def _neighbours_rdf(self, mimetype):
query = '''
SELECT * WHERE {
<%(uri)s> ?p ?o .
}
''' % {
'uri': self.uri
}
g = Graph()
g.bind('prov', Namespace('http://www.w3.org/ns/prov#'))
for r in _database.query(query)['results']['bindings']:
if r['o']['type'] == 'literal':
g.add((URIRef(self.uri), URIRef(r['p']['value']),
Literal(r['o']['value'])))
else:
g.add((URIRef(self.uri), URIRef(r['p']['value']),
URIRef(r['o']['value'])))
query2 = '''
SELECT * WHERE {
?s ?p <%(uri)s> .
}
''' % {
'uri': self.uri
}
for r in _database.query(query2)['results']['bindings']:
g.add((URIRef(r['s']['value']), URIRef(r['p']['value']),
URIRef(self.uri)))
return Response(
g.serialize(format=LDAPI.get_rdf_parser_for_mimetype(mimetype)),
status=200,
mimetype=mimetype)
def lodge_reportingsystem():
"""Insert a ReportingSystem into the provenance _database"""
# only accept RDF documents
acceptable_mimes = LDAPI.get_rdf_mimetypes_list()
ct = request.content_type
if ct not in acceptable_mimes:
return api_functions.client_error_response(
'The ReportingSystem posted is not encoded with a valid RDF Content-Type. Must be one of: '
+ ', '.join(acceptable_mimes) + '.')
# validate ReportingSystem
rs = class_reportingsystems.IncomingReportingSystem(request)
if not rs.valid():
return api_functions.client_error_response(
'The ReportingSystem posted is not valid for the following reasons: '
+ ', '.join(rs.error_messages) + '.')
# get the ReportingSystem's URI
rs.determine_uri()
rs.generate_named_graph_metadata()
# store the ReportingSystem
if not rs.stored():
return api_functions.server_error_response(
'ReportingSystem posted is valid but cannot be stored for the following reasons: '
+ ', '.join(rs.error_messages) + '.')
# reply to sender
return Response(rs.uri, status=201, mimetype='text/plain')
def render(self, view, mimetype):
if view == 'neighbours':
if mimetype in LDAPI.get_rdf_mimetypes_list():
return self._neighbours_rdf(mimetype)
elif mimetype == 'text/html':
self._get_details()
return self._neighbours_html()
elif view == 'prov':
if mimetype in LDAPI.get_rdf_mimetypes_list():
return Response(self._prov_rdf().serialize(
format=LDAPI.get_rdf_parser_for_mimetype(mimetype)),
status=200,
mimetype=mimetype)
elif mimetype == 'text/html':
self._get_details()
return self._prov_html()
def lodge_agent():
"""Insert an Agent into the provenance _database"""
# only accept RDF documents
acceptable_mimes = LDAPI.get_rdf_mimetypes_list()
ct = request.content_type
if ct not in acceptable_mimes:
return api_functions.client_error_response(
'The Agent posted is not encoded with a valid RDF Content-Type. Must be one of: '
+ ', '.join(acceptable_mimes) + '.')
# validate Agent
sr = class_agents.IncomingAgent(request.data, request.content_type)
if not sr.valid():
return api_functions.client_error_response(
'The Agent posted is not valid for the following reasons: ' +
', '.join(sr.error_messages) + '.')
# get the Agent's URI
sr.determine_uri()
# store the Agent
if not sr.stored():
return api_functions.server_error_response(
'The Agent posted is valid but cannot be stored for the following reasons: '
+ ', '.join(sr.error_messages) + '.')
