def get_csdh_schemes():
"""Loads SKOS Schemes (code lists) from the CSDH"""
log.debug("Querying CSDH Cloud")
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?uri ?label WHERE {
{
?c skos:inScheme ?uri .
?uri rdfs:label ?label .
}
UNION
{
?uri skos:member ?c .
?uri rdfs:label ?label .
}
}
"""
schemes_results = sc.sparql(query)
log.debug(schemes_results)
schemes = sc.dictize(schemes_results)
log.debug(schemes)
return schemes
def get_csdh_schemes():
"""Loads SKOS Schemes (code lists) from the CSDH"""
log.debug("Querying CSDH Cloud")
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?uri ?label WHERE {
{
?c skos:inScheme ?uri .
?uri rdfs:label ?label .
}
UNION
{
?uri skos:member ?c .
?uri rdfs:label ?label .
}
}
"""
schemes_results = sc.sparql(query)
log.debug(schemes_results)
schemes = sc.dictize(schemes_results)
log.debug(schemes)
return schemes
def get_concepts(uri):
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?uri ?label ?notation WHERE {{
{{ ?uri skos:inScheme <{URI}> . }}
UNION
{{ <{URI}> skos:member+ ?uri . }}
?uri skos:prefLabel ?label .
OPTIONAL {{ ?uri skos:notation ?notation . }}
}}
""".format(URI=uri)
lod_codelist = []
sdh_codelist = []
try:
log.debug("Querying the LOD cloud cache")
# First we go to the LOD cloud
sparql = SPARQLWrapper('http://lod.openlinksw.com/sparql')
sparql.setTimeout(1)
sparql.setReturnFormat(JSON)
sparql.setQuery(query)
lod_codelist_results = sparql.query().convert()['results']['bindings']
if len(lod_codelist_results) > 0:
lod_codelist = sc.dictize(lod_codelist_results)
else:
lod_codelist = []
log.debug(lod_codelist)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the LOD cloud')
lod_codelist = []
try:
log.debug("Querying the SDH")
# Then we have a look locally
sdh_codelist_results = sc.sparql(query)
if len(sdh_codelist_results) > 0:
sdh_codelist = sc.dictize(sdh_codelist_results)
else:
sdh_codelist = []
log.debug(sdh_codelist)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the SDH')
sdh_codelist = []
return lod_codelist + sdh_codelist
def get_concepts(uri):
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?uri ?label ?notation WHERE {{
{{ ?uri skos:inScheme <{URI}> . }}
UNION
{{ <{URI}> skos:member+ ?uri . }}
?uri skos:prefLabel ?label .
OPTIONAL {{ ?uri skos:notation ?notation . }}
}}
""".format(URI=uri)
lod_codelist = []
sdh_codelist = []
try:
log.debug("Querying the LOD cloud cache")
# First we go to the LOD cloud
sparql = SPARQLWrapper('http://lod.openlinksw.com/sparql')
sparql.setTimeout(1)
sparql.setReturnFormat(JSON)
sparql.setQuery(query)
lod_codelist_results = sparql.query().convert()['results']['bindings']
if len(lod_codelist_results) > 0:
lod_codelist = sc.dictize(lod_codelist_results)
else:
lod_codelist = []
log.debug(lod_codelist)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the LOD cloud')
lod_codelist = []
try:
log.debug("Querying the SDH")
# Then we have a look locally
sdh_codelist_results = sc.sparql(query)
if len(sdh_codelist_results) > 0:
sdh_codelist = sc.dictize(sdh_codelist_results)
else:
sdh_codelist = []
log.debug(sdh_codelist)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the SDH')
sdh_codelist = []
return lod_codelist + sdh_codelist
def get_datasets():
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX qb: <http://purl.org/linked-data/cube#>
PREFIX prov: <http://www.w3.org/ns/prov#>
SELECT DISTINCT ?uri ?label ?owner ?nanopublication WHERE {
?nanopublication a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri .
