From dee508d46c916caa5080da87a264347479576dd2 Mon Sep 17 00:00:00 2001
From: John Nduli
Date: Wed, 19 Jun 2024 20:53:53 +0300
Subject: fix: use correct prefix and index key; group wiki cache query

---
 gn3/api/search.py         | 2 +-
 scripts/index-genenetwork | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gn3/api/search.py b/gn3/api/search.py
index b3e67cd..588e11d 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -212,7 +212,7 @@ def parse_query(synteny_files_directory: Path, query: str):
     queryparser.add_boolean_prefix("peakchr", "XPC")
     queryparser.add_prefix("description", "XD")
     queryparser.add_prefix("rif", "XRF")
-    queryparser.add_prefix("wikidata", "XRWD")
+    queryparser.add_prefix("wiki", "XWK")
     range_prefixes = ["mean", "peak", "position", "peakmb", "additive", "year"]
     for i, prefix in enumerate(range_prefixes):
         # Treat position specially since it needs its own field processor.
diff --git a/scripts/index-genenetwork b/scripts/index-genenetwork
index 8efe955..5c22b3b 100755
--- a/scripts/index-genenetwork
+++ b/scripts/index-genenetwork
@@ -147,14 +147,14 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX gnt: <http://genenetwork.org/term/>
 PREFIX gnc: <http://genenetwork.org/category/>
 
-SELECT * WHERE {
+SELECT ?symbolName ?speciesName GROUP_CONCAT(DISTINCT ?comment ; separator=\"\\n\") AS ?comment WHERE {
     ?symbol rdfs:comment _:node ;
             rdfs:label ?symbolName .
 _:node rdf:type gnc:NCBIWikiEntry ;
        gnt:belongsToSpecies ?species ;
        rdfs:comment ?comment .
 ?species gnt:shortName ?speciesName .
-}
+} GROUP BY ?speciesName ?symbolName
 """
 
 
@@ -346,7 +346,7 @@ def index_genes(xapian_build_directory: pathlib.Path, chunk_index: int, namespac
 
             Maybe.apply(index_from_dictionary).to_arguments(
                     Just((trait["species"].value, trait["symbol"].value)),
-                    Just("XRWD"),
+                    Just("XWK"),
                     Just(share.wiki_cache)
                     )
 
@@ -488,7 +488,7 @@ def is_data_modified(xapian_directory: str,
                      sparql_uri: str) -> None:
     dir_ = pathlib.Path(xapian_directory)
     with locked_xapian_writable_database(dir_) as db, database_connection(sql_uri) as conn:
-        checksums = ""
+        checksums = "-1"
         if db.get_metadata('tables'):
             checksums = " ".join([
                 str(result["Checksum"].value)
-- 
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