R/loadDatabaseSchema.R

In compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

loadDatabaseSchema <-
function(con, updateSchema = FALSE, file = ""){

  if(updateSchema){
    response <- readline("You have set 'updateSchema' equal to 'TRUE'. This will update your current schema and delete all data in the compendium database (if any).\nType 'y' if you want to continue, type 'n' if you don't want to update the schema:\n")
    if(response=='y'){
      connect <- con$connect
      dir <- path.package("compendiumdb")
      if(file==""){
        file <- paste(dir,"/extdata/compendiumSchema.sql",sep="")
      }
	
      File <- readLines(file)
      dbFile <- gsub('^--.*',"",File)
      dbFile <- strsplit(paste(dbFile,collapse=""),";")
      dbFile <- unlist(dbFile)
		
      rs <- dbSendQuery(connect,paste("use",con$dbname))
      print("Loading database ...")
		
      for(i in 1:length(dbFile))
        {
          percent <- round((i*100)/length(dbFile))
          print(paste("....",percent,"%"))
          rs <- dbSendQuery(connect,dbFile[i])
        }
	
      ## Load organism table to the compendium database. This table has been constructed using information 
      ## from NCBI Taxonomy and from the field organism in GEO according to the package GEOmetadb
      orgFile <- paste(dir,"/extdata/compendiumOrganismTable.txt",sep="")
      query <- paste("LOAD DATA LOCAL INFILE '",orgFile,"' INTO TABLE organism FIELDS TERMINATED BY '@' LINES TERMINATED BY '\n' (ncbiorgid,officialname,shortname)",sep="")
      rs <- dbSendQuery(connect, query)	
	
      print("... Done!")
    }
  }else{cat("Set updateSchema equal to 'TRUE' to (re)load the schema and delete all data in the compendium database \n")}
}