def get_configurations(cls, item_type: str, config_id: str, url: str):
if not cls.__instance:
cls()
cls.__init_graph()
validated_item = validate_config_id(cls.__source_base_uri, item_type,
config_id)
if validated_item:
item_type = unquote(item_type)
item_type = re.sub(' ', '.', item_type)
url = unquote(url)
url = re.sub(' ', '.', url)
container = Resource(cls.__graph, URIRef(url))
streams = load_streams(cls.__source_base_uri, item_type, config_id)
for stream in streams.keys():
member = Resource(
cls.__graph,
URIRef(
url.replace('configurations', 'stream') +
f'/{stream}'))
container.add(RDFS.member, member)
return container
else:
return False
def output_rdf(data, code, headers=None):
"""Makes a Flask response with a JSON encoded body"""
content_type = request.headers.get('accept')
representation = get_content_type(content_type)
if code == OK:
data = data.to_rdf(representation)
else:
g = Graph()
g.bind('oslc', OSLC)
rsrc = Resource(g, URIRef(request.base_url))
rsrc.add(RDF.type, OSLC.Error)
if isinstance(data, dict):
for attr in data:
rsrc.add(OSLC.term(attr), Literal(data[attr]))
data = g.serialize(format=representation)
resp = make_response(data, code)
resp.headers.extend(headers or {})
return resp
def __get_query_capability(cls, item_type_name: str,
item_type_name_url: str, uri: str) -> Resource:
qc = Resource(cls.__graph, BNode())
qc.add(RDF.type, OSLC.QueryCapability)
qc.add(DCTERMS.title,
Literal(f'Query Capability for ItemType: {item_type_name}'))
qc.add(OSLC.queryBase, URIRef(uri))
qc.add(OSLC.resourceType, URIRef(ARAS.term(item_type_name_url)))
qc.add(OSLC.resourceShape, URIRef(uri + '/resourceShape'))
return qc
def convert_calendar_dates(self, csv_filename):
read_dates = self.__open_file(csv_filename)
for row in read_dates:
service = self.get_service(str.strip(row["service_id"]))
calendar_date = Resource(self.graph, URIRef(self.uri + str.strip(row["service_id"]) + "_cal" + "_" + str.strip(row["date"])))
service.add(self.GTFS.serviceRule, calendar_date)
calendar_date.set(RDF.type, self.GTFS.CalendarDateRule)
calendar_date.add(DCTERMS.date, self.get_date_literal(str.strip(row["date"])))
exception_type = str.strip(row["exception_type"])
if exception_type is "2":
exception_type = "0"
calendar_date.add(self.GTFS.dateAddition, Literal(exception_type, datatype=XSD.boolean))
def convert_frequencies(self, csv_filename):
read_freqs = self.__open_file(csv_filename)
for row in read_freqs:
freq = Resource(self.graph, URIRef(self.uri + str.strip(row["trip_id"]) + str.strip(row["start_time"]) + str.strip(row["end_time"])))
freq.set(RDF.type, self.GTFS.Frequency)
freq.add(self.GTFS.trip, self.get_trip(str.strip(row["trip_id"])))
freq.add(self.GTFS.startTime, Literal(str.strip(row["start_time"]), datatype=XSD.string))
freq.add(self.GTFS.endTime, Literal(str.strip(row["end_time"]), datatype=XSD.string))
freq.add(self.GTFS.headwaySeconds, Literal(str.strip(row["headway_secs"]), datatype=XSD.nonNegativeInteger))
if "exact_times" in row:
exact = False
if str.strip(row["exact_times"]) == "1":
exact = True
freq.add(self.GTFS.exactTimes, Literal(exact, datatype=XSD.boolean))
def get_resource_shape(cls, item_type: str, url: str, url_sp: str):
if not cls.__instance:
cls()
cls.__init_graph()
resource_shape = Resource(cls.__graph, URIRef(url))
resource_shape.add(RDF.type, OSLC.ResourceShape)
rs = cls.__get_resource_shape(item_type, url_sp, cls.__source_base_uri)
if rs:
for subject in rs.subjects(RDF.type, OSLC.Property):
prop = Resource(cls.__graph, subject)
prop.add(RDF.type, OSLC.Property)
for p, o in rs.predicate_objects(subject):
prop.add(p, o)
resource_shape.add(OSLC.property, prop)
return resource_shape
else:
return False
def get_service_provider(cls, url: str):
if not cls.__instance:
cls()
cls.__init_graph()
service_provider = None
service = cls.__get_service(url=url)
if service:
service_provider = Resource(cls.__graph, URIRef(url))
service_provider.add(RDF.type, OSLC.ServiceProvider)
service_provider.add(OSLC.service, service)
return service_provider
else:
return False
def convert_calendar(self, csv_filename):
read_calendar = self.__open_file(csv_filename)
for row in read_calendar:
service = self.get_service(str.strip(row["service_id"]))
calendar = Resource(self.graph, URIRef(self.uri + str.strip(row["service_id"]) + "_cal"))
service.add(self.GTFS.serviceRule, calendar)
calendar.set(RDF.type, self.GTFS.CalendarRule)
calendar.set(self.GTFS.monday, Literal(str.strip(row["monday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.tuesday, Literal(str.strip(row["tuesday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.wednesday, Literal(str.strip(row["wednesday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.thursday, Literal(str.strip(row["thursday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.friday, Literal(str.strip(row["friday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.saturday, Literal(str.strip(row["saturday"]), datatype=XSD.boolean))
