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This R script contains usage examples for accessing the KeyPathwayMinerWeb RESTful API defined at http://tomcat.compbio.sdu.dk/keypathwayminer/documentation/rest/ Usage examples depend on methods defined in RESTful_KeyPathwayMiner.r
### R functions to consume the KeyPathwayMinerWeb RESTful API ###
### Authors: Markus List and Martin Dissing-Hansen ###
# Package dependencies. Make sure those are installed
library(RCurl)
library(rjson)
library(foreach)
# Helper method for base64 encoding. Needed to transfer network and dataset files #
base64EncFile <- function(fileName){
return(base64(readChar(fileName, file.info(fileName)$size)))
}
# Function to set up a JSON object in preparation of the job submission
setup.KPM <- function(list.of.indicator.matrices,
algorithm="Greedy", strategy="GLONE", graphID=1,
graph.file,
removeBENs=FALSE, range,
Kmin=0, Lmin=0, Kmax=0, Lmax=0, Kstep=1, Lstep=1,
l_same_percentage = FALSE,
same_percentage = 0,
ATTACHED_TO_ID,
computed.pathways=20,
with.perturbation=FALSE,
unmapped_nodes="Add to negative list",
linkType="OR"){
#base64 encode datasetfiles files
datasetList <- datasetList.KPM(list.of.indicator.matrices, ATTACHED_TO_ID)
#create a run id
RUN_ID <- paste(sample(c(LETTERS[1:6],0:9),6,replace=TRUE),collapse="")
# setup the json settings:
settings <- toJSON(
list(
parameters=c(
name=paste("R demo client run", RUN_ID),
algorithm=algorithm,
strategy=strategy,
removeBENs=tolower(as.character(removeBENs)),
unmapped_nodes=unmapped_nodes,
computed_pathways=computed.pathways,
graphID=graphID,
l_samePercentage=tolower(as.character(l_same_percentage)),
samePercentage_val=same_percentage,
k_values=list(c(val=Kmin, val_step=Kstep, val_max=Kmax, use_range=tolower(as.character(range)), isPercentage="false")),
l_values=list(
c(val=Lmin, val_step=Lstep, val_max=Lmax, use_range=tolower(as.character(range)), isPercentage="false", datasetName=paste("dataset", 1, sep=""))
)
),
withPerturbation=tolower(as.character(with.perturbation)),
perturbation=list(c( # perturbation can be left out, if withPeturbation parameter is set to false.
technique="Node-swap",
startPercent=5,
stepPercent=1,
maxPercent=15,
graphsPerStep=1
)),
linkType=linkType,
attachedToID=ATTACHED_TO_ID,
positiveNodes="",
negativeNodes=""
))
# Add custom network if provided
graph <- graph.KPM(graph.file, ATTACHED_TO_ID)
return(list(settings, datasetList, graph))
}
# Helper method to encode a list of datasets (indicator matrices) for the job submission
datasetList.KPM <- function(list.of.indicator.matrices, ATTACHED_TO_ID)
{
counter <- 0
datasetList <- foreach(indicator.matrix = list.of.indicator.matrices) %do% {
txt.con <- textConnection("tmp.file", "w")
write.table(indicator.matrix, txt.con, sep="\t",quote=F, col.names = F, row.names = F)
enc.file <- base64(paste(tmp.file, collapse="\n"))
close(txt.con)
counter <- counter + 1
c(name=paste("dataset", counter, sep=""), attachedToID=ATTACHED_TO_ID, contentBase64=enc.file)
}
return(toJSON(datasetList))
}
# Helper method to encode custom network file
graph.KPM <- function(graph.file, ATTACHED_TO_ID){
if(!is.null(graph.file))
{
graph <- base64EncFile(graph.file)
graph <- toJSON(c(name=basename(graph.file), attachedToID=ATTACHED_TO_ID, contentBase64=graph))
}
else{
graph <- NULL
}
return(graph)
}
# Method used to create a job submission
call.KPM <- function(indicator.matrices, ATTACHED_TO_ID=NULL, url="http://localhost:8080/kpm-web/", async=TRUE, ...){
# generate random UUID for the session if none was provided
if(is.null(ATTACHED_TO_ID))
ATTACHED_TO_ID = paste(sample(c(LETTERS[1:6],0:9),32,replace=TRUE),collapse="")
#Create settings object
kpmSetup <- setup.KPM(indicator.matrices, ATTACHED_TO_ID=ATTACHED_TO_ID, ...)
#prepare result object
result <- NULL
#print out settings for debugging purposes
print(sprintf("url: %s", url))
print(sprintf("settings: %s", kpmSetup[[1]]))
#submit
result <- submit.KPM(url, kpmSetup, async)
return(result)
}
# helper method for error handling
withTryCatch <- function(surroundedFunc){
tryCatch({
surroundedFunc()
}, error = function(e) {
if("COULDNT_CONNECT" %in% class(e)){
stop("Couldn't connect to url.")
