R/nlp.R
In statsmaths/coreNLP: Wrappers Around Stanford CoreNLP Tools
# http://nlp.stanford.edu/software/stanford-corenlp-full-2015-01-29.zip
volatiles = new.env(parent=emptyenv())
#' Initialize the CoreNLP java object
#'
#' This must be run prior to calling any other CoreNLP
#' functions. It may be called multiple times in order
#' to specify a different parameter set, but note that
#' if you use a different configuration during the same
#' R session it must have a unique name.
#'
#' @importFrom rJava .jinit .jaddClassPath .jcall .jnew
#' @param libLoc a string giving the location of the CoreNLP java
#' files. This should point to a directory which
#' contains, for
#' example the file "stanford-corenlp-*.jar", where "*" is the
#' version number. If missing, the function will try to find the
#' library in the environment variable CORENLP_HOME, and otherwise
#' will fail.
#' @param type type of model to load. Ignored if parameterFile is set.
#' @param parameterFile the path to a parameter file. See the CoreNLP documentation for
#' an extensive list of options. If missing, the package will simply
#' specify a list of standard annotators and otherwise only use default
#' values.
#' @param mem a string giving the amount of memory to be assigned to the rJava
#' engine. For example, "6g" assigned 6 gigabytes of memory. At least
#' 2 gigabytes are recommended at a minimum for running the CoreNLP
#' package. On a 32bit machine, where this is not possible, setting
#' "1800m" may also work. This option will only have an effect the first
#' time \code{initCoreNLP} is called, and also will not have an effect if
#' the java engine is already started by a seperate process.
#'@examples
#'\dontrun{
#'initCoreNLP()
#'sIn <- "Mother died today. Or, maybe, yesterday; I can't be sure."
#'annoObj <- annotateString(sIn)
#'}
#' @export
initCoreNLP = function(libLoc, type = c("english", "english_all", "english_fast", "arabic", "chinese", "french", "german", "spanish"),
parameterFile = NULL, mem = "4g") {
# Find location of the CoreNLP Libraries
if (missing(libLoc)) {
libLoc = paste0(system.file("extdata",package="coreNLP"),
"/stanford-corenlp-full-2015-12-09")
if (!file.exists(libLoc))
stop("Please run downloadCoreNLP() in order to install required jar files.")
}
if (!file.exists(libLoc) || !file.info(libLoc)$isdir)
stop("libLoc does not point to an existing directory path")
path = Sys.glob(paste0(libLoc,"/*.jar"))
# Start java engine, if not already done, and add to classpath
options(java.parameters = paste0("-Xmx", mem))
rJava::.jinit()
rJava::.jaddClassPath(path)
# Determine if the corenlp files have been loaded correctly
len = length(grep("stanford-corenlp-", basename(rJava::.jclassPath())))
if (len == 0L)
stop("The coreNLP jar files are were not found in libLoc.")
if (len < 4L)
warning("The set of coreNLP jar files may be incomplete. Proceed with caution")
# Read parameter file and add to classpath
if (is.null(parameterFile)) {
type = match.arg(type)
basepath = system.file("extdata",package="coreNLP")
if (type == "english") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP.properties")
if (type == "english_all") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-english-all.properties")
if (type == "english_fast") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-english-fast.properties")
if (type == "arabic") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-arabic.properties")
if (type == "chinese") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-chinese.properties")
if (type == "french") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-french.properties")
if (type == "german") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-german.properties")
if (type == "spanish") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-spanish.properties")
} else {
path = Sys.glob(paste0(parameterFile[[1]]))
}
rJava::.jaddClassPath(dirname(path))
if (!is.null(volatiles$cNLP))
rJava::.jcall(volatiles$cNLP, "V", "clearAnnotatorPool")
volatiles$cNLP = rJava::.jnew("edu.stanford.nlp.pipeline.StanfordCoreNLP", basename(path))
volatiles$xmlOut = rJava::.jnew("edu.stanford.nlp.pipeline.XMLOutputter")
}
#' Annotate a string of text
#'
#' Runs the CoreNLP annotators over a given string of text. The details
#' for which annotators to run and how to run them are specified in the
#' properties file loaded in via the \code{initCoreNLP} function (which
#' must be run prior to any annotation).
#'
#' @importFrom rJava .jcall
#' @param text a vector of strings for which an annotation is desired.
#' Will be collapsed to length 1 using new line characters
#' prior to the annotation.
#' @param format the desired output format. Option \code{obj}, the default,
#' returns an R object of class \code{annotation} and will
#' likely be the desired choice for most users. The \code{xml}
#' and \code{text} exist primarily for subsequently saving
#' to disk.
#' @param outputFile character string indicating where to put the output. If
#' set to NA, the output will be returned by the function.
#' @param includeXSL boolean. Whether the xml style sheet should be included
#' in the output. Only used if format is \code{xml} and
#' outputFile is not \code{NA}.
#'@examples
#'\dontrun{
#'initCoreNLP()
#'sIn <- "Mother died today. Or, maybe, yesterday; I can't be sure."