calendar.set(self.GTFS.sunday, Literal(str.strip(row["sunday"]), datatype=XSD.boolean))
temporal = Resource(self.graph, URIRef(self.uri + str.strip(row["service_id"]) + "_cal" + "_temporal"))
calendar.set(DCTERMS.temporal, temporal)
temporal.add(self.SCHEMA.startDate, self.get_date_literal(str.strip(row["start_date"])))
temporal.add(self.SCHEMA.endDate, self.get_date_literal(str.strip(row["end_date"])))
def get_components(cls,
item_type: str,
url: str,
paging: bool = False,
page_size: int = 0,
page_no: int = 0):
if not cls.__instance:
cls()
cls.__init_graph()
if not cls.__item_types:
cls.__item_types = cls.__get_item_types()
if re.sub('\\.', ' ', item_type) in cls.__item_types.values():
item_type = unquote(item_type)
item_type = re.sub(' ', '.', item_type)
url = unquote(url)
url = re.sub(' ', '.', url)
container = Resource(cls.__graph, URIRef(url))
container.add(RDF.type, LDP.BasicContainer)
config_ids = load_items(cls.__source_base_uri, item_type,
page_size, page_no)
ri, config_ids = cls.__get_paging(item_type, config_ids, url,
paging, page_size, page_no)
if ri:
container.add(OSLC.responseInfo, ri)
for config_id in config_ids:
member_url = url + f'/{config_id}'
member = Resource(cls.__graph, URIRef(member_url))
member.add(RDF.type, OSLC_CONFIG.Component)
member.add(DCTERMS.title,
Literal(config_ids[config_id]['keyed_name']))
container.add(LDP.contains, member)
return container
else:
return False
def __get_response_info(cls, item_type: str, url: str, url_sp: str,
paging: bool, page_size: int,
page_no: int) -> Resource:
items = load_items(cls.__source_base_uri, item_type, page_size,
page_no)
resource = Resource(cls.__graph, URIRef(url))
ri, items = cls.__get_paging(item_type, items, url, paging, page_size,
page_no)
if ri:
resource.add(OSLC.responseInfo, ri)
for item in items:
item_url = url + '/' + re.sub(' ', '.', item)
member = Resource(cls.__graph, URIRef(item_url))
resource.add(RDFS.member, member)
return resource
def convert_transfers(self, csv_filename):
read_transfers = self.__open_file(csv_filename)
for row in read_transfers:
from_stop = str.strip(row["from_stop_id"])
to_stop = str.strip(row["to_stop_id"])
transfers = Resource(self.graph, URIRef(self.uri + "_" + from_stop + "_" + to_stop))
transfers.set(RDF.type, self.GTFS.TransferRule)
transfers.add(self.GTFS.originStop, self.get_stop(from_stop))
transfers.add(self.GTFS.destinationStop, self.get_stop(to_stop))
transfers.add(self.GTFS.transferType, self.get_transfer_type(str.strip(row["transfer_type"])))
if "min_transfer_time" in row and str.strip(row["min_transfer_time"]):
transfers.add(self.GTFS.minimumTransferTime, Literal(str.strip(row["min_transfer_time"]), datatype=XSD.nonNegativeInteger))
def to_rdf(self, graph):
super(Preview, self).to_rdf(graph)
p = Resource(graph, BNode())
p.add(RDF.type, OSLC.Preview)
if self.document:
p.add(OSLC.document, URIRef(self.document))
if self.hint_height:
p.add(OSLC.hintHeight, Literal(self.hint_height, datatype=XSD.string))
if self.hint_width:
p.add(OSLC.hintWidth, Literal(self.hint_width, datatype=XSD.string))
if self.initial_height:
p.add(OSLC.initialHeight, Literal(self.initial_height, datatype=XSD.string))
return p
def __get_paging(cls, item_type: str, items: dict, url: str, paging: bool,
page_size: int, page_no: int) -> tuple:
ri = None
paging = paging if paging else page_size > 0
if paging:
page_size = page_size if page_size else 50
page_no = page_no if page_no else 1
params = {'oslc.paging': 'true'}
if page_size:
params['oslc.pageSize'] = page_size
if page_no:
params['oslc.pageNo'] = page_no
ri_url = cls.__get_url(url, params)
ri = Resource(cls.__graph, URIRef(ri_url))
ri.add(RDF.type, OSLC.ResponseInfo)
ri.add(DCTERMS.title, Literal(f'Query Results for {item_type}'))
params['oslc.pageNo'] = page_no + 1
ri_url = cls.__get_url(url, params)
ri.add(OSLC.nextPage, URIRef(ri_url))
return ri, items
def get_stream(cls, item_type: str, config_id: str, stream_id: str,
url: str):
if not cls.__instance:
cls()
cls.__init_graph()
validated_item = validate_config_id(cls.__source_base_uri, item_type,
config_id)
if validated_item:
item_type = unquote(item_type)
item_type = re.sub(' ', '.', item_type)
url = unquote(url)
url = re.sub(' ', '.', url)
streams = load_streams(cls.__source_base_uri, item_type, config_id)
if stream_id in streams.keys():
stream = streams[stream_id]
configuration = Resource(cls.__graph, URIRef(url))
