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-rw-r--r--gn3/api/metadata.py98
1 files changed, 8 insertions, 90 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"])