# reply to sender
return Response(sr.uri, status=201, mimetype='text/plain')
def render(self, view, mimetype):
if mimetype == 'text/html':
self._get_details()
return self._html()
else:
self._get_details()
return Response(self._rdf().serialize(
format=LDAPI.get_rdf_parser_for_mimetype(mimetype)),
mimetype=mimetype)
def instance():
"""
Responds with one of a number of HTTP responses according to an allowed model and format of this object in the graph
:return: and HTTP response
"""
# must have the URI of an object in the graph
instance_uri = request.args.get('_uri')
try:
g = get_class_object(instance_uri)
if not g:
return client_error_response(
'No URI of an object in the provenance database was supplied. '
'Expecting a query string argument \'_uri\'.')
except ConnectionError:
return render_template('error_db_connection.html'), 500
# the URI is of something in the graph so now we validate the requested model and format
# find the class of the URI
for s, p, o in g:
if str(p) == 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type':
# validate this request's model and format
class_uri = str(o)
views_formats = objects_functions.get_classes_views_formats().get(
class_uri)
try:
view, mime_format = LDAPI.get_valid_view_and_format(
request.args.get('_view'), request.args.get('_format'),
views_formats)
# if alternates model, return this info from file
if view == 'alternates':
instance_uri_encoded = urllib.parse.quote_plus(
request.args.get('_uri'))
class_uri_encoded = urllib.parse.quote_plus(class_uri)
del views_formats['renderer']
return api_functions.render_alternates_view(
class_uri, class_uri_encoded, instance_uri,
instance_uri_encoded, views_formats, mime_format)
else:
# chooses a class to render this instance based on the specified renderer in
# classes_views_formats.json
# no need for further validation as instance_uri, model & format are already validated
renderer = getattr(__import__('model'),
views_formats['renderer'])
endpoints = {
'instance': url_for('.instance'),
'sparql': url_for('api.sparql')
}
return renderer(instance_uri,
endpoints).render(view, mime_format)
except LdapiParameterError as e:
return client_error_response(e)
def render(self, view, mimetype):
if view == 'reg':
# is an RDF format requested?
if mimetype in LDAPI.get_rdf_mimetypes_list():
# it is an RDF format so make the graph for serialization
self._make_dpr_graph(view)
rdflib_format = LDAPI.get_rdf_parser_for_mimetype(mimetype)
return Response(self.g.serialize(format=rdflib_format),
status=200,
mimetype=mimetype)
elif mimetype == 'text/html':
return render_template(
'class_register.html',
class_name=self.request.args.get('_uri'),
register=self.register)
else:
return Response(
'The requested model model is not valid for this class',
status=400,
mimetype='text/plain')
def _convert_proms_pingback_to_rdf(self):
PROMS = Namespace('http://promsns.org/def/proms#')
self.graph.bind('proms', PROMS)
# type this pingback specifically
self.graph.add(
(URIRef(self.named_graph_uri), RDF.type, PROMS.PromsPingback))
# convert the data to RDF (just de-serialise it)
self.graph += Graph().parse(data=self.request.data,
format=LDAPI.get_rdf_parser_for_mimetype(
self.request.mimetype))
def render(self, view, mimetype):
if view == 'neighbours':
# no work to be done as we have already loaded the triples
if mimetype in LDAPI.get_rdf_mimetypes_list():
return self._neighbours_rdf(mimetype)
elif mimetype == 'text/html':
self._get_details()
return self._neighbours_html()
elif view == 'prov':
if mimetype in LDAPI.get_rdf_mimetypes_list():
return Response(self._prov_rdf().serialize(
format=LDAPI.get_rdf_parser_for_mimetype(mimetype)),
status=200,
mimetype=mimetype)
# TODO: pre-render the viz.js image and serve static image
# elif mimetype == 'image/svg':
# return Response(
#
# )
elif mimetype == 'text/html':
self._get_details()
return self._prov_html()
def register():
"""
Responds with a Register model response for classes listed in the graph
Supported classes statically loaded from classes_views_formats.json
In the future, we will dynamically work out which classes are supported.