configuration.add(RDF.type, OSLC_CONFIG.Stream)
configuration.add(DCTERMS.identifier, Literal(stream['id']))
configuration.add(DCTERMS.title, Literal(stream['keyed_name']))
return configuration
else:
return False
else:
return False
def get_component(cls, item_type: str, config_id: str, url: str):
if not cls.__instance:
cls()
cls.__init_graph()
validated_item = validate_config_id(cls.__source_base_uri, item_type,
config_id)
if validated_item:
item_type = unquote(item_type)
item_type = re.sub(' ', '.', item_type)
url = unquote(url)
url = re.sub(' ', '.', url)
component = Resource(cls.__graph, URIRef(url))
component.add(RDF.type, OSLC_CONFIG.Component)
keyed_name = None
for item in validated_item['value']:
keyed_name = item['keyed_name']
if keyed_name:
component.add(DCTERMS.title, Literal(keyed_name))
component.add(OSLC_CONFIG.configurations,
URIRef(url + '/configurations'))
return component
else:
return False
def to_rdf(self):
g = Graph()
p = Resource(g, self.uri)
p.add(RDF.type, FOAF.Person)
p.set(RDFS.label, Literal(self._label()))
p.set(CONVERIS.converisId, Literal(self.cid))
if hasattr(self, 'cfresint'):
p.set(VIVO.researchOverview, Literal(self.cfresint))
if hasattr(self, 'orcid'):
p.set(VIVO.orcidId, self.orcid_uri)
# Confirm the orcid
g.add((self.orcid_uri, RDF.type, OWL.Thing))
# Todo - review if we want to confirm all orcids
g.add((self.orcid_uri, VIVO.confirmedOrcidId, self.uri))
# Vcard individual
vci_uri = URIRef(self.vcard_uri)
p.set(OBO['ARG_2000028'], vci_uri)
g.add((vci_uri, RDF.type, VCARD.Individual))
# Vcard Name
g += self._vcard_name()
g.add((vci_uri, VCARD.hasName, URIRef(self.vcard_name_uri)))
# Vcard title
vtg = self._vcard_title()
if vtg is not None:
g += vtg
g.add((vci_uri, VCARD.hasTitle, URIRef(self.vcard_title_uri)))
# Vcard email
vte = self._vcard_email()
if vte is not None:
g += vte
g.add((vci_uri, VCARD.hasEmail, URIRef(self.vcard_email_uri)))
# positions
g += self.get_positions()
return g
def convert_fare_rules(self, csv_filename):
read_fares = self.__open_file(csv_filename)
for row in read_fares:
fare = self.get_fare(str.strip(row["fare_id"]))
fare_rule = Resource(self.graph, URIRef(self.uri + str.strip(row["fare_id"]) + "_rule_" + str(self.next_fare_rule_num)))
self.next_fare_rule_num += 1
fare_rule.set(RDF.type, self.GTFS.FareRule)
fare_rule.set(self.GTFS.fareClass, fare_rule)
if "route_id" in row and str.strip(row["route_id"]) != "":
fare_rule.add(self.GTFS.route, self.get_route(str.strip(row["route_id"])))
if "origin_id" in row and str.strip(row["origin_id"]) != "":
fare_rule.add(self.GTFS.originZone, self.get_zone(str.strip(row["origin_id"])))
if "destination_id" in row and str.strip(row["destination_id"]) != "":
fare_rule.add(self.GTFS.destinationZone, self.get_zone(str.strip(row["destination_id"])))
if "contains_id" in row and str.strip(row["contains_id"]) != "":
fare_rule.add(self.GTFS.zone, self.get_zone(str.strip(row["contains_id"])))
def authorships(self):
g = Graph()
aus = self.authors()
for au in aus:
aship_uri = self.aship_uri(au['rank'])
r = Resource(g, aship_uri)
r.set(RDFS.label, Literal(au["display_name"]))
r.set(RDF.type, VIVO.Authorship)
r.set(VIVO.rank, Literal(au['rank']))
data_props = [
('rank', VIVO.rank),
('full_name', WOS.fullName),
('display_name', WOS.displayName),
('wos_standard', WOS.standardName),
('first', WOS.firstName),
('last', WOS.lastName),
('email', WOS.email),
('dais_ng', WOS.daisNg),
('reprint', WOS.reprint),
]
for key, prop in data_props:
value = au.get(key)
if value is not None:
r.set(prop, Literal(value))
# relations
r.add(VIVO.relates, self.uri)
# relate to addresses too
# address nums are a space separated list of numbers
addr_nums = au["address"]
if addr_nums is None:
continue
else:
for anum in addr_nums.split():
addr_uris = self.addr_uris_from_number(anum)
for auri in addr_uris:
r.add(VIVO.relates, auri)
return g
def addressships(self):
g = Graph()
addresses = self.addresses()
for addr in addresses:
addr_uri = self.addr_uri(addr["full_address"], addr["number"])
org = addr["organization"]
r = Resource(g, addr_uri)
r.set(RDF.type, WOS.Address)
r.set(RDFS.label, Literal(addr['full_address']))
r.set(WOS.organizationName, Literal(org))
r.set(WOS.sequenceNumber, Literal(addr['number']))
# relation to author set by authorship
# relate to pub
r.set(VIVO.relates, self.uri)
# sub orgs
for idx, suborg in enumerate(addr["sub_organizations"]):
label = "{}, {}".format(suborg, org)
so_uri = self.sub_org_uri(label)
r.add(VIVO.relates, so_uri)
# relate unified orgs
for uorg in addr["unified_orgs"]:
uo_uri = waan_uri(uorg)
r.add(VIVO.relates, uo_uri)
return g
def to(self):
"""
Core publication metadata mapped to VIVO RDF.
