Nothing
R/ndex_RCX.r
In ndexr: NDEx R client library
Defines functions
print.RCX
rcx_updateMetaData
rcx_new
rcx_asNewNetwork
rcx_aspect_toJSON
rcx_toJSON
rcx_fromJSON
Documented in
print.RCX
rcx_asNewNetwork
rcx_aspect_toJSON
rcx_fromJSON
rcx_new
rcx_toJSON
rcx_updateMetaData
################################################################################
## Authors:
## Frank Kramer [frank.kramer@med.uni-goettingen.de]
## Florian Auer [florian.auer@med.uni-goettingen.de]
## Zaynab Hammoud [zaynab.hammoud@med.uni-goettingen.de]
##
## History:
## Created on 20 September 2016 by Kramer
## Restructured on 10 January 2017 by Auer
##
## Description:
## Base functions to create, parse, modify CX networks from/to JSON data
################################################################################
####################################################
## Conversion from/to JSON
####################################################
#' Create RCX object from JSON data
#'
#' This function creates an RCX object from a supplied JSON-encoded CX object.
#' RCX objects store the CX data as a named list of data.frames containing metaData and all aspects of the network.
#'
#' The structure of an RCX object, as shown via str(rcx) could be a list like this:\cr
#' \preformatted{
#' > str(rcx)
#'
#' List of 12
#' $ metaData :'data.frame': 11 obs. of 7 variables:
#' ..$ name : chr [1:11] "citations" "@context" "edgeAttributes" "edgeCitations" ...
#' ..$ consistencyGroup: int [1:11] 1 1 1 1 1 1 1 1 1 1 ...
#' ..$ elementCount : int [1:11] 4 23 NA NA 11 1 NA NA NA 5 ...
#' ..$ lastUpdate : num [1:11] 1.44e+12 1.44e+12 1.44e+12 1.44e+12 1.44e+12 ...
#' ..$ version : chr [1:11] "1.0" "1.0" "1.0" "1.0" ...
#' ..$ idCounter : int [1:11] 60714397 NA NA NA 60714399 NA NA NA NA 60714395 ...
#' ..$ properties :List of 11
#' $ numberVerification:'data.frame': 1 obs. of 1 variable:
#' ..$ longNumber: num 2.81e+14
#' $ ndexStatus :'data.frame': 1 obs. of 10 variables:
#' ..$ externalId : chr "eac8a4b8-6194-11e5-8ac5-06603eb7f303"
#' ..$ creationTime : num 1.44e+12
#' ..$ modificationTime: num 1.44e+12
#' ..$ visibility : chr "PUBLIC"
#' ..$ published : logi FALSE
#' ..$ nodeCount : int 5
#' ..$ edgeCount : int 11
#' ..$ owner : chr "nci-pid"
#' ..$ ndexServerURI : chr "http://public.ndexbio.org"
#' ..$ readOnly : logi FALSE
#' $ @context :'data.frame': 1 obs. of 23 variables:
#' ..$ GENPEPT : chr "http://www.ncbi.nlm.nih.gov/protein/"
#' ..$ NCBI GENE : chr "http://identifiers.org/ncbigene/"
#' ..$ ENSEMBL : chr "http://identifiers.org/ensembl/"
#' [...]
#' $ networkAttributes :'data.frame': 4 obs. of 2 variables:
#' ..$ n: chr [1:4] "name" "description" "version" "ndex:sourceFormat"
#' ..$ v: chr [1:4] "PLK3 signaling events" "This network ..." [...]
#' $ citations :'data.frame': 4 obs. of 7 variables:
#' ..$ @id : int [1:4] 60714380 60714383 60714386 60714397
#' ..$ dc:identifier : chr [1:4] "pmid:17264206" "pmid:14968113" "pmid:12242661" "pmid:11551930"
#' ..$ dc:type : chr [1:4] "URI" "URI" "URI" "URI"
#' ..$ attributes :List of 4 [...]
#' $ nodes :'data.frame': 5 obs. of 2 variables:
#' ..$ @id: int [1:5] 60714376 60714377 60714381 60714384 60714395
#' ..$ n : chr [1:5] "CCNE1" "PLK3" "MPIP3" "CHK2" ...
#' $ nodeAttributes :'data.frame': 10 obs. of 4 variables:
#' ..$ po: int [1:10] 60714376 60714376 60714377 60714377 60714381 60714381 60714384 60714384 60714395 60714395
#' ..$ n : chr [1:10] "alias" "relatedTo" "alias" "relatedTo" ...
#' ..$ v :List of 10
#' .. ..$ : chr [1:6] "UniProt Knowledgebase:Q92501" "UniProt Knowledgebase:Q9UD21" ...
#' .. ..$ : chr [1:98] "GENE ONTOLOGY:GO:0003713" "GENE ONTOLOGY:GO:0005515" ...
#' [...]
#' ..$ d : chr [1:10] "list_of_string" ...
#' $ edges :'data.frame': 11 obs. of 4 variables:
#' ..$ @id: int [1:11] 60714379 60714382 ...
#' ..$ s : int [1:11] 60714376 60714381 ...
#' ..$ t : int [1:11] 60714377 60714377 ...
#' ..$ i : chr [1:11] "neighbor-of" "neighbor-of" ...
#' $ edgeCitations :'data.frame': 11 obs. of 2 variables:
#' ..$ po :List of 11
#' .. ..$ : int 60714379
#' .. ..$ : int 60714382
#' [...]
#' ..$ citations:List of 11
#' .. ..$ : int 60714380
#' .. ..$ : int 60714383
#' [...]
