def return_collection_or_concept_from_main_cache(uri):
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT *
WHERE {{
<{uri}> a ?c .
OPTIONAL {{
{{ <{uri}> skos:inScheme ?cs . }}
UNION
{{ <{uri}> skos:topConcpetOf ?cs . }}
UNION
{{ ?cs skos:member <{uri}> . }}
}}
}}
""".format(uri=uri)
for r in u.sparql_query(q):
if r["c"]["value"] in source.Source.VOC_TYPES:
# if we find it and it's of a known class, return it
# since, for a Concept or a Collection, we know the relevant vocab as vocab == CS == graph
# in VocPrez's models of a vocabs
vocab_uri = r["cs"]["value"]
if r["c"][
"value"] == "http://www.w3.org/2004/02/skos/core#Collection":
try:
c = getattr(source, g.VOCABS[vocab_uri].source) \
(vocab_uri, request, language=request.values.get("lang")).get_collection(uri)
return CollectionRenderer(request, c)
except:
pass
elif r["c"][
"value"] == "http://www.w3.org/2004/02/skos/core#Concept":
try:
c = getattr(source, g.VOCABS[vocab_uri].source) \
(vocab_uri, request, language=request.values.get("lang")).get_concept(uri)
return ConceptRenderer(request, c)
except:
pass
return None
def collect(details):
"""
For this source, one SPARQL endpoint is given for a series of vocabs which are all separate ConceptSchemes
'ga-jena-fuseki': {
'source': VocabSource.SPARQL,
'sparql_endpoint': 'http://dev2.nextgen.vocabs.ga.gov.au/fuseki/vocabs',
'sparql_username': '******', # Optional username for SPARQL endpoint
'sparql_password': '******', # Optional password for SPARQL endpoint
#'uri_filter_regex': '.*', # Regular expression to filter vocabulary URIs - Everything
#'uri_filter_regex': '^http(s?)://pid.geoscience.gov.au/def/voc/ga/', # Regular expression to filter vocabulary URIs - GA
#'uri_filter_regex': '^https://gcmdservices.gsfc.nasa.gov', # Regular expression to filter vocabulary URIs - GCMD
'uri_filter_regex': '^http(s?)://resource.geosciml.org/', # Regular expression to filter vocabulary URIs - CGI
},
"""
logging.debug("SPARQL collect()...")
# Get all the ConceptSchemes from the SPARQL endpoint
# Interpret each CS as a Vocab
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT *
WHERE {{
?cs a skos:ConceptScheme .
OPTIONAL {{ ?cs skos:prefLabel ?title .
FILTER(lang(?title) = "{language}" || lang(?title) = "") }}
OPTIONAL {{ ?cs dcterms:created ?created }}
OPTIONAL {{ ?cs dcterms:issued ?issued }}
OPTIONAL {{ ?cs dcterms:modified ?modified }}
OPTIONAL {{ ?cs dcterms:creator ?creator }}
OPTIONAL {{ ?cs dcterms:publisher ?publisher }}
OPTIONAL {{ ?cs owl:versionInfo ?version }}
OPTIONAL {{ ?cs skos:definition ?description .
FILTER(lang(?description) = "{language}" || lang(?description) = "") }}
}}
ORDER BY ?title
""".format(language=config.DEFAULT_LANGUAGE)
# record just the IDs & title for the VocPrez in-memory vocabs list
concept_schemes = u.sparql_query(
q,
details[
"sparql_endpoint"], # must specify a SPARQL endpoint if this source is to be a SPARQL source
details.get("sparql_username"),
details.get("sparql_password"),
)
assert concept_schemes is not None, "Unable to query for ConceptSchemes"
sparql_vocabs = {}
vocab_ids = []
for cs in concept_schemes:
vocab_id = cs["cs"]["value"]
part = cs["cs"]["value"].split("#")[-1].split("/")[-1]
if len(part) < 1:
part = cs["cs"]["value"].split("#")[-1].split("/")[-2]
id = part.lower()
if id in vocab_ids:
if id[-1].isnumeric():
id = id[:-1] + str(int(id[-1]) + 1)
else:
id = id + "1"
vocab_ids.append(id)
sparql_vocabs[vocab_id] = Vocabulary(
id,
cs["cs"]["value"],
cs["title"].get("value") or vocab_id if cs.get("title") else
vocab_id, # Need str for sorting, not None
markdown(cs["description"].get("value"))
if cs.get("description") is not None else None,
cs["creator"].get("value")
if cs.get("creator") is not None else None,
dateutil.parser.parse(cs.get("created").get("value"))
if cs.get("created") is not None else None,
# dct:issued not in Vocabulary
# dateutil.parser.parse(cs.get('issued').get('value')) if cs.get('issued') is not None else None,
dateutil.parser.parse(cs.get("modified").get("value"))
if cs.get("modified") is not None else None,
cs["version"].get("value")
if cs.get("version") is not None else None, # versionInfo
config.VocabSource.SPARQL,
sparql_endpoint=details["sparql_endpoint"],
sparql_username=details.get("sparql_username"),
sparql_password=details.get("sparql_password"),
)
g.VOCABS = {**g.VOCABS, **sparql_vocabs}
logging.debug("SPARQL collect() complete.")