:return: Graph
"""
g = Graph()
r = Resource(g, self.uri)
r.set(RDFS.label, Literal(self.title()))
for vtype in self.rec_type():
r.add(RDF.type, vtype)
r.set(WOS.wosId, Literal(self.ut))
meta = self.meta()
# data properties
data_props = [
#('author_list', WOS.authorList),
('abstract', BIBO.abstract),
('funding_acknowledgement', WOS.fundingText),
('volume', BIBO.volume),
('issue', BIBO.issue),
('start', BIBO.pageStart),
('end', BIBO.pageEnd),
('page_count', BIBO.numPages),
('doi', BIBO.doi),
#('cite_key', WOS.citeKey),
('reference_count', WOS.referenceCount),
('citation_count', WOS.citationCount)
]
for key, prop in data_props:
value = meta.get(key)
if value is not None:
g.add((self.uri, prop, Literal(value)))
g += self.add_pub_date()
return g
def to_rdf(self, graph):
if not self.about:
raise Exception("The title is missing")
oac = Resource(graph, URIRef(self.about))
oac.add(RDF.type, URIRef(OSLC.oauthConfiguration))
if self.authorization_uri:
oac.add(OSLC.authorizationURI, URIRef(self.authorization_uri))
if self.oauth_access_token_uri:
oac.add(OSLC.oauthAccessTokenURI, URIRef(self.oauth_access_token_uri))
if self.oauth_request_token_uri:
oac.add(OSLC.oauthRequestTokenURI, URIRef(self.oauth_request_token_uri))
return oac
def to_rdf(self, graph):
super(PrefixDefinition, self).to_rdf(graph)
pd = Resource(graph, BNode())
pd.add(RDF.type, OSLC.PrefixDefinition)
if self.prefix:
pd.add(OSLC.prefix, Literal(self.prefix))
if self.prefix_base:
pd.add(OSLC.prefixBase, URIRef(self.prefix_base.uri))
return pd
def to_rdf(self, graph):
super(ResponseInfo, self).to_rdf(graph)
uri = self.about
ri = Resource(graph, URIRef(uri))
ri.add(RDF.type, OSLC.ResponseInfo)
if self.title:
ri.add(DCTERMS.title, Literal(self.title, datatype=XSD.Literal))
if self.members:
for item in self.members:
item_url = uri + '/' + item.identifier
member = Resource(graph, URIRef(item_url))
ri.add(RDFS.member, member)
if self.total_count and self.total_count > 0:
ri.add(OSLC.totalCount, Literal(self.total_count))
return ri
def add_pub_date(self):
"""
Publication dates in VIVO's expected format.
"""
g = Graph()
value = self.pub_date()
if value is None:
return g
date_uri = self.make_date_uri(self.ut, value)
date = Resource(g, date_uri)
date.set(RDF.type, VIVO.DateTimeValue)
date.set(VIVO.dateTimePrecision, VIVO.yearMonthDayPrecision)
date.add(VIVO.dateTime,
Literal("%sT00:00:00" % (value), datatype=XSD.dateTime))
date.add(RDFS.label, Literal(value))
date.set(RDF.type, VIVO.DateTimeValue)
date.set(VIVO.dateTimePrecision, VIVO.yearMonthDayPrecision)
date.add(VIVO.dateTime,
Literal("%sT00:00:00" % (value), datatype=XSD.dateTime))
date.add(RDFS.label, Literal(value))
g.add((self.uri, VIVO.dateTimeValue, date_uri))
return g
def __get_service(cls, url: str) -> Resource:
service = None
cls.__item_types = cls.__get_item_types()
if cls.__item_types:
service = Resource(cls.__graph, BNode())
service.add(RDF.type, OSLC.Service)
service.add(OSLC.domain, URIRef(ARAS))
qc_url = url + '/{itemType}'
for item_type in cls.__item_types:
item_type_name = cls.__item_types.get(item_type)
item_type_name_url = re.sub(' ', '.', item_type_name)
uri = urlparse(
qc_url.format(**{'itemType': item_type_name_url}))
qc = cls.__get_query_capability(item_type_name,
item_type_name_url,
uri.geturl())
service.add(OSLC.queryCapability, qc)
return service
def to_rdf(self, graph):
super(ServiceProviderCatalog, self).to_rdf(graph)
spc = Resource(graph, URIRef(self.about))
spc.add(RDF.type, OSLC.ServiceProviderCatalog)
if self.title:
spc.add(DCTERMS.title, Literal(self.title))
if self.description:
spc.add(DCTERMS.description, Literal(self.description))
if self.publisher:
spc.add(DCTERMS.publisher, URIRef(self.publisher.about))
if self.domain:
for item in self.domain:
spc.add(OSLC.domain, URIRef(item))
if self.service_provider:
for sp in self.service_provider:
r = sp.to_rdf(graph)
spc.add(OSLC.serviceProvider, r)
if self.service_provider_catalog:
for item in self.service_provider_catalog:
spc.add(OSLC.serviceProviderCatalog, URIRef(item.about))
if self.oauth_configuration:
spc.add(OSLC.oauthConfiguration, URIRef(self.oauth_configuration.about))
spc.add(OSLC.domain, JAZZ_PROCESS.uri)
return spc
def to_rdf(self, graph):
super(Compact, self).to_rdf(graph)
uri = self.about if self.about else ''
d = Resource(graph, URIRef(uri))
d.add(RDF.type, OSLC.Compact)
if self.icon:
d.add(OSLC.icon, URIRef(self.icon))
if self.short_title:
d.add(DCTERMS.shortTitle, Literal(self.short_title, datatype=XSD.string))
if self.title:
d.add(DCTERMS.title, Literal(self.title, datatype=XSD.string))
if self.small_preview:
sp = self.small_preview.to_rdf(graph)
d.add(OSLC.smallPreview, sp)
if self.large_preview:
sp = self.large_preview.to_rdf(graph)
d.add(OSLC.largePreview, sp)