#' $ status :'data.frame': 1 obs. of 2 variables:
#' ..$ error : chr ""
#' ..$ success: logi TRUE
#'- attr(*, "class")= chr [1:2] "RCX" "list"
#' }
#'
#' The data.frames representing nodes and edges could look like this:\cr
#' \preformatted{
#' > rcx[["nodes"]]
#' @id n
#' 1 60714376 CCNE1
#' 2 60714377 PLK3
#' 3 60714381 MPIP3
#' 4 60714384 CHK2
#' 5 60714395 P53
#'
#' > rcx[["edges"]]
#' @id s t i
#' 1 60714379 60714376 60714377 neighbor-of
#' 2 60714382 60714381 60714377 neighbor-of
#' 3 60714385 60714384 60714377 neighbor-of
#' 4 60714388 60714377 60714376 controls-expression-of
#' 5 60714390 60714377 60714381 controls-phosphorylation-of
#' 6 60714392 60714377 60714381 controls-state-change-of
#' 7 60714393 60714377 60714384 controls-phosphorylation-of
#' 8 60714394 60714377 60714384 controls-state-change-of
#' 9 60714396 60714377 60714395 controls-phosphorylation-of
#' 10 60714398 60714377 60714395 controls-state-change-of
#' 11 60714399 60714377 60714395 neighbor-of
#' }
#'
#'
#' @param json JSON data
#' @param verbose logical; whether to print out extended feedback
#'
#' @return returns object of class RCX if successfull, NULL otherwise
#'
#' @seealso \code{\link{rcxgraph_fromRCX}} \code{\link{rcxgraph_toRCX}} \code{\link{rcx_toJSON}}
#' @aliases RCX
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert to JSON
#' json = rcx_toJSON(rcx)
#' ## Convert it back from JSON
#' rcx = rcx_fromJSON(json)
#' @export
rcx_fromJSON <- function(json, verbose = FALSE){
#!TODO: add a better way for datatype columns ("d") of properties and nodeAttributes, edgeAttributes, etc.
if(!jsonlite::validate(json)) {
stop("rcx_fromJSON: parameter json does not contain valid JSON")
}
json = jsonlite::fromJSON(json)
## this created a data.frame of size n x m, where n = (columns) number of individual aspects and m = (rows) overall number of aspects received
## this means: most entries within each column are NULL. if they are not null, they contain a data.frame containing the aspect according to the column name.
## note: not all data.frames contained within a column must have matching column, e.g. pre- and post-metdata
## implementation:
#break up data.frame columns into a list
#merge pre- and post-metadata
#consolidate other aspects using rbind which also removes NULLs
jsonlist = as.list(json)
aspectlist = list()
### merge pre- and post-metadata. this is special as pre- and post-metadata can have the entries of the same name.
sel = which(!sapply(jsonlist[["metaData"]], is.null))
if(length(sel)==1) {
aspectlist[["metaData"]] = jsonlist[["metaData"]][[sel[1]]]
}
if(length(sel)==2) {
aspectlist[["metaData"]] = merge(jsonlist[["metaData"]][[sel[1]]],jsonlist[["metaData"]][[sel[2]]],by="name",all = TRUE)
if("properties.x" %in% names(aspectlist$metaData)) {
aspectlist[["metaData"]]$properties = aspectlist$metaData$properties.x
aspectlist[["metaData"]]$properties.x = NULL
aspectlist[["metaData"]]$properties.y = NULL
}
}
## correction for the "properties" element in "metaData"
## since 2018.01.20 "properties" is optional, it casts to NULL instead of list
## this leads to a conversion to an json object, which is wrong
## this is done to prevent this behavor!
if("properties" %in% names(aspectlist$metaData)) {
propTmp = aspectlist[["metaData"]]$properties
aspectlist[["metaData"]]$properties = lapply(propTmp, function(x){
if(is.null(x)){
return(as.list(NULL))
}else{
return(x)
}
})
}
## more than 2 metaData elements in the json defined
if(!(length(sel) %in% c(1,2))) {
warning(paste0("JSON2RCX: data contained ",length(sel), " parts of metaData. Must be 1 or 2. Returning NULL." ))
return(NULL)
}
### remaining aspects must have same structure: rbind them
for(i in names(jsonlist)) {
if(i == "metaData") next
aspectlist[[i]] = plyr::rbind.fill(jsonlist[[i]])
}
#set class
class(aspectlist) = c("RCX",class(aspectlist))
return(aspectlist)
}
#' Generate JSON data from RCX object
#'
#' @param rcx RCX object
#' @param verbose logical; whether to print out extended feedback
#' @param pretty logical; adds indentation whitespace to JSON output
#'
#' @return json jsonlite json object if successfull, NULL otherwise
#' @seealso \code{\link{rcxgraph_fromRCX}} \code{\link{rcxgraph_toRCX}} \code{\link{rcx_fromJSON}}
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert to JSON
#' json = rcx_toJSON(rcx)
#' @export
rcx_toJSON <- function(rcx, verbose = FALSE, pretty = FALSE){
if(is.null(rcx) || !("RCX" %in% class(rcx))) {
stop("rcx_toJSON: parameter rcx does not contain RCX object")
}
## numberVerification has to be 2^48 = 281,474,976,710,655
rcx$numberVerification = data.frame(longNumber=281474976710655)
jsonCol = c()
## remove empty "properties" elements column in "metaData"
if("properties" %in% names(rcx$metaData)) {
propTmp = rcx$metaData$properties
if(! any(! sapply(propTmp, is.null))){
rcx$metaData$properties = NULL
}
}
## specify the order of the elemnets in the sent CX json
## numberVerifiction has to be first!!
## metaData has to be second!!
rcxNames = names(rcx)
rcxNames = rcxNames[rcxNames!="numberVerification"]
rcxNames = rcxNames[rcxNames!="metaData"]
rcxNames = c("numberVerification", "metaData", rcxNames)
for(aspect in rcxNames){
jsonCol = c(jsonCol,paste0('{"',aspect,'":',rcx_aspect_toJSON(rcx[[aspect]], verbose, pretty),'}'))
}
return(paste0('[',paste0(jsonCol, collapse=','),']'))
}
#' Generate JSON data for a single aspect of a RCX object
#'
#' @param rcxAspect aspect in RCX object (rcx[[aspectName]])
#' @param verbose logical; whether to print out extended feedback
#' @param pretty logical; adds indentation whitespace to JSON output
#'
#' @return json object if successfull, empty string otherwise
#' @seealso \code{\link{rcx_toJSON}} and \code{\link{rcx_fromJSON}}
#'
#' @keywords internal
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert RCX aspect to JSON
#' rcxNodesJson = ndexr:::rcx_aspect_toJSON(rcx$nodes)
rcx_aspect_toJSON <- function(rcxAspect, verbose = FALSE, pretty = FALSE){
result = ''
## if any of the aspects has a datatype ('d') property, at least one of the datatypes is not of 'string' (default datatype).
