Mercurial > repos > prog > lcmsmatching
diff PeakforestConn.R @ 6:f86fec07f392 draft default tip
planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce
| author | prog |
|---|---|
| date | Fri, 22 Feb 2019 16:04:22 -0500 |
| parents | fb9c0409d85c |
| children |
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--- a/PeakforestConn.R Wed Apr 19 10:00:05 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,176 +0,0 @@ -##################### -# CLASS DECLARATION # -##################### -#'A class to connect to peakforest -#'@export -#'@field .url An urel to the database -PeakforestConn <- methods::setRefClass("PeakforestConn", contains = c("RemotedbConn","MassdbConn"), fields = list( .url = "character" )) # TODO Inherits also from MassdbConn - -########################## -# GET ENTRY CONTENT TYPE # -########################## - -PeakforestConn$methods( getEntryContentType = function(type) { - return(BIODB.JSON) -}) - -##################### -# GET ENTRY CONTENT # -##################### - -PeakforestConn$methods( getEntryContent = function(id) { - - - # Initialize return values - content <- rep(NA_character_, length(id)) - # Request - - url <- get.entry.url(BIODB.PEAKFOREST, id[i], BIODB.JSON,token = .self$.token) - jsonstr <- .self$.get.url(url) - if(startsWith("<html>", jsonstr) ){ - next - } - - return(content) -}) - - -########################################## -# SEARCH FOR SPECTRA IN GIVEN MASS RANGE # -########################################## - -PeakforestConn$methods( searchMzRange = function(mzmin, mzmax, rtype = c("object","spec","peak")){ - - rtype <- match.arg(rtype) - if(mzmin>mzmax){ - stop("mzmin shloud be inferior to mzmax in searchMzRange.") - } - - url <- paste0("https://rest.peakforest.org/spectra/lcms/peaks/get-range/",mzmin,"/",mzmax) - - contents <- .self$.get.url(url) - - jsontree <- fromJSON(contents) - - ###No match form the output. - if( length(jsontree)==0 ) return(NULL) - - # Getting a list of all the id. - lid <- sapply(jsontree,function(x){ - x$source$id - }) - - # Returning the content for all the spectra - contents <- .self$getEntryContent(lid) - - entries <- .self$createEntry(contents) - - # Checking the return type - if( rtype=="object" ){ - return( entries ) - } - - ### XXXX See if we don't want to reduce the output and factorize this shit. - toreturn <- NULL - if( rtype=="spec" ){ - toreturn <- sapply(entries,function(x){ - x$getFieldsAsDataFrame() - }) - } - if( rtype=="peak" ){ - toreturn <- lapply(entries,function(x){ - temp <- as.data.frame( x$getFieldValue( BIODB.PEAKS )) - temp$accession = x$getFieldValue( BIODB.ACCESSION) - return(temp) - - }) - } - ###Trying to convert in data.frame - if(!is.data.frame(toreturn)){ - temp <- colnames(toreturn[[1]]) - toreturn <- do.call("rbind.fill",toreturn) - colnames(toreturn) <- temp - } - - return(toreturn) -}) - - -################################################# -# SEARCH FOR SPECTRA IN A TOLERANCE AROUND A MZ # -################################################# - -PeakforestConn$methods( searchMzTol = function(mz, tol, tolunit=BIODB.MZTOLUNIT.VALS, - rtype = c("object","spec","peak")){ - - rtype <- match.arg(rtype) - tolunit <- match.arg(tolunit) - - if( tolunit == BIODB.MZTOLUNIT.PPM){ - tol <- tol * mz * 10^-6 - } - - mzmin <- mz - tol - mzmax <- mz + tol - - return(.self$searchMzRange(mzmin, mzmax, rtype = rtype)) - -}) - -################################################## -# SEARCH FOR MSMS SPECTRA PRECUSOR AROUND A MASS # -################################################## - - -PeakforestConn$methods( - searchSpecPrecTol = function(mz, - tol, - tolunit = "plain", - mode = NULL) { - #TODO handle the units - #tolunit <- match.arg(tolunit) - - strmode <- '' - - if (!is.null(mode)) { - if (mode %in% c(BIODB.MSMODE.NEG, BIODB.MSMODE.POS)) { - strmode <- paste0('?polarity=', mode) - } - - } - - if (tolunit == BIODB.MZTOLUNIT.PPM) { - tol <- tol * mz * 10 ^ -6 - } - - ##Request which return peak and not spectra. - url <- - paste0( - "https://rest.peakforest.org/spectra/lcms/search-naive/", - mz, - "/", - tol, - strmode - ) - contents <- .self$.get.url(url) - entries <- .self$createReducedEntry(contents, drop = TRUE) - return(entries) - } -) - - -################ -# CREATE ENTRY # -################ - -# Creates a Spectrum instance from file content. -# content A file content, downloaded from the public database. -# RETURN A spectrum instance. -PeakforestConn$methods( createEntry = function(content, drop = TRUE) { - return(createPeakforestSpectraFromJSON(content, drop = drop)) -}) - -PeakforestConn$methods( createReducedEntry = function(content , drop = TRUE){ - entries <- createReducedSpectraFromJSON(content, drop = drop) - return(entries) -})