return d
def convert_feed(self, csv_filename):
read_feed = self.__open_file(csv_filename)
for row in read_feed:
feed = Resource(self.graph, URIRef(str.strip(row["publisher"])))
feed.set(RDF.type, self.GTFS.Feed)
feed.add(DCTERMS.publisher, Literal(str.strip(row["publisher"]), datatype=XSD.string))
feed.add(DCTERMS.title, Literal(str.strip(row["feed_publisher_name"]), datatype=XSD.string))
feed.add(DCTERMS.language, Literal(str.strip(row["feed_lang"]), datatype=XSD.string))
if "feed_version" in row and str.strip(row["feed_version"]) != "":
feed.add(self.SCHEMA.version, Literal(row["feed_version"], datatype=XSD.string))
if "feed_start_date" in row and str.strip(row["feed_start_date"]) != "" and "feed_end_date" in row and str.strip(row["feed_end_date"]) != "":
temporal = Resource(self.graph, URIRef(feed.identifier + "_temporal"))
temporal.set(RDF.type, DCTERMS.temporal)
temporal.add(self.SCHEMA.startDate, self.get_date_literal(str.strip(row["feed_start_date"])))
temporal.add(self.SCHEMA.endDate, self.get_date_literal(str.strip(row["feed_end_date"])))
def _createProvenance(self, result):
provdata = IProvenanceData(result)
from rdflib import URIRef, Literal, Namespace, Graph
from rdflib.namespace import RDF, RDFS, FOAF, DCTERMS, XSD
from rdflib.resource import Resource
PROV = Namespace(u"http://www.w3.org/ns/prov#")
BCCVL = Namespace(u"http://ns.bccvl.org.au/")
LOCAL = Namespace(u"urn:bccvl:")
graph = Graph()
# the user is our agent
member = api.user.get_current()
username = member.getProperty('fullname') or member.getId()
user = Resource(graph, LOCAL['user'])
user.add(RDF['type'], PROV['Agent'])
user.add(RDF['type'], FOAF['Person'])
user.add(FOAF['name'], Literal(username))
user.add(FOAF['mbox'],
URIRef('mailto:{}'.format(member.getProperty('email'))))
# add software as agent
software = Resource(graph, LOCAL['software'])
software.add(RDF['type'], PROV['Agent'])
software.add(RDF['type'], PROV['SoftwareAgent'])
software.add(FOAF['name'], Literal('BCCVL ALA Importer'))
# script content is stored somewhere on result and will be exported with zip?
# ... or store along with pstats.json ? hidden from user
# -> execenvironment after import -> log output?
# -> source code ... maybe some link expression? stored on result ? separate entity?
activity = Resource(graph, LOCAL['activity'])
activity.add(RDF['type'], PROV['Activity'])
# TODO: this is rather queued or created time for this activity ... could capture real start time on running status update (or start transfer)
now = datetime.now().replace(microsecond=0)
activity.add(PROV['startedAtTime'],
Literal(now.isoformat(), datatype=XSD['dateTime']))
activity.add(PROV['hasAssociationWith'], user)
activity.add(PROV['hasAssociationWith'], software)
# add job parameters to activity
provdata.data = graph.serialize(format="turtle")
def to_rdf(self, graph):
super(Dialog, self).to_rdf(graph)
d = Resource(graph, BNode())
d.add(RDF.type, OSLC.Dialog)
if self.label:
d.add(OSLC.label, Literal(self.label))
if self.title:
d.add(DCTERMS.title, Literal(self.title))
if self.hint_width:
d.add(DCTERMS.hintWidth, Literal(self.hint_width))
if self.hint_height:
d.add(DCTERMS.hintHeight, Literal(self.hint_height))
if self.dialog:
d.add(OSLC.dialog, URIRef(self.dialog))
if self.resource_type:
for item in self.resource_type:
d.add(OSLC.resourceType, URIRef(item))
if self.usage:
for item in self.usage:
d.add(OSLC.usage, URIRef(item))
return d
def to_rdf(self, graph):
super(QueryCapability, self).to_rdf(graph)
qc = Resource(graph, BNode())
qc.add(RDF.type, OSLC.QueryCapability)
if self.title:
qc.add(DCTERMS.title, Literal(self.title))
if self.label:
qc.add(OSLC.label, Literal(self.label, datatype=XSD.string))
else:
qc.add(OSLC.label, Literal(self.title, datatype=XSD.string))
if self.query_base:
qc.add(OSLC.queryBase, URIRef(self.query_base))
if self.resource_shape:
qc.add(OSLC.resourceShape, URIRef(self.resource_shape))
if self.resource_type:
for item in self.resource_type:
qc.add(OSLC.resourceType, URIRef(item))
if self.usage:
for item in self.usage.items():
qc.add(OSLC.usage, URIRef(item[1]))
return qc
logging.debug(owl_sameas[match_id])
else:
# we want a way to catalog things that end up without any kind of match. Let's start here.
if left_labels[key] not in unmatched:
unmatched.append(left_labels[key])
out_graph = Graph()
nsm = NamespaceManager(out_graph)
nsm.bind('owl', OWL, override=False)
print("Count of matches: " + str(len(match_ids)))
for i in match_ids:
osa = owl_sameas[i]
if osa['score'] >= min_score:
f = Resource(out_graph, URIRef(osa['left']))
r = Resource(out_graph, URIRef(osa['right']))
f.add(OWL.sameAs, r)
r.add(OWL.sameAs, f)
else:
# The match was excluded by score
print("Excluding " + str(osa) + " because the score was too low.")