def get_collection(self, collection_uri):
print("OGC get_collection()")
# get the collection's metadata and members
q = """
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT *
WHERE {
<xxxx> a skos:Collection ;
?p ?o .
FILTER(!isLiteral(?o) || lang(?o) = "en" || lang(?o) = "")
OPTIONAL {
?p skos:prefLabel|rdfs:label ?ppl .
FILTER(!isLiteral(?o) || lang(?o) = "en" || lang(?o) = "")
}
OPTIONAL {
?o skos:prefLabel|rdfs:label ?opl .
FILTER(!isLiteral(?o) || lang(?o) = "en" || lang(?o) = "")
}
}
""".replace("xxxx", collection_uri)
vocab_uri = None
pl = None
d = None
c = None
s = {
"provenance": None,
"source": None,
"wasDerivedFrom": None,
}
m = []
found = False
for r in u.sparql_query(q, config.SPARQL_ENDPOINT, config.SPARQL_USERNAME, config.SPARQL_PASSWORD):
prop = r["p"]["value"]
val = r["o"]["value"]
found = True
if val == "http://www.w3.org/2004/02/skos/core#Concept":
return None
if prop == "http://www.w3.org/2004/02/skos/core#prefLabel":
pl = val
elif prop == "http://www.w3.org/2004/02/skos/core#definition":
d = val
elif prop == "http://www.w3.org/2000/01/rdf-schema#comment":
c = val
elif prop == "http://purl.org/dc/terms/provenance":
s["provenance"] = val
elif prop == "http://purl.org/dc/terms/source":
s["source"] = val
elif prop == "http://www.w3.org/2004/02/skos/core#inScheme":
s["inScheme"] = val
vocab_uri = val
elif prop == "http://www.w3.org/ns/prov#wasDerivedFrom":
s["wasDerivedFrom"] = val
elif prop == "http://www.w3.org/2004/02/skos/core#member":
m.append(Property(prop, "Member", val, r["opl"]["value"]))
if not found:
return None
from vocprez.model.collection import Collection
if not d:
d = c
return Collection(vocab_uri, collection_uri, pl, d, s, sorted(m, key=lambda x: x.value_label.lower()))
def search():
if request.values.get("search"):
last_search = request.values.get("search")
if request.values.get("from") and request.values.get("from") != "all":
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?uri ?pl (SUM(?weight) AS ?weight)
WHERE {{
GRAPH <{grf}> {{
{{ # exact match on a prefLabel always wins
?uri a skos:Concept ;
skos:prefLabel ?pl .
BIND (50 AS ?weight)
FILTER REGEX(?pl, "^{input}$", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:prefLabel ?pl .
BIND (10 AS ?weight)
FILTER REGEX(?pl, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:altLabel ?al ;
skos:prefLabel ?pl .
BIND (5 AS ?weight)
FILTER REGEX(?al, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:hiddenLabel ?hl ;
skos:prefLabel ?pl .
BIND (5 AS ?weight)
FILTER REGEX(?hl, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:definition ?d ;
skos:prefLabel ?pl .
BIND (1 AS ?weight)
FILTER REGEX(?d, "{input}", "i")
}}
}}
}}
GROUP BY ?uri ?pl
ORDER BY DESC(?weight)
""".format(
**{
"grf": request.values.get("from"),
"input": request.values.get("search")
})
results = []
else:
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?g ?uri ?pl (SUM(?weight) AS ?weight)
WHERE {{
GRAPH ?g {{
{{ # exact match on a prefLabel always wins
?uri a skos:Concept ;
skos:prefLabel ?pl .
BIND (50 AS ?weight)
FILTER REGEX(?pl, "^{input}$", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:prefLabel ?pl .
