw1)){
- index <- which(cpdIDsw2[i] == cpdIDsw1)
- w1@specs[[index]]$peaks <- c(w1@specs[[index]]$peaks,w2@specs[[i]]$peaks)
- w1@specs[[index]]$childScans <- c(w1@specs[[index]]$childScans,w2@specs[[i]]$childScans)
- w1@specs[[index]]$childHeaders <- rbind(w1@specs[[index]]$childHeaders, w2@specs[[i]]$childHeaders)
-
- ##Fake seqNums and/or acquisitionNums if the concatenation has doubled some of them
-
- seqNums <- w1@specs[[index]]$childHeaders[,"seqNum"]
- if(length(seqNums) != length(unique(seqNums))){
- w1@specs[[index]]$childHeaders[,"seqNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
- w1@specs[[index]]$childScans <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
- }
+ index <- which(cpdIDsw2[i] == cpdIDsw1)
- acqNums <- w1@specs[[index]]$childHeaders[,"acquisitionNum"]
- if(length(acqNums) != length(unique(acqNums))){
- w1@specs[[index]]$childHeaders[,"acquisitionNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
- }
+ w1@specs[[index]]$peaks <- c(w1@specs[[index]]$peaks,w2@specs[[i]]$peaks)
+ w1@specs[[index]]$childScans <- c(w1@specs[[index]]$childScans,w2@specs[[i]]$childScans)
+ w1@specs[[index]]$childHeaders <- rbind(w1@specs[[index]]$childHeaders, w2@specs[[i]]$childHeaders)
+
+ ##Fake seqNums and/or acquisitionNums if the concatenation has doubled some of them
+
+ seqNums <- w1@specs[[index]]$childHeaders[,"seqNum"]
+ if(length(seqNums) != length(unique(seqNums))){
+ w1@specs[[index]]$childHeaders[,"seqNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
+ w1@specs[[index]]$childScans <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
+ }
+
+
+ acqNums <- w1@specs[[index]]$childHeaders[,"acquisitionNum"]
+ if(length(acqNums) != length(unique(acqNums))){
+ w1@specs[[index]]$childHeaders[,"acquisitionNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
+ }
}
if(all(cpdIDsw2[i] != cpdIDsw1)){
w1@specs[[length(w1@specs) + 1]] <- w2@specs[[i]]
+ w1@files <- c(w1@files,w2@files[i])
}
}
return(w1)
diff --git a/R/msmsRead.R b/R/msmsRead.R
index 42516f55c8d4ae4ceaae542883c633ffdddf151a..e8b9ac910d9e145f921d85d0e9f12f944d17ead4 100644
--- a/R/msmsRead.R
+++ b/R/msmsRead.R
@@ -303,7 +303,7 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
## 3rd Best: find pspec closest to RT from spreadsheet
##psp <- which.min( abs(getRT(anmsms) - RT) )
if((plots == TRUE) && (length(psp[[i]]) > 0)){
- plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE, mzrange=c(0, findMz(cpdids)[[3]]), maxlabel=10)
+ plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE, mzrange=c(0, findMz(cpdids[1])[[3]]), maxlabel=10)
}
if(length(psp[[i]]) != 0){
spectra[[i]] <- getpspectra(anmsms[[i]], psp[[i]])
@@ -315,12 +315,18 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
spectra[[i]] <- matrix(0,2,7)
}
}
+
if(length(w@specs) != 0){
w@specs <- c(w@specs,list(toRMB(spectra,cpdids[1],mode)))
} else {
w@specs[[1]] <- toRMB(spectra,cpdids[1],mode)
}
- w@files <- c(w@files,xRAW[[1]]@filepath)
- names(w@specs)[length(w@specs)] <- basename(xRAW[[1]]@filepath)
+
+ if(all(w@files != xRAW[[1]]@filepath)){
+ w@files <- c(w@files,xRAW[[1]]@filepath)
+ } else{
+ w@files <- c(w@files,paste0(xRAW[[1]]@filepath,"_2"))
+ }
+ names(w@specs)[length(w@specs)] <- basename(w@files[length(w@files)])
return(w)
}
\ No newline at end of file
diff --git a/R/validateMassBank.R b/R/validateMassBank.R
index 21a927f74f1955db1247fb2e86ea13471e4afc09..0085e1e3cc5f50f4a6ee9daab0eb6201405a2df6 100644
--- a/R/validateMassBank.R
+++ b/R/validateMassBank.R
@@ -9,7 +9,7 @@
#' "report.html" in the working directory.