:param class_name: the name of a class of object in the graph db
:return: an HTTP message based on a particular model and format of the class
"""
# check for a class URI
uri = request.args.get('_uri')
# ensure the class URI is one of the classes in the views_formats
class_uris = objects_functions.get_class_uris()
if uri not in class_uris:
return client_error_response(
'No URI of a class in the provenance database was supplied. Expecting a query string argument \'_uri\' '
'equal to one of the following: ' +
', '.join(class_uris)
)
# validate this request's model and format
class_uri = 'http://purl.org/linked-data/registry#Register'
views_formats = objects_functions.get_classes_views_formats().get(class_uri)
try:
view, mime_format = LDAPI.get_valid_view_and_format(
request.args.get('_view'),
request.args.get('_format'),
views_formats
)
except LdapiParameterError as e:
return client_error_response(e)
# if alternates model, return this info from file
if view == 'alternates':
del views_formats['renderer']
return api_functions.render_alternates_view(uri, uriparse.parse.quote_plus(uri), None, None, views_formats, mime_format)
# get the register of this class of thing from the provenance database
try:
class_register = get_class_register(uri)
except ConnectionError:
return render_template('error_db_connection.html'), 500
# since everything's valid, use the Renderer to return a response
endpoints = {
'instance': url_for('.instance'),
'sparql': url_for('api.sparql')
}
return model.RegisterRenderer(request, uri, endpoints, class_register).render(view, mime_format)
def lodge_report():
"""Insert a Report into the provenance database
This function should be edited if any custom actions are to be undertaken by PROMS on reciept of a Report, such as
Ppingbacks
"""
# only accept RDF documents
acceptable_mimes = LDAPI.get_rdf_mimetypes_list()
ct = request.content_type
if ct not in acceptable_mimes:
return api_functions.client_error_response(
'The Report posted is not encoded with a valid RDF Content-Type. Must be one of: '
+ ', '.join(acceptable_mimes) + '.')
# validate Report, using the controller validator class, IncomingReport
r = class_reports.IncomingReport(request)
if not r.valid():
return api_functions.client_error_response(
'The Report posted is not valid for the following reasons: ' +
', '.join(r.error_messages) + '.')
# generate Named Graph metadata
r.determine_uri()
r.generate_named_graph_metadata()
# store the Report
# since it is valid and NG metadata has been built, we can store it
if not r.stored():
return api_functions.server_error_response(
'Report posted is valid but cannot be stored for the following reasons: '
+ ', '.join(r.error_messages) + '.')
# Custom Actions
# Only try to any custom actions, e.g. Pingbacks, if the module is turned on
if conf.MODULES.get('pingbacks').get('valid'):
# kick off any Pingbacks for this Report, as per chosen Pingbacks strategies
# TODO: split Pingbacks process off into another thread
from modules.pingbacks.engine import Engine
e = Engine(r.graph, r.uri, url_for('modelx.instance'),
url_for('.sparql'))
# reply to sender
return r.uri, 201
def valid(self):
"""Validates an incoming Pingback using direct _tests using the Pingbacks RuleSet"""
# PROV Pingbacks can only be of mimtype text/uri-list
if self.request.mimetype == 'text/uri-list':
print(self.request.headers)
conformant_pingback = ProvPingback(self.request)
# ensure that this Pingback has the URI(s) of the Resource(s) it is for
if self.request.args.get('resource_uri') is None:
error_message = 'No resource URI is indicated for this pingback. Pingbacks sent to a PROMS Server ' \
'instance must be posted to ' \
'http://{POROMS_INTANCE}/function/lodge-pingback?resource_uri={RESOURCE_URI}'
if self.error_messages is not None:
self.error_messages.append(error_message)
else:
self.error_messages = [error_message]
return False
elif not LDAPI.is_a_uri(self.request.args.get('resource_uri')):
error_message = 'The resource URI indicated for this pingback does not validate as a URI'
if self.error_messages is not None:
self.error_messages.append(error_message)
else:
self.error_messages = [error_message]
return False
# PROMS Pingbacks can only be of an RDF mimetype
else:
conformant_pingback = PromsPingback(self.request,
self.pingback_endpoint)
if not conformant_pingback.passed:
self.error_messages = conformant_pingback.fail_reasons
return False
return True
def lodge_report():
"""Insert a Report into the provenance database"""
# only accept RDF documents
acceptable_mimes = LDAPI.get_rdf_mimetypes_list()
ct = request.content_type
if ct not in acceptable_mimes:
return api_functions.client_error_response(
'The Report posted is not encoded with a valid RDF Content-Type. Must be one of: '
+ ', '.join(acceptable_mimes) + '.')
