oai-ore

A Clojure library used to generate Open Archives Initiative Object Reuse and Exchange files for the CyVerse Data Commons repository. The primary purpose of this library is to make it easier to generate OAI-ORE files from a set of URIs and attribute metdata stored in the CyVerse Data Store.

Usage

All examples assume that these commands have been executed in the REPL:

(defn- file-info-from-id [id] {:id  id :uri (str "http://foo.org/" id)})
(require '[org.cyverse.oai-ore :as ore])
(require '[clojure.data.xml :refer :all])
(def agg-uri "http://foo.org")
(def arch (file-info-from-id "bar"))
(def metadata (file-info-from-id "baz"))
(def archived-files (mapv file-info-from-id ["bar1" "bar2"]))

The suggested way to build an OAI-ORE file is to use the build-ore function. The result of this function is an instance of org.cyverse.oai-ore.Ore, which can then be converted to RDF/XML and serialized. The simplest such file is an empty archive:

(def empty-ore (ore/build-ore agg-uri arch []))

Once you have the org.cyverse.oai-ore.Ore instance, you can convert it to RDF/XML by calling its to-rdf method:

(def rdf (ore/to-rdf empty-ore))

The result of calling this method is an instance of clojure.data.xml.Element, which can then be serialized using any serialization method available in org.clojure/data.xml. For example, you can use the following commands to emit pretty-printed RDF/XML:

(print (indent-str rdf))

An empty OAI-ORE file is good for an example, but not very useful. It's possible to add aggregated entites by including some file information in the third argument to build-ore:

(def populated-ore (ore/build-ore agg-uri arch archived-files))

This library also supports several of the metadata attributes that are used when a data set is published to the CyVerse Data Commons repository. The following attributes are currently supported:

CyVerse Attribute	ORE Element
datacite.title	dc:title
datacite.publisher	dc:publisher
datacite.creator	dc:creator
datacite.resourcetype	dc:type
contributorName	dc:contributor
Subject	dc:subject
Rights	dc:rights
Description	dc:description
Identifier	dcterms:identifier
geoLocationBox	dcterms:Box
geoLocationPlace	dcterms:Location
geoLocationPoint	dcterms:Point

Any attribute that is associated with the data set that is not in this list is ignored. Similarly, any attribute that is in the list but either contains an empty value or is not associated with the data set is ignored:

(def attr-ore (ore/build-ore agg-uri arch archived-files [{:attr "datacite.title" :value "The Title"}
                                                          {:attr "datacite.creator" :value "The Creator"}
                                                          {:attr "ignored.attribute" :value "Who Cares?"}
                                                          {:attr "Subject" :value ""}]
                             metadata))

Serializing the RDF using (print (indent-str (ore/to-rdf attr-ore))) should produce the following output:

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/"
         xmlns:owl="http://www.w3.org/2002/07/owl#"
         xmlns:foaf="http://xmlns.com/foaf/0.1/"
         xmlns:dcterms="http://purl.org/dc/terms/"
         xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:ore="http://www.openarchives.org/ore/terms/"
         xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
         xmlns:cito="http://purl.org/spar/cito/">
  <rdf:Description rdf:about="http://foo.org">
    <rdf:type rdf:resource="http://www.openarchives.org/ore/terms/Aggregation"/>
    <ore:aggregates rdf:resource="http://foo.org/baz"/>
    <ore:aggregates rdf:resource="http://foo.org/bar1"/>
    <ore:aggregates rdf:resource="http://foo.org/bar2"/>
    <dc:title>The Title</dc:title>
    <dc:creator>The Creator</dc:creator>
  </rdf:Description>
  <rdf:Description rdf:about="http://foo.org/bar">
    <dcterms:identifier>bar</dcterms:identifier>
    <rdf:type rdf:resource="http://www.openarchives.org/ore/terms/ResourceMap"/>
    <ore:describes rdf:resource="http://foo.org"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://foo.org/baz">
    <dcterms:identifier>baz</dcterms:identifier>
    <cito:documents rdf:resource="http://foo.org/bar1"/>
    <cito:documents rdf:resource="http://foo.org/bar2"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://foo.org/bar1">
    <dcterms:identifier>bar1</dcterms:identifier>
    <cito:isDocumentedBy rdf:resource="http://foo.org/baz"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://foo.org/bar2">
    <dcterms:identifier>bar2</dcterms:identifier>
    <cito:isDocumentedBy rdf:resource="http://foo.org/baz"/>
  </rdf:Description>
</rdf:RDF>

Note: the namespace declarations have been reformatted for readability.

License

http://www.cyverse.org/license