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"""Sparql queries to get metadata about WIKI and RIF metadata.
NOTE: In the CONSTRUCT queries below, we manually sort the arrays from
the result of a CONSTRUCT. This is because the SPARQL engine does
not provide a guarantee that it will support an ORDER BY clause in a
CONSTRUCT. Using ORDER BY on a solution sequence for a CONSTRUCT or
DESCRIBE query has no direct effect because only SELECT returns a
sequence of results. See:
<https://stackoverflow.com/questions/78186393>
<https://www.w3.org/TR/rdf-sparql-query/#modOrderBy>
"""
from string import Template
from gn3.db.rdf import (
BASE_CONTEXT,
RDF_PREFIXES,
query_frame_and_compact,
update_rdf,
)
WIKI_CONTEXT = BASE_CONTEXT | {
"foaf": "http://xmlns.com/foaf/0.1/",
"dct": "http://purl.org/dc/terms/",
"categories": "gnt:belongsToCategory",
"web_url": "foaf:homepage",
"version": "gnt:hasVersion",
"symbol": "rdfs:label",
"reason": "gnt:reason",
"species": "gnt:species",
"pubmed_ids": "dct:references",
"email": "foaf:mbox",
"initial": "gnt:initial",
"comment": "rdfs:comment",
"created": "dct:created",
"id": "dct:identifier",
}
def __sanitize_result(result: dict) -> dict:
"""Make sure `categories` and `pubmed_ids` are always arrays"""
if not result:
return {}
categories = result.get("categories")
if isinstance(categories, str):
result["categories"] = [categories] if categories else []
result["categories"] = sorted(result["categories"])
pmids = result.get("pubmed_ids")
if isinstance(pmids, str):
result["pubmed_ids"] = [pmids] if pmids else []
if isinstance(pmids, int):
result["pubmed_ids"] = [pmids]
result["pubmed_ids"] = [
int(pmid.split("/")[-1]) if isinstance(pmid, str) else pmid
for pmid in result["pubmed_ids"]
]
result["pubmed_ids"] = sorted(result["pubmed_ids"])
return result
def get_wiki_entries_by_symbol(
symbol: str, sparql_uri: str, graph: str = "<http://genenetwork.org>"
) -> dict:
"""Fetch all the Wiki entries using the symbol"""
# This query uses a sub-query to fetch the latest comment by the
# version id.
query = Template(
"""
$prefix
CONSTRUCT {
?comment rdfs:label ?symbol;
gnt:reason ?reason ;
gnt:species ?species ;
dct:references ?pmid ;
foaf:homepage ?weburl ;
rdfs:comment ?text ;
foaf:mbox ?email ;
gnt:initial ?usercode ;
gnt:belongsToCategory ?category ;
gnt:hasVersion ?max ;
dct:created ?created ;
dct:identifier ?id_ .
} FROM $graph WHERE {
?comment rdfs:label ?text_ ;
gnt:symbol ?symbol ;
rdf:type gnc:GNWikiEntry ;
dct:identifier ?id_ ;
dct:created ?createTime .
FILTER ( LCASE(?symbol) = LCASE('$symbol') ) .
{
SELECT (MAX(?vers) AS ?max) ?id_ WHERE {
?comment dct:identifier ?id_ ;
dct:hasVersion ?vers .
}
}
?comment dct:hasVersion ?max .
OPTIONAL { ?comment gnt:reason ?reason_ } .
OPTIONAL {
?comment gnt:belongsToSpecies ?speciesId .
?speciesId gnt:shortName ?species_ .
} .
OPTIONAL { ?comment dct:references ?pmid_ } .
OPTIONAL { ?comment foaf:homepage ?weburl_ } .
OPTIONAL { ?comment gnt:initial ?usercode_ } .
OPTIONAL { ?comment foaf:mbox ?email_ } .
OPTIONAL { ?comment gnt:belongsToCategory ?category_ } .
BIND (str(?createTime) AS ?created) .
BIND (str(?text_) AS ?text) .
BIND (STR(COALESCE(?pmid_, "")) AS ?pmid) .
BIND (COALESCE(?reason_, "") AS ?reason) .
BIND (STR(COALESCE(?weburl_, "")) AS ?weburl) .
BIND (COALESCE(?usercode_, "") AS ?usercode) .
BIND (STR(COALESCE(?email_, "")) AS ?email) .
BIND (COALESCE(?species_, "") AS ?species) .
BIND (COALESCE(?category_, "") AS ?category) .
}
"""
).substitute(
prefix=RDF_PREFIXES,
graph=graph,
symbol=symbol,
)
results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri)
data = [__sanitize_result(result) for result in results.get("data", {})]
# See note above in the doc-string
results["data"] = sorted(data, key=lambda d: d["created"])
if not data:
return results
return results
def get_comment_history(
comment_id: int, sparql_uri: str, graph: str = "<http://genenetwork.org>"
) -> dict:
"""Get all the historical data for a given id"""
query = Template(
"""
$prefix
CONSTRUCT {
?comment rdfs:label ?symbolName ;
gnt:reason ?reason ;
gnt:species ?species ;
dct:references ?pmid ;
foaf:homepage ?weburl ;
rdfs:comment ?text ;
foaf:mbox ?email ;
gnt:initial ?usercode ;
gnt:belongsToCategory ?category ;
gnt:hasVersion ?version ;
dct:created ?created .