# validate Report
r = class_reports.IncomingReport(request)
print(str(r))
if not r.valid():
return api_functions.client_error_response(
'The Report posted is not valid for the following reasons: ' +
', '.join(r.error_messages) + '.')
# get the Report's URI
r.determine_uri()
r.generate_named_graph_metadata()
# store the Report
if not r.stored():
return api_functions.server_error_response(
'Report posted is valid but cannot be stored for the following reasons: '
+ ', '.join(r.error_messages) + '.')
# kick off any Pingbacks for this Report, as per chosen Pingbacks strategies
# TODO: split this off into another thread
from modules.pingbacks.engine import Engine
e = Engine(r.graph, r.uri, url_for('modelx.instance'), url_for('.sparql'))
# reply to sender
return r.uri, 201
def render_alternates_view(class_uri, class_uri_encoded, instance_uri,
instance_uri_encoded, views_formats, mimetype):
"""Renders an HTML table, a JSON object string or a serialised RDF representation of the alternate views of an
object"""
if mimetype == 'application/json':
del views_formats[
'renderer'] # the renderer used is not for public consumption!
return Response(json.dumps(views_formats),
status=200,
mimetype='application/json')
elif mimetype in LDAPI.get_rdf_mimetypes_list():
g = Graph()
LDAPI_O = Namespace('http://promsns.org/def/ldapi#')
g.bind('ldapi', LDAPI_O)
DCT = Namespace('http://purl.org/dc/terms/')
g.bind('dct', DCT)
class_uri_ref = URIRef(uriparse.unquote_plus(class_uri))
if instance_uri:
instance_uri_ref = URIRef(instance_uri)
g.add((instance_uri_ref, RDF.type, class_uri_ref))
else:
g.add((class_uri_ref, RDF.type, LDAPI_O.ApiResource))
# alternates model
alternates_view = BNode()
g.add((alternates_view, RDF.type, LDAPI_O.View))
g.add((alternates_view, DCT.title,
Literal('alternates', datatype=XSD.string)))
g.add((class_uri_ref, LDAPI_O.view, alternates_view))
# default model
default_view = BNode()
g.add((default_view, DCT.title, Literal('default',
datatype=XSD.string)))
g.add((class_uri_ref, LDAPI_O.defaultView, default_view))
default_title = views_formats['default']
# the ApiResource is incorrectly assigned to the class URI
for view_name, formats in views_formats.items():
if view_name == 'alternates':
for f in formats:
g.add((alternates_view,
URIRef('http://purl.org/dc/terms/format'),
Literal(f, datatype=XSD.string)))
elif view_name == 'default':
pass
elif view_name == 'renderer':
pass
else:
x = BNode()
if view_name == default_title:
g.add((default_view, RDF.type, x))
g.add((class_uri_ref, LDAPI_O.view, x))
g.add((x, DCT.title, Literal(view_name, datatype=XSD.string)))
for f in formats:
g.add((x, URIRef('http://purl.org/dc/terms/format'),
Literal(f, datatype=XSD.string)))
rdflib_format = [
item[1] for item in LDAPI.MIMETYPES_PARSERS if item[0] == mimetype
][0]
return Response(g.serialize(format=rdflib_format),
status=200,
mimetype=mimetype)
else: # HTML
return render_template('alternates_view.html',
class_uri=class_uri,
class_uri_encoded=class_uri_encoded,
instance_uri=instance_uri,
instance_uri_encoded=instance_uri_encoded,
views_formats=views_formats)
class IncomingPingback(IncomingClass):
acceptable_mimes = LDAPI.get_rdf_mimetypes_list() + ['text/uri-list']
def __init__(self, request):
IncomingClass.__init__(self, request)
self.pingback_endpoint = request.url
self.determine_uri()
self._generate_named_graph_uri()
def valid(self):
"""Validates an incoming Pingback using direct tests using the Pingbacks RuleSet"""