GRAPH ?assertion_uri {
?uri a qb:DataSet ;
rdfs:label ?label .
}
GRAPH ?pubinfo_uri {
?nanopublication prov:wasAttributedTo ?owner .
}
}
"""
dataset_list = []
try:
log.debug("Querying the SDH")
# Then we have a look locally
sdh_datasets_results = sc.sparql(query)
if len(sdh_datasets_results) > 0:
dataset_list = sc.dictize(sdh_datasets_results)
else:
dataset_list = []
log.debug(dataset_list)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the SDH')
dataset_list = []
return dataset_list
def get_datasets():
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX qb: <http://purl.org/linked-data/cube#>
PREFIX prov: <http://www.w3.org/ns/prov#>
SELECT DISTINCT ?uri ?label ?owner ?nanopublication WHERE {
?nanopublication a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri .
GRAPH ?assertion_uri {
?uri a qb:DataSet ;
rdfs:label ?label .
}
GRAPH ?pubinfo_uri {
?nanopublication prov:wasAttributedTo ?owner .
}
}
"""
dataset_list = []
try:
log.debug("Querying the SDH")
# Then we have a look locally
sdh_datasets_results = sc.sparql(query)
if len(sdh_datasets_results) > 0:
dataset_list = sc.dictize(sdh_datasets_results)
else:
dataset_list = []
log.debug(dataset_list)
except Exception as e:
log.error(e)
log.error('Could not retrieve anything from the SDH')
dataset_list = []
return dataset_list
def get_csdh_dimensions():
"""Loads the list of Linked Statistical Data dimensions (variables) from the CSDH"""
log.debug("Loading dimensions from the CSDH")
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT DISTINCT ?uri ?label ("CSDH" as ?refs) WHERE {
{
?uri a qb:DimensionProperty .
?uri rdfs:label ?label .
}
UNION
{
?uri a qb:MeasureProperty .
?uri rdfs:label ?label .
}
UNION
{
?uri a qb:AttributeProperty .
?uri rdfs:label ?label .
}
}
"""
sdh_dimensions_results = sc.sparql(query)
try:
if len(sdh_dimensions_results) > 0:
sdh_dimensions = sc.dictize(sdh_dimensions_results)
else:
sdh_dimensions = []
except Exception as e:
log.error(e)
sdh_dimensions = []
return sdh_dimensions
def get_csdh_dimensions():
"""Loads the list of Linked Statistical Data dimensions (variables) from the CSDH"""
log.debug("Loading dimensions from the CSDH")
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT DISTINCT ?uri ?label ("CSDH" as ?refs) WHERE {
{
?uri a qb:DimensionProperty .
?uri rdfs:label ?label .
}
UNION
{
?uri a qb:MeasureProperty .
?uri rdfs:label ?label .
}
UNION
{
?uri a qb:AttributeProperty .
?uri rdfs:label ?label .
}
}
"""
sdh_dimensions_results = sc.sparql(query)
try:
if len(sdh_dimensions_results) > 0:
sdh_dimensions = sc.dictize(sdh_dimensions_results)
else:
sdh_dimensions = []
except Exception as e:
log.error(e)
sdh_dimensions = []
return sdh_dimensions
def delete_dataset(uri):
log.warning("TODO: Untested! Unsafe!")
uri = uri.strip()
query = """
PREFIX np: <http://www.nanopub.org/nschema#>
SELECT DISTINCT ?assertion_uri ?pubinfo_uri ?provenance_uri WHERE {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
}}
""".format(URI=uri)
def clear_graph(uri):
clear_query_template = """
DEFINE sql:log-enable 2
CLEAR GRAPH <{}>
"""
clear_query = clear_query_template.format(uri)
log.debug("Clearing graph {}".format(uri))
return sc.sparql_update(clear_query)
def delete_publication(uri):
delete_query = """
PREFIX np: <http://www.nanopub.org/nschema#>
DELETE {{ GRAPH ?g {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
?assertion_uri a np:Assertion .
?pubinfo_uri a np:PublicationInfo .