## this means, the corresponding values ('v') have to be wrapped in arrays, if they are defined as kind of list (e.g. 'list_of_string', 'list_of_integer',...)
if(('v' %in% names(rcxAspect))&&('d' %in% names(rcxAspect))){
tmp = rcxAspect
isListVector = (!is.na(tmp$d)&(substr(tmp[,'d'],1,nchar("list_of_"))=="list_of_"))
tmpList = rcxAspect[isListVector,] # has to be wrapped
tmpNoList = rcxAspect[!isListVector,] # doesn't have to be wrapped
tmpList$v = as.list(tmpList$v) # forces toJSON to encode the elements as arrays
jsonCol = c()
## don't add an empty aspect, if all v's are lists
if(dim(tmpNoList)[1]!=0){
tmpNoList$v <- unlist(tmpNoList$v)
# tmpTxt = jsonlite::toJSON(tmpNoList, na='string', pretty = pretty) # TODO!! [fauer:20.03.2017]: NA as string or NULL? for citations$`dc:contributor` it has to be NULL!
tmpTxt = jsonlite::toJSON(tmpNoList, na=NULL, pretty = pretty)
tmpTxt = sub('\n*$','',substr(tmpTxt,2,nchar(tmpTxt)-1))
jsonCol = c(jsonCol, tmpTxt)
}
## don't add an empty aspect, if none v is a list (but might be an integer)
if(dim(tmpList)[1]!=0){
# tmpTxt = jsonlite::toJSON(tmpList, na='string', pretty = pretty)
tmpTxt = jsonlite::toJSON(tmpList, na=NULL, pretty = pretty)
tmpTxt = substr(tmpTxt,2,nchar(tmpTxt)-1)
jsonCol = c(jsonCol, tmpTxt)
}
result = paste0('[',paste0(jsonCol, collapse=','),']')
}else{
tmpList = rcxAspect
# result = jsonlite::toJSON(tmpList, na='string', pretty = pretty)
result = jsonlite::toJSON(tmpList, na=NULL, pretty = pretty)
}
return(result)
}
####################################################
## Some convenience functions for RCX
####################################################
#' Remove all interfering NDEx artefacts from RCX object
#'
#' @param rcx RCX object
#'
#' @return \code{\link{RCX}} object
#' @seealso \code{\link{rcx_fromJSON}}
#'
#' @details After a RCX object is downloaded from an NDEx server, it will contain some aspects that are not present in a newly generated network, i.e. ndexStatus', provenanceHistory' and 'status'.
#' Removing those aspects might be useful in some cases.
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Remove NDEx artefacts
#' rcx = rcx_asNewNetwork(rcx)
#' \dontrun{
#' rcxjson = rcx_toJSON(rcx)
#' ndex_create_network(ndexcon, rcxjson)
#' }
#' @export
rcx_asNewNetwork = function(rcx){
rcx['ndexStatus'] = NULL # a newly created network doesn't have an ndex-status yet
rcx['provenanceHistory'] = NULL # ... also not an provenance history
rcx['status'] = NULL # fragment from retrieving the network from the server
return(rcx)
}
#' Create a blank rcx object
#'
#' This function generates a (blank) RCX object. For a valid RCX, at least one node has to be specified. Optional attributes are 'n' for names and 'r' for represents.
#' Ids have to be unique (in nodes) and may not contain 'NA' values. For names and represents attributes, 'NA' values are allowed.
#'
#' @param nodes vector or data.frame (default: c('@id'=1) ) node(s)
#'
#' @return RCX object
#'
#' @examples
#' rcx = rcx_new()
#' rcx = rcx_new(c('@id'=1)) #same as one before
#' rcx = rcx_new(nodes=c('@id'=1)) #same as one before
#' rcx = rcx_new(data.frame('@id'=c(1), check.names=FALSE)) #same as one before
#' rcx = rcx_new(c('@id'=1, n='Some Name'))
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' #same as one before:
#' rcx = rcx_new(data.frame('@id'=c(1),n=c('Some Name'), r=c('HGNC:Symbol'), check.names=FALSE))
#' rcx = rcx_new(data.frame('@id'=c(1,2,3),n=c('Some Name','And another name',NA),
#' r=c('HGNC:Symbol',NA,'UniProt:C3P0'), check.names=FALSE))
#' @export
rcx_new = function(nodes=c('@id'=1)){
# TODO : add parameters for edges and other core aspects
# rcx_new = function(nodes=c('@id'=1), edges, nodeAttributes, edgeAttributes, networkAttributes){
if(is.null(nodes)) stop('rcx_new: At least one node is necessary!')
if(!'@id' %in% names(nodes)) stop('rcx_new: No "@id" column in nodes!')
ids = as.character(nodes[['@id']])
if(length(unique(ids)) != length(ids)) stop('rcx_new: Some ids in "@id" column are duplicated!')
if(any(NA %in% nodes[['@id']])) stop('rcx_new: Some ids in "@id" column have "NA" value!')
rcx <- list(nodes=data.frame('@id'=ids, stringsAsFactors=FALSE, check.names=FALSE))
if('n' %in% names(nodes)) rcx$nodes$n = as.character(nodes[['n']])
if('r' %in% names(nodes)) rcx$nodes$r = as.character(nodes[['r']])
class(rcx) = c("RCX",class(rcx))
rcx = rcx_updateMetaData(rcx)
return(rcx)
}
#' Updating the meta-data of an RCX object
#'
#' @param rcx RCX object
#' @param mandatoryAspects character vector; Aspects, that are mandatory for a valid RCX object (by default: "nodes")
#' @param excludeAspects character vector; Aspects, that are excluded for generating metaData (by default: "metaData", "numberVerification" and "status")
#' @param force logical; force the creation of new metaData (even if the RCX object already contains metaData)
#' @param verbose logical; whether to print out extended feedback
#'
#' @return \code{\link{RCX}} object
#'
#' @details For a given RCX object the meta-data is updated, i.e. the counted elements and id counter are updated. If an aspect was added/removed, it will also added/removed from the meta-data.