# PROV Pingbacks can only be of mimtype text/uri-list
if self.request.mimetype == 'text/uri-list':
print((self.request.headers))
conformant_pingback = ProvPingback(self.request)
# ensure that this Pingback has the URI(s) of the Resource(s) it is for
if self.request.args.get('resource_uri') is None:
error_message = 'No resource URI is indicated for this pingback. Pingbacks sent to a PROMS Server ' \
'instance must be posted to ' \
'http://{POROMS_INTANCE}/function/lodge-pingback?resource_uri={RESOURCE_URI}'
if self.error_messages is not None:
self.error_messages.append(error_message)
else:
self.error_messages = [error_message]
return False
elif not LDAPI.is_a_uri(self.request.args.get('resource_uri')):
error_message = 'The resource URI indicated for this pingback does not validate as a URI'
if self.error_messages is not None:
self.error_messages.append(error_message)
else:
self.error_messages = [error_message]
return False
# PROMS Pingbacks can only be of an RDF mimetype
else:
conformant_pingback = PromsPingback(self.request, self.pingback_endpoint)
if not conformant_pingback.passed:
self.error_messages = conformant_pingback.fail_reasons
return False
return True
def determine_uri(self):
pass # no need for this!
def _generate_named_graph_uri(self):
self.named_graph_uri = settings.PINGBACK_NAMED_GRAPH_BASE_URI + str(uuid.uuid4())
def convert_pingback_to_rdf(self):
# the URI of the Named Graph for this Pingback must have been generated before doing this
# so we can refer to the graph
if self.named_graph_uri is not None:
self.graph = Graph()
# PROV Pingbacks can only be of mimtype text/uri-list
if self.request.mimetype == 'text/uri-list':
self._convert_prov_pingback_to_rdf()
# PROMS Pingbacks can only be of an RDF mimetype
else:
self._convert_proms_pingback_to_rdf()
else:
raise Exception('The Incoming Pingback must have had a URI generated for it by PROMS Server before the data'
'for it is stored. The function determine_uri() generated the URI.')
def _convert_prov_pingback_to_rdf(self):
# every URI in the PROV-AQ message is treated as a provenance statement about the resource
PROV = Namespace('http://www.w3.org/ns/prov#')
self.graph.bind('prov', PROV)
for uri_line in self.request.data.split('\n'):
self.graph.add((
URIRef(self.request.args.get('resource_uri')),
PROV.has_provenance,
URIRef(uri_line)
))
# if there are Link headers about other resources, create DCT provenance indicators for them too
if self.request.headers.get('Link'):
for link_header in self.request.headers.get('Link').split(','):
uri, rel, anchor = link_header.split(';')
self.graph.add((
URIRef(uri.strip('<>')),
URIRef(rel.strip().replace('rel=', '').strip('"')),
URIRef(anchor.strip().replace('anchor=', '').strip('"'))
))
def _convert_proms_pingback_to_rdf(self):
PROMS = Namespace('http://promsns.org/def/proms#')
self.graph.bind('proms', PROMS)
# type this pingback specifically
self.graph.add((
URIRef(self.named_graph_uri),
RDF.type,
PROMS.PromsPingback
))
# convert the data to RDF (just de-serialise it)
self.graph += Graph().parse(
data=self.request.data,
format=LDAPI.get_rdf_parser_for_mimetype(self.request.mimetype)
)
def generate_named_graph_metadata(self):
# add graph metadata, regardless of the type of Pingback
PROV = Namespace('http://www.w3.org/ns/prov#')
self.graph.bind('prov', PROV)
PROMS = Namespace('http://promsns.org/def/proms#')
self.graph.bind('proms', PROMS)
