def load_single(orcid_id, person_uri, person_id, person_class, data_path, endpoint, username, password,
namespace=None, skip_person=False, confirmed_orcid_id=False):
with Store(data_path) as store:
#Crosswalk
(graph, profile, person_uri) = default_execute(orcid_id, namespace=namespace, person_uri=person_uri,
person_id=person_id, skip_person=skip_person,
person_class=person_class, confirmed_orcid_id=confirmed_orcid_id)
graph_filepath = os.path.join(data_path, "%s.ttl" % orcid_id.lower())
previous_graph = Graph(namespace_manager=ns_manager)
#Load last graph
if os.path.exists(graph_filepath):
log.debug("Loading previous graph %s", graph_filepath)
previous_graph.parse(graph_filepath, format="turtle")
#Diff against last graph
(both_graph, delete_graph, add_graph) = graph_diff(previous_graph, graph)
#SPARQL Update
log.info("Adding %s, deleting %s triples for %s", len(add_graph), len(delete_graph), orcid_id)
sparql_delete(delete_graph, endpoint, username, password)
sparql_insert(add_graph, endpoint, username, password)
#Save new last graph
log.debug("Saving new graph %s", graph_filepath)
with codecs.open(graph_filepath, "w") as out:
graph.serialize(format="turtle", destination=out)
#Touch
store.touch(orcid_id)
return graph, add_graph, delete_graph
def load_single(orcid_id, person_uri, person_id, person_class, data_path, endpoint, username, password,
namespace=None, skip_person=False, confirmed_orcid_id=False):
with Store(data_path) as store:
#Crosswalk
(graph, profile, person_uri) = default_execute(orcid_id, namespace=namespace, person_uri=person_uri,
person_id=person_id, skip_person=skip_person,
person_class=person_class, confirmed_orcid_id=confirmed_orcid_id)
graph_filepath = os.path.join(data_path, "%s.ttl" % orcid_id.lower())
previous_graph = Graph(namespace_manager=ns_manager)
#Load last graph
if os.path.exists(graph_filepath):
log.debug("Loading previous graph %s", graph_filepath)
previous_graph.parse(graph_filepath, format="turtle")
#Diff against last graph
(both_graph, delete_graph, add_graph) = graph_diff(previous_graph, graph)
#SPARQL Update
log.info("Adding %s, deleting %s triples for %s", len(add_graph), len(delete_graph), orcid_id)
sparql_delete(delete_graph, endpoint, username, password)
sparql_insert(add_graph, endpoint, username, password)
#Save new last graph
log.debug("Saving new graph %s", graph_filepath)
with codecs.open(graph_filepath, "w") as out:
graph.serialize(format="turtle", destination=out)
#Touch
store.touch(orcid_id)
return graph, add_graph, delete_graph
def crosswalk():
session["format"] = request.form.get("format")
endpoint = request.form.get("endpoint")
session["endpoint"] = endpoint
session["username"] = request.form.get("username")
session["password"] = request.form.get("password")
person_class = request.form.get("person_class")
session["person_class"] = person_class
session["skip_person"] = True if "skip_person" in request.form else False
session["confirmed"] = True if "confirmed" in request.form else False
session["output"] = request.form.get("output")
session["output_html"] = True if "output_html" in request.form else False
session[
"output_profile"] = True if "output_profile" in request.form else False
#Excute with default strategies
(g, p, per_uri) = default_execute(
request.form["orcid_id"],
namespace=request.form["namespace"],
person_uri=request.form["person_uri"],
person_id=request.form["person_id"],
skip_person=True if "skip_person" in request.form else False,
person_class=person_class if person_class != "Person" else None,
confirmed_orcid_id=True if "confirmed" in request.form else False)
if "output" in request.form and request.form["output"] == "vivo":
utility.sparql_insert(g, endpoint, request.form["username"],
request.form["password"])
msg = "Loaded to VIVO"
if endpoint.endswith("api/sparqlUpdate"):
