def _render_nvs_rdf(self):
if "/standard_name/" in self.concept.uri:
api_concept_uri = "$DB2RDF_STANDARD_NAME_URI" + self.concept.uri.split(
"/standard_name/")[1]
else:
api_concept_uri = "$DB2RDF_COLLECTIONS_URI" + self.concept.uri.split(
"/collection/")[1]
r = requests.get(api_concept_uri)
if self.mediatype in [
"application/rdf+xml", "application/xml", "text/xml"
]:
return Response(
r.text,
mimetype=self.mediatype,
headers=self.headers,
)
else:
g = Graph().parse(data=r.text, format="xml")
# serialise in other RDF format
if self.mediatype in ["application/rdf+json", "application/json"]:
graph_text = g.serialize(format="json-ld")
else:
graph_text = g.serialize(format=self.mediatype)
return Response(
graph_text,
mimetype=self.mediatype,
headers=self.headers,
)
def pickle_to_file(vocab_id, g):
logging.debug("Pickling file: {}".format(vocab_id))
path = os.path.join(config.APP_DIR, "vocab_files", vocab_id)
# TODO: Check if file_name already has extension
with open(path + ".p", "wb") as f:
pickle.dump(g, f)
f.close()
g.serialize(path + ".ttl", format="turtle")
def _render_skos_rdf(self):
# get Collection RDF
# TODO: re-assemble RDF from Concept object
g = Graph()
# serialise in the appropriate RDF format
if self.mediatype in ["application/rdf+json", "application/json"]:
return g.serialize(format="json-ld")
else:
return g.serialize(format=self.mediatype)
def get_sparql_service_description(rdf_format="turtle"):
"""Return an RDF description of PROMS' read only SPARQL endpoint in a requested format
:param rdf_format: 'turtle', 'n3', 'xml', 'json-ld'
:return: string of RDF in the requested format
"""
sd_ttl = """
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sd: <http://www.w3.org/ns/sparql-service-description#> .
@prefix sdf: <http://www.w3.org/ns/formats/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://gnafld.net/sparql>
a sd:Service ;
sd:endpoint <%(BASE_URI)s/function/sparql> ;
sd:supportedLanguage sd:SPARQL11Query ; # yes, read only, sorry!
sd:resultFormat sdf:SPARQL_Results_JSON ; # yes, we only deliver JSON results, sorry!
sd:feature sd:DereferencesURIs ;
sd:defaultDataset [
a sd:Dataset ;
sd:defaultGraph [
a sd:Graph ;
void:triples "100"^^xsd:integer
]
]
.
"""
g = Graph().parse(io.StringIO(sd_ttl), format="turtle")
rdf_formats = list(set([x for x in Renderer.RDF_SERIALIZER_TYPES_MAP]))
if rdf_format in rdf_formats:
return g.serialize(format=rdf_format)
else:
raise ValueError("Input parameter rdf_format must be one of: " +
", ".join(rdf_formats))
def edit_glass(id):
""" Edit the name of a glass-type.
| **URL:** /beer/api/v0.1/glasses/<glass_id>
| **Method:** PUT
| **Query Args:** None
| **Authentication:** Token/Password
Example:
*Rename glass with id# 2 to 'Goblet'* ::
PUT http://domain.tld/beer/api/v0.1/glasses/2
data={"name":"Goblet"}
"""
g = Glass.query.get_or_404(id)
if 'name' in request.json and type(request.json['name']) != str:
flash(u'Invalid input', 'error')
abort(400)
name = request.json.get('name')
if name is not None:
if Glass.query.filter_by(name=name).first() is not None:
flash(u'Glass with that name already exists', 'error')
abort(400)
g.name = name
db.session.commit()
return jsonify({'status': 'Glass-type updated successfully',\
'results': g.serialize()})
def list_glasses():
""" List glass types in the database.
