Fetch all the wiki entries by symbol.

* gn3/api/metadata.py: Import "get_wiki_entries_by_symbol".
(get_gn_genewiki_entries): Rename this to...
(get_wiki_entries): this; and update the URL endpoint.
* gn3/db/rdf.py: Import constants.BASE_CONTEXT.
(get_wiki_entries_by_symbol): New function.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 67 insertions, 2 deletions

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