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
- 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
- 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/.
GLSS-F0G5RP:orcid2vivo justinlittman$ curl --data "orcid_id=0000-0003-1527-0030&format=turtle" http://localhost:5000/
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 "O2V_USERNAME=vivo_root@mydomain.edu" -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.