def sparql(self, select='*', body=None, inject_prefixes=None, single_column=False):
"""
Execute a SPARQL query.
The query is specified using `select` and `body` parameters.
The argument for the Named Graph is injected into the query.
The select parameter should be either '*' or a list of vars (not prefixed with '?').
- If '*' is passed, then the result is a list of dicts, { $var: {value: $val } }
- If a list of vars is passed, then the result is a list of lists
- Unless single_column=True, in which case the results are a simple list of values from the first var
The inject_prefixes argument can be used to inject a list of prefixes - these are expanded
using the prefixcommons library
"""
if inject_prefixes is None:
inject_prefixes = []
namedGraph = get_named_graph(self.handle)
cols = []
select_val = None
if select is None or select=='*':
if not single_column:
cols=None
select_val='*'
else:
if isinstance(cols,list):
cols = [select]
else:
cols = select
select_val = ", ".join(['?'+c for c in cols])
prefixes = ""
if inject_prefixes is not None:
plist = ["prefix {}: <{}> ".format(p,expand_uri(p+":")) for p in inject_prefixes if p != "" and p is not None]
prefixes = "\n".join(plist)
query = """
{prefixes}
SELECT {s} WHERE {{
GRAPH <{g}> {{
{b}
}}
}}
""".format(prefixes=prefixes, s=select_val, b=body, g=namedGraph)
bindings = run_sparql(query)
if len(bindings) == 0:
return []
if cols is None:
return bindings
else:
if single_column:
c = list(bindings[0].keys())[0]
return [r[c]['value'] for r in bindings]
else:
return [r[c]['value'] for c in cols for r in bindings]
def subsets(self):
"""
Find all subsets for an ontology
"""
# note subsets have an unusual encoding
query = """
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT DISTINCT ?s WHERE {{
GRAPH <{g}> {{
?c oboInOwl:inSubset ?s
}}
}}
""".format(g=self.graph_name)
bindings = run_sparql(query)
return [r['s']['value'] for r in bindings]
def _search(self, searchterm, pred, **args):
"""
Search for things using labels
"""
# TODO: DRY with sparql_ontol_utils
searchterm = searchterm.replace('%','.*')
namedGraph = get_named_graph(self.handle)
query = """
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT ?c WHERE {{
GRAPH <{g}> {{
?c {pred} ?l
FILTER regex(?l,'{s}','i')
}}
}}
""".format(pred=pred, s=searchterm, g=namedGraph)
bindings = run_sparql(query)
return [r['c']['value'] for r in bindings]
def extract_subset(self, subset):
"""
Find all nodes in a subset.
We assume the oboInOwl encoding of subsets, and subset IDs are IRIs
"""
# note subsets have an unusual encoding
query = """
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT ?c WHERE {{
GRAPH <{g}> {{
?c oboInOwl:inSubset ?s
FILTER regex(?s,'#{s}$','i')
}}
}}
""".format(s=subset, g=self.graph_name)
bindings = run_sparql(query)
return [r['c']['value'] for r in bindings]