BIND (10 AS ?weight)
FILTER REGEX(?pl, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:altLabel ?al ;
skos:prefLabel ?pl .
BIND (5 AS ?weight)
FILTER REGEX(?al, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:hiddenLabel ?hl ;
skos:prefLabel ?pl .
BIND (5 AS ?weight)
FILTER REGEX(?hl, "{input}", "i")
}}
UNION
{{
?uri a skos:Concept ;
skos:definition ?d ;
skos:prefLabel ?pl .
BIND (1 AS ?weight)
FILTER REGEX(?d, "{input}", "i")
}}
}}
}}
GROUP BY ?g ?uri ?pl
ORDER BY DESC(?weight)
""".format(**{"input": request.values.get("search")})
results = {}
for r in u.sparql_query(q):
if r.get("uri") is None:
break # must do this check as r["weight"] will appear at least once with value 0 for no results
if request.values.get(
"from") and request.values.get("from") != "all":
results.append((r["uri"]["value"], r["pl"]["value"]))
else:
if r["g"]["value"] not in results.keys():
results[r["g"]["value"]] = []
results[r["g"]["value"]].append(
(r["uri"]["value"], r["pl"]["value"]))
return render_template("search.html",
vocabs=[(v.uri, v.title)
for k, v in g.VOCABS.items()],
last_search=last_search,
selected_vocab=request.values.get("from"),
results=results)
else:
return render_template("search.html",
vocabs=[(v.uri, v.title)
for k, v in g.VOCABS.items()])
def object():
"""
This is the general RESTful endpoint and corresponding Python function to handle requests for individual objects,
be they a Vocabulary (ConceptScheme), a Collection or Concept. Only those 3 classes of object are supported for the
moment.
An HTTP URI query string argument parameter 'uri' must be supplied, indicating the URI of the object being requested
:return: A Flask Response object
:rtype: :class:`flask.Response`
"""
uri = request.values.get("uri")
# must have a URI or Vocab URI supplied
if uri is None:
return return_vocprez_error(
"Input Error", 400,
"A Query String Argument of 'uri' must be supplied for this endpoint"
)
if uri == config.SYSTEM_BASE_URI or uri == config.SYSTEM_BASE_URI + "/":
return index()
if uri == config.VOCS_URI or uri == config.VOCS_URI + "/":
return vocabularies()
# get the class of the object
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?cs
WHERE {
GRAPH ?g {
<xxx> a ?c .
OPTIONAL {
VALUES ?memberof { skos:inScheme skos:topConceptOf }
<xxx> ?memberof ?cs .
}
}
}
""".replace("xxx", uri)
cs = None
for r in u.sparql_query(q):
if r["c"][
"value"] == "http://www.w3.org/2004/02/skos/core#ConceptScheme":
if uri in g.VOCABS.keys():
# get vocab details using appropriate source handler
vocab = source.SPARQL(request).get_vocabulary(uri)
return VocabularyRenderer(request, vocab).render()
else:
return None
elif r["c"][
"value"] == "http://www.w3.org/2004/02/skos/core#Collection":
try:
c = source.SPARQL(request).get_collection(uri)
return CollectionRenderer(request, c).render()
except:
return None
elif r["c"]["value"] == "http://www.w3.org/2004/02/skos/core#Concept":
try:
if r.get("cs"):
cs = r["cs"]["value"]
c = source.SPARQL(request).get_concept(cs, uri)
return ConceptRenderer(request, c).render()
except:
return None
return return_vocprez_error(
"Input Error", 400,
"The object with URI {} is not of type skos:ConceptScheme, skos:Collection or skos:Concept "
"and only these classes of object are understood by VocPrez".format(
uri))
def get_concept(self, uri):
vocab = g.VOCABS[self.vocab_uri]
q = """
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT *
WHERE {{
<{concept_uri}> a skos:Concept ;
?p ?o .
OPTIONAL {{
?o skos:prefLabel ?ropl .