#'annoObj <- annotateString(sIn)
#'}
#' @export
annotateString = function(text, format=c("obj", "xml", "text"), outputFile=NA,
includeXSL=FALSE) {
if (is.null(volatiles$cNLP))
stop("Must initilize with 'initCoreNLP'!")
format = match.arg(format)
if (length(text) > 1L) text = paste(text,collapse="\n")
if (!is.na(outputFile) & format == "obj") {
warning("Cannot output 'obj' as text file, saving xml instead.")
format = "xml"
}
anno = rJava::.jcall(volatiles$cNLP, "Ledu/stanford/nlp/pipeline/Annotation;", "process", text)
# Parse the output
if (format == "text") {
rJava::.jcall(volatiles$cNLP, "V", "prettyPrint", anno, .jnew("java.io.PrintWriter", tf <- tempfile()))
on.exit(file.remove(tf))
out = readLines(tf)
} else {
d = rJava::.jcall(volatiles$xmlOut, "Lnu/xom/Document;", "annotationToDoc", anno, volatiles$cNLP)
xml = rJava::.jcall(d, "Ljava/lang/String;", "toXML")
if (format == "xml") out = xml else out = parseAnnoXML(xml)
}
# Return the output if asked for; otherwise just write to disk
if (is.na(outputFile)) return(out)
outputCon = file(outputFile, "w")
on.exit(close(outputCon),add=TRUE)
writeLines(out, outputCon)
if (includeXSL & format == "xml")
file.copy(from=paste0(system.file("extdata",package="coreNLP"), "/CoreNLP-to-HTML.xsl"),
to=dirname(outputFile))
invisible(outputFile)
}
#' Annotate a text file
#'
#' Runs the CoreNLP annotators for the text contained in a given file.
#' The details for which annotators to run and how to run them are
#' specified in the properties file loaded in via the \code{initCoreNLP}
#' function (which must be run prior to any annotation).
#'
#' @importFrom rJava .jcall
#' @param file a string giving the location of the file to be loaded.
#' @param format the desired output format. Option \code{obj}, the default,
#' returns an R object of class \code{annotation} and will
#' likely be the desired choice for users loading the output
#' into R. The \code{xml} and \code{text} exist primarily for
#' saving the files on the disk.
#' @param outputFile character string indicating where to put the output. If
#' set to NA, the output will be returned by the function.
#' @param includeXSL boolean. Whether the xml style sheet should be included
#' in the output. Only used if format is \code{xml} and
#' outputFile is not \code{NA}.
#' @export
annotateFile = function(file, format=c("obj", "xml", "text"), outputFile=NA,
includeXSL=FALSE) {
if (is.null(volatiles$cNLP))
stop("Must initilize with 'initCoreNLP'!")
# Processing inputs
format = match.arg(format)
if (!is.na(outputFile) & format == "obj") {
warning("Cannot output 'obj' as text file, saving xml instead.")
format = "xml"
}
if (is.character(file)) {
file = file(file, "r")
on.exit(close(file))
}
# Read input into R and annotate
# TODO: Use native java interface instead of reading into R.
text = readLines(file)
if (length(text) > 1L) text = paste(text,collapse="\n")
anno = rJava::.jcall(volatiles$cNLP, "Ledu/stanford/nlp/pipeline/Annotation;",
"process", text)
# Parse the output
if (format == "text") {
rJava::.jcall(volatiles$cNLP, "V", "prettyPrint", anno, .jnew("java.io.PrintWriter", tf <- tempfile()))
on.exit(file.remove(tf))
out = readLines(tf)
} else {
d = rJava::.jcall(volatiles$xmlOut, "Lnu/xom/Document;", "annotationToDoc", anno, volatiles$cNLP)
xml = rJava::.jcall(d, "Ljava/lang/String;", "toXML")
if (format == "xml") out = xml else out = parseAnnoXML(xml)
}
# Return the output if asked for asked for; otherwise just write to disk
if (is.na(outputFile)) return(out)
outputCon = file(outputFile, "w")
on.exit(close(outputCon),add=TRUE)
writeLines(out, outputCon)
if (includeXSL && format == "xml")
file.copy(from=paste0(system.file("extdata",package="coreNLP"), "CoreNLP-to-HTML.xsl"),
to=dirname(outputFile))
}
#' Print a summary of an annotation object
#'
#' @method print annotation
#' @param x an annotation object
#' @param ... other arguments. Currently unused.
#'
#'@examples
#'print(annoEtranger)
#'
#' @export
print.annotation = function(x, ...) {
cat("\nA CoreNLP Annotation:\n")
cat(" num. sentences:", x$token[nrow(x$token),1], "\n")
cat(" num. tokens:", nrow(x[[1]]), "\n")
cat("\n")
invisible(x)
}
#' Get tokens as data frame
#'
#' Returns a data frame of the tokens from an annotation
#' object.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getToken(annoEtranger)
#'
#' @export
getToken = function(annotation) {
annotation$token
}
#' Get parse tree as character vector
#'
#' Returns a character vector of the parse trees.
#' Mostly use for visualization; the output of
#' \code{\link{getToken}} will generally be more
#' conveniant for manipulating in R.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getParse(annoEtranger)
#'
#' @export
getParse = function(annotation) {
annotation$parse
}
#' Get Dependencies
#'
#' Returns a data frame of the coreferences of an annotation
#'
#' @param annotation an annotation object
#' @param type the class of coreference desired
#'
#'@examples
#'getDependency(annoEtranger)
#'getDependency(annoHp)
#'
#' @export
getDependency = function(annotation, type=c("CCprocessed","basic","collapsed")) {
type = match.arg(type)
dep <- if (type == "basic") annotation$basicDep
else if (type == "collapsed") annotation$collapsedDep
else if (type == "CCprocessed") annotation$collapsedProcDep
dep$govIndex = match(paste0(dep$sentence,"-",dep$governorIdx),
paste0(annotation$token$sentence,"-",annotation$token$id))
dep$depIndex = match(paste0(dep$sentence,"-",dep$dependentIdx),
paste0(annotation$token$sentence,"-",annotation$token$id))
dep
}
#' Get Sentiment scores
#'
#' Returns a data frame of the sentiment scores from an annotation
#'
#' @param annotation an annotation object
#'
#'@examples
#'getSentiment(annoEtranger)
#'getSentiment(annoHp)
#'
#' @export
getSentiment = function(annotation) {
annotation$sentiment
}
#' Get Coreference
#'
#' Returns a dataframe containing all coreferences detected in the text.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getCoreference(annoHp)
#'
#' @export
getCoreference = function(annotation) {
coref = annotation$coref[,-grep("text",names(annotation$coref))]
coref$startIndex = match(paste0(coref$sentence,"-",coref$start),
paste0(annotation$token$sentence,"-",annotation$token$id))
coref$endIndex = match(paste0(coref$sentence,"-",as.numeric(coref$end)-1),
paste0(annotation$token$sentence,"-",annotation$token$id))
coref
}
#' Get OpenIE
#'
#' Returns a dataframe containing all OpenIE triples.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getOpenIE(annoHp)
#'
#' @export
getOpenIE = function(annotation) {
annotation$openie
}
#' Load CoreNLP XML file
#'
#' Loads a properly formated XML file output by the CoreNLP
#' library into an \code{annotation} object in R.