} FROM $graph WHERE {
?comment rdf:type gnc:GNWikiEntry ;
rdfs:label ?text_ ;
gnt:symbol ?symbol ;
dct:created ?createTime ;
dct:hasVersion ?version ;
dct:identifier $comment_id .
OPTIONAL { ?comment gnt:reason ?reason_ } .
OPTIONAL {
?comment gnt:belongsToSpecies ?speciesId .
?speciesId gnt:shortName ?species_ .
} .
OPTIONAL { ?comment dct:references ?pmid_ . } .
OPTIONAL { ?comment foaf:homepage ?weburl_ . } .
OPTIONAL { ?comment gnt:initial ?usercode_ . } .
OPTIONAL { ?comment foaf:mbox ?email_ . } .
OPTIONAL { ?comment gnt:belongsToCategory ?category_ . } .
BIND (str(?text_) AS ?text) .
BIND (str(?createTime) AS ?created) .
BIND (STR(COALESCE(?pmid_, "")) AS ?pmid) .
BIND (COALESCE(?reason_, "") AS ?reason) .
BIND (STR(COALESCE(?weburl_, "")) AS ?weburl) .
BIND (COALESCE(?usercode_, "") AS ?usercode) .
BIND (STR(COALESCE(?email_, "")) AS ?email) .
BIND (COALESCE(?species_, "") AS ?species) .
BIND (COALESCE(?category_, "") AS ?category) .
}
"""
).substitute(prefix=RDF_PREFIXES, graph=graph, comment_id=comment_id)
results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri)
data = [__sanitize_result(result) for result in results.get("data", {})]
# See note above in the doc-string
results["data"] = sorted(data, key=lambda d: d["version"], reverse=True)
return results
def update_wiki_comment(
insert_dict: dict,
sparql_user: str,
sparql_password: str,
sparql_auth_uri: str,
graph: str = "<http://genenetwork.org>",
) -> str:
"""Update a wiki comment by inserting a comment with the same
identifier but an updated version id. The End form of this query
looks like:
INSERT {
GRAPH <http://genenetwork.org> {
[ rdfs:label '''XXXX'''@en] rdf:type gnc:GNWikiEntry ;
gnt:symbol "XXXX" ;
foaf:mbox <XXXX> ;
gnt:initial "XXXX" ;
gnt:belongsToSpecies ?speciesId ;
gnt:reason "XXXX" ;
foaf:homepage <XXXX> ;
dct:references pmid:XXXX ;
dct:references pmid:XXXX ;
gnt:belongsToCategory "XXXX";
gnt:belongsToCategory "XXXX";
dct:hasVersion "123"^^xsd:integer ;
dct:identifier "1"^^xsd:integer ;
dct:created "2024-09-11 11:00"^^xsd:datetime .
} USING <http://genenetwork.org> WHERE {
?speciesId gnt:shortName "{species}" .
}
}
"""
name = f"gn:wiki-{insert_dict['Id']}-{insert_dict['versionId']}"
comment_triple = Template("""$name rdf:label '''$comment'''@en ;
rdf:type gnc:GNWikiEntry ;
gnt:symbol "$symbol" ;
dct:identifier "$comment_id"^^xsd:integer ;
dct:hasVersion "$next_version"^^xsd:integer ;
dct:created "$created"^^xsd:datetime .
""").substitute(
comment=insert_dict["comment"],
name=name, symbol=insert_dict['symbol'],
comment_id=insert_dict["Id"], next_version=insert_dict["versionId"],
created=insert_dict["createtime"])
using = ""
if insert_dict["email"]:
comment_triple += f"{name} foaf:mbox <{insert_dict['email']}> .\n"
if insert_dict["initial"]:
comment_triple += f"{name} gnt:initial \"{insert_dict['initial']}\" .\n"
if insert_dict["species"]:
comment_triple += f"{name} gnt:belongsToSpecies ?speciesId .\n"
using = Template(
""" USING $graph WHERE { ?speciesId gnt:shortName "$species" . } """).substitute(
graph=graph, species=insert_dict["species"]
)
if insert_dict["reason"]:
comment_triple += f"{name} gnt:reason \"{insert_dict['reason']}\" .\n"
if insert_dict["weburl"]:
comment_triple += f"{name} foaf:homepage <{insert_dict['weburl']}> .\n"
for pmid in insert_dict["PubMed_ID"].split():
comment_triple += f"{name} dct:references pubmed:{pmid} .\n"
for category in insert_dict["categories"]:
comment_triple += f'{name} gnt:belongsToCategory "{category}".\n'
return update_rdf(
query=Template(
"""
$prefix
INSERT {
GRAPH $graph {
$comment_triple}
} $using
""").substitute(prefix=RDF_PREFIXES,
graph=graph,
comment_triple=comment_triple,
using=using),
sparql_user=sparql_user,
sparql_password=sparql_password,
sparql_auth_uri=sparql_auth_uri,
)
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