#' If mandatory aspects (specified in mandatoryAspects parameter) are missing in the RCX object, an error is thrown.
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## update meta-data
#' rcx = rcx_updateMetaData(rcx)
#' # or with explicitly set default values
#' rcx = rcx_updateMetaData(rcx, mandatoryAspects=c('nodes'),
#' excludeAspects=c("metaData", "numberVerification", "status"),
#' force=FALSE, verbose=FALSE)
#' @export
rcx_updateMetaData = function(rcx, mandatoryAspects=c('nodes'), excludeAspects=c("metaData", "numberVerification", "status"), force=FALSE, verbose=FALSE){
if(missing(rcx) || is.null(rcx) || !("RCX" %in% class(rcx))) stop("rcx_updateMetaData: Parameter rcx does not contain RCX object")
# check if mandatoryAspects are present in the RCX object
if(any(!(mandatoryAspects %in% names(rcx)))) stop(paste0("rcx_updateMetaData: Mandatory aspects are missing in the RCX object: ", paste0(mandatoryAspects[!(mandatoryAspects %in% names(rcx))], collapse=', ')))
# get meta data from RCX object
# create it, if it doesn't exist (or if it is forced)
metaData = rcx$metaData
if(is.null(metaData) || force) {
if(verbose) print('rcx_updateMetaData: MetaData will be created')
metaData = data.frame(consistencyGroup=1, elementCount=0, lastUpdate=1, name = sort(names(rcx)[!(names(rcx) %in% excludeAspects)]), version='1.0', idCounter=NA, stringsAsFactors = FALSE)
}else{
if(verbose) print('rcx_updateMetaData: Existing metaData will be updated')
if(!('consistencyGroup' %in% names(metaData))){
metaData$consistencyGroup = 1
if(verbose) warning('rcx_updateMetaData: No consistancy groups specified (Set by default to "1")! Check manually for consistency!')
}
if(!('elementCount' %in% names(metaData))) metaData$elementCount = 0
if(!('lastUpdate' %in% names(metaData))) metaData$lastUpdate = 1
if(!('version' %in% names(metaData))) metaData$version = '1.0'
if(!('idCounter' %in% names(metaData))) metaData$idCounter = NA
properties = NULL
if('properties' %in% names(metaData)){
properties = metaData$properties
metaData$properties = NULL
}else{
properties = rep(list(), length.out=dim(metaData)[1])
}
aspects = names(rcx)[!(names(rcx) %in% excludeAspects)]
aspectsAlreadyInMDIndex = which(metaData$name %in% aspects)
# exclude rows, that are no aspects and order columns
metaData = metaData[aspectsAlreadyInMDIndex,sort(colnames(metaData))]
properties = properties[aspectsAlreadyInMDIndex]
# find aspects missing in meta-data
aspectsNotYetInMD = aspects[!aspects %in% metaData$name]
# add missing aspects to metaData
if(length(aspectsNotYetInMD)!=0) {
metaData = rbind(metaData, data.frame(consistencyGroup=1, elementCount=0, idCounter=NA, lastUpdate=1, name = aspectsNotYetInMD, version='1.0', stringsAsFactors = FALSE))
properties = c(properties,rep(list(),length.out=length(aspectsNotYetInMD)))
}
# add the properties column again
metaData$properties = properties
}
if(verbose) print('rcx_updateMetaData: idCounter will be updated')
# id exporting aspects are required to have specified an id counter (max id in the aspect)
metaData$idCounter = sapply(metaData$name, function(x){return(ifelse('@id' %in% colnames(rcx[[x]]), max(rcx[[x]]$'@id'), NA))})
if(verbose) print('rcx_updateMetaData: Consistency groups will be checked')
# get the current consistency group(s)
consistencyGroups = unique(metaData$consistencyGroup)
if(verbose && (length(consistencyGroups)>1)){
warn = paste0("rcx_updateMetaData: RCX object contains ",length(consistencyGroups), " consistency groups! Check the groups manually for consistency!\n")
for(cgNr in consistencyGroups){
warn = paste0(warn, 'Group ',cgNr, ': ', paste0(metaData$name[metaData$consistencyGroup==cgNr], collapse = ', '),'\n')
}
warning(warn)
}
# update element count
metaData$elementCount = sapply(metaData$name, function(x){return(max(dim(rcx[[x]])[1],0))}) # max(0,NULL) = 0 to set default value to 0
# set properties (if not already set)
if(!('list' %in% class(metaData$properties))){
metaData$properties=rep(list(), length.out=dim(metaData)[1])
}
# order meta-data elements by names and correct the row numbering
metaData = metaData[order(metaData$name),order(colnames(metaData))]
rownames(metaData) = 1:dim(metaData)[1]
rcx$metaData = metaData
return(rcx)
}
####################################################
###
### Print functions
###
####################################################
#' Print a RCX object
#'
#' @param x RCX object; stores the CX data as a named list of data.frames containing metaData and all aspects of the network.
#' @param ... further arguments passed to or from other methods.
#'
#' @return Just prints the RCX object
#'
#' @keywords internal
#' @examples
#' rcx = rcx_new(data.frame('@id'=c(1,2,3),n=c('Some Name','And another name',NA),
#' r=c('HGNC:Symbol',NA,'UniProt:C3P0'), check.names=FALSE))
#' print(rcx)
#' @seealso \code{\link{rcx_fromJSON}} and \code{\link{rcx_new}}
#' @export
print.RCX <- function(x,...){
cat('RCX object containing the following aspects:\n')
tmpColNames = colnames(x$metaData)
tmpColNames = tmpColNames[order(tmpColNames)]
tmpColNames = c('name',tmpColNames[tmpColNames!='name'])
print(x$metaData[tmpColNames])
tmpNames = names(x)
tmpAspects = x$metaData$name
metaAspects = tmpNames[!tmpNames %in% tmpAspects]
if(length(metaAspects)!=0){
cat('\nAdditionally the following aspects contain meta-data:\n')
print(metaAspects)
}
invisible(x)
}
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Defines functions print.RCX rcx_updateMetaData rcx_new rcx_asNewNetwork rcx_aspect_toJSON rcx_toJSON rcx_fromJSON
Documented in print.RCX rcx_asNewNetwork rcx_aspect_toJSON rcx_fromJSON rcx_new rcx_toJSON rcx_updateMetaData
################################################################################
## Authors:
## Frank Kramer [frank.kramer@med.uni-goettingen.de]
## Florian Auer [florian.auer@med.uni-goettingen.de]
## Zaynab Hammoud [zaynab.hammoud@med.uni-goettingen.de]
##
## History:
## Created on 20 September 2016 by Kramer
## Restructured on 10 January 2017 by Auer
##
## Description:
## Base functions to create, parse, modify CX networks from/to JSON data
################################################################################
####################################################
## Conversion from/to JSON
####################################################
#' Create RCX object from JSON data
#'
#' This function creates an RCX object from a supplied JSON-encoded CX object.