#'
#' @aliases validate
-#' @usage validate(path)
+#' @usage validate(path, simple = TRUE)
#' @param path The filepath to a single record, or a directory to search recursively
#' @param simple If TRUE the function creates a simpler form of the RUnit .html report, better readable for humans. If FALSE it returns the unchanged RUnit report.
#' @examples
diff --git a/man/gatherDataBabel.Rd b/man/gatherDataBabel.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..4727d5b58ed78f4ea03cae15af63ea890dc90536
--- /dev/null
+++ b/man/gatherDataBabel.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/createMassBank.R
+\name{gatherDataBabel}
+\alias{gatherDataBabel}
+\title{Retrieve annotation data}
+\usage{
+gatherDataBabel(id)
+}
+\arguments{
+\item{id}{The compound ID.}
+}
+\value{
+Returns a list of type \code{list(id= \var{compoundID}, ...,
+'ACCESSION' = '', 'RECORD_TITLE' = '', )} etc. %% ...
+}
+\description{
+Retrieves annotation data for a compound by using babel,
+based on the SMILES code and name of the compounds stored in the
+compound list.
+}
+\details{
+Composes the "upper part" of a MassBank record filled with chemical data
+about the compound: name, exact mass, structure, CAS no..
+The instrument type is also written into this block (even
+if not strictly part of the chemical information). Additionally, index
+fields are added at the start of the record, which will be removed later:
+\code{id, dbcas, dbname} from the compound list.
+
+Additionally, the fields \code{ACCESSION} and \code{RECORD_TITLE} are
+inserted empty and will be filled later on.
+
+This function is an alternative to gatherData, in case CTS is down or if information
+on one or more of the compounds in the compound list are sparse
+}
+\examples{
+# Gather data for compound ID 131
+\dontrun{gatherDataBabel(131)}
+}
+\author{
+Michael Stravs, Erik Mueller
+}
+\references{
+MassBank record format:
+\url{http://www.massbank.jp/manuals/MassBankRecord_en.pdf}
+}
+\seealso{
+\code{\link{mbWorkflow}}
+}
+
diff --git a/man/mbWorkflow.Rd b/man/mbWorkflow.Rd
index 275ef1d8065e13d30a671792771f81e4acc485bd..dc7b756da95c2507e96d08568f332bd41ebf3e47 100755
--- a/man/mbWorkflow.Rd
+++ b/man/mbWorkflow.Rd
@@ -3,7 +3,7 @@
\title{MassBank record creation workflow}
\usage{
mbWorkflow(mb, steps = c(1, 2, 3, 4, 5, 6, 7, 8),
- infolist_path = "./infolist.csv")
+ infolist_path = "./infolist.csv", useCTS = TRUE)
}
\arguments{
\item{steps}{Which steps in the workflow to perform.}
@@ -13,6 +13,11 @@
manually inspected.}
\item{mb}{The \code{mbWorkspace} to work in.}
+
+ \item{useCTS}{A boolean variable denoting whether
+ to retrieve information using CTS or to use babel to
+ retrieve minimal information.}
+
}
\value{
The processed \code{mbWorkspace}.
diff --git a/man/validate.Rd b/man/validate.Rd
index 7bbedf117ff3c12e44a281b59a96b06708fc5ef5..3c0b19deab568e8cef91983a89cada2c45660f96 100644
--- a/man/validate.Rd
+++ b/man/validate.Rd
@@ -8,6 +8,7 @@ validate(path, simple=TRUE)
}
\arguments{
\item{path}{The filepath to a single record, or a directory to search recursively}
+
\item{simple}{If TRUE the function creates a simpler form of the RUnit .html report, better readable for humans. If FALSE it returns the unchanged RUnit report.}
}
\description{