#'
#' @param file connection or character string giving the file name to load
#' @param encoding encoding to be assumed for input strings. It is used to mark
#' character strings as known to be in Latin-1 or UTF-8: it is
#' not used to re-encode the input. Passed to \code{readLines}.
#' @export
loadXMLAnnotation = function(file, encoding="unknown") {
if (is.character(file)) {
file = file(file, "r")
on.exit(close(file))
}
x = readLines(file)
tryCatch(output <- parseAnnoXML(x),
error = function(e) stop("Not a valid CoreNLP XML file."))
output
}
#' Convert Penn TreeBank POS to Universal Tagset
#'
#' Maps a character string of English Penn TreeBank
#' part of speech tags into the universal tagset
#' codes. This provides a reduced set of tags (12), and
#' a better cross-linguist model of speech.
#'
#' @param pennPOS a character vector of penn tags to match
#'
#'@examples
#'tok <- getToken(annoEtranger)
#'cbind(tok$POS,universalTagset(tok$POS))
#'
#' @export
universalTagset = function(pennPOS) {
mtab = structure(c("!", "#", "$", "''", "(", ")", ",", "-LRB-",
"-RRB-", ".", ":", "?", "CC", "CD", "CD|RB", "DT", "EX", "FW", "IN",
"IN|RP", "JJ", "JJR", "JJRJR", "JJS", "JJ|RB", "JJ|VBG", "LS", "MD", "NN",
"NNP", "NNPS", "NNS", "NN|NNS", "NN|SYM", "NN|VBG", "NP", "PDT", "POS", "PRP",
"PRP$", "PRP|VBP", "PRT", "RB", "RBR", "RBS", "RB|RP", "RB|VBG", "RN", "RP", "SYM",
"TO", "UH", "VB", "VBD", "VBD|VBN", "VBG", "VBG|NN", "VBN", "VBP", "VBP|TO",
"VBZ", "VP", "WDT", "WH", "WP", "WP$", "WRB", "``", ".", ".", ".", ".", ".",
".", ".", ".", ".", ".", ".", ".", "CONJ", "NUM", "X", "DET", "DET", "X",
"ADP", "ADP", "ADJ", "ADJ", "ADJ", "ADJ", "ADJ", "ADJ", "X", "VERB", "NOUN",
"NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "DET", "PRT", "PRON",
"PRON", "PRON", "PRT", "ADV", "ADV", "ADV", "ADV", "ADV", "X", "PRT", "X",
"PRT", "X", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB",
"VERB", "VERB", "DET", "X", "PRON", "PRON", "ADV", "."), .Dim = c(68L, 2L))
index = match(pennPOS, mtab[,1])
output = rep("X", length(pennPOS))
output[!is.na(index)] = mtab[index[!is.na(index)],2]
output
}
#' Parse annotation xml
#'
#' Returns an annotation object from a character vector containing
#' the xml. Not exported; use \code{loadXMLAnnotation} instead.
#'
#' @importFrom XML xmlRoot xmlParse xmlToDataFrame xmlChildren xmlAttrs xmlValue
#' @param xml character vector containing the xml file from an annotation
parseAnnoXML = function(xml) {
xml = XML::xmlRoot(XML::xmlParse(xml))[[1]]
coref = xml[[2]]
xml = xml[[1]]
sentences = XML::xmlChildren(xml)
out = list(token = NULL,parse = NULL,basicDep = NULL,collapsedDep = NULL,
collapsedProcDep = NULL, coref = NULL, openie = NULL)
if (length(sentences)==0L) {
class(out) = "annotation"
return(out)
}
tokenNames = c("sentence", "id", "word", "lemma", "CharacterOffsetBegin",
"CharacterOffsetEnd", "POS", "NER", "Speaker")
depNames = c("sentence", "governor", "dependent", "type", "governorIdx",
"dependentIdx")
corefNames = c("corefId", "sentence", "start", "end", "head", "text")
sentNames = c("id", "sentimentValue", "sentiment")
openieNames = c("subject_start", "subject_end", "subject",
"relation_start", "relation_end", "relation",
"object_start", "object_end", "object")
for (i in 1:length(sentences)) {
sent = sentences[[i]]
df = data.frame(sentence=i, id=sapply(XML::xmlChildren(sent[[1L]]),function(v) XML::xmlAttrs(v)[1]),
XML::xmlToDataFrame(sent[[1]], stringsAsFactors=FALSE), stringsAsFactors=FALSE)
index = match(tokenNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, tokenNames)
df = df[,tokenNames]
out$token = rbind(out$token, df)
elementNames <- names(XML::xmlChildren(sent))
elementAttributes <- sapply(XML::xmlChildren(sent),
function(v) {v <- as.character(XML::xmlAttrs(v)['type']); if (length(v)) v else "" })
names(elementAttributes) <- NULL
parseIndex <- which(elementNames == "parse" & elementAttributes == "")[1]
basicDepIndex <- which(elementNames == "dependencies" & elementAttributes == "basic-dependencies")[1]
collapsedDepIndex <- which(elementNames == "dependencies" & elementAttributes == "collapsed-dependencies")[1]
collapsedProcDepIndex <- which(elementNames == "dependencies" & elementAttributes == "collapsed-ccprocessed-dependencies")[1]
openieIndex <- which(elementNames == "openie" & elementAttributes == "")[1]
machineReadingIndex <- which(elementNames == "MachineReading" & elementAttributes == "")[1]
if (!is.na(parseIndex))
out$parse = c(out$parse, XML::xmlValue(sent[[parseIndex]]))