#' RCX objects store the CX data as a named list of data.frames containing metaData and all aspects of the network.
#'
#' The structure of an RCX object, as shown via str(rcx) could be a list like this:\cr
#' \preformatted{
#' > str(rcx)
#'
#' List of 12
#' $ metaData :'data.frame': 11 obs. of 7 variables:
#' ..$ name : chr [1:11] "citations" "@context" "edgeAttributes" "edgeCitations" ...
#' ..$ consistencyGroup: int [1:11] 1 1 1 1 1 1 1 1 1 1 ...
#' ..$ elementCount : int [1:11] 4 23 NA NA 11 1 NA NA NA 5 ...
#' ..$ lastUpdate : num [1:11] 1.44e+12 1.44e+12 1.44e+12 1.44e+12 1.44e+12 ...
#' ..$ version : chr [1:11] "1.0" "1.0" "1.0" "1.0" ...
#' ..$ idCounter : int [1:11] 60714397 NA NA NA 60714399 NA NA NA NA 60714395 ...
#' ..$ properties :List of 11
#' $ numberVerification:'data.frame': 1 obs. of 1 variable:
#' ..$ longNumber: num 2.81e+14
#' $ ndexStatus :'data.frame': 1 obs. of 10 variables:
#' ..$ externalId : chr "eac8a4b8-6194-11e5-8ac5-06603eb7f303"
#' ..$ creationTime : num 1.44e+12
#' ..$ modificationTime: num 1.44e+12
#' ..$ visibility : chr "PUBLIC"
#' ..$ published : logi FALSE
#' ..$ nodeCount : int 5
#' ..$ edgeCount : int 11
#' ..$ owner : chr "nci-pid"
#' ..$ ndexServerURI : chr "http://public.ndexbio.org"
#' ..$ readOnly : logi FALSE
#' $ @context :'data.frame': 1 obs. of 23 variables:
#' ..$ GENPEPT : chr "http://www.ncbi.nlm.nih.gov/protein/"
#' ..$ NCBI GENE : chr "http://identifiers.org/ncbigene/"
#' ..$ ENSEMBL : chr "http://identifiers.org/ensembl/"
#' [...]
#' $ networkAttributes :'data.frame': 4 obs. of 2 variables:
#' ..$ n: chr [1:4] "name" "description" "version" "ndex:sourceFormat"
#' ..$ v: chr [1:4] "PLK3 signaling events" "This network ..." [...]
#' $ citations :'data.frame': 4 obs. of 7 variables:
#' ..$ @id : int [1:4] 60714380 60714383 60714386 60714397
#' ..$ dc:identifier : chr [1:4] "pmid:17264206" "pmid:14968113" "pmid:12242661" "pmid:11551930"
#' ..$ dc:type : chr [1:4] "URI" "URI" "URI" "URI"
#' ..$ attributes :List of 4 [...]
#' $ nodes :'data.frame': 5 obs. of 2 variables:
#' ..$ @id: int [1:5] 60714376 60714377 60714381 60714384 60714395
#' ..$ n : chr [1:5] "CCNE1" "PLK3" "MPIP3" "CHK2" ...
#' $ nodeAttributes :'data.frame': 10 obs. of 4 variables:
#' ..$ po: int [1:10] 60714376 60714376 60714377 60714377 60714381 60714381 60714384 60714384 60714395 60714395
#' ..$ n : chr [1:10] "alias" "relatedTo" "alias" "relatedTo" ...
#' ..$ v :List of 10
#' .. ..$ : chr [1:6] "UniProt Knowledgebase:Q92501" "UniProt Knowledgebase:Q9UD21" ...
#' .. ..$ : chr [1:98] "GENE ONTOLOGY:GO:0003713" "GENE ONTOLOGY:GO:0005515" ...
#' [...]
#' ..$ d : chr [1:10] "list_of_string" ...
#' $ edges :'data.frame': 11 obs. of 4 variables:
#' ..$ @id: int [1:11] 60714379 60714382 ...
#' ..$ s : int [1:11] 60714376 60714381 ...
#' ..$ t : int [1:11] 60714377 60714377 ...
#' ..$ i : chr [1:11] "neighbor-of" "neighbor-of" ...
#' $ edgeCitations :'data.frame': 11 obs. of 2 variables:
#' ..$ po :List of 11
#' .. ..$ : int 60714379
#' .. ..$ : int 60714382
#' [...]
#' ..$ citations:List of 11
#' .. ..$ : int 60714380
#' .. ..$ : int 60714383
#' [...]
