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"""RDF utilities
This module is a collection of functions that handle SPARQL queries.
"""
from typing import Tuple
from string import Template
from urllib.parse import unquote
from urllib.parse import urlparse
from SPARQLWrapper import JSON, SPARQLWrapper
from pymonad.maybe import Just
from gn3.monads import MonadicDict
RDF_PREFIXES = """PREFIX dct: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
PREFIX gn: <http://genenetwork.org/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
"""
def sparql_query(
sparql_conn: SPARQLWrapper, query: str,
) -> Tuple[MonadicDict, ...]:
"""Run a SPARQL query and return the bound variables."""
sparql_conn.setQuery(query)
sparql_conn.setReturnFormat(JSON)
parsed_response = MonadicDict()
results = sparql_conn.queryAndConvert()["results"]["bindings"] # type: ignore
if results:
for result in results:
if "s" in result: # A CONSTRUCT
parsed_response[
get_url_local_name(
result["p"]["value"] # type: ignore
)
] = Just(result["o"]["value"]) # type: ignore
elif "key" in result: # A SELECT
parsed_response[
result["key"] # type: ignore
] = Just(result["value"]) # type: ignore
return (parsed_response,)
def get_url_local_name(string: str) -> str:
"""Get the last item after a '/" from a URL"""
if string.startswith("http"):
url = urlparse(string)
return unquote(url.path).rpartition("/")[-1]
return string
def get_dataset_metadata(
sparql_conn: SPARQLWrapper, name: str
) -> MonadicDict:
"""Return info about dataset with a given NAME"""
__metadata_query = """
$prefix
CONSTRUCT {
gn:dataset ?datasetTerm ?datasetValue .
gn:dataset ?platformName ?platform_name .
gn:dataset gn:normalization ?normalization .
gn:dataset gn:investigatorName ?investigatorName .
gn:dataset gn:investigatorWebUrl ?investigatorWebUrl .
gn:dataset gn:tissueName ?tissueName .
gn:dataset gn:organism ?speciesDisplayName .
gn:dataset gn:organismUrl ?ncbiReference .
gn:dataset gn:inbredSetName ?inbredSetName .
gn:dataset gn:geoPlatformUrl ?geoPlatform .
gn:dataset gn:platformName ?platform_name .
} WHERE {
?subClass rdf:subClassOf gn:dataset .
?dataset rdf:type ?subclass ;
gn:name "$name";
?datasetTerm ?datasetValue .
OPTIONAL {
?dataset gn:datasetOfInvestigator ?investigator .
?investigator foaf:name ?investigatorName .
?investigator foaf:homepage ?investigatorWebUrl .
} .
OPTIONAL{
?dataset gn:normalization ?normalizationType .
?normalizationType gn:name ?normalization .
} .
OPTIONAL{
?dataset gn:datasetOfSpecies ?species .
?species gn:displayName ?speciesDisplayName .
?species gn:organism ?ncbiReference .
} .
OPTIONAL {
?dataset gn:datasetOfInbredSet ?inbredSet .
?inbredSet gn:binomialName ?inbredSetName .
?inbredSet gn:inbredSetOfSpecies ?species .
?species gn:displayName ?speciesDisplayName .
?species gn:organism ?ncbiReference .
} .
OPTIONAL{
?dataset gn:datasetOfPlatform ?platform .
?platform gn:name ?platform_name .
?platform gn:geoPlatform ?geoPlatform .
} .
OPTIONAL{
?dataset gn:datasetOfTissue ?tissue .
?tissue gn:name ?tissueName .
} .
VALUES ?datasetTerm {
dct:created gn:aboutCases gn:aboutDataProcessing gn:aboutPlatform
gn:aboutTissue gn:accessionId gn:acknowledgment gn:citation
gn:contributors gn:datasetGroup gn:datasetOfinvestigator
gn:experimentDesign gn:geoSeries gn:name gn:notes
gn:specifics gn:summary gn:title gn:publicationTitle
gn:datasetStatusName gn:datasetOfOrganization
}
}
"""
response: MonadicDict = MonadicDict()
for key, value in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(
prefix=RDF_PREFIXES,
name=name
)
)[0].items():
if key.endswith("Url") or key == "geoSeries":
response[key] = value
else:
response[key] = value.map(get_url_local_name)
return response
def get_trait_metadata(
sparql_conn: SPARQLWrapper,
trait_name: str,
dataset_name: str
):
"""Return metadata about a given trait"""
__metadata_query = """
PREFIX gn: <http://genenetwork.org/>
SELECT strafter((str(?key)), "http://genenetwork.org/sampledata:") as ?key
?value WHERE {
gn:sampledata_$trait_name gn:sampledata:dataset "$dataset_name" .
gn:sampledata_$trait_name ?key ?value .
}
"""
result: MonadicDict = MonadicDict()
for _r in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(trait_name=trait_name,
dataset_name=dataset_name)
):
_key = _r["key"].bind(lambda x: x["value"]) # type:ignore
if _key:
result[_key] = _r["value"].bind(lambda x: Just(x["value"])) # type:ignore
return result
|