?provenance_uri a np:Provenance .
}}}}
WHERE {{ GRAPH ?g {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
?assertion_uri a np:Assertion .
?pubinfo_uri a np:PublicationInfo .
?provenance_uri a np:Provenance .
}}}}
""".format(URI=uri)
log.debug("Removing the nanopublication {}...".format(uri))
return sc.sparql_update(delete_query)
nanopub = {}
try:
log.debug("Querying the SDH")
# Then we have a look locally
nanopub_results = sc.sparql(query)
if len(nanopub_results) > 0:
nanopub = sc.dictize(nanopub_results)[0]
log.debug(nanopub)
t_assertion = Thread(target=clear_graph, args=(nanopub['assertion_uri'],))
t_assertion.start()
t_provenance = Thread(target=clear_graph, args=(nanopub['provenance_uri'],))
t_provenance.start()
t_pubinfo = Thread(target=clear_graph, args=(nanopub['pubinfo_uri'],))
t_pubinfo.start()
t_publication = Thread(target=delete_publication, args=(uri,))
t_publication.start()
return "Called delete functions for {}".format(uri)
else:
return "No matching nanopublication found"
log.debug(nanopub)
except Exception as e:
log.error(e)
log.error("Could not retrieve anything from the SDH")
log.debug(nanopub_results)
return "Could not retrieve anything from the SDH"
return "Not implemented"
def get_definition(uri):
exists = sc.ask(uri, template="""
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
ASK {{<{}> rdfs:label ?l .}}""")
if not exists:
success, visited = sc.resolve(uri, depth=2)
print "Resolved ", visited
else:
success = True
if success:
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT (<{URI}> as ?uri) ?type ?label ?description ?concept_uri WHERE {{
OPTIONAL
{{
<{URI}> rdfs:label ?label .
}}
OPTIONAL
{{
<{URI}> rdfs:comment ?description .
}}
OPTIONAL
{{
<{URI}> a qb:DimensionProperty .
BIND(qb:DimensionProperty AS ?type )
}}
OPTIONAL
{{
<{URI}> qb:concept ?measured_concept .
}}
OPTIONAL
{{
<{URI}> a qb:MeasureProperty .
BIND(qb:MeasureProperty AS ?type )
}}
OPTIONAL
{{
<{URI}> a qb:AttributeProperty .
BIND(qb:AttributeProperty AS ?type )
}}
}}
""".format(URI=uri)
results = sc.sparql(query)
log.debug(results)
# Turn into something more manageable, and take only the first element.
variable_definition = sc.dictize(results)[0]
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT DISTINCT ?uri ?label WHERE {{
<{URI}> a qb:CodedProperty .
BIND(qb:DimensionProperty AS ?type )
<{URI}> qb:codeList ?uri .
?uri rdfs:label ?label .
}}""".format(URI=uri)
codelist_results = sc.sparql(query)
log.debug(codelist_results)
if len(codelist_results) > 0:
codelist = sc.dictize(codelist_results)
log.debug(codelist)
# Only take the first result (won't allow multiple code lists)
# TODO: Check how this potentially interacts with user-added codes and lists
variable_definition['codelist'] = codelist[0]
else:
log.debug("No codelist for this variable")
log.debug("Definition for: {}".format(uri))
log.debug(variable_definition)
return variable_definition
else:
raise(Exception("Could not find the definition for <{}> online, nor in the CSDH".format(uri)))
def delete_dataset(uri):
log.warning("TODO: Untested! Unsafe!")
uri = uri.strip()
query = """
PREFIX np: <http://www.nanopub.org/nschema#>
SELECT DISTINCT ?assertion_uri ?pubinfo_uri ?provenance_uri WHERE {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
}}
""".format(URI=uri)
def clear_graph(uri):
clear_query_template = """
DEFINE sql:log-enable 2
CLEAR GRAPH <{}>
"""
clear_query = clear_query_template.format(uri)
log.debug("Clearing graph {}".format(uri))
return sc.sparql_update(clear_query)
def delete_publication(uri):
delete_query = """
PREFIX np: <http://www.nanopub.org/nschema#>
DELETE {{ GRAPH ?g {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
?assertion_uri a np:Assertion .