#' $ status :'data.frame': 1 obs. of 2 variables:
#' ..$ error : chr ""
#' ..$ success: logi TRUE
#'- attr(*, "class")= chr [1:2] "RCX" "list"
#' }
#'
#' The data.frames representing nodes and edges could look like this:\cr
#' \preformatted{
#' > rcx[["nodes"]]
#' @id n
#' 1 60714376 CCNE1
#' 2 60714377 PLK3
#' 3 60714381 MPIP3
#' 4 60714384 CHK2
#' 5 60714395 P53
#'
#' > rcx[["edges"]]
#' @id s t i
#' 1 60714379 60714376 60714377 neighbor-of
#' 2 60714382 60714381 60714377 neighbor-of
#' 3 60714385 60714384 60714377 neighbor-of
#' 4 60714388 60714377 60714376 controls-expression-of
#' 5 60714390 60714377 60714381 controls-phosphorylation-of
#' 6 60714392 60714377 60714381 controls-state-change-of
#' 7 60714393 60714377 60714384 controls-phosphorylation-of
#' 8 60714394 60714377 60714384 controls-state-change-of
#' 9 60714396 60714377 60714395 controls-phosphorylation-of
#' 10 60714398 60714377 60714395 controls-state-change-of
#' 11 60714399 60714377 60714395 neighbor-of
#' }
#'
#'
#' @param json JSON data
#' @param verbose logical; whether to print out extended feedback
#'
#' @return returns object of class RCX if successfull, NULL otherwise
#'
#' @seealso \code{\link{rcxgraph_fromRCX}} \code{\link{rcxgraph_toRCX}} \code{\link{rcx_toJSON}}
#' @aliases RCX
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert to JSON
#' json = rcx_toJSON(rcx)
#' ## Convert it back from JSON
#' rcx = rcx_fromJSON(json)
#' @export
rcx_fromJSON <- function(json, verbose = FALSE){
#!TODO: add a better way for datatype columns ("d") of properties and nodeAttributes, edgeAttributes, etc.
if(!jsonlite::validate(json)) {
stop("rcx_fromJSON: parameter json does not contain valid JSON")
}
json = jsonlite::fromJSON(json)
## this created a data.frame of size n x m, where n = (columns) number of individual aspects and m = (rows) overall number of aspects received
## this means: most entries within each column are NULL. if they are not null, they contain a data.frame containing the aspect according to the column name.
## note: not all data.frames contained within a column must have matching column, e.g. pre- and post-metdata
## implementation:
#break up data.frame columns into a list
#merge pre- and post-metadata
#consolidate other aspects using rbind which also removes NULLs
jsonlist = as.list(json)
aspectlist = list()
### merge pre- and post-metadata. this is special as pre- and post-metadata can have the entries of the same name.
sel = which(!sapply(jsonlist[["metaData"]], is.null))
if(length(sel)==1) {
aspectlist[["metaData"]] = jsonlist[["metaData"]][[sel[1]]]
}
if(length(sel)==2) {
aspectlist[["metaData"]] = merge(jsonlist[["metaData"]][[sel[1]]],jsonlist[["metaData"]][[sel[2]]],by="name",all = TRUE)
if("properties.x" %in% names(aspectlist$metaData)) {
aspectlist[["metaData"]]$properties = aspectlist$metaData$properties.x
aspectlist[["metaData"]]$properties.x = NULL
aspectlist[["metaData"]]$properties.y = NULL
}
}
## correction for the "properties" element in "metaData"
## since 2018.01.20 "properties" is optional, it casts to NULL instead of list
## this leads to a conversion to an json object, which is wrong
## this is done to prevent this behavor!
if("properties" %in% names(aspectlist$metaData)) {
propTmp = aspectlist[["metaData"]]$properties
aspectlist[["metaData"]]$properties = lapply(propTmp, function(x){
if(is.null(x)){
return(as.list(NULL))
}else{
return(x)
}
})
}
## more than 2 metaData elements in the json defined
if(!(length(sel) %in% c(1,2))) {
warning(paste0("JSON2RCX: data contained ",length(sel), " parts of metaData. Must be 1 or 2. Returning NULL." ))
return(NULL)
}
### remaining aspects must have same structure: rbind them
for(i in names(jsonlist)) {
if(i == "metaData") next
aspectlist[[i]] = plyr::rbind.fill(jsonlist[[i]])
}
#set class
class(aspectlist) = c("RCX",class(aspectlist))
return(aspectlist)
}
#' Generate JSON data from RCX object
#'
#' @param rcx RCX object
#' @param verbose logical; whether to print out extended feedback
#' @param pretty logical; adds indentation whitespace to JSON output
#'
#' @return json jsonlite json object if successfull, NULL otherwise
#' @seealso \code{\link{rcxgraph_fromRCX}} \code{\link{rcxgraph_toRCX}} \code{\link{rcx_fromJSON}}
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert to JSON
#' json = rcx_toJSON(rcx)
#' @export
rcx_toJSON <- function(rcx, verbose = FALSE, pretty = FALSE){
if(is.null(rcx) || !("RCX" %in% class(rcx))) {
stop("rcx_toJSON: parameter rcx does not contain RCX object")
}
## numberVerification has to be 2^48 = 281,474,976,710,655
rcx$numberVerification = data.frame(longNumber=281474976710655)
jsonCol = c()
## remove empty "properties" elements column in "metaData"
if("properties" %in% names(rcx$metaData)) {
propTmp = rcx$metaData$properties
if(! any(! sapply(propTmp, is.null))){
rcx$metaData$properties = NULL
}
}
## specify the order of the elemnets in the sent CX json
## numberVerifiction has to be first!!
## metaData has to be second!!
rcxNames = names(rcx)
rcxNames = rcxNames[rcxNames!="numberVerification"]
rcxNames = rcxNames[rcxNames!="metaData"]
rcxNames = c("numberVerification", "metaData", rcxNames)
for(aspect in rcxNames){
jsonCol = c(jsonCol,paste0('{"',aspect,'":',rcx_aspect_toJSON(rcx[[aspect]], verbose, pretty),'}'))
}
return(paste0('[',paste0(jsonCol, collapse=','),']'))
}
#' Generate JSON data for a single aspect of a RCX object
#'
#' @param rcxAspect aspect in RCX object (rcx[[aspectName]])
#' @param verbose logical; whether to print out extended feedback
#' @param pretty logical; adds indentation whitespace to JSON output
#'
#' @return json object if successfull, empty string otherwise
#' @seealso \code{\link{rcx_toJSON}} and \code{\link{rcx_fromJSON}}
#'
#' @keywords internal
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Convert RCX aspect to JSON
#' rcxNodesJson = ndexr:::rcx_aspect_toJSON(rcx$nodes)
rcx_aspect_toJSON <- function(rcxAspect, verbose = FALSE, pretty = FALSE){
result = ''
## if any of the aspects has a datatype ('d') property, at least one of the datatypes is not of 'string' (default datatype).
