In ropensci/codemetar: Generate 'CodeMeta' Metadata for R Packages

library("jsonld")
library("jsonlite")
library("redland")
library("tidyverse")
library("codemetar")

Practice examples

We'll start by generating a codemeta json-ld file, and converting this to RDF using the jsonld library. The official jsonld serialization uses nquads format for RDF, (it is not clear if any others are supported at this time)

write_codemeta("codemetar")
jsonld::jsonld_to_rdf("codemeta.json") %>% 
  writeLines("codemeta.nquads")

Now we can use the redland library to parse and query the resulting RDF. Note that the we must tell rdflib what parser and mime type to use, matching the names and q 1.0 recognized mimeTypes as listed here: http://librdf.org/raptor/api/raptor-formats-types-by-parser.html.

world <- new("World")
storage <- new("Storage", world, "hashes", name="", options="hash-type='memory'")
model <- new("Model", world=world, storage, options="")
parser <- new("Parser", world, name="nquads", mimeType="text/x-nquads")
parseFileIntoModel(parser, world, "codemeta.nquads", model)

We now have a model object loaded into memory. We can serialize this into different formats, e.g. rdf+xml:

serializer <- new("Serializer", world, name="rdfxml", mimeType="application/rdf+xml")
status <- serializeToFile(serializer, world, model, "codemeta.xml")

against which we can make SPARQL queries:

queryString <- '
PREFIX schema: <http://schema.org>
SELECT ?name
WHERE { 
  ?a schema:name ?name .
}'
query <- new("Query", world, queryString, base_uri=NULL, query_language="sparql", query_uri=NULL)
queryResult <- executeQuery(query, model)
result <- getNextResult(queryResult)

result

xmlrdf <- 
'<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:dc="http://purl.org/dc/elements/1.1/">
  <rdf:Description rdf:about="http://www.dajobe.org/">
    <dc:title>Dave Becketts Home Page</dc:title>
    <rdf:type>Webpage</rdf:type>
    <dc:creator>Dave Beckett</dc:creator>
    <dc:address>
      <dc:state>California</dc:state>
    </dc:address>
    <dc:description>The generic home page of Dave Beckett.</dc:description>
  </rdf:Description> 
</rdf:RDF>
'
writeLines(xmlrdf, "ex.rdf")

#f <- system.file("extdata", "dc.rdf", package="redland")
#cat(readLines(f), sep="\n")
f <- "ex.rdf"
parseFileIntoModel(parser, world, f, model)

queryString <- '
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT *
WHERE { 
  ?a dc:creator ?creator ;
     dc:title ?title ;
     dc:description ?description .
  FILTER (?title = "Dave Beckett\'s Home Page") .

}'
query <- new("Query", world, queryString, base_uri=NULL, query_language="sparql", query_uri=NULL)
queryResult <- executeQuery(query, model)
result <- getNextResult(queryResult)

result

rOpenSci corpus

#nquads <- jsonld_to_rdf("ropensci.json") 
#xml <- jsonld_to_rdf("ropensci.json", options = list(format="application/rdf+xml")) 
#writeLines(nquads, "ropensci.nquads")

world <- new("World")
storage <- new("Storage", world, "hashes", name="", options="hash-type='memory'")
model <- new("Model", world, storage, options="")
# Create the default "rdfxml" parser
parser <- new("Parser", world)
parseFileIntoModel(parser, world, "ropensci.rdf", model)

queryString <- '
PREFIX schema: <http://schema.org>
SELECT ?name
WHERE { 
  ?a schema:name ?name .
}'
query <- new("Query", world, queryString, base_uri=NULL, query_language="sparql", query_uri=NULL)
queryResult <- executeQuery(query, model)
result <- getNextResult(queryResult)

result