if (!is.na(basicDepIndex) && length(XML::xmlToDataFrame(sent[[basicDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[basicDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[basicDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[basicDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[basicDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]),
stringsAsFactors=FALSE)
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$basicDep = rbind(out$basicDep, df)
}
if (!is.na(collapsedDepIndex) && length(XML::xmlToDataFrame(sent[[collapsedDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[collapsedDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]))
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$collapsedDep = rbind(out$collapsedDep, df)
}
if (!is.na(collapsedProcDepIndex) && length(XML::xmlToDataFrame(sent[[collapsedProcDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[collapsedProcDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]))
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$collapsedProcDep = rbind(out$collapsedProcDep, df)
}
if (!is.na(openieIndex) && length(XML::xmlToDataFrame(sent[[openieIndex]]))) {
these <- XML::xmlChildren(sent[[openieIndex]])
ids <-
cbind(t(sapply(these, function(v) XML::xmlAttrs(v[[1]]))),
sapply(these, function(v) XML::xmlValue(v[[1]][[1]])),
t(sapply(these, function(v) XML::xmlAttrs(v[[2]]))),
sapply(these, function(v) XML::xmlValue(v[[2]][[1]])),
t(sapply(these, function(v) XML::xmlAttrs(v[[3]]))),
sapply(these, function(v) XML::xmlValue(v[[3]][[1]])))
ids <- data.frame(ids, stringsAsFactors=FALSE, row.names=NULL)
colnames(ids) <- openieNames
out$openie = rbind(out$openie, ids)
}
# if (!is.na(machineReadingIndex) && length(XML::xmlToDataFrame(sent[[machineReadingIndex]]))) {
# these <- XML::xmlChildren(sent[[machineReadingIndex]])
# ids <-
# cbind(t(sapply(these, function(v) XML::xmlAttrs(v[[1]]))),
# sapply(these, function(v) XML::xmlValue(v[[1]][[1]])),
# t(sapply(these, function(v) XML::xmlAttrs(v[[2]]))),
# sapply(these, function(v) XML::xmlValue(v[[2]][[1]])),
# t(sapply(these, function(v) XML::xmlAttrs(v[[3]]))),
# sapply(these, function(v) XML::xmlValue(v[[3]][[1]])))
# ids <- data.frame(ids, stringsAsFactors=FALSE, row.names=NULL)
# colnames(ids) <- openieNames
# out$mr = rbind(out$mr, ids)
# }
sm = XML::xmlAttrs(sent)
df = data.frame(matrix(sm,nrow=1),stringsAsFactors=FALSE)
names(df) = names(sm)
index = match(sentNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)],drop=FALSE]
if (any(is.na(index))) df = fillDF(df, sentNames)
if (nrow(df)) out$sentiment = rbind(out$sentiment, df)
}
if (!is.null(out$token)) {
if (!is.na(index <- match("word", names(out$token))[1]))
names(out$token)[index] = "token"
if (sum(!is.na((index <- match(c("CharacterOffsetBegin","CharacterOffsetEnd"),names(out$token))))))
out$token[,index] = apply(out$token[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$basicDep)) {
if (sum(is.na((index <- match(c("governorIdx","dependentIdx"),names(out$basicDep))))))
out$basicDep[,index] = apply(out$basicDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$collapsedDep)) {
if (sum(!is.na((index <- match(c("governorIdx","dependentIdx"),names(out$collapsedDep))))))
out$collapsedDep[,index] = apply(out$collapsedDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$collapsedProcDep)) {
if (sum(!is.na((index <- match(c("governorIdx","dependentIdx"),names(out$collapsedProcDep))))))
out$collapsedProcDep[,index] = apply(out$collapsedProcDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(coref)) {
coref = XML::xmlChildren(coref)
for (corefId in 1:length(coref)) {
df = data.frame(corefId=corefId, XML::xmlToDataFrame(coref[[corefId]], stringsAsFactors=FALSE),
stringsAsFactors=FALSE)
index = match(corefNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, corefNames)
out$coref = rbind(out$coref, df)
}
}
if (!is.null(out$sentiment)) {
if (sum(!is.na(index <- match(c("id","sentimentValue"),names(out$sentiment)))))
out$sentiment[,index[!is.na(index)]] = apply(out$sentiment[,index[!is.na(index)],drop=FALSE],2,as.integer)
}
class(out) = "annotation"
out
}
fillDF = function(df, nameVec) {
if (nrow(df) == 0L) return(df)
index = match(nameVec, names(df))
df[,nameVec[is.na(index)]] = NA
return(df)
}
statsmaths/coreNLP documentation built on May 30, 2019, 10:41 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# http://nlp.stanford.edu/software/stanford-corenlp-full-2015-01-29.zip
volatiles = new.env(parent=emptyenv())
#' Initialize the CoreNLP java object
#'
#' This must be run prior to calling any other CoreNLP
#' functions. It may be called multiple times in order
#' to specify a different parameter set, but note that
#' if you use a different configuration during the same
#' R session it must have a unique name.