## this means, the corresponding values ('v') have to be wrapped in arrays, if they are defined as kind of list (e.g. 'list_of_string', 'list_of_integer',...)
if(('v' %in% names(rcxAspect))&&('d' %in% names(rcxAspect))){
tmp = rcxAspect
isListVector = (!is.na(tmp$d)&(substr(tmp[,'d'],1,nchar("list_of_"))=="list_of_"))
tmpList = rcxAspect[isListVector,] # has to be wrapped
tmpNoList = rcxAspect[!isListVector,] # doesn't have to be wrapped
tmpList$v = as.list(tmpList$v) # forces toJSON to encode the elements as arrays
jsonCol = c()
## don't add an empty aspect, if all v's are lists
if(dim(tmpNoList)[1]!=0){
tmpNoList$v <- unlist(tmpNoList$v)
# tmpTxt = jsonlite::toJSON(tmpNoList, na='string', pretty = pretty) # TODO!! [fauer:20.03.2017]: NA as string or NULL? for citations$`dc:contributor` it has to be NULL!
tmpTxt = jsonlite::toJSON(tmpNoList, na=NULL, pretty = pretty)
tmpTxt = sub('\n*$','',substr(tmpTxt,2,nchar(tmpTxt)-1))
jsonCol = c(jsonCol, tmpTxt)
}
## don't add an empty aspect, if none v is a list (but might be an integer)
if(dim(tmpList)[1]!=0){
# tmpTxt = jsonlite::toJSON(tmpList, na='string', pretty = pretty)
tmpTxt = jsonlite::toJSON(tmpList, na=NULL, pretty = pretty)
tmpTxt = substr(tmpTxt,2,nchar(tmpTxt)-1)
jsonCol = c(jsonCol, tmpTxt)
}
result = paste0('[',paste0(jsonCol, collapse=','),']')
}else{
tmpList = rcxAspect
# result = jsonlite::toJSON(tmpList, na='string', pretty = pretty)
result = jsonlite::toJSON(tmpList, na=NULL, pretty = pretty)
}
return(result)
}
####################################################
## Some convenience functions for RCX
####################################################
#' Remove all interfering NDEx artefacts from RCX object
#'
#' @param rcx RCX object
#'
#' @return \code{\link{RCX}} object
#' @seealso \code{\link{rcx_fromJSON}}
#'
#' @details After a RCX object is downloaded from an NDEx server, it will contain some aspects that are not present in a newly generated network, i.e. ndexStatus', provenanceHistory' and 'status'.
#' Removing those aspects might be useful in some cases.
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## Remove NDEx artefacts
#' rcx = rcx_asNewNetwork(rcx)
#' \dontrun{
#' rcxjson = rcx_toJSON(rcx)
#' ndex_create_network(ndexcon, rcxjson)
#' }
#' @export
rcx_asNewNetwork = function(rcx){
rcx['ndexStatus'] = NULL # a newly created network doesn't have an ndex-status yet
rcx['provenanceHistory'] = NULL # ... also not an provenance history
rcx['status'] = NULL # fragment from retrieving the network from the server
return(rcx)
}
#' Create a blank rcx object
#'
#' This function generates a (blank) RCX object. For a valid RCX, at least one node has to be specified. Optional attributes are 'n' for names and 'r' for represents.
#' Ids have to be unique (in nodes) and may not contain 'NA' values. For names and represents attributes, 'NA' values are allowed.
#'
#' @param nodes vector or data.frame (default: c('@id'=1) ) node(s)
#'
#' @return RCX object
#'
#' @examples
#' rcx = rcx_new()
#' rcx = rcx_new(c('@id'=1)) #same as one before
#' rcx = rcx_new(nodes=c('@id'=1)) #same as one before
#' rcx = rcx_new(data.frame('@id'=c(1), check.names=FALSE)) #same as one before
#' rcx = rcx_new(c('@id'=1, n='Some Name'))
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' #same as one before:
#' rcx = rcx_new(data.frame('@id'=c(1),n=c('Some Name'), r=c('HGNC:Symbol'), check.names=FALSE))
#' rcx = rcx_new(data.frame('@id'=c(1,2,3),n=c('Some Name','And another name',NA),
#' r=c('HGNC:Symbol',NA,'UniProt:C3P0'), check.names=FALSE))
#' @export
rcx_new = function(nodes=c('@id'=1)){
# TODO : add parameters for edges and other core aspects
# rcx_new = function(nodes=c('@id'=1), edges, nodeAttributes, edgeAttributes, networkAttributes){
if(is.null(nodes)) stop('rcx_new: At least one node is necessary!')
if(!'@id' %in% names(nodes)) stop('rcx_new: No "@id" column in nodes!')
ids = as.character(nodes[['@id']])
if(length(unique(ids)) != length(ids)) stop('rcx_new: Some ids in "@id" column are duplicated!')
if(any(NA %in% nodes[['@id']])) stop('rcx_new: Some ids in "@id" column have "NA" value!')
rcx <- list(nodes=data.frame('@id'=ids, stringsAsFactors=FALSE, check.names=FALSE))
if('n' %in% names(nodes)) rcx$nodes$n = as.character(nodes[['n']])
if('r' %in% names(nodes)) rcx$nodes$r = as.character(nodes[['r']])
class(rcx) = c("RCX",class(rcx))
rcx = rcx_updateMetaData(rcx)
return(rcx)
}
#' Updating the meta-data of an RCX object
#'
#' @param rcx RCX object
#' @param mandatoryAspects character vector; Aspects, that are mandatory for a valid RCX object (by default: "nodes")
#' @param excludeAspects character vector; Aspects, that are excluded for generating metaData (by default: "metaData", "numberVerification" and "status")
#' @param force logical; force the creation of new metaData (even if the RCX object already contains metaData)
#' @param verbose logical; whether to print out extended feedback
#'
#' @return \code{\link{RCX}} object
#'
#' @details For a given RCX object the meta-data is updated, i.e. the counted elements and id counter are updated. If an aspect was added/removed, it will also added/removed from the meta-data.