}}
}}
""".format(concept_uri=uri)
pl = None
d = None
s = {
"provenance": None,
"source": None,
"wasDerivedFrom": None,
}
annotation_types = {
"http://www.opengis.net/def/metamodel/ogc-na/status": "Status",
'http://www.w3.org/2004/02/skos/core#altLabel':
"Alternative Label",
'http://www.w3.org/2004/02/skos/core#note': "Note",
'http://www.w3.org/2004/02/skos/core#scopeNote': "Scope Note",
'http://www.w3.org/2004/02/skos/core#hostryNote': "History Note",
}
annotations = []
agent_types = {
'http://purl.org/dc/terms/contributor': "Contributor",
'http://purl.org/dc/terms/creator': "Creator",
'http://purl.org/dc/terms/publisher': "Publisher",
}
agent = {}
related_instance_types = {
'http://www.w3.org/2004/02/skos/core#exactMatch': "Exact Match",
'http://www.w3.org/2004/02/skos/core#closeMatch': "Close Match",
'http://www.w3.org/2004/02/skos/core#broadMatch': "Broad Match",
'http://www.w3.org/2004/02/skos/core#narrowMatch': "Narrow Match",
'http://www.w3.org/2004/02/skos/core#broader': "Broader",
'http://www.w3.org/2004/02/skos/core#narrower': "Narrower"
}
provenance_property_types = {
"http://purl.org/pav/hasCurrentVersion": "Has Current Version",
"http://purl.org/pav/version": "Version",
"http://www.w3.org/2002/07/owl#deprecated": "Deprecated",
"http://purl.org/pav/previousVersion": "Previous Version",
"http://purl.org/dc/terms/isVersionOf": "Is Version Of",
"http://purl.org/pav/authoredOn": "Authored On"
}
related_instances = {}
other_properties = []
for r in u.sparql_query(q, vocab.sparql_endpoint,
vocab.sparql_username, vocab.sparql_password):
if r["p"][
"value"] == "http://www.w3.org/2004/02/skos/core#prefLabel":
pl = r["o"]["value"]
elif r["p"][
"value"] == "http://www.w3.org/2004/02/skos/core#definition":
d = r["o"]["value"]
elif r["p"]["value"] == "http://purl.org/dc/terms/provenance":
s["provenance"] = r["o"]["value"]
elif r["p"]["value"] == "http://purl.org/dc/terms/source":
s["source"] = r["o"]["value"]
elif r["p"]["value"] == "http://www.w3.org/ns/prov#wasDerivedFrom":
s["wasDerivedFrom"] = r["o"]["value"]
elif r["p"]["value"] in annotation_types.keys():
annotations.append(
Property(r["p"]["value"],
annotation_types[r["p"]["value"]],
r["o"]["value"]))
elif r["p"]["value"] in related_instance_types.keys():
if related_instances.get(r["p"]["value"]) is None:
related_instances[r["p"]["value"]] = {}
related_instances[r["p"]["value"]] = {
"instances": [],
"label": related_instance_types[r["p"]["value"]]
}
related_instances[r["p"]["value"]]["instances"].append(
(r["o"]["value"], r["ropl"]["value"]
if r.get("ropl") is not None else None))
elif r["p"]["value"] in provenance_property_types.keys():
other_properties.append(
Property(r["p"]["value"],
provenance_property_types[r["p"]["value"]],
r["o"]["value"].rstrip(".0")))
elif r["p"][
"value"] == "http://www.w3.org/2004/02/skos/core#altLabel":
other_properties.append(
Property(r["p"]["value"], "Alternative Label",
r["o"]["value"]))
# TODO: Agents
# TODO: more Annotations
if pl is None:
return None
from vocprez.model.concept import Concept
return Concept(self.vocab_uri,
uri,
pl,
d,
related_instances,
annotations=annotations,
other_properties=other_properties)
def list_concepts_for_a_collection(self, acc_dep=None):
vocab = g.VOCABS[self.vocab_uri]
if acc_dep == "accepted":
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?dep
WHERE {{
<{vocab_uri}> skos:member ?c .
?c <http://www.w3.org/2002/07/owl#deprecated> "false" .
OPTIONAL {{
?c <http://www.w3.org/2002/07/owl#deprecated> ?dep .
}}
?c skos:prefLabel ?pl .
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
elif acc_dep == "deprecated":
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?dep
WHERE {{
<{vocab_uri}> skos:member ?c .
?c <http://www.w3.org/2002/07/owl#deprecated> "true" .
OPTIONAL {{
?c <http://www.w3.org/2002/07/owl#deprecated> ?dep .
}}
?c skos:prefLabel ?pl .
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
else:
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?dep
WHERE {{
<{vocab_uri}> skos:member ?c .
OPTIONAL {{
?c <http://www.w3.org/2002/07/owl#deprecated> ?dep .
}}
?c skos:prefLabel ?pl .