#'
#' @importFrom rJava .jinit .jaddClassPath .jcall .jnew
#' @param libLoc a string giving the location of the CoreNLP java
#' files. This should point to a directory which
#' contains, for
#' example the file "stanford-corenlp-*.jar", where "*" is the
#' version number. If missing, the function will try to find the
#' library in the environment variable CORENLP_HOME, and otherwise
#' will fail.
#' @param type type of model to load. Ignored if parameterFile is set.
#' @param parameterFile the path to a parameter file. See the CoreNLP documentation for
#' an extensive list of options. If missing, the package will simply
#' specify a list of standard annotators and otherwise only use default
#' values.
#' @param mem a string giving the amount of memory to be assigned to the rJava
#' engine. For example, "6g" assigned 6 gigabytes of memory. At least
#' 2 gigabytes are recommended at a minimum for running the CoreNLP
#' package. On a 32bit machine, where this is not possible, setting
#' "1800m" may also work. This option will only have an effect the first
#' time \code{initCoreNLP} is called, and also will not have an effect if
#' the java engine is already started by a seperate process.
#'@examples
#'\dontrun{
#'initCoreNLP()
#'sIn <- "Mother died today. Or, maybe, yesterday; I can't be sure."
#'annoObj <- annotateString(sIn)
#'}
#' @export
initCoreNLP = function(libLoc, type = c("english", "english_all", "english_fast", "arabic", "chinese", "french", "german", "spanish"),
parameterFile = NULL, mem = "4g") {
# Find location of the CoreNLP Libraries
if (missing(libLoc)) {
libLoc = paste0(system.file("extdata",package="coreNLP"),
"/stanford-corenlp-full-2015-12-09")
if (!file.exists(libLoc))
stop("Please run downloadCoreNLP() in order to install required jar files.")
}
if (!file.exists(libLoc) || !file.info(libLoc)$isdir)
stop("libLoc does not point to an existing directory path")
path = Sys.glob(paste0(libLoc,"/*.jar"))
# Start java engine, if not already done, and add to classpath
options(java.parameters = paste0("-Xmx", mem))
rJava::.jinit()
rJava::.jaddClassPath(path)
# Determine if the corenlp files have been loaded correctly
len = length(grep("stanford-corenlp-", basename(rJava::.jclassPath())))
if (len == 0L)
stop("The coreNLP jar files are were not found in libLoc.")
if (len < 4L)
warning("The set of coreNLP jar files may be incomplete. Proceed with caution")
# Read parameter file and add to classpath
if (is.null(parameterFile)) {
type = match.arg(type)
basepath = system.file("extdata",package="coreNLP")
if (type == "english") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP.properties")
if (type == "english_all") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-english-all.properties")
if (type == "english_fast") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-english-fast.properties")
if (type == "arabic") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-arabic.properties")
if (type == "chinese") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-chinese.properties")
if (type == "french") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-french.properties")
if (type == "german") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-german.properties")
if (type == "spanish") path = sprintf("%s/%s", basepath, "/StanfordCoreNLP-spanish.properties")
} else {
path = Sys.glob(paste0(parameterFile[[1]]))
}
rJava::.jaddClassPath(dirname(path))
if (!is.null(volatiles$cNLP))
rJava::.jcall(volatiles$cNLP, "V", "clearAnnotatorPool")
volatiles$cNLP = rJava::.jnew("edu.stanford.nlp.pipeline.StanfordCoreNLP", basename(path))
volatiles$xmlOut = rJava::.jnew("edu.stanford.nlp.pipeline.XMLOutputter")
}
#' Annotate a string of text
#'
#' Runs the CoreNLP annotators over a given string of text. The details
#' for which annotators to run and how to run them are specified in the
#' properties file loaded in via the \code{initCoreNLP} function (which
#' must be run prior to any annotation).
#'
#' @importFrom rJava .jcall
#' @param text a vector of strings for which an annotation is desired.
#' Will be collapsed to length 1 using new line characters
#' prior to the annotation.
#' @param format the desired output format. Option \code{obj}, the default,
#' returns an R object of class \code{annotation} and will
#' likely be the desired choice for most users. The \code{xml}
#' and \code{text} exist primarily for subsequently saving
#' to disk.
#' @param outputFile character string indicating where to put the output. If
#' set to NA, the output will be returned by the function.
#' @param includeXSL boolean. Whether the xml style sheet should be included
#' in the output. Only used if format is \code{xml} and
#' outputFile is not \code{NA}.
#'@examples
#'\dontrun{
#'initCoreNLP()
#'sIn <- "Mother died today. Or, maybe, yesterday; I can't be sure."
#'annoObj <- annotateString(sIn)
#'}
#' @export
annotateString = function(text, format=c("obj", "xml", "text"), outputFile=NA,
includeXSL=FALSE) {
if (is.null(volatiles$cNLP))
stop("Must initilize with 'initCoreNLP'!")
format = match.arg(format)
if (length(text) > 1L) text = paste(text,collapse="\n")
if (!is.na(outputFile) & format == "obj") {
warning("Cannot output 'obj' as text file, saving xml instead.")
format = "xml"
}
anno = rJava::.jcall(volatiles$cNLP, "Ledu/stanford/nlp/pipeline/Annotation;", "process", text)
# Parse the output
if (format == "text") {
rJava::.jcall(volatiles$cNLP, "V", "prettyPrint", anno, .jnew("java.io.PrintWriter", tf <- tempfile()))
on.exit(file.remove(tf))
out = readLines(tf)
} else {
d = rJava::.jcall(volatiles$xmlOut, "Lnu/xom/Document;", "annotationToDoc", anno, volatiles$cNLP)
xml = rJava::.jcall(d, "Ljava/lang/String;", "toXML")
if (format == "xml") out = xml else out = parseAnnoXML(xml)
}
# Return the output if asked for; otherwise just write to disk
if (is.na(outputFile)) return(out)
outputCon = file(outputFile, "w")
on.exit(close(outputCon),add=TRUE)
writeLines(out, outputCon)
if (includeXSL & format == "xml")
file.copy(from=paste0(system.file("extdata",package="coreNLP"), "/CoreNLP-to-HTML.xsl"),
to=dirname(outputFile))
invisible(outputFile)
}
#' Annotate a text file
#'
#' Runs the CoreNLP annotators for the text contained in a given file.