#' If mandatory aspects (specified in mandatoryAspects parameter) are missing in the RCX object, an error is thrown.
#'
#' @examples
#' ## Create an RCX object
#' rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
#' ## update meta-data
#' rcx = rcx_updateMetaData(rcx)
#' # or with explicitly set default values
#' rcx = rcx_updateMetaData(rcx, mandatoryAspects=c('nodes'),
#' excludeAspects=c("metaData", "numberVerification", "status"),
#' force=FALSE, verbose=FALSE)
#' @export
rcx_updateMetaData = function(rcx, mandatoryAspects=c('nodes'), excludeAspects=c("metaData", "numberVerification", "status"), force=FALSE, verbose=FALSE){
if(missing(rcx) || is.null(rcx) || !("RCX" %in% class(rcx))) stop("rcx_updateMetaData: Parameter rcx does not contain RCX object")
# check if mandatoryAspects are present in the RCX object
if(any(!(mandatoryAspects %in% names(rcx)))) stop(paste0("rcx_updateMetaData: Mandatory aspects are missing in the RCX object: ", paste0(mandatoryAspects[!(mandatoryAspects %in% names(rcx))], collapse=', ')))
# get meta data from RCX object
# create it, if it doesn't exist (or if it is forced)
metaData = rcx$metaData
if(is.null(metaData) || force) {
if(verbose) print('rcx_updateMetaData: MetaData will be created')
metaData = data.frame(consistencyGroup=1, elementCount=0, lastUpdate=1, name = sort(names(rcx)[!(names(rcx) %in% excludeAspects)]), version='1.0', idCounter=NA, stringsAsFactors = FALSE)
}else{
if(verbose) print('rcx_updateMetaData: Existing metaData will be updated')
if(!('consistencyGroup' %in% names(metaData))){
metaData$consistencyGroup = 1
if(verbose) warning('rcx_updateMetaData: No consistancy groups specified (Set by default to "1")! Check manually for consistency!')
}
if(!('elementCount' %in% names(metaData))) metaData$elementCount = 0
if(!('lastUpdate' %in% names(metaData))) metaData$lastUpdate = 1
if(!('version' %in% names(metaData))) metaData$version = '1.0'
if(!('idCounter' %in% names(metaData))) metaData$idCounter = NA
properties = NULL
if('properties' %in% names(metaData)){
properties = metaData$properties
metaData$properties = NULL
}else{
properties = rep(list(), length.out=dim(metaData)[1])
}
aspects = names(rcx)[!(names(rcx) %in% excludeAspects)]
aspectsAlreadyInMDIndex = which(metaData$name %in% aspects)
# exclude rows, that are no aspects and order columns
metaData = metaData[aspectsAlreadyInMDIndex,sort(colnames(metaData))]
properties = properties[aspectsAlreadyInMDIndex]
# find aspects missing in meta-data
aspectsNotYetInMD = aspects[!aspects %in% metaData$name]
# add missing aspects to metaData
if(length(aspectsNotYetInMD)!=0) {
metaData = rbind(metaData, data.frame(consistencyGroup=1, elementCount=0, idCounter=NA, lastUpdate=1, name = aspectsNotYetInMD, version='1.0', stringsAsFactors = FALSE))
properties = c(properties,rep(list(),length.out=length(aspectsNotYetInMD)))
}
# add the properties column again
metaData$properties = properties
}
if(verbose) print('rcx_updateMetaData: idCounter will be updated')
# id exporting aspects are required to have specified an id counter (max id in the aspect)
metaData$idCounter = sapply(metaData$name, function(x){return(ifelse('@id' %in% colnames(rcx[[x]]), max(rcx[[x]]$'@id'), NA))})
if(verbose) print('rcx_updateMetaData: Consistency groups will be checked')
# get the current consistency group(s)
consistencyGroups = unique(metaData$consistencyGroup)
if(verbose && (length(consistencyGroups)>1)){
warn = paste0("rcx_updateMetaData: RCX object contains ",length(consistencyGroups), " consistency groups! Check the groups manually for consistency!\n")
for(cgNr in consistencyGroups){
warn = paste0(warn, 'Group ',cgNr, ': ', paste0(metaData$name[metaData$consistencyGroup==cgNr], collapse = ', '),'\n')
}
warning(warn)
}
# update element count
metaData$elementCount = sapply(metaData$name, function(x){return(max(dim(rcx[[x]])[1],0))}) # max(0,NULL) = 0 to set default value to 0
# set properties (if not already set)
if(!('list' %in% class(metaData$properties))){
metaData$properties=rep(list(), length.out=dim(metaData)[1])
}
# order meta-data elements by names and correct the row numbering
metaData = metaData[order(metaData$name),order(colnames(metaData))]
rownames(metaData) = 1:dim(metaData)[1]
rcx$metaData = metaData
return(rcx)
}
####################################################
###
### Print functions
###
####################################################
#' Print a RCX object
#'
#' @param x RCX object; stores the CX data as a named list of data.frames containing metaData and all aspects of the network.
#' @param ... further arguments passed to or from other methods.
#'
#' @return Just prints the RCX object
#'
#' @keywords internal
#' @examples
#' rcx = rcx_new(data.frame('@id'=c(1,2,3),n=c('Some Name','And another name',NA),
#' r=c('HGNC:Symbol',NA,'UniProt:C3P0'), check.names=FALSE))
#' print(rcx)
#' @seealso \code{\link{rcx_fromJSON}} and \code{\link{rcx_new}}
#' @export
print.RCX <- function(x,...){
cat('RCX object containing the following aspects:\n')
tmpColNames = colnames(x$metaData)
tmpColNames = tmpColNames[order(tmpColNames)]
tmpColNames = c('name',tmpColNames[tmpColNames!='name'])
print(x$metaData[tmpColNames])
tmpNames = names(x)
tmpAspects = x$metaData$name
metaAspects = tmpNames[!tmpNames %in% tmpAspects]
if(length(metaAspects)!=0){
cat('\nAdditionally the following aspects contain meta-data:\n')
print(metaAspects)
}
invisible(x)
}
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