From b9fb2c69136fe243fc9c6f7c3c4f8917814a401e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 12 Aug 2023 13:52:25 +0200
Subject: Add SPARQL prefix

---
 README.md        |  6 ++++++
 gn/db/sparql.scm | 22 ++++++++++++----------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index cf753b0..12f3050 100644
--- a/README.md
+++ b/README.md
@@ -21,6 +21,12 @@ Note the leading dot. The .guix-shell is defined in `genenetwork3/gn3-guile/web`
 
 Next fire up emacs with `emacs-geiser-guile` and connect to the running web server with `M-x geiser-connect` and the port `1970`. Now you can not only inspect procedures, but also update any prodedure on the live server using `C-M-x` and get updated output from the webserver!
 
+# Development
+
+```
+git remote add gn git.genenetwork.org:/home/git/public/gn-guile
+```
+
 # LICENSE
 
 This software is published by the GeneNetwork team under the AGPL3. See [LICENSE](LICENSE.txt).
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm
index 6c3b5b2..95b4e1d 100644
--- a/gn/db/sparql.scm
+++ b/gn/db/sparql.scm
@@ -24,6 +24,16 @@
 (define (wd-sparql-endpoint-url)
   "https://query.wikidata.org/sparql")
 
+(define (gn-sparql-prefix query)
+  (string-append
+  "
+PREFIX gn:  <http://genenetwork.org/id/>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+" query))
+
 (define (wdt-taxon-name) "wdt:P225")
 
 (define (sparql-exec endpoint-url query)
@@ -56,7 +66,8 @@
 
 (define (sparql-scm endpoint-url query)
   "Return dual S-exp 'resultset' of varnames and results"
-  (let ((response (json-string->scm (sparql-exec endpoint-url query))))
+  (let ((response (json-string->scm
+                   (sparql-exec endpoint-url (gn-sparql-prefix query)))))
    (values (sparql-names response) (sparql-results response))))
 
 (define (tsv->scm text)
@@ -136,10 +147,6 @@ gn:Mus_musculus gnt:organism taxon:10090 .
 
 (define (sparql-species)
   (sparql-scm (gn-sparql-endpoint-url) "
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-
 SELECT DISTINCT ?species WHERE {
     ?species rdf:type gnc:species .
 }"))
@@ -150,11 +157,6 @@ SELECT DISTINCT ?species WHERE {
 (define (sparql-species-meta)
   "Return values names recs"
   (sparql-scm (gn-sparql-endpoint-url) "
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <http://genenetwork.org/term/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-
 SELECT ?species ?p ?o WHERE {
    MINUS { ?species rdf:type ?o . }
 {
-- 
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