#' The details for which annotators to run and how to run them are
#' specified in the properties file loaded in via the \code{initCoreNLP}
#' function (which must be run prior to any annotation).
#'
#' @importFrom rJava .jcall
#' @param file a string giving the location of the file to be loaded.
#' @param format the desired output format. Option \code{obj}, the default,
#' returns an R object of class \code{annotation} and will
#' likely be the desired choice for users loading the output
#' into R. The \code{xml} and \code{text} exist primarily for
#' saving the files on the disk.
#' @param outputFile character string indicating where to put the output. If
#' set to NA, the output will be returned by the function.
#' @param includeXSL boolean. Whether the xml style sheet should be included
#' in the output. Only used if format is \code{xml} and
#' outputFile is not \code{NA}.
#' @export
annotateFile = function(file, format=c("obj", "xml", "text"), outputFile=NA,
includeXSL=FALSE) {
if (is.null(volatiles$cNLP))
stop("Must initilize with 'initCoreNLP'!")
# Processing inputs
format = match.arg(format)
if (!is.na(outputFile) & format == "obj") {
warning("Cannot output 'obj' as text file, saving xml instead.")
format = "xml"
}
if (is.character(file)) {
file = file(file, "r")
on.exit(close(file))
}
# Read input into R and annotate
# TODO: Use native java interface instead of reading into R.
text = readLines(file)
if (length(text) > 1L) text = paste(text,collapse="\n")
anno = rJava::.jcall(volatiles$cNLP, "Ledu/stanford/nlp/pipeline/Annotation;",
"process", text)
# Parse the output
if (format == "text") {
rJava::.jcall(volatiles$cNLP, "V", "prettyPrint", anno, .jnew("java.io.PrintWriter", tf <- tempfile()))
on.exit(file.remove(tf))
out = readLines(tf)
} else {
d = rJava::.jcall(volatiles$xmlOut, "Lnu/xom/Document;", "annotationToDoc", anno, volatiles$cNLP)
xml = rJava::.jcall(d, "Ljava/lang/String;", "toXML")
if (format == "xml") out = xml else out = parseAnnoXML(xml)
}
# Return the output if asked for asked for; otherwise just write to disk
if (is.na(outputFile)) return(out)
outputCon = file(outputFile, "w")
on.exit(close(outputCon),add=TRUE)
writeLines(out, outputCon)
if (includeXSL && format == "xml")
file.copy(from=paste0(system.file("extdata",package="coreNLP"), "CoreNLP-to-HTML.xsl"),
to=dirname(outputFile))
}
#' Print a summary of an annotation object
#'
#' @method print annotation
#' @param x an annotation object
#' @param ... other arguments. Currently unused.
#'
#'@examples
#'print(annoEtranger)
#'
#' @export
print.annotation = function(x, ...) {
cat("\nA CoreNLP Annotation:\n")
cat(" num. sentences:", x$token[nrow(x$token),1], "\n")
cat(" num. tokens:", nrow(x[[1]]), "\n")
cat("\n")
invisible(x)
}
#' Get tokens as data frame
#'
#' Returns a data frame of the tokens from an annotation
#' object.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getToken(annoEtranger)
#'
#' @export
getToken = function(annotation) {
annotation$token
}
#' Get parse tree as character vector
#'
#' Returns a character vector of the parse trees.
#' Mostly use for visualization; the output of
#' \code{\link{getToken}} will generally be more
#' conveniant for manipulating in R.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getParse(annoEtranger)
#'
#' @export
getParse = function(annotation) {
annotation$parse
}
#' Get Dependencies
#'
#' Returns a data frame of the coreferences of an annotation
#'
#' @param annotation an annotation object
#' @param type the class of coreference desired
#'
#'@examples
#'getDependency(annoEtranger)
#'getDependency(annoHp)
#'
#' @export
getDependency = function(annotation, type=c("CCprocessed","basic","collapsed")) {
type = match.arg(type)
dep <- if (type == "basic") annotation$basicDep
else if (type == "collapsed") annotation$collapsedDep
else if (type == "CCprocessed") annotation$collapsedProcDep
dep$govIndex = match(paste0(dep$sentence,"-",dep$governorIdx),
paste0(annotation$token$sentence,"-",annotation$token$id))
dep$depIndex = match(paste0(dep$sentence,"-",dep$dependentIdx),
paste0(annotation$token$sentence,"-",annotation$token$id))
dep
}
#' Get Sentiment scores
#'
#' Returns a data frame of the sentiment scores from an annotation
#'
#' @param annotation an annotation object
#'
#'@examples
#'getSentiment(annoEtranger)
#'getSentiment(annoHp)
#'
#' @export
getSentiment = function(annotation) {
annotation$sentiment
}
#' Get Coreference
#'
#' Returns a dataframe containing all coreferences detected in the text.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getCoreference(annoHp)
#'
#' @export
getCoreference = function(annotation) {
coref = annotation$coref[,-grep("text",names(annotation$coref))]
coref$startIndex = match(paste0(coref$sentence,"-",coref$start),
paste0(annotation$token$sentence,"-",annotation$token$id))
coref$endIndex = match(paste0(coref$sentence,"-",as.numeric(coref$end)-1),
paste0(annotation$token$sentence,"-",annotation$token$id))
coref
}
#' Get OpenIE
#'
#' Returns a dataframe containing all OpenIE triples.
