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orcid2vivo

About this fork

This fork includes some small modifications to the orcid2vivo script created by GWU's Justin Littman. Namely, URI generation is performed by generating a random number and calling the VIVO Query API to ensure it does not already exist. Additionally, the script has been changed to only create one new SKOS concept, journal, or publisher rather than numerous identical objects. Original readme below...

#________ Proof of concept code for retrieving data from the ORCID API and crosswalking to VIVO-ISF.

Try it at http://gw-orcid2vivo.wrlc.org/orcid2vivo

Commandline

  • Supports outputting to:
    • screen / stdout
    • file
    • load to VIVO instance (via SPARQL Update)
  • Supports multiple RDF serializations.
  • Allows specifying:
    • VIVO namespace
    • An id for the person.
    • Class for the person.

(ENV)GLSS-F0G5RP:orcid2vivo justinlittman$ python orcid2vivo.py -h
usage: orcid2vivo.py [-h] [--format {xml,n3,turtle,nt,pretty-xml,trix}]
                     [--file FILE] [--endpoint ENDPOINT] [--username USERNAME]
                     [--password PASSWORD] [--person-id PERSON_ID]
                     [--namespace NAMESPACE]
                     [--person-class {FacultyMember,FacultyMemberEmeritus,Librarian,LibrarianEmeritus,NonAcademic,NonFacultyAcademic,ProfessorEmeritus,Student}]
                     [--skip-person]
                     orcid_id

positional arguments:
  orcid_id

optional arguments:
  -h, --help            show this help message and exit
  --format {xml,n3,turtle,nt,pretty-xml,trix}
                        The RDF format for serializing. Default is turtle.
  --file FILE           Filepath to which to serialize.
  --endpoint ENDPOINT   Endpoint for SPARQL Update of VIVO instance,e.g.,
                        http://localhost/vivo/api/sparqlUpdate. Also provide
                        --username and --password.
  --username USERNAME   Username for VIVO root.
  --password PASSWORD   Password for VIVO root.
  --person-id PERSON_ID
                        Id for the person to use when constructing the
                        person's URI. If not provided, the orcid id will be
                        used.
  --namespace NAMESPACE
                        VIVO namespace. Default is
                        http://vivo.mydomain.edu/individual/.
  --person-class {FacultyMember,FacultyMemberEmeritus,Librarian,LibrarianEmeritus,NonAcademic,NonFacultyAcademic,ProfessorEmeritus,Student}
                        Class (in VIVO Core ontology) for a person. Default is
                        a FOAF Person.
  --skip-person         Skip adding triples declaring the person and the
                        person's name

For example:

(ENV)GLSS-F0G5RP:orcid2vivo justinlittman$ python orcid2vivo.py 0000-0003-1527-0030

Web application

  • Supports outputting to:
    • web page
    • download
    • load to VIVO instance (via SPARQL Update)
  • Also supports outputting of ORCID profile to web page.
  • Can be invoked from web form and http client.
  • Supports multiple RDF serializations.
  • Allows specifying:
    • VIVO namespace
    • An id for the person.
    • Class for the person.
  • Allows providing various default values when starting the application.

(ENV)GLSS-F0G5RP:orcid2vivo justinlittman$ python orcid2vivo_service.py -h
usage: orcid2vivo_service.py [-h]
                             [--format {xml,n3,turtle,nt,pretty-xml,trix}]
                             [--endpoint ENDPOINT] [--username USERNAME]
                             [--password PASSWORD] [--namespace NAMESPACE]
                             [--person-class {FacultyMember,FacultyMemberEmeritus,Librarian,LibrarianEmeritus,NonAcademic,NonFacultyAcademic,ProfessorEmeritus,Student}]
                             [--skip-person] [--debug] [--port PORT]

optional arguments:
  -h, --help            show this help message and exit
  --format {xml,n3,turtle,nt,pretty-xml,trix}
                        The RDF format for serializing. Default is turtle.
  --endpoint ENDPOINT   Endpoint for SPARQL Update of VIVO instance,e.g.,
                        http://localhost/vivo/api/sparqlUpdate.
  --username USERNAME   Username for VIVO root.
  --password PASSWORD   Password for VIVO root.
  --namespace NAMESPACE
                        VIVO namespace. Default is
                        http://vivo.mydomain.edu/individual/.
  --person-class {FacultyMember,FacultyMemberEmeritus,Librarian,LibrarianEmeritus,NonAcademic,NonFacultyAcademic,ProfessorEmeritus,Student}
                        Class (in VIVO Core ontology) for a person. Default is
                        a FOAF Person.
  --skip-person         Skip adding triples declaring the person and the
                        person's name.
  --debug
  --port PORT           The port the service should run on. Default is 5000.

For example, to start:

(ENV)GLSS-F0G5RP:orcid2vivo justinlittman$ python orcid2vivo_service.py

The web form will now be available at http://localhost:5000/.

Invoke using curl

GLSS-F0G5RP:orcid2vivo justinlittman$ curl --data "orcid_id=0000-0003-1527-0030&format=turtle" http://localhost:5000/

Docker

The web application can be deployed to a Docker container.

GLSS-F0G5RP:orcid2vivo justinlittman$ docker build -t orcid2vivo .
GLSS-F0G5RP:orcid2vivo justinlittman$ docker run -e "O2V_ENDPOINT=http://vivo:8080/vivo/api/sparqlUpdate" -e "[email protected]" -e "O2V_PASSWORD=password" -e "O2V_NAMESPACE=http://vivo.mydomain.edu/" -p "5000:5000" -d orcid2vivo

The web form will now be available at http://localhost:5000/. (Note: If using boot2docker, use result of boot2docker ip instead of localhost.)

##Caveats:

  • All data is not cross walked to VIVO-ISF.
  • Not ready for production use.
  • Password for SPARQL Update is not handled securely.

##Other:

  • Feedback / tickets / pull requests welcome.
  • Consider using with vivo-docker to put together an environment for experimenting with crosswalking ORCID to VIVO.