}else{
stop(paste("Unexpected error:", e$message))
}
return(NULL)
})
}
# method for submitting a job to KeyPathwayMinerWeb asynchronously (returns immediately) or blocking (returns when job is complete)
submit.KPM <- function(url, kpmSetup, async=TRUE){
withTryCatch(function(){
if(async)
url <- paste(url, "requests/submitAsync", sep="")
else
url <- paste(url, "requests/submit", sep="")
#if a default graph is used we should not send the graph attribute
if(is.null(kpmSetup[[3]]))
result <- postForm(url, kpmSettings=kpmSetup[[1]], datasets=kpmSetup[[2]])
else
result <- postForm(url, kpmSettings=kpmSetup[[1]], datasets=kpmSetup[[2]], graph=kpmSetup[[3]])
#get results
jsonResult <- fromJSON(result)
#print status to console
print(jsonResult["comment"])
#return results
return(jsonResult)
})
}
# Method to check up on a submitted job. Useful to monitor its progress and current status.
getStatus <- function(url, questId){
withTryCatch(function(){
url <- paste(url, "requests/runStatus", sep="")
print(sprintf("url: %s", url))
result <- postForm(url, questID=questId)
jsonResult <- fromJSON(result)
if(tolower(jsonResult["success"]) == "cancelled"){
print("Run has been cancelled.")
return
}
print(jsonResult["completed"])
print(jsonResult["progress"])
return(jsonResult)
})
}
# Once the run is complete, we can obtain the results
getResults <- function(url, questId){
withTryCatch(function(){
url <- paste(url, "requests/results", sep="")
print(sprintf("url: %s", url))
result <- postForm(url, questID=questId)
jsonResult <- fromJSON(result)
if(tolower(jsonResult["success"]) == "true"){
return(jsonResult)
}
else{
return(NULL)
}
})
}
# Get a data frame of available networks
getNetworks <- function(url){
kpm.url <- paste(url, "rest/availableNetworks/", sep="")
result <- getURL(kpm.url)
jsonResult <- fromJSON(result)
networks <- foreach(network = jsonResult, .combine=append) %do% {network[[1]]}
names(networks) <- foreach(network = jsonResult, .combine=append) %do% {network[[2]]}
return(networks)
}
# Get url to see progress in the browser and see the results
quest.progress.url <- function(url, ATTACHED_TO_ID){
kpm.url <- paste(url, "requests/quests?attachedToId=", sep="")
paste(kpm.url, ATTACHED_TO_ID, "&hideTitle=false", sep="")
}
### Example calls to demonstrate the usage of the KeyPathwayMinerWeb RESTful API ###
### Authors: Markus List and Martin Dissing-Hansen ###
# Load test data and R functions to access KeyPathwayMiner Web
source("RESTful_KeyPathwayMiner.R")
# KeyPathWayMiner URL:
url <- "http://tomcat.compbio.sdu.dk/keypathwayminer/"
url <- "http://localhost:8080/kpm-web/"
huntington_disease_up <- as.data.frame.matrix(read.delim("matrix-hd-up.dat", header=FALSE))
huntington_disease_down <- as.data.frame.matrix(read.delim("matrix-hd-down.dat", header=FALSE))
huntington_list <- list(huntington_disease_up, huntington_disease_down)
# Generate a unique identifier for this session
ATTACHED_TO_ID <- paste(sample(c(LETTERS[1:6],0:9),32,replace=TRUE),collapse="")
# List available networks
availableNetworks <- getNetworks(url)
print(availableNetworks)
# Use the I2D network
I2D.id <- availableNetworks[["I2D entrez"]]
test <- call.KPM(list(ind.matrix), ATTACHED_TO_ID, url=url,
async=FALSE, Lmin=22, Kmin=1,
strategy="INES", removeBENs=TRUE,
graphID=I2D.id, graph.file=NULL,
range=FALSE, linkType="OR")
# Start with a simple run on one dataset with fixed parameters for K and L using INES in a blocking call.
result.fixed.parameters.one.dataset <- call.KPM(list(huntington_disease_up), ATTACHED_TO_ID, url=url,
async=FALSE, Lmin=8, Kmin=1,
strategy="INES", removeBENs=TRUE,
graphID=I2D.id, graph.file=NULL,
range=FALSE, linkType="OR")
#results
print(paste("browse to", result.fixed.parameters.one.dataset$resultUrl, "to see the results"))
# Start a ranged run on one dataset with fixed parameters for K and L using INES in a blocking call.
result.ranged.parameters.one.dataset <- call.KPM(list(huntington_disease_up), ATTACHED_TO_ID, url=url,
async=FALSE, Lmin=4, Lmax=8, Lstep=4,
Kmin=0, Kmax=1, Kstep=1,
strategy="INES", removeBENs=TRUE,
graphID=I2D.id, graph.file=NULL,
range=TRUE, linkType="OR")
#results
print(paste("browse to", result.ranged.parameters.one.dataset$resultUrl, "to see the results"))
# Start a run with INES and K = 1 where we use a percentage of L = 10% for the two datasets.
# Note: The web service does not allow individual fixed parameters to be set for each dataset at the moment.
result.fixed.percentage.two.datasets <- call.KPM(huntington_list, ATTACHED_TO_ID, url=url,
async=TRUE, l_same_percentage = TRUE, strategy="INES",
removeBENs=TRUE, same_percentage=10, Kmin=1,
graphID=I2D.id, graph.file=NULL, range=FALSE,
linkType="OR")
# Now we want to monitor progress in the client or in the browser:
#extract job id (called quest id)
quest.id <- result.fixed.percentage.two.datasets$questID
# open the result page where you can monitor the progress of both tasks
print(quest.progress.url(url, ATTACHED_TO_ID))
#check status of the second job
getStatus(url, quest.id)
#if complete, download results of the second job
if(status$completed){
result.fixed.percentage.two.datasets <- getResults(url, quest.id)
}
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