#'
#' @param annotation an annotation object
#'
#'@examples
#'getOpenIE(annoHp)
#'
#' @export
getOpenIE = function(annotation) {
annotation$openie
}
#' Load CoreNLP XML file
#'
#' Loads a properly formated XML file output by the CoreNLP
#' library into an \code{annotation} object in R.
#'
#' @param file connection or character string giving the file name to load
#' @param encoding encoding to be assumed for input strings. It is used to mark
#' character strings as known to be in Latin-1 or UTF-8: it is
#' not used to re-encode the input. Passed to \code{readLines}.
#' @export
loadXMLAnnotation = function(file, encoding="unknown") {
if (is.character(file)) {
file = file(file, "r")
on.exit(close(file))
}
x = readLines(file)
tryCatch(output <- parseAnnoXML(x),
error = function(e) stop("Not a valid CoreNLP XML file."))
output
}
#' Convert Penn TreeBank POS to Universal Tagset
#'
#' Maps a character string of English Penn TreeBank
#' part of speech tags into the universal tagset
#' codes. This provides a reduced set of tags (12), and
#' a better cross-linguist model of speech.
#'
#' @param pennPOS a character vector of penn tags to match
#'
#'@examples
#'tok <- getToken(annoEtranger)
#'cbind(tok$POS,universalTagset(tok$POS))
#'
#' @export
universalTagset = function(pennPOS) {
mtab = structure(c("!", "#", "$", "''", "(", ")", ",", "-LRB-",
"-RRB-", ".", ":", "?", "CC", "CD", "CD|RB", "DT", "EX", "FW", "IN",
"IN|RP", "JJ", "JJR", "JJRJR", "JJS", "JJ|RB", "JJ|VBG", "LS", "MD", "NN",
"NNP", "NNPS", "NNS", "NN|NNS", "NN|SYM", "NN|VBG", "NP", "PDT", "POS", "PRP",
"PRP$", "PRP|VBP", "PRT", "RB", "RBR", "RBS", "RB|RP", "RB|VBG", "RN", "RP", "SYM",
"TO", "UH", "VB", "VBD", "VBD|VBN", "VBG", "VBG|NN", "VBN", "VBP", "VBP|TO",
"VBZ", "VP", "WDT", "WH", "WP", "WP$", "WRB", "``", ".", ".", ".", ".", ".",
".", ".", ".", ".", ".", ".", ".", "CONJ", "NUM", "X", "DET", "DET", "X",
"ADP", "ADP", "ADJ", "ADJ", "ADJ", "ADJ", "ADJ", "ADJ", "X", "VERB", "NOUN",
"NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "NOUN", "DET", "PRT", "PRON",
"PRON", "PRON", "PRT", "ADV", "ADV", "ADV", "ADV", "ADV", "X", "PRT", "X",
"PRT", "X", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB", "VERB",
"VERB", "VERB", "DET", "X", "PRON", "PRON", "ADV", "."), .Dim = c(68L, 2L))
index = match(pennPOS, mtab[,1])
output = rep("X", length(pennPOS))
output[!is.na(index)] = mtab[index[!is.na(index)],2]
output
}
#' Parse annotation xml
#'
#' Returns an annotation object from a character vector containing
#' the xml. Not exported; use \code{loadXMLAnnotation} instead.
#'
#' @importFrom XML xmlRoot xmlParse xmlToDataFrame xmlChildren xmlAttrs xmlValue
#' @param xml character vector containing the xml file from an annotation
parseAnnoXML = function(xml) {
xml = XML::xmlRoot(XML::xmlParse(xml))[[1]]
coref = xml[[2]]
xml = xml[[1]]
sentences = XML::xmlChildren(xml)
out = list(token = NULL,parse = NULL,basicDep = NULL,collapsedDep = NULL,
collapsedProcDep = NULL, coref = NULL, openie = NULL)
if (length(sentences)==0L) {
class(out) = "annotation"
return(out)
}
tokenNames = c("sentence", "id", "word", "lemma", "CharacterOffsetBegin",
"CharacterOffsetEnd", "POS", "NER", "Speaker")
depNames = c("sentence", "governor", "dependent", "type", "governorIdx",
"dependentIdx")
corefNames = c("corefId", "sentence", "start", "end", "head", "text")
sentNames = c("id", "sentimentValue", "sentiment")
openieNames = c("subject_start", "subject_end", "subject",
"relation_start", "relation_end", "relation",
"object_start", "object_end", "object")
for (i in 1:length(sentences)) {
sent = sentences[[i]]
df = data.frame(sentence=i, id=sapply(XML::xmlChildren(sent[[1L]]),function(v) XML::xmlAttrs(v)[1]),
XML::xmlToDataFrame(sent[[1]], stringsAsFactors=FALSE), stringsAsFactors=FALSE)
index = match(tokenNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, tokenNames)
df = df[,tokenNames]
out$token = rbind(out$token, df)
elementNames <- names(XML::xmlChildren(sent))
elementAttributes <- sapply(XML::xmlChildren(sent),
function(v) {v <- as.character(XML::xmlAttrs(v)['type']); if (length(v)) v else "" })
names(elementAttributes) <- NULL
parseIndex <- which(elementNames == "parse" & elementAttributes == "")[1]
basicDepIndex <- which(elementNames == "dependencies" & elementAttributes == "basic-dependencies")[1]
collapsedDepIndex <- which(elementNames == "dependencies" & elementAttributes == "collapsed-dependencies")[1]
collapsedProcDepIndex <- which(elementNames == "dependencies" & elementAttributes == "collapsed-ccprocessed-dependencies")[1]
openieIndex <- which(elementNames == "openie" & elementAttributes == "")[1]
machineReadingIndex <- which(elementNames == "MachineReading" & elementAttributes == "")[1]
if (!is.na(parseIndex))
out$parse = c(out$parse, XML::xmlValue(sent[[parseIndex]]))
