metadata-files

A Clojure library designed to generate metadata files for the CyVerse Data Commons repository.

Usage

This library is intended to support the generation of multiple file formats. New formats can be added in the future as necessary.

DataCite 3.1

The suggested way to build a DataCite file is to use org.cyverse.metadata-files.datacite/build-datacite. This function accepts a list of AVUs in the format returned by the metadata service and returns an instance of clojure.data.xml.Element representing the metadata file, which can be serialized using any of the serialization methods in org.clojure/data.xml.

The following metadata attributes are currently supported. Note that multiple CyVerse attributes might be associated with a single DataCite element. For example the CyVerse attributes, Identifier and identifierType both map to DataCite's identifier element. The Identifier attribute maps to the element's content whereas the identifierType attribute maps to the element's identifierType attribute.

CyVerse Attribute	DataCite Element
Identifier	identifier
identifierType	identifier
datacite.creator	creators
creatorAffiliation	creators
creatorNameIdentifier	creators
datacite.title	titles
datacite.publisher	publishers
datacite.publicationyear	publicationYear
datacite.resourcetype	resourceType
Subject	subjects
contributorName	contributors
contributorType	contributors
AlternateIdentifier	alternateIdentifiers
alternateIdentifierType	alternateIdentifiers
RelatedIdentifier	relatedIdentifiers
relatedIdentifierType	relatedIdentifiers
relationType	relatedIdentifiers
Rights	rightsList
Description	descriptions
descriptionType	descriptions
geoLocationPlace	geoLocations
geoLocationPoint	geoLocations
geoLocationBox	geoLocations

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.

Example:

user=> (defn build-attributes
  #_=>   "Provides a convenient way to generate metadata attributes in the format returned by the metadata service. The
  #_=>    attributes can be defined as a map if there are no duplicate attribute names. Otherwise, a sequence of vectors
  #_=>    must be used."
  #_=>   [attrs]
  #_=>   (mapv (fn [[attr value]] {:attr attr :value value}) attrs))

user=> (def ^:private min-attrs
  #_=>   {"Identifier"               "the-identifier"
  #_=>    "identifierType"           "DOI"
  #_=>    "datacite.creator"         "Nobody Inparticular"
  #_=>    "creatorAffiliation"       "The University of Nowhere"
  #_=>    "datacite.title"           "A Very Important Data Set"
  #_=>    "datacite.publisher"       "CyVerse Data Commons"
  #_=>    "datacite.publicationyear" "2018"
  #_=>    "datacite.resourcetype"    "Data Set"})

user=> (require '[clojure.data.xml :refer :all] '[org.cyverse.metadata-files.datacite :refer [build-datacite]])
nil

user=> (def xml (build-datacite (build-attributes min-attrs)))
#'user/xml

user=> (println (indent-str xml))
;; output omitted for brevity.

DataCite 4.1

The primary interface for creating a DataCite 4.1 file is essentially the same as the interface for creating a DataCite 3.1 file. The function org.cyverse.metadata-files.datacite-4-2/build-datacite returns an instance of clojure.data.xml.Element representing the metadata file. This metadata file generator works with the DOI Request - DataCite 4.1 template in the Discovery Environment, which is a nested metadata template. Because the template is nested, the attributes can have the same names as the DataCite elements. The following attributes are supported.

• title
  • titleType
  • xml:lang
• creator
  • affiliation
  • nameIdentifier
    • nameIdentifierScheme
    • schemeURI
• publisher
• publicationYear
• resourceType
  • resourceTypeGeneral
• contributor
  • contributorType
  • affiliation
  • nameIdentifier
    • nameIdentifierScheme
    • schemeURI
• description
  • descriptionType
  • xml:lang
• subject
  • subjectScheme
  • schemeURI
  • xml:lang
• identifier
• rights
  • rightsURI
• version
• alternateIdentifier
  • alternateIdentifierType
• relatedIdentifier
  • relatedIdentifierType
  • relationType
• geoLocation
  • geoLocationPlace
  • geoLocationPoint
    • pointLongitude
    • pointLatitude
  • geoLocationBox
    • northBoundLatitude
    • southBoundLatitude
    • westBoundLongitude
    • eastBoundLongitude
• fundingreference
  • funderName
    • funderIdentifier
      • funderIdentifierType
• language
• size
• format

As with DataCite 3.1, any attribute that is not in this list is ignored.

Example:

user=> (require '[org.cyverse.metadata-files.datacite-4-2 :refer [build-datacite]]
  #_=>          '[clojure.data.xml :refer :all]
  #_=>          :reload-all)


user=> (def min-attrs
  #_=>   [{:attr  "identifier",
  #_=>     :value "   doi:10.1000/182",
  #_=>     :avus  [{:attr  "identifierType",
  #_=>              :value "DOI"}]}
  #_=>    {:attr  "creator",
  #_=>     :value "the-creator"}
  #_=>    {:attr  "title",
  #_=>     :value "the-title"}
  #_=>    {:attr  "publisher",
  #_=>     :value "CyVerse"}
  #_=>    {:attr  "publicationYear",
  #_=>     :value "2019"}
  #_=>    {:attr  "resourceType",
  #_=>     :value "XML",
  #_=>     :avus  [{:attr  "resourceTypeGeneral",
  #_=>              :value "Dataset"}]}])


user=> (println (indent-str (build-datacite min-attrs)))
;; output omitted for brevity.

License

http://www.cyverse.org/license