diff options
| -rw-r--r-- | gn3/api/metadata.py | 98 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 69 |
2 files changed, 75 insertions, 92 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 2e26489..d8f16f9 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -16,7 +16,8 @@ from gn3.db.datasets import (retrieve_metadata, get_history) from gn3.db.rdf import RDF_PREFIXES from gn3.db.rdf import (query_frame_and_compact, - query_and_compact) + query_and_compact, + get_wiki_entries_by_symbol) from gn3.db.constants import ( RDF_PREFIXES, BASE_CONTEXT, DATASET_CONTEXT, SEARCH_CONTEXT, @@ -394,95 +395,12 @@ CONSTRUCT { ) -@metadata.route("/genewikis/gn/<symbol>", methods=["GET"]) -def get_gn_genewiki_entries(symbol): - """Fetch the GN and NCBI GeneRIF entries""" - args = request.args - page = args.get("page", 0) - page_size = args.get("per-page", 10) - _query = Template(""" -$prefix - -CONSTRUCT { - ?symbol ex:entries [ - rdfs:comment ?comment ; - ex:species ?species_ ; - dct:created ?createTime ; - dct:references ?pmids ; - dct:creator ?creator ; - gnt:belongsToCategory ?categories ; - ] . - ?symbol rdf:type gnc:GNWikiEntry ; - ex:totalCount ?totalCount ; - ex:currentPage $offset . -} WHERE { -{ - SELECT ?symbol ?comment - (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_) - ?createTime ?creator - (GROUP_CONCAT(DISTINCT ?pubmed; SEPARATOR='; ') AS ?pmids) - (GROUP_CONCAT(DISTINCT ?category; SEPARATOR='; ') AS ?categories) - WHERE { - ?symbol rdfs:label ?label ; - rdfs:comment _:entry . - ?label bif:contains "'$symbol'" . - _:entry rdf:type gnc:GNWikiEntry ; - rdfs:comment ?comment . - OPTIONAL { - ?species ^xkos:classifiedUnder _:entry ; - ^skos:member gnc:Species ; - skos:prefLabel ?speciesName . - } . - OPTIONAL { _:entry dct:created ?createTime . } . - OPTIONAL { _:entry dct:references ?pubmed . } . - OPTIONAL { - ?investigator foaf:name ?creator ; - ^dct:creator _:entry . - } . - OPTIONAL { _:entry gnt:belongsToCategory ?category . } . - } GROUP BY ?comment ?symbol ?createTime - ?creator ORDER BY ?createTime LIMIT $limit OFFSET $offset -} - -{ - SELECT (COUNT(DISTINCT ?comment)/$limit+1 AS ?totalCount) WHERE { - ?symbol rdfs:comment _:entry ; - rdfs:label ?label . - _:entry rdfs:comment ?comment ; - rdf:type gnc:GNWikiEntry . - ?label bif:contains "'$symbol'" . - } -} -} -""").substitute(prefix=RDF_PREFIXES, symbol=symbol, - limit=page_size, offset=page) - _context = { - "@context": BASE_CONTEXT | { - "ex": "http://example.org/stuff/1.0/", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "gnt": "http://genenetwork.org/term/", - "gnc": "http://genenetwork.org/category/", - "dct": "http://purl.org/dc/terms/", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "entries": "ex:entries", - "comment": "rdfs:comment", - "species": "ex:species", - "category": 'gnt:belongsToCategory', - "author": "dct:creator", - "pubmed": "dct:references", - "currentPage": "ex:currentPage", - "pages": "ex:totalCount", - "created": { - "@id": "dct:created", - "@type": "xsd:datetime" - }, - }, - "type": "gnc:GNWikiEntry" - } - return query_frame_and_compact( - _query, _context, - current_app.config.get("SPARQL_ENDPOINT") - ) +@metadata.route("/wiki/<symbol>", methods=["GET"]) +def get_wiki_entries(symbol): + """Fetch wiki entries""" + return get_wiki_entries_by_symbol( + symbol=symbol, + sparql_uri=current_app.config.get("SPARQL_ENDPOINT")) @metadata.route("/genewikis/ncbi/<symbol>", methods=["GET"]) diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index c5a8d7f..9d6346b 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -4,11 +4,11 @@ This module is a collection of functions that handle SPARQL queries. """ import json - +from string import Template from SPARQLWrapper import SPARQLWrapper from pyld import jsonld # type: ignore from gn3.db.constants import ( - RDF_PREFIXES + RDF_PREFIXES, BASE_CONTEXT ) @@ -43,3 +43,68 @@ def query_and_frame(query: str, context: dict, endpoint: str) -> dict: if not results: return {} return jsonld.frame(results, context) + + +def get_wiki_entries_by_symbol(symbol: str, sparql_uri: str) -> dict: + """Fetch all the Wiki entries using the symbol""" + # FIXME: Get the latest VersionId of a comment. + query = Template(""" +$prefix + +CONSTRUCT { + _:node rdfs:label '$symbol'; + gnt:reason ?reason ; + gnt:species ?species ; + dct:references ?pmid ; + foaf:homepage ?weburl ; + rdfs:comment ?wikientry ; + foaf:mbox ?email ; + gnt:initial ?usercode ; + gnt:belongsToCategory ?category ; + gnt:hasVersion ?versionId +} WHERE { + ?symbolId rdfs:comment _:node ; + rdfs:label '$symbol' . + _:node rdf:type gnc:GNWikiEntry ; + dct:hasVersion "0"^^xsd:int ; + dct:hasVersion ?version ; + rdfs:comment ?wikientry . + OPTIONAL { _:node gnt:reason ?reason } . + OPTIONAL { + _:node gnt:belongsToSpecies ?speciesId . + ?speciesId gnt:shortName ?species . + } . + OPTIONAL { _:node dct:references ?pubmedId . } . + OPTIONAL { _:node foaf:homepage ?weburl . } . + OPTIONAL { _:node gnt:initial ?usercode . } . + OPTIONAL { _:node gnt:mbox ?email . } . + OPTIONAL { _:node gnt:belongsToCategory ?category . } + BIND (str(?version) AS ?versionId) . + BIND (str(?pubmedId) AS ?pmid) +} +""").substitute(prefix=RDF_PREFIXES, symbol=symbol,) + 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_id": "dct:references", + "web_url": "foaf:homepage", + "email": "foaf:mbox", + "initial": "gnt:initial", + "comment": "rdfs:comment" + } + results = query_frame_and_compact( + query, context, + sparql_uri + ) + if data := results.get("data"): + for result in data: + if result.get("categories"): + result["categories"] = list(map(str.strip, + result.get("categories").split(";"))) + return results |