if (!is.na(basicDepIndex) && length(XML::xmlToDataFrame(sent[[basicDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[basicDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[basicDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[basicDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[basicDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]),
stringsAsFactors=FALSE)
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$basicDep = rbind(out$basicDep, df)
}
if (!is.na(collapsedDepIndex) && length(XML::xmlToDataFrame(sent[[collapsedDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[collapsedDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[collapsedDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]))
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$collapsedDep = rbind(out$collapsedDep, df)
}
if (!is.na(collapsedProcDepIndex) && length(XML::xmlToDataFrame(sent[[collapsedProcDepIndex]]))) {
df = data.frame(sentence=i, XML::xmlToDataFrame(sent[[collapsedProcDepIndex]],stringsAsFactors=FALSE),
type=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]),function(v) XML::xmlAttrs(v)[[1]]),
governorIdx=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]), function(v) XML::xmlAttrs(v[[1]])[1]),
dependentIdx=sapply(XML::xmlChildren(sent[[collapsedProcDepIndex]]), function(v) XML::xmlAttrs(v[[2]])[1]))
index = match(depNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, depNames)
out$collapsedProcDep = rbind(out$collapsedProcDep, df)
}
if (!is.na(openieIndex) && length(XML::xmlToDataFrame(sent[[openieIndex]]))) {
these <- XML::xmlChildren(sent[[openieIndex]])
ids <-
cbind(t(sapply(these, function(v) XML::xmlAttrs(v[[1]]))),
sapply(these, function(v) XML::xmlValue(v[[1]][[1]])),
t(sapply(these, function(v) XML::xmlAttrs(v[[2]]))),
sapply(these, function(v) XML::xmlValue(v[[2]][[1]])),
t(sapply(these, function(v) XML::xmlAttrs(v[[3]]))),
sapply(these, function(v) XML::xmlValue(v[[3]][[1]])))
ids <- data.frame(ids, stringsAsFactors=FALSE, row.names=NULL)
colnames(ids) <- openieNames
out$openie = rbind(out$openie, ids)
}
# if (!is.na(machineReadingIndex) && length(XML::xmlToDataFrame(sent[[machineReadingIndex]]))) {
# these <- XML::xmlChildren(sent[[machineReadingIndex]])
# ids <-
# cbind(t(sapply(these, function(v) XML::xmlAttrs(v[[1]]))),
# sapply(these, function(v) XML::xmlValue(v[[1]][[1]])),
# t(sapply(these, function(v) XML::xmlAttrs(v[[2]]))),
# sapply(these, function(v) XML::xmlValue(v[[2]][[1]])),
# t(sapply(these, function(v) XML::xmlAttrs(v[[3]]))),
# sapply(these, function(v) XML::xmlValue(v[[3]][[1]])))
# ids <- data.frame(ids, stringsAsFactors=FALSE, row.names=NULL)
# colnames(ids) <- openieNames
# out$mr = rbind(out$mr, ids)
# }
sm = XML::xmlAttrs(sent)
df = data.frame(matrix(sm,nrow=1),stringsAsFactors=FALSE)
names(df) = names(sm)
index = match(sentNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)],drop=FALSE]
if (any(is.na(index))) df = fillDF(df, sentNames)
if (nrow(df)) out$sentiment = rbind(out$sentiment, df)
}
if (!is.null(out$token)) {
if (!is.na(index <- match("word", names(out$token))[1]))
names(out$token)[index] = "token"
if (sum(!is.na((index <- match(c("CharacterOffsetBegin","CharacterOffsetEnd"),names(out$token))))))
out$token[,index] = apply(out$token[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$basicDep)) {
if (sum(is.na((index <- match(c("governorIdx","dependentIdx"),names(out$basicDep))))))
out$basicDep[,index] = apply(out$basicDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$collapsedDep)) {
if (sum(!is.na((index <- match(c("governorIdx","dependentIdx"),names(out$collapsedDep))))))
out$collapsedDep[,index] = apply(out$collapsedDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(out$collapsedProcDep)) {
if (sum(!is.na((index <- match(c("governorIdx","dependentIdx"),names(out$collapsedProcDep))))))
out$collapsedProcDep[,index] = apply(out$collapsedProcDep[,index,drop=FALSE],2,as.integer)
}
if (!is.null(coref)) {
coref = XML::xmlChildren(coref)
for (corefId in 1:length(coref)) {
df = data.frame(corefId=corefId, XML::xmlToDataFrame(coref[[corefId]], stringsAsFactors=FALSE),
stringsAsFactors=FALSE)
index = match(corefNames, names(df))
if (length(index) != ncol(df)) df = df[,index[!is.na(index)]]
if (any(is.na(index))) df = fillDF(df, corefNames)
out$coref = rbind(out$coref, df)
}
}
if (!is.null(out$sentiment)) {
if (sum(!is.na(index <- match(c("id","sentimentValue"),names(out$sentiment)))))
out$sentiment[,index[!is.na(index)]] = apply(out$sentiment[,index[!is.na(index)],drop=FALSE],2,as.integer)
}
class(out) = "annotation"
out
}
fillDF = function(df, nameVec) {
if (nrow(df) == 0L) return(df)
index = match(nameVec, names(df))
df[,nameVec[is.na(index)]] = NA
return(df)
}
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