vivo_profile_url = "%s/individual?%s" % (
endpoint[:-17], urllib.urlencode({"uri": per_uri}))
msg += ". Try <a href=\"%s\">%s</a>." % (vivo_profile_url,
vivo_profile_url)
flash(Markup(msg))
return crosswalk_form()
else:
#Serialize
rdf = g.serialize(format=request.form['format'], encoding="utf-8")
if "output_html" in request.form or "output_profile" in request.form:
return crosswalk_form(
rdf=rdf if "output_html" in request.form else None,
orcid_profile=p if "output_profile" in request.form else None)
else:
return Response(rdf,
content_type=content_types[request.form['format']])
def crosswalk():
session["format"] = request.form.get("format")
endpoint = request.form.get("endpoint")
session["endpoint"] = endpoint
session["username"] = request.form.get("username")
session["password"] = request.form.get("password")
person_class = request.form.get("person_class")
session["person_class"] = person_class
session["skip_person"] = True if "skip_person" in request.form else False
session["confirmed"] = True if "confirmed" in request.form else False
session["output"] = request.form.get("output")
session["output_html"] = True if "output_html" in request.form else False
session["output_profile"] = True if "output_profile" in request.form else False
#Excute with default strategies
(g, p, per_uri) = default_execute(request.form["orcid_id"],
namespace=request.form["namespace"],
person_uri=request.form["person_uri"],
person_id=request.form["person_id"],
skip_person=True if "skip_person" in request.form else False,
person_class=person_class if person_class != "Person" else None,
confirmed_orcid_id=True if "confirmed" in request.form else False)
if "output" in request.form and request.form["output"] == "vivo":
utility.sparql_insert(g, endpoint, request.form["username"], request.form["password"])
msg = "Loaded to VIVO"
if endpoint.endswith("api/sparqlUpdate"):
vivo_profile_url = "%s/individual?%s" % (endpoint[:-17], urllib.urlencode({"uri": per_uri}))
msg += ". Try <a href=\"%s\">%s</a>." % (vivo_profile_url, vivo_profile_url)
flash(Markup(msg))
return crosswalk_form()
else:
#Serialize
rdf = g.serialize(format=request.form['format'], encoding="utf-8")
if "output_html" in request.form or "output_profile" in request.form:
return crosswalk_form(rdf=rdf if "output_html" in request.form else None,
orcid_profile=p if "output_profile" in request.form else None)
else:
return Response(rdf, content_type=content_types[request.form['format']])
parser.add_argument("--person-class", dest="person_class",
choices=["FacultyMember", "FacultyMemberEmeritus", "Librarian", "LibrarianEmeritus",
"NonAcademic", "NonFacultyAcademic", "ProfessorEmeritus", "Student"],
help="Class (in VIVO Core ontology) for a person. Default is a FOAF Person.")
parser.add_argument("--skip-person", dest="skip_person", action="store_true",
help="Skip adding triples declaring the person and the person's name.")
parser.add_argument("--confirmed", action="store_true", help="Mark the orcid id as confirmed.")
# Parse
args = parser.parse_args()
# Excute with default strategies
(g, p, per_uri) = default_execute(args.orcid_id, namespace=args.namespace, person_uri=args.person_uri,
person_id=args.person_id, skip_person=args.skip_person,
person_class=args.person_class, confirmed_orcid_id=args.confirmed)
# Write to file
if args.file:
with codecs.open(args.file, "w") as out:
g.serialize(format=args.format, destination=out)
# Post to SPARQL Update
if args.endpoint:
if not args.username or not args.password:
raise Exception("If an endpoint is specified, --username and --password must be provided.")
sparql_insert(g, args.endpoint, args.username, args.password)
# If not writing to file to posting to SPARQL Update then serialize to stdout
if not args.file and not args.endpoint:
print g.serialize(format=args.format)