R/Getter_Functions.R

In frankkramer-lab/Multipath2Neo4j: A package for collecting, modeling, visualizing and storing biological pathways networks in Neo4j

#' Get the number of labels in a Neo4j graph
#'
#' Get the number of labels in a Neo4j graph
#' @param connection The Neo4j connection object.
#'
#' @return The labels count in case of success, otherwise the result from the Neo4j call.
#' @importFrom neo4r call_neo4j
#'
#' @export
#'
#' @examples
#' \dontrun{
#' #To get the labels count
#' result = getLabelsCount(connection)
#' }
getLabelsCount <- function(connection){
  #If the function is called without passing a neo4j connection, raise an exception
  if(missing(connection)){
    stop("Neo4j Connection must be specified")
  }
  if(connection$ping() == FALSE){
    stop("Check your connection")
  }

  query = "CALL db.labels()"

  result = call_neo4j(query, connection, type = c("row", "graph"), output = c("r","json"), include_stats = FALSE, include_meta = FALSE)

  if(is.null(result$error_code))
  {
    return(length(unlist(result)))
  }
  return(result)
}


#' Verify if the label exists in a graph
#'
#' Verify if the label exists in a graph
#' @param connection The Neo4j connection object.
#' @param label The name of the label.
#'
#' @return A boolean value in case of success, otherwise the result from the Neo4j call.
#' @importFrom neo4r call_neo4j
#'
#' @export
#' @examples
#' \dontrun{
#' #To get the labels count
#' isLabel(connection, "DrUGs")
#' }
isLabel <- function(connection, label){
  #If the function is called without passing a neo4j connection, raise an exception
  if(missing(connection)){
    stop("Neo4j Connection must be specified")
  }
  if(connection$ping() == FALSE){
    stop("Check your connection")
  }

  #If the function is called without passing a label, raise an exception
  if(missing(label) || is.null(label) || label == ""){
    stop("Node Label must be specified")
  }

  query = "CALL db.labels()"

  result = call_neo4j(query, connection, type = c("row", "graph"), output = c("r","json"), include_stats = FALSE, include_meta = FALSE)

  tmp = result
  if(is.null(result$error_code))
  {
    labels_names = lapply(unlist(result), function(x){tolower(x)})
    if (tolower(label) %in% labels_names) {
      tmp = TRUE
    }
    else{
      tmp = FALSE
    }
  }
  return(tmp)
}


#' Get the attributes of a node, or all nodes in a Neo4j graph
#'
#' Get the attributes of a node, or all nodes in a Neo4j graph
#' @param connection The Neo4j connection object.
#' @param property_key The node property key name to be identified by.
#' @param property_key_value The started node property key value to be found within.
#'
#' @return A dataframe containing the attributes of the specified node. If the node property key and value are not specified,
#' all nodes with their attributes are returned, in case of success, otherwise the result from the Neo4j call.
#' @importFrom neo4r call_neo4j
#'
#' @export
#'
#' @examples
#' \dontrun{
#' #To get all the nodes with their attributes
#' nodes = getNodeAttributes(connection)
#'
#' #To get the nodes of name Complex70 with its attributes
#' nodes = getNodeAttributes(connection,"name","Complex70")
#' }
getNodeAttributes <- function(connection, property_key = NULL, property_key_value = NULL){
  #If the function is called without passing a neo4j connection, raise an exception
  if(missing(connection)){
    stop("Neo4j Connection must be specified")
  }
  if(connection$ping() == FALSE){
    stop("Check your connection")
  }

  #If the function is called by passing one of the arguments property key and value, raise an exception
  if((missing(property_key) && !missing(property_key_value)) || (!missing(property_key) && missing(property_key_value))){
    stop("Property key and value must be both NULL or specified")
  }
  if((!missing(property_key) && !missing(property_key_value)) && ((property_key == "" && property_key_value != "") || (property_key != "" && property_key_value == ""))){
    stop("Property key and value must be both NULL or specified")
  }

  query = "MATCH (n"

  if(!is.null(property_key) && property_key != ""){
    query = paste0(query, " {", property_key, ": '", property_key_value ,"'}")
  }
  query = query = paste0(query, ") RETURN n")

  result = call_neo4j(query, connection, type = c("row", "graph"), output = c("r","json"), include_stats = FALSE, include_meta = FALSE)

  tmp = result
  if(is.null(result$error_code) && length(tmp))
  {
    tmp = as.data.frame(result, col.names = "")
  }
  return(tmp)
}


#' Get the nodes on a layer in a Neo4j graph
#'
#' Get the nodes on a layer in a Neo4j graph
#' @param connection The Neo4j connection object.
#' @param label The name of the label.
#' @param property_key The node property key name to be extracted.
#'
#' @return A list of nodes having the label, with their property key values.
#' @importFrom neo4r call_neo4j
#'
#' @export
#'
#' @examples
#' \dontrun{
#' #To get the list of Proteins' names
#' result = getLabel(connection, "Protein", "name")
#' }
getLabel <- function(connection, label, property_key){
  #If the function is called without passing a neo4j connection, raise an exception
  if(missing(connection)){
    stop("Neo4j Connection must be specified")
  }
  if(connection$ping() == FALSE){
    stop("Check your connection")
  }