| **URL:** /beer/api/v0.1/glasses
| **Method:** GET
| **Query Args:** sort_by=<column name> <desc>
| **Authentication:** None
Example:
*List all glass styles in the database* ::
GET http://domain.tld/beer/api/v0.1/glasses
*List glass styles by name descending* ::
GET http://domain.tld/beer/api/v0.1/glasses?sort_by=name%20desc
"""
sort = request.args.get('sort_by') or None
if sort:
try:
glasses = Glass.query.order_by(sort).all()
except OperationalError:
flash(u'Invalid sorting value specified', 'error')
abort(400)
else:
glasses = Glass.query.all()
return jsonify(results=[g.serialize() for g in glasses])
def _render_skos_rdf(self):
g = Graph()
g.bind("dct", DCTERMS)
g.bind("skos", SKOS)
c = URIRef(self.concept.uri)
# Concept SKOS metadata
g.add((c, RDF.type, SKOS.Concept))
g.add((c, SKOS.prefLabel,
Literal(self.concept.prefLabel, lang=config.DEFAULT_LANGUAGE)))
g.add((c, SKOS.definition,
Literal(self.concept.definition, lang=config.DEFAULT_LANGUAGE)))
for k, v in self.concept.related_instances.items():
for k2, v2 in v.items():
if k2 == "instances":
for inst in v2:
g.add((
c,
URIRef(k),
URIRef(inst[0]
) # only URIs for RDF, not prefLabels too
))
if self.concept.other_properties is not None:
for prop in self.concept.other_properties:
if str(prop.value).startswith("http"):
g.add((c, URIRef(prop.uri), URIRef(prop.value)))
else:
g.add((c, URIRef(prop.uri), Literal(prop.value)))
# serialise in the appropriate RDF format
if self.mediatype in ["application/rdf+json", "application/json"]:
graph_text = g.serialize(format="json-ld")
else:
graph_text = g.serialize(format=self.mediatype)
return Response(
graph_text,
mimetype=self.mediatype,
headers=self.headers,
)
def get_glass(id):
""" Get data about a particular glass in the database.
| **URL:** /beer/api/v0.1/glasses/<glass_id>
| **Method:** GET
| **Query Args:** None
| **Authentication:** None
Example:
*Get data about glass with id# 3* ::
GET http://domain.tld/beer/api/v0.1/glasses/3
"""
g = Glass.query.get_or_404(id)
return jsonify(results=g.serialize())
def tobj(objname):
SCHEMA = Namespace('http://schema.org/')
SPDX = Namespace('http://www.spdx.org/rdf/terms#')
n = NamespaceManager(Graph())
n.bind("schema", SCHEMA)
n.bind("spdx", SPDX)
c = get_db().cursor()
c.execute('SELECT * FROM objects WHERE id=?', (objname,))
obj = c.fetchone()
g = Graph()
g.namespace_manager = n
objuri = URIRef("http://localhost:5000/b/" + obj[0])
robjuri = URIRef("http://localhost:5000/r/" + obj[0])
md5node = BNode()
g.add((md5node, SPDX.checksumValue, Literal(obj[2])))
g.add((md5node, SPDX.algorithm, URIRef("http://packages.qa.debian.org/#checksumAlgorithm_md5sum")))
g.add((objuri, SPDX.checksum, md5node))
g.add((objuri, SCHEMA.fileSize, Literal(obj[1])))
return Response(g.serialize(format="turtle"), mimetype="text/plain")
def _render_skos_rdf(self):
# make Collection RDF from Collection object in memory
# (this is faster than re-querying for RDF from the main cache or a vocab's source)
# this is the SKOS view - only SKOS stuff
g = Graph()
g.bind("dcterms", DCTERMS)
g.bind("skos", SKOS)
c = URIRef(self.collection.uri)
# Collection metadata
g.add((
c,
RDF.type,
SKOS.Collection
))
g.add((
c,
SKOS.prefLabel,
Literal(self.collection.prefLabel, lang=config.DEFAULT_LANGUAGE)
))
if self.collection.definition is not None:
g.add((
c,
SKOS.definition,
Literal(self.collection.definition, lang=config.DEFAULT_LANGUAGE)
))
for k, v in self.collection.source.items():
if k == "provenance" and v is not None:
g.add((
c,
DCTERMS.provenance,
Literal(self.collection.source["provenance"], lang=config.DEFAULT_LANGUAGE)
))
elif k == "source" and v is not None:
g.add((
c,
DCTERMS.source,
URIRef(self.collection.source["source"])
))
elif k == "wasDerivedFrom" and v is not None:
g.add((
c,
DCTERMS.provenance,
URIRef(self.collection.source["wasDerivedFrom"])
))
# vocab
if self.collection.vocab_uri is not None:
g.add((
c,
SKOS.inScheme,
URIRef(self.collection.vocab_uri),
))
# members
for m in self.collection.members:
g.add((
c,
SKOS.member,
URIRef(m[0]),
))
# serialise in the appropriate RDF format
if self.mediatype in ["application/rdf+json", "application/json"]:
graph_text = g.serialize(format="json-ld")
else:
graph_text = g.serialize(format=self.mediatype)
return Response(
graph_text,
mimetype=self.mediatype,
headers=self.headers,
)