?pubinfo_uri a np:PublicationInfo .
?provenance_uri a np:Provenance .
}}}}
WHERE {{ GRAPH ?g {{
<{URI}> a np:Nanopublication ;
np:hasAssertion ?assertion_uri ;
np:hasPublicationInfo ?pubinfo_uri ;
np:hasProvenance ?provenance_uri .
?assertion_uri a np:Assertion .
?pubinfo_uri a np:PublicationInfo .
?provenance_uri a np:Provenance .
}}}}
""".format(URI=uri)
log.debug("Removing the nanopublication {}...".format(uri))
return sc.sparql_update(delete_query)
nanopub = {}
try:
log.debug("Querying the SDH")
# Then we have a look locally
nanopub_results = sc.sparql(query)
if len(nanopub_results) > 0:
nanopub = sc.dictize(nanopub_results)[0]
log.debug(nanopub)
t_assertion = Thread(target=clear_graph,
args=(nanopub['assertion_uri'], ))
t_assertion.start()
t_provenance = Thread(target=clear_graph,
args=(nanopub['provenance_uri'], ))
t_provenance.start()
t_pubinfo = Thread(target=clear_graph,
args=(nanopub['pubinfo_uri'], ))
t_pubinfo.start()
t_publication = Thread(target=delete_publication, args=(uri, ))
t_publication.start()
return "Called delete functions for {}".format(uri)
else:
return "No matching nanopublication found"
log.debug(nanopub)
except Exception as e:
log.error(e)
log.error("Could not retrieve anything from the SDH")
log.debug(nanopub_results)
return "Could not retrieve anything from the SDH"
return "Not implemented"
def get_definition(uri):
exists = sc.ask(uri,
template="""
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
ASK {{<{}> rdfs:label ?l .}}""")
if not exists:
success, visited = sc.resolve(uri, depth=2)
print "Resolved ", visited
else:
success = True
if success:
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT (<{URI}> as ?uri) ?type ?label ?description ?concept_uri WHERE {{
OPTIONAL
{{
<{URI}> rdfs:label ?label .
}}
OPTIONAL
{{
<{URI}> rdfs:comment ?description .
}}
OPTIONAL
{{
<{URI}> a qb:DimensionProperty .
BIND(qb:DimensionProperty AS ?type )
}}
OPTIONAL
{{
<{URI}> qb:concept ?measured_concept .
}}
OPTIONAL
{{
<{URI}> a qb:MeasureProperty .
BIND(qb:MeasureProperty AS ?type )
}}
OPTIONAL
{{
<{URI}> a qb:AttributeProperty .
BIND(qb:AttributeProperty AS ?type )
}}
}}
""".format(URI=uri)
results = sc.sparql(query)
log.debug(results)
# Turn into something more manageable, and take only the first element.
variable_definition = sc.dictize(results)[0]
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX qb: <http://purl.org/linked-data/cube#>
SELECT DISTINCT ?uri ?label WHERE {{
<{URI}> a qb:CodedProperty .
BIND(qb:DimensionProperty AS ?type )
<{URI}> qb:codeList ?uri .
?uri rdfs:label ?label .
}}""".format(URI=uri)
codelist_results = sc.sparql(query)
log.debug(codelist_results)
if len(codelist_results) > 0:
codelist = sc.dictize(codelist_results)
log.debug(codelist)
# Only take the first result (won't allow multiple code lists)
# TODO: Check how this potentially interacts with user-added codes and lists
variable_definition['codelist'] = codelist[0]
else:
log.debug("No codelist for this variable")
log.debug("Definition for: {}".format(uri))
log.debug(variable_definition)
return variable_definition
else:
raise (Exception(
"Could not find the definition for <{}> online, nor in the CSDH".
format(uri)))