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
return [(concept["c"]["value"], concept["pl"]["value"],
True if concept.get("dep")
and concept["dep"]["value"] == "true" else False)
for concept in
u.sparql_query(q, vocab.sparql_endpoint, vocab.sparql_username,
vocab.sparql_password)]
def list_concepts(self, acc_dep=None):
vocab = g.VOCABS[self.vocab_uri]
if acc_dep == "accepted":
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?broader ?dep
WHERE {{
{{?c skos:inScheme <{vocab_uri}>}}
?c a skos:Concept ;
skos:prefLabel ?pl .
?c <http://www.w3.org/2002/07/owl#deprecated> "false" .
OPTIONAL {{
{{?c skos:broader ?broader}}
UNION
{{?broader skos:narrower ?c}}
}}
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
elif acc_dep == "deprecated":
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?broader ?dep
WHERE {{
{{?c skos:inScheme <{vocab_uri}>}}
?c a skos:Concept ;
skos:prefLabel ?pl .
?c <http://www.w3.org/2002/07/owl#deprecated> "true" .
OPTIONAL {{
{{?c skos:broader ?broader}}
UNION
{{?broader skos:narrower ?c}}
}}
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
else:
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?c ?pl ?broader ?dep
WHERE {{
{{?c skos:inScheme <{vocab_uri}>}}
?c a skos:Concept ;
skos:prefLabel ?pl .
OPTIONAL {{
{{?c skos:broader ?broader}}
UNION
{{?broader skos:narrower ?c}}
}}
FILTER(lang(?pl) = "{language}" || lang(?pl) = "")
}}
ORDER BY ?pl
""".format(vocab_uri=vocab.uri, language=self.language)
return [
(concept["c"]["value"], concept["pl"]["value"],
concept["broader"]["value"] if concept.get("broader") else None)
for concept in u.sparql_query(q, vocab.sparql_endpoint,
vocab.sparql_username,
vocab.sparql_password)
]
def collect(details):
"""
For this source, one SPARQL endpoint is given for a series of vocabs which are all separate ConceptSchemes
'ga-jena-fuseki': {
'source': VocabSource.SPARQL,
'sparql_endpoint': 'http://dev2.nextgen.vocabs.ga.gov.au/fuseki/vocabs',
'sparql_username': '******', # Optional username for SPARQL endpoint
'sparql_password': '******', # Optional password for SPARQL endpoint
#'uri_filter_regex': '.*', # Regular expression to filter vocabulary URIs - Everything
#'uri_filter_regex': '^http(s?)://pid.geoscience.gov.au/def/voc/ga/', # Regular expression to filter vocabulary URIs - GA
#'uri_filter_regex': '^https://gcmdservices.gsfc.nasa.gov', # Regular expression to filter vocabulary URIs - GCMD
'uri_filter_regex': '^http(s?)://resource.geosciml.org/', # Regular expression to filter vocabulary URIs - CGI
},
"""
logging.debug("SPARQL collect()...")
# Get all the ConceptSchemes from the SPARQL endpoint
# Interpret each CS as a Vocab
q = """
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT * WHERE {{
{{?cs a skos:ConceptScheme .}}
UNION
{{?cs a skos:Collection .}}
?cs a ?t .
OPTIONAL {{ ?cs skos:prefLabel ?title .
FILTER(lang(?title) = "{language}" || lang(?title) = "") }}
OPTIONAL {{ ?cs dcterms:created ?created }}
OPTIONAL {{ ?cs dcterms:issued ?issued }}
OPTIONAL {{ ?cs dcterms:date ?modified }}
OPTIONAL {{ ?cs dcterms:modified ?modified }}
OPTIONAL {{ ?cs dcterms:creator ?creator }}
OPTIONAL {{ ?cs dcterms:publisher ?publisher }}
OPTIONAL {{ ?cs owl:versionInfo ?version }}
OPTIONAL {{ ?cs dcterms:description ?description .
FILTER(lang(?description) = "{language}" || lang(?description) = "") }}
# NVS special properties
OPTIONAL {{
?cs <http://www.isotc211.org/schemas/grg/RE_RegisterManager> ?registermanager .
?cs <http://www.isotc211.org/schemas/grg/RE_RegisterOwner> ?registerowner .