DCT = Namespace('http://purl.org/dc/terms/')
self.graph.bind('dct', DCT)
# ... the date this Pingback was sent to this PROMS Server
self.graph.add((
URIRef(self.named_graph_uri),
DCT.dateSubmitted,
Literal(datetime.now().isoformat(), datatype=XSD.dateTime)
))
# ... who contributed this Pingback
self.graph.add((
URIRef(self.named_graph_uri),
DCT.contributor,
URIRef(self.request.remote_addr)
))
# TODO: add other useful metadata variables gleaned from the HTTP message headers
# PROV Pingbacks can only be of mimtype text/uri-list
if self.request.mimetype == 'text/uri-list':
self._generate_prov_pingback_named_graph_metadata()
else:
self._generate_proms_pingback_named_graph_metadata()
def _generate_prov_pingback_named_graph_metadata(self):
PROMS = Namespace('http://promsns.org/def/proms#')
self.graph.bind('proms', PROMS)
# type this pingback specifically
self.graph.add((
URIRef(self.named_graph_uri),
RDF.type,
PROMS.ProvAqPingbackNamedGraph
))
def _generate_proms_pingback_named_graph_metadata(self):
PROMS = Namespace('http://promsns.org/def/proms#')
self.graph.bind('proms', PROMS)
# type this pingback specifically
self.graph.add((
URIRef(self.named_graph_uri),
RDF.type,
PROMS.PromsPingbackNamedGraph
))
def instance():
"""
Responds with one of a number of HTTP responses according to an allowed model and format of this object in the graph
:return: and HTTP response
"""
# must have the URI of an object in the graph
instance_uri = request.args.get('_uri')
try:
g = get_class_object(instance_uri)
if not g:
return client_error_response(
'No URI of an object in the provenance _database was supplied. '
'Expecting a query string argument \'_uri\'.')
except ConnectionError:
return render_template('error_db_connection.html'), 500
# the URI is of something in the graph so now we validate the requested model and format
# find the class of the URI
q = '''
SELECT DISTINCT ?o WHERE {
<%s> a ?o .
}
''' % instance_uri
for r in g.query(q):
class_uri = str(str(r['o']))
# first preference render
if class_uri in [
'http://www.w3.org/ns/prov#Activity',
'http://www.w3.org/ns/prov#Agent',
'http://www.w3.org/ns/prov#Entity',
'http://promsns.org/def/proms#BasicReport',
'http://promsns.org/def/proms#ExternalReport',
'http://promsns.org/def/proms#InternalReport',
'http://promsns.org/def/proms#ReportingSystem'
]:
# validate this request's model and format
views_formats = objects_functions.get_classes_views_formats().get(class_uri)
try:
view, mime_format = LDAPI.get_valid_view_and_format(
request.args.get('_view'),
request.args.get('_format'),
views_formats
)
# if alternates model, return this info from file
if view == 'alternates':
instance_uri_encoded = uriparse.quote_plus(request.args.get('_uri'))
class_uri_encoded = uriparse.quote_plus(class_uri)
del views_formats['renderer']
return api_functions.render_alternates_view(
class_uri,
class_uri_encoded,
instance_uri,
instance_uri_encoded,
views_formats,
mime_format
)
else:
# chooses a class to render this instance based on the specified renderer in
# classes_views_formats.json
# no need for further validation as instance_uri, model & format are already validated
renderer = getattr(__import__('model'), views_formats['renderer'])
endpoints = {
'instance': url_for('.instance'),
'sparql': url_for('api.sparql')
}
return renderer(
instance_uri,
endpoints
).render(view, mime_format)
except LdapiParameterError as e:
return client_error_response(e)