  #If the function is called without passing a label, raise an exception
  if(missing(label) || label == ""){
    stop("Label must be specified")
  }
  #If the function is called without passing a node property key, raise an exception
  if(missing(property_key) || property_key == ""){
    stop("Node Property Key must be specified")
  }

  query = paste0("MATCH (n:", label, ") RETURN n.", property_key)

  result = call_neo4j(query, connection, type = c("row", "graph"), output = c("r","json"), include_stats = FALSE, include_meta = FALSE)

  tmp = result
  if(is.null(result$error_code))
  {
    tmp = unlist(result, use.names = FALSE)
  }
  return(tmp)
}


#' Get the attributes of the relationships connecting two nodes, or all nodes in a Neo4j graph
#'
#' Get the attributes of the relationships connecting two nodes, or all nodes in a Neo4j graph
#' @param connection The Neo4j connection object.
#' @param returned_started_node_property The name of the attribute identifying the started node.
#' @param returned_end_node_property The name of the attribute identifying the end node.
#' @param started_node_property The started node property key name to be identified by.
#' @param started_node_property_value The started node property key value to be found within.
#' @param end_node_property The end node property key name to be identified by.
#' @param end_node_property_value The end node property key value to be found within.
#'
#' @return A dataframe containing the relationships with their attributes. If both nodes' properties and values are missing,
#' it returns all the relationships with their attributes. If the started node's property name and value are given,
#' it returns all the relationships starting from this node. If the end node's property name and value are given,
#' it returns all the relationships ending with this node.
#' @importFrom neo4r call_neo4j
#' @importFrom stringr str_remove
#'
#' @export
#' @examples
#' \dontrun{
#' #To get all the edges with their attributes
#' edges = getRelationshipAttributes(connection, "name", "name")
#'
#' #To get all the edges starting from the node of name Complex1 with their attributes
#' edges = getRelationshipAttributes(connection, "name", "name", "name", "Complex1")
#'
#' #To get all the edges ending with the node of name Complex10 with their attributes
#' edges = getRelationshipAttributes(connection, "name", "name",
#' end_node_property = "name", end_node_property_value = "Complex10")
#' }
getRelationshipAttributes <- function(connection, returned_started_node_property,
                                      returned_end_node_property,
                                      started_node_property = NULL,
                                      started_node_property_value = NULL,
                                      end_node_property = NULL,
                                      end_node_property_value = NULL){
  #If the function is called without passing a neo4j connection, raise an exception
  if(missing(connection)){
    stop("Neo4j Connection must be specified")
  }
  if(connection$ping() == FALSE){
    stop("Check your connection")
  }

  #If the function is called without passing the started node property key to be returned, raise an exception
  if(missing(returned_started_node_property) || is.null(returned_started_node_property) || returned_started_node_property == ""){
    stop("Started Node Property Key to be returned must be specified")
  }

  #If the function is called without passing the end node property key to be returned, raise an exception
  if(missing(returned_end_node_property) || is.null(returned_end_node_property) || returned_end_node_property == ""){
    stop("End Node Property Key to be returned must be specified")
  }

  if((is.null(started_node_property) && !is.null(started_node_property_value))
     ||
     (!is.null(started_node_property) && is.null(started_node_property_value))){
    stop("Started Node property key and value must be both NULL or specified.")
  }


  if((is.null(end_node_property) && !is.null(end_node_property_value))
     ||
     (!is.null(end_node_property) && is.null(end_node_property_value))){
    stop("End Node property key and value must be both NULL or specified.")
  }

  query = "MATCH (n"

  if(!is.null(started_node_property)){
    started_node_property_c = gsub(started_node_property, pattern = " ", replacement = "_")
    started_node_property_value_c = started_node_property_value

    if(grepl("'", started_node_property_value, fixed = TRUE))
    {
      started_node_property_value_c = unlist(strsplit(as.character(started_node_property_value), "'"))
      started_node_property_value_c = paste0(unlist(started_node_property_value_c), sep = "", collapse = "\\'")
    }
    query = paste0(query, " {", started_node_property_c, ": '",started_node_property_value_c, "'}")
  }

  query = paste0(query, ")-[r]->(m")

  if(!is.null(end_node_property)){
    end_node_property_c = gsub(end_node_property, pattern = " ", replacement = "_")
    end_node_property_value_c = end_node_property_value

    if(grepl("'", end_node_property_value, fixed = TRUE))
    {
      end_node_property_value_c = unlist(strsplit(as.character(end_node_property_value), "'"))
      end_node_property_value_c = paste0(unlist(end_node_property_value_c), sep = "", collapse = "\\'")
    }
    query = paste0(query, " {", end_node_property_c, ": '",end_node_property_value_c, "'}")
  }

  returned_started_node_property_c = gsub(returned_started_node_property, pattern = " ", replacement = "_")
  returned_end_node_property_c = gsub(returned_end_node_property, pattern = " ", replacement = "_")
  query = paste0(query, ") RETURN n.", returned_started_node_property_c, ",m.", returned_end_node_property_c, ",r")

  result = call_neo4j(query, connection, type = c("row", "graph"), output = c("r","json"), include_stats = FALSE, include_meta = FALSE)

  tmp = result
  if(is.null(result$error_code) && length(result) != 0)
  {

    tmp = as.data.frame(result)

    colnames(tmp)[which(names(tmp) == "value")] = "V1"
    colnames(tmp)[which(names(tmp) == "value.1")] = "V2"
    colnames(tmp)[startsWith(colnames(tmp),"r.")] = str_remove(colnames(tmp)[startsWith(colnames(tmp),"r.")],"r.")

  }
  return(tmp)
}