out_graph.serialize(outfile,format=left_format)
if len(unmatched) > 0:
if len(unmatched_deletions) > 0:
unmatched = list(set(unmatched) - set(unmatched_deletions))
for u in unmatched:
print(u + " matched nothing in the target set.")
def generate_rdf(data):
DCO = Namespace("http://info.deepcarbon.net/schema#")
VIVO = Namespace("http://vivoweb.org/ontology/core#")
SKOS = Namespace("http://www.w3.org/2004/02/skos/core#")
BIBO = Namespace("http://purl.org/ontology/bibo/")
g = Graph()
g.bind("dco", DCO)
g.bind("bibo", BIBO)
g.bind("vivo", VIVO)
for (uri, record) in data:
try:
publication = Publication(record)
pub = Resource(g, URIRef(uri))
if publication.issue is not None:
pub.add(BIBO.issue, Literal(publication.issue))
if publication.issued is not None and publication.issued["year"] is not None:
pub.add(DCO.yearOfPublicationYear, Literal(publication.issued["year"], datatype=XSD.gYear))
if publication.volume is not None:
pub.add(BIBO.volume, Literal(publication.volume))
if publication.issn is not None:
pub.add(BIBO.issn, Literal(publication.issn))
if publication.pages is not None:
if "-" in publication.pages:
pageStart = publication.pages[:publication.pages.find("-")]
pageEnd = publication.pages[publication.pages.find("-") + 1:]
if pageStart != "n/a":
pub.add(BIBO.pageStart, Literal(pageStart))
if pageEnd != "n/a":
pub.add(BIBO.pageEnd, Literal(pageEnd))
else:
#pub.add(BIBO.pages, Literal(publication.pages))
pass
except ValueError as err:
#print((uri,str(err)))
pass
with open("pub-info.ttl", "w") as out:
out.write(g.serialize(format="turtle", encoding="UTF-8").decode(encoding="UTF-8"))
def convert_agency(self, csv_filename):
read_agency = self.__open_file(csv_filename)
for row in read_agency:
if "agency_id" in row:
agency = self.get_agency(str.strip(row["agency_id"]))
else:
agency = Resource(self.graph, URIRef(row['agency_url']))
agency.add(RDF.type, self.GTFS.Agency)
name = Literal(row['agency_name'], datatype=XSD.string)
agency.add(FOAF.name, name)
timezone = Literal(row['agency_timezone'], datatype=XSD.string)
agency.add(self.GTFS.timeZone, timezone)
if 'agency_lang' in row and str.strip(row["agency_lang"]) != "":
agency.add(DCTERMS.language, Literal(row['agency_lang'], datatype=XSD.string))
if 'agency_phone' in row and str.strip(row["agency_phone"]) != "":
agency.add(FOAF.phone, Literal(row['agency_phone'], datatype=XSD.string))
if 'agency_fare_url' in row and str.strip(row["agency_fare_url"]) != "":
agency.add(self.GTFS.fareUrl, URIRef(row['agency_fare_url']))
def __iter__(self):
"""missing docstring."""
for item in self.previous:
# check if we have a dataset
if item['_type'] not in ('org.bccvl.content.dataset',
'org.bccvl.content.remotedataset'):
# not a dataset
yield item
continue
pathkey = self.pathkey(*item.keys())[0]
# no path .. can't do anything
if not pathkey:
yield item
continue
path = item[pathkey]
# Skip the Plone site object itself
if not path:
yield item
continue
obj = self.context.unrestrictedTraverse(
path.encode().lstrip('/'), None)
# FIXME: this is really not a great way to check where to find provenenace data
# check if we are inside an experiment (means we import result)
if IExperiment.providedBy(self.context.__parent__):
# result import
context = self.context
else:
# dataset import?
context = obj
# TODO: do some sanity checks
provdata = IProvenanceData(context)
PROV = Namespace(u"http://www.w3.org/ns/prov#")
BCCVL = Namespace(u"http://ns.bccvl.org.au/")
LOCAL = Namespace(u"urn:bccvl:")
graph = Graph()
graph.parse(data=provdata.data or '', format='turtle')
activity = Resource(graph, LOCAL['activity'])
# FIXME: shouldn't I use uuid instead of id?
entity = Resource(graph, LOCAL[obj.id])
# create this dataset as new entity -> output of activity
entity.add(RDF['type'], PROV['Entity'])
# generated by
entity.add(PROV['wasGeneratedBy'], activity)
# PROV['prov:wasAttributedTo'] to user and software?
# File metadata
entity.add(DCTERMS['creator'], Literal(obj.Creator()))
entity.add(DCTERMS['title'], Literal(obj.title))
entity.add(DCTERMS['description'], Literal(obj.description))
entity.add(DCTERMS['rights'], Literal(obj.rights))
if obj.portal_type == 'org.bccvl.content.dataset':
entity.add(DCTERMS['format'], Literal(obj.file.contentType))
else:
# FIXME: this doesn't seem to do the right thing
entity.add(DCTERMS['format'], Literal(obj.format))
