R/startGraph.R

In neo2R: Neo4j to R

#' Prepare connection to neo4j database
#'
#' @param url the DB url
#' @param database the name of the database. If NA (default) it will use "data"
#' with versions 3.. of Neo4j and "neo4j" with versions 4..
#' @param username the neo4j user name
#' (default: NA; works only if authentication has been disabled in neo4j by
#' setting NEO4J.AUTH=none)
#' @param password the neo4j user password
#' (default: NA; works only if authentication has been disabled in neo4j by
#' setting NEO4J.AUTH=none)
#' @param importPath path to the import directory
#' (default: NA => no import directory). Import only works with local neo4j
#' instance.
#' @param .opts a named list identifying the curl
#' options for the handle (see [httr::config()] and [httr::httr_options()]
#' for a complete list of available options;
#' for example: `.opts = list(ssl_verifypeer = 0)`). Moreover, this parameter
#' can be used to pass additional headers to the graph requests as
#' "extendedHeaders": it is useful, for example, for OAuth access
#' delegation (see details).
#'
#'
#' @details The "ssl.verifypeer" logical option available in the RCurl package
#' used in former versions of neo2R (<= 2.2.0) is
#' not recognized by [httr::config()].
#' However, for backward compatibility, if it used, it is translated into
#' "ssl_verifypeer" integer option recognized by the httr package with a
#' warning message.
#'
#' Headers in `.opts$extendedHeaders` are added to, or overwrite,
#' the default Neo4j headers.
#' If there is a `.opts$extendedHeaders[["Authorization"]]` value, the
#' default Neo4j "Authorization" header (user credentials) is provided
#' automaticaly as "X-Authorization". This mechanism is used for OAuth access
#' delegation.
#'
#' @return A connection to the graph DB:
#' a list with the url and necessary headers
#'
#' @export
#'
startGraph <- function(
   url, database=NA, username=NA, password=NA, importPath=NA, .opts=list()
){

   if("ssl.verifypeer" %in% names(.opts)){
      .opts$ssl_verifypeer <- as.integer(.opts$ssl.verifypeer)
      .opts$ssl.verifypeer <- NULL
      warning(
         "'ssl.verifypeer' option has been automatically converted into ",
         "'ssl_verifypeer' option recognized by `httr::config()`. ",
         "You should use the 'ssl_verifypeer' integer option ",
         "to avoid this warning."
      )
   }

   ## Process URL and guess protocol ----
   protocol <- grep("^https://", url)
   if(length(protocol)==1){
      protocol="https://"
      url <- sub("^https://", "", url)
   }else{
      protocol <- "http://"
      url <- sub("^http://", "", url)
   }
   url <- paste0(
      protocol,
      sub("[/]db.*$", "", url)
   )
   ## Set general header ----
   neo4jHeaders <- list(
      'Accept' = 'application/json; charset=UTF-8;',
      'Content-Type' = 'application/json',
      'X-Stream' = TRUE,
      'Authorization' = paste(
         "Basic",
         base64enc::base64encode(charToRaw(
            paste(username, password, sep=":")
         ))
      )
   )

   ## Append other headers - swap Authorization headers for OAuth ----
   extendedHeaders <- .opts$extendedHeaders
   .opts$extendedHeaders <- NULL
   if(!is.null(extendedHeaders[["Authorization"]])){
      temp_auth <- neo4jHeaders[["Authorization"]]
      neo4jHeaders[["Authorization"]] <- extendedHeaders[["Authorization"]]
      neo4jHeaders[["X-Authorization"]] <- temp_auth
      extendedHeaders <- extendedHeaders[setdiff(
         names(extendedHeaders), "Authorization"
      )]
   }
   overw <- intersect(names(extendedHeaders), names(neo4jHeaders))
   if(length(overw) > 0){
      warning(
         "The following default headers are overwritten by user values: ",
         paste(overw, sep=", ")
      )
      neo4jHeaders <- neo4jHeaders[setdiff(
         names(neo4jHeaders), names(extendedHeaders)
      )]
   }
   neo4jHeaders <- c(neo4jHeaders, extendedHeaders)

   toRet <- list(
      url=url,
      headers=neo4jHeaders,
      importPath=importPath,
      .opts=.opts
   )
   ## Find neo4j version and database name ----
   conStatus <- graphRequest(toRet, "", "GET", "")
   if(is.na(conStatus$header["status"]) || conStatus$header["status"]!="200"){
      print(conStatus$header)
      stop("Cannot connect to the Neo4j database")
   }
   if("neo4j_version" %in% names(conStatus$result)){
      toRet$version=unlist(strsplit(
         conStatus$result$neo4j_version, split="[.]"
      ))
   }else{
      if(is.na(database)){
         database <- "data"
      }
      conStatus <- graphRequest(toRet, sprintf("/db/%s/", database), "GET", "")
      if(
         is.na(conStatus$header["status"]) || conStatus$header["status"]!="200"
      ){
         print(conStatus$header)
         stop("Cannot connect to the Neo4j database")
      }
      if("neo4j_version" %in% names(conStatus$result)){
         toRet$version=unlist(strsplit(
            conStatus$result$neo4j_version, split="[.]"
         ))
      }else{
         stop("Unknown version of neo4j")
      }
   }
   if(!toRet$version[1] %in% c("3", "4", "5")){
      print(toRet["version"])
      stop("Only version 3, 4 and 5 of Neo4j are supported")
   }
   ## Define cypher transaction endpoint ----
   if(toRet$version[1]=="3"){
      toRet$database=ifelse(is.na(database), "data", database)
      toRet$cypher_endpoint <- sprintf(
         "/db/%s/transaction/commit", toRet$database
      )
   }
   if(toRet$version[1]=="4"){
      toRet$database <- ifelse(is.na(database), "neo4j", database)
      toRet$cypher_endpoint <- sprintf("/db/%s/tx/commit", toRet$database)
   }
   if(toRet$version[1]=="5"){
      toRet$database <- ifelse(is.na(database), "neo4j", database)
      toRet$cypher_endpoint <- sprintf("/db/%s/tx/commit", toRet$database)
   }
   ## Final connection check ----
   cypher(toRet, "match (n) return n limit 1", result="graph")
   return(toRet)
}