R/modules/search/search.R

In benhid/Rpath: A Web-App for Biologic Pathway Exploration

output$searchResults <-  renderDataTable({
  return(getResultsDf())
}, options = list(pageLength = 10, searching = FALSE, lengthChange = FALSE), escape=FALSE, selection = 'single'
)

output$downloadOWL <- downloadHandler(
  filename = function() {
    paste('rpath-owl-', Sys.Date(), '.owl', sep='')
  },
  content = function(file) {
    showNotification("Downloading file...")
    URL <- getRowFromDf()
    owl <- getPc(URL)

    saveXML(owl, file)
  }
)

# Auxiliar functions to prettify the output table
createLink <- function(val) {
  sprintf('<a href="%s" target="_blank" class="btn btn-default">GO</a>', val)
}

createImg <- function(val) {
  db <- gsub("http://pathwaycommons.org/pc2/","",val)
  url_img <- paste(db, ".png", sep="")
  sprintf('<img src="img/search/%s" class="img-rounded" alt="%s"></img>', url_img, db)
}

getRowFromDf <- function(){
  if(length(input$searchResults_rows_selected) > 0){
    URL <- strsplit(as.character(finalSearchResultsDf$uri[input$searchResults_rows_selected]), "\"")[[1]][2]
    print(paste("Reading url: ", URL, sep=''))
    return(URL)
  }
  else if(!is.null(input$owlFile)){
    print("Reading file")

    inFile <- input$owlFile

    if (is.null(inFile)){
      showNotification("Error parsing file")
      return(NULL)
    } else{
      # todo Validate BIOPAX file
      return(inFile)
    }
  }
}

getResultsDf <- eventReactive(input$searchButton, {
  term <- input$term
  dataSources <- input$dataSources
  organism <- input$organism
  numberOfResults <- input$numberOfResults

  shinyjs::disable(id = "searchButton")

  # Validation
  if (term == ""){
    showNotification("No term provided. Executing example query...", type="error")
    term <- "name:gl?coly*"
  }
  if (is.null(dataSources)){
    showNotification("No datasource selected. Searching on Reactome only...", type="error")
    dataSources <- "reactome"
  }
  if (numberOfResults<0 || numberOfResults>100){
    showNotification("No valid number of results range (1:100). Showing 10 results...", type="error")
    numberOfResults <- 10
  }

  # Loading bar
  withProgress(message = 'Loading', value = 0, {
    incProgress(0.1, detail = paste("Searching on selected databases..."))
    searchResults <- searchPc(q = term,
                              datasource = paste(dataSources, sep="&"),
                              type = "Pathway", organism = organism, verbose = TRUE)

    incProgress(0.5, detail = paste("Parsing results..."))
    searchResultsDf <- ldply(xmlToList(searchResults), data.frame)

    incProgress(0.8, detail = paste("Simplifying results..."))
    searchResultsDf <- subset(searchResultsDf, .id=="searchHit") # we only keep searchHits (NOT .attrs)
    headSearchResultsDf <- head(searchResultsDf,  numberOfResults)

    # If we have searchHit>=1 then create links, images and
    # return a subset of the original dataframe
    if("uri" %in% colnames(headSearchResultsDf))
    {
      headSearchResultsDf$uri <- createLink(headSearchResultsDf$uri)
      headSearchResultsDf$dataSource <- createImg(headSearchResultsDf$dataSource)
      headSearchResultsDf <- headSearchResultsDf[, c("name", "dataSource", "numParticipants", "numProcesses", "size", "uri")]
    }

    incProgress(1.0, detail = paste("Done!"))
    finalSearchResultsDf <<- headSearchResultsDf # global variable
  })

  if(!is.data.frame(finalSearchResultsDf)){
    # Error in search; replace with empty dataframe
    finalSearchResultsDf <- data.frame()
  }

  shinyjs::enable(id = "searchButton")

  return(finalSearchResultsDf)
})