# TODO: add metadata about file?
# genre, layers, emsc, gcm, year
# set activities end time
# first one wins
if activity.value(PROV['endedAtTime']) is None:
activity.add(PROV['endedAtTime'],
Literal(datetime.now().replace(microsecond=0).isoformat(), datatype=XSD['dateTime']))
# TODO: extend activity metadata with execution environment data
# (logfile import?, pstats import) .. and script + params.json file
# ALA import url
pd = item.get('_ala_provenance', {})
if pd:
entity.add(BCCVL['download_url'], Literal(pd['url']))
# store prov data
provdata.data = graph.serialize(format="turtle")
yield item
def _createProvenance(self, result):
provdata = IProvenanceData(result)
from rdflib import URIRef, Literal, Namespace, Graph
from rdflib.namespace import RDF, RDFS, FOAF, DCTERMS, XSD
from rdflib.resource import Resource
PROV = Namespace(u"http://www.w3.org/ns/prov#")
BCCVL = Namespace(u"http://ns.bccvl.org.au/")
LOCAL = Namespace(u"urn:bccvl:")
graph = Graph()
# the user is our agent
member = api.user.get_current()
username = member.getProperty('fullname') or member.getId()
user = Resource(graph, LOCAL['user'])
user.add(RDF['type'], PROV['Agent'])
user.add(RDF['type'], FOAF['Person'])
user.add(FOAF['name'], Literal(username))
user.add(FOAF['mbox'],
URIRef('mailto:{}'.format(member.getProperty('email'))))
# add software as agent
software = Resource(graph, LOCAL['software'])
software.add(RDF['type'], PROV['Agent'])
software.add(RDF['type'], PROV['SoftwareAgent'])
software.add(FOAF['name'], Literal('BCCVL Job Script'))
# script content is stored somewhere on result and will be exported with zip?
# ... or store along with pstats.json ? hidden from user
# -> execenvironment after import -> log output?
# -> source code ... maybe some link expression? stored on result ? separate entity?
activity = Resource(graph, LOCAL['activity'])
activity.add(RDF['type'], PROV['Activity'])
# TODO: this is rather queued or created time for this activity ... could capture real start time on running status update (or start transfer)
now = datetime.now().replace(microsecond=0)
activity.add(PROV['startedAtTime'],
Literal(now.isoformat(), datatype=XSD['dateTime']))
activity.add(PROV['hasAssociationWith'], user)
activity.add(PROV['hasAssociationWith'], software)
# add job parameters to activity
for idx, (key, value) in enumerate(result.job_params.items()):
param = Resource(graph, LOCAL[u'param_{}'.format(idx)])
activity.add(BCCVL['algoparam'], param)
param.add(BCCVL['name'], Literal(key))
# We have only dataset references as parameters
if key in ('data_table',):
param.add(BCCVL['value'], LOCAL[dsuuid])
else:
param.add(BCCVL['value'], Literal(value))
# iterate over all input datasets and add them as entities
for key in ('data_table',):
dsbrain = uuidToCatalogBrain(result.job_params[key])
if not dsbrain:
continue
ds = dsbrain.getObject()
dsprov = Resource(graph, LOCAL[result.job_params[key]])
dsprov.add(RDF['type'], PROV['Entity'])
#dsprov.add(PROV['..'], Literal(''))
dsprov.add(DCTERMS['creator'], Literal(ds.Creator()))
dsprov.add(DCTERMS['title'], Literal(ds.title))
dsprov.add(DCTERMS['description'], Literal(ds.description))
dsprov.add(DCTERMS['rights'], Literal(ds.rights)) # ds.rightsstatement
dsprov.add(DCTERMS['format'], Literal(ds.file.contentType))
# location / source
# graph.add(uri, DCTERMS['source'], Literal(''))
# TODO: genre ...
# TODO: resolution
# species metadata
md = IBCCVLMetadata(ds)
# dsprov.add(BCCVL['scientificName'], Literal(md['species']['scientificName']))
# dsprov.add(BCCVL['taxonID'], URIRef(md['species']['taxonID']))
# ... species data, ... species id
for layer in md.get('layers_used',()):
dsprov.add(BCCVL['layer'], LOCAL[layer])
# link with activity
activity.add(PROV['used'], dsprov)
provdata.data = graph.serialize(format="turtle")
def to_rdf(self, graph):
super(ServiceProvider, self).to_rdf(graph)
uri = self.about if self.about.__contains__(self.identifier) \
else self.about + '/{}'.format(self.identifier) if self.identifier else ''
sp = Resource(graph, URIRef(uri))
sp.add(RDF.type, OSLC.ServiceProvider)
if self.identifier:
sp.add(DCTERMS.identifier, Literal(self.identifier, datatype=XSD.string))
if self.title:
sp.add(DCTERMS.title, Literal(self.title, datatype=XSD.Literal))
if self.description:
sp.add(DCTERMS.description, Literal(self.description))
if self.publisher:
sp.add(DCTERMS.publisher, URIRef(self.publisher.about))
if self.service:
for s in self.service:
r = s.to_rdf(graph)
sp.add(OSLC.service, r)
if self.details:
sp.add(OSLC.details, URIRef(self.details))
if self.oauth_configuration:
sp.add(OSLC.oauthConfiguration, URIRef(self.oauth_configuration.about))
if self.prefix_definition:
for pd in self.prefix_definition:
r = pd.to_rdf(graph)
sp.add(OSLC.prefixDefinition, r)
sp.add(JAZZ_PROCESS.supportContributionsToLinkIndexProvider, Literal(True, datatype=XSD.boolean))
sp.add(JAZZ_PROCESS.supportLinkDiscoveryViaLinkIndexProvider, Literal(True, datatype=XSD.boolean))
sp.add(JAZZ_PROCESS.supportOSLCSimpleQuery, Literal(True, datatype=XSD.boolean))
sp.add(JAZZ_PROCESS.globalConfigurationAware, Literal('yes', datatype=XSD.String))
return sp
def to_rdf(self, graph):
super(Service, self).to_rdf(graph)
# uri = self.about if self.about.__contains__(self.identifier) else self.about + '/{}'.format(
# self.identifier) if self.identifier else ''
s = Resource(graph, BNode())
s.add(RDF.type, OSLC.Service)
if self.title:
s.add(DCTERMS.title, Literal(self.title, datatype=XSD.Literal))
if self.description:
s.add(DCTERMS.description, Literal(self.description, datatype=XSD.Literal))
if self.domain:
s.add(OSLC.domain, URIRef(self.domain))
if self.creation_factory:
for cf in self.creation_factory:
r = cf.to_rdf(graph)
s.add(OSLC.creationFactory, r)
if self.query_capability:
for qc in self.query_capability:
r = qc.to_rdf(graph)
s.add(OSLC.queryCapability, r)
if self.selection_dialog:
for sd in self.selection_dialog:
r = sd.to_rdf(graph)
s.add(OSLC.selectionDialog, r)
if self.creation_dialog:
for cd in self.creation_dialog:
r = cd.to_rdf(graph)
s.add(OSLC.creationDialog, r.identifier)
return s
nsm = NamespaceManager(g)