}}
OPTIONAL {{ ?cs rdfs:seeAlso ?seeAlso }}
}}
ORDER BY ?title
""".format(language=config.DEFAULT_LANGUAGE)
# record just the IDs & title for the VocPrez in-memory vocabs list
concept_schemes = u.sparql_query(
q,
details[
"sparql_endpoint"], # must specify a SPARQL endpoint if this source is to be a SPARQL source
details.get("sparql_username"),
details.get("sparql_password"),
)
assert concept_schemes is not None, "Unable to query for ConceptSchemes"
sparql_vocabs = {}
for cs in concept_schemes:
vocab_id = cs["cs"]["value"]
other_properties = []
other_properties.append(
Property(
"http://purl.org/dc/terms/identifier", "Identifier",
Literal(cs["cs"]["value"].replace(
"http://vocab.nerc.ac.uk/collection/",
"").replace("http://vocab.nerc.ac.uk/scheme/",
"").replace("/current/", ""))))
if cs.get("registermanager") is not None:
other_properties.append(
Property(
"http://www.isotc211.org/schemas/grg/RE_RegisterManager",
"Register Manager",
Literal(cs["registermanager"]["value"])))
if cs.get("registerowner") is not None:
other_properties.append(
Property(
"http://www.isotc211.org/schemas/grg/RE_RegisterOwner",
"Register Owner",
Literal(cs["registerowner"]["value"])))
if cs.get("seeAlso") is not None:
other_properties.append(
Property("http://www.w3.org/2000/01/rdf-schema#seeAlso",
"See Also", URIRef(cs["seeAlso"]["value"])))
sparql_vocabs[vocab_id] = Vocabulary(
cs["cs"]["value"],
cs["cs"]["value"],
cs["title"].get("value") or vocab_id if cs.get("title") else
vocab_id, # Need str for sorting, not None
cs["description"].get("value")
if cs.get("description") is not None else None,
cs["creator"].get("value")
if cs.get("creator") is not None else None,
dateutil.parser.parse(cs.get("created").get("value"))
if cs.get("created") is not None else None,
# dct:issued not in Vocabulary
# dateutil.parser.parse(cs.get('issued').get('value')) if cs.get('issued') is not None else None,
dateutil.parser.parse(cs.get("modified").get("value"))
if cs.get("modified") is not None else None,
cs["version"].get("value")
if cs.get("version") is not None else None, # versionInfo
config.VocabSource.
NvsSPARQL, # TODO: replace this var with a reference to self class type (Source type)
collections=str(cs["t"]["value"]).split("#")[-1],
sparql_endpoint=details["sparql_endpoint"],
sparql_username=details.get("sparql_username"),
sparql_password=details.get("sparql_password"),
other_properties=other_properties)
logging.debug("pickle latest standard_name")
import requests
from pathlib import Path
import pickle
r = requests.get("http://vocab.nerc.ac.uk/standard_name/")
gr = Graph()
gr.parse(data=r.text, format="xml")
with open(Path(config.APP_DIR) / "cache" / "standard_name.p",
"wb") as f:
pickle.dump(gr, f)
for cs in gr.query(q):
vocab_id = str(cs["cs"])
other_properties = []
other_properties.append(
Property("http://purl.org/dc/terms/identifier", "Identifier",
Literal("standard_name")))
# the following properties are filled with blanks, not None, in the vocab
# if cs.get("registermanager") is not None:
# other_properties.append(
# Property(
# "http://www.isotc211.org/schemas/grg/RE_RegisterManager",
# "Register Manager",
# Literal(cs["registermanager"])
# )
# )
# if cs.get("registerowner") is not None:
# other_properties.append(
# Property(
# "http://www.isotc211.org/schemas/grg/RE_RegisterOwner",
# "Register Owner",
# Literal(cs["registerowner"])
# )
# )
# if cs.get("seeAlso") is not None:
# other_properties.append(
# Property(
# "http://www.w3.org/2000/01/rdf-schema#seeAlso",
# "See Also",
# URIRef(cs["seeAlso"])
# )
# )
sparql_vocabs[vocab_id] = Vocabulary(
"standard_name",
vocab_id,
str(cs["title"]),
str(cs["description"]),
str(cs["creator"]),
None,
# dct:issued not in Vocabulary
# dateutil.parser.parse(cs.get('issued').get('value')) if cs.get('issued') is not None else None,
dateutil.parser.parse(cs.get("modified")),
str(cs["version"]), # versionInfo
config.VocabSource.NvsSPARQL,
collections="Collection", # just like the other Collections
sparql_endpoint=details["sparql_endpoint"],
sparql_username=details.get("sparql_username"),
sparql_password=details.get("sparql_password"),
other_properties=other_properties)
g.VOCABS = {}
g.VOCABS.update(**sparql_vocabs)
logging.debug("NvsSPARQL collect() complete.")
