R/common_datasets.R

In m-raheel/ShinyBeads: Interface for RnBeads generated reports

#' Datasets List used in RnBeads Analysis
#'
#' Takes in a results directory and returns a list of grouped directories that used the same set of datasets
#' @param rd A path to the rnbeads results repository
#' @return list of directories
#' @export


datasets_common <- function(rd) {


  folders <- list.files(rd,full.names = FALSE)
  folders


  if ( length(folders) != 0 ){

    path.lists <- list()
    for (i in 1:length(folders)) {


      if ( file.exists( isolate({ paste(rd, folders[i], 'data_import_data','annotation.csv',sep="/") }) ) ){



        #filepath <- file.path(rd, folders[i], 'data_import_data','annotation.csv')

        tmp = toString(paste(rd, folders[i], 'data_import_data','annotation.csv',sep="/"))
        # len = nchar(tmp)
        # last_character = substr(tmp,len,len)
        #
        # if (last_character == '/'){
        #
        #
        #
        #   tmp = substr(tmp,len,len - 1)
        #
        # }

        filepath <- tmp



        # removing the last character from the path '/' cause error in the server




        if (file.exists( isolate({ paste(filepath) }) ) ){
          filename <- as.character(filepath)

          path.lists[i] <- filename


        }
      }
      else{

      }

    }

    if (length(path.lists) != 0){


      # this for loops store the combination of results folder that uses the same  dataset
      same.sample.list <- list()
      same.sample.list2 <- list()

      temp.list <- list()
      temp.counter <- 1

      counter <- 1
      for (i in 1:length(folders)) {

          if ( file.exists( isolate({ paste(rd, folders[i], 'data_import_data','annotation.csv',sep="/") }) ) ){


            A <- try(read.csv((toString(path.lists[i]))))

            #A <- read.csv((toString(path.lists[i])))[ ,2:3]

            if(inherits(A, "try-error")){
              print ('error occured in try block of A')
            }

            else
            {
              for (j in i:length(folders)) {

                if ( file.exists( isolate({ paste(rd, folders[j], 'data_import_data','annotation.csv',sep="/") }) ) ){

                  B <- try(read.csv((toString(path.lists[j]))))

                  if(inherits(B, "try-error")){
                    print ('error occured in try block of B')
                  }

                  else
                  {
                    if (length(A) == length(B) && j != i){
                      comparison <- identical(A,B)
                      comparison
                      if (comparison == TRUE){

                        temp.list[temp.counter] <- folders[j]
                        temp.counter = temp.counter+1

                        if ((folders[i] %in% temp.list) & (folders[j] %in% temp.list) ){
                        }
                        else{
                          same.sample.list[counter] <- list(c(folders[i],folders[j]))
                          same.sample.list2[counter] <- folders[j]

                          counter = counter+1

                          }
                      }

                    }
                  }#end else try-error of B
                }#end of if for checking file

              }

            }#end else try-error of A

        }
      }


      # datastructure logic of storing the list of folders as a list that share the common folders
      temp.list <- list()
      actual.list <- list()
      actual.counter <- 1
      length(same.sample.list)

      increament <- 1
      k <- 1
      actual.list


      apath.lists <- list()
      apath.counter <- 1

      while (k <= length(same.sample.list)) {

        a <- unlist(same.sample.list[k], use.names = FALSE)
        temp.variable <- a[1]
        temp.list <- append(temp.list, temp.variable)

        # bn <- basename(file.path(rd, temp.variable,'data_import_data', c("annotation.csv")))
        # dn <- dirname(file.path(rd, temp.variable,'data_import_data/annotation.csv'))
        # full.path <- file.path(dn,'annotation.csv')


        filepath <- file.path(rd, temp.variable, 'data_import_data','annotation.csv')

        filepath= as.character(filepath)


        #filename <- paste(filepath, 'annotation.csv', sep="/")

        if (file.exists( isolate({ paste(filepath) }) ) ){

          filename <- filepath
          #removing space


          #tmp <- file.path(rd, paste(temp.variable,'/data_import_data/annotation.csv'),sep='')
          #removing space
          #tmp <- gsub(" /", "/", tmp)
          apath.lists[apath.counter] <- filename
          apath.counter <- apath.counter + 1


          for (l in k:length(same.sample.list)) {
            b <- unlist(same.sample.list[l], use.names = FALSE)
            b1 <- b[1]
            if (b1 == temp.variable){

              temp.list <- append(temp.list, b[2])

            }
            else{
              increament = l -1

              break
            }

          }

          #message(paste0("Value of K =  ", k))

          k <- k + increament

          temp.variable <- b

          actual.list[actual.counter] <- list(temp.list)
          temp.list <- list()


          actual.counter <- actual.counter + 1
        }


      }

      return(actual.list)

    }
    else{
      common.datasets <- list()

      return(common.datasets)
    }
  }
  else{

    common.datasets <- list()

    return(common.datasets)


  }

}