# r_namespace should == p_namespace, otherwise how can they really be reciprocals?
(p_namespace,p_verb) = predicate.split(":")
(r_namespace,r_verb) = reciprocal.split(":")
assert p_namespace == r_namespace, "Prefixes don't match. This would probably create weird reciprocations."
# find out if the namespaces are already registered via the graph, because they *should* be
# I wonder if there's a more efficient way of doing this. Namespaces aren't usually prohibitively numerous, but still.
nuri = ''
for (p,n) in g.namespaces():
if p == p_namespace:
nuri = Namespace(n)
nsm.bind(p,nuri,override=False)
if nuri == '':
# we lack a proper prefix/namespace definition and can't continue
sys.exit("\nError: Can't find the prefix in the namespace list for this graph. Are you sure it's there?\n")
found_p = getattr(nuri,p_verb)
found_r = getattr(nuri,r_verb)
for (s,o) in g.subject_objects(predicate = found_p):
new_subject = Resource(g, o)
new_object = Resource(g, s)
new_subject.add(found_r,new_object)
g.serialize(outfile,guess_format(infile))
def to_rdf(self, graph):
super(CreationFactory, self).to_rdf(graph)
cf = Resource(graph, BNode())
cf.add(RDF.type, OSLC.CreationFactory)
if self.title:
cf.add(DCTERMS.title, Literal(self.title))
if self.label:
cf.add(OSLC.label, Literal(self.label, datatype=XSD.string))
if self.creation:
cf.add(OSLC.creation, URIRef(self.creation))
if self.resource_shape:
for item in self.resource_shape:
cf.add(OSLC.resourceShape, URIRef(item))
if self.resource_type:
for item in self.resource_type:
cf.add(OSLC.resourceType, URIRef(item))
if self.usage:
for item in self.usage:
cf.add(OSLC.usage, URIRef(item))
return cf
def to_rdf(self, graph):
super(Publisher, self).to_rdf(graph)
graph.bind('jfs', JFS)
p = Resource(graph, URIRef(self.about))
p.add(RDF.type, DCTERMS.Publisher)
if self.title:
p.add(DCTERMS.title, Literal(self.title))
if self.label:
p.add(OSLC.label, Literal(self.label))
if self.identifier:
p.add(DCTERMS.identifier, Literal(self.identifier))
if self.icon:
p.add(OSLC.icon, URIRef(self.icon))
p.add(JFS.nonLocalizedTitle, Literal('Configuration'))
p.add(JFS.version, Literal('7.0'))
p.add(JFS.instanceName, Literal('/pyoslc'))
return p
def convert_stop_times(self, csv_filename):
read_stop_times = self.__open_file(csv_filename)
for row in read_stop_times:
stop_id = str.strip(row["stop_id"])
sequence_num = str.strip(row["stop_sequence"])
trip_id = str.strip(row["trip_id"])
stop_time = Resource(self.graph, URIRef(self.uri + trip_id + "_" + stop_id + "_StopTime_" + sequence_num))
stop_time.set(RDF.type, self.GTFS.StopTime)
stop_time.add(self.GTFS.trip, self.get_trip(trip_id))
stop_time.add(self.GTFS.arrivalTime, Literal(str.strip(row["arrival_time"]), datatype=XSD.time))
stop_time.add(self.GTFS.departureTime, Literal(str.strip(row["departure_time"]), datatype=XSD.time))
stop_time.add(self.GTFS.stop, self.get_stop(stop_id))
stop_time.add(self.GTFS.stopSequence, Literal(sequence_num, datatype=XSD.nonNegativeInteger))
if "stop_headsign" in row:
stop_time.add(self.GTFS.headsign, Literal(str.strip(row["stop_headsign"]), datatype=XSD.string))
if "pickup_type" in row:
pickup_type = self.get_stop_type(str.strip(row["pickup_type"]))
stop_time.add(self.GTFS.pickupType, pickup_type)
if "drop_off_type" in row:
dropoff_type = self.get_stop_type(str.strip(row["drop_off_type"]))
stop_time.add(self.GTFS.dropOffType, dropoff_type)
if "shape_dist_traveled" in row:
# stop_time.add(self.GTFS.distanceTraveled,
# Literal(float(str.strip(row["shape_dist_traveled"])), datatype=XSD.nonNegativeInteger))
stop_time.add(self.GTFS.distanceTraveled, Literal(float(str.strip(row["shape_dist_traveled"]))))
def get_agency(self, agency_id):
agency = Resource(self.graph, URIRef(self.uri + "agency_" + agency_id))
agency.add(RDF.type, self.GTFS.Agency)
agency.set(DCTERMS.identifier, Literal(agency_id, datatype=XSD.string))
return agency
