create_exfor_mongodb.R

#  The MIT License
#  
#  Copyright (c) 2019 Georg Schnabel 
#  
#  Permission is hereby granted, free of charge, 
#  to any person obtaining a copy of this software and 
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#  copies of the Software, and to permit persons to whom 
#  the Software is furnished to do so, 
#  subject to the following conditions:
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#  The above copyright notice and this permission notice 
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#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 
#  OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
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# load necessary packages and script modules

library(mongolite)
library(data.table)
library(exforParser)

exforFiles <- list.files("<PATH TO DIRECTORY WITH EXFOR ENTRIES>",
                         pattern="entry.*txt", full.names=TRUE)

m <- mongo("entries",db="exfor",url="mongodb://localhost")

errorCounter <- 0
errorFiles <- character(0)

# loop over entries
for (idx in seq_along(exforFiles)) {

    cat("read file ", idx, " of ", length(exforFiles), "\n")
    curFile <- exforFiles[idx]
    curText <- try(readChar(curFile, file.info(curFile)$size), silent=TRUE) 
    if ("try-error" %in% class(curText)) 
    {
        cat("Problems reading ", curFile, "\n")
        errorCounter <- errorCounter + 1
        errorFiles <- c(errorFiles, curFile)
        next
    }
    curEntry <- parseEntry(curText)
    firstSub <- NULL

    # loop over subentries
    for (idx2 in seq_along(curEntry$SUBENT)) {
        curSub <- curEntry$SUBENT[[idx2]]
        if (idx2==1) 
        {
            firstSub <- curSub
        }
        else
        {
            curSub <- transformSubent(firstSub,curSub)
        }
        jsonObj <- convToJSON(curSub)
        m$insert(jsonObj)
    }
}