From 2a8ae48a36cc88105c9a4c056132c9a47e2f120a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 27 Aug 2023 11:24:08 +0200
Subject: Shortnames

---
 gn/data/species.scm | 5 +++++
 gn/db/sparql.scm    | 2 +-
 test/runner.scm     | 6 ++++++
 web/gn-uri.scm      | 7 ++++---
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/gn/data/species.scm b/gn/data/species.scm
index a712bae..100cccf 100644
--- a/gn/data/species.scm
+++ b/gn/data/species.scm
@@ -11,9 +11,11 @@
 
   #:export (
             gnid-species
+            get-species
             get-species-meta
             get-species-data
             get-species-shortnames
+            get-species-binominal-names
             get-expanded-species
             get-expanded-taxon-meta
             get-expanded-taxon-data
@@ -95,6 +97,9 @@
 (define (get-species-shortnames recs)
   (map (lambda r (assoc-ref (car r) "shortName")) recs))
 
+(define (get-species-binominal-names recs)
+  (map (lambda r (url-parse-id (car (car r)))) recs))
+
 (define (get-species-meta2 recs)
   "Return a list of short names and expand them to URIs"
   (map (lambda r
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm
index 7e512ff..c413b9a 100644
--- a/gn/db/sparql.scm
+++ b/gn/db/sparql.scm
@@ -100,7 +100,7 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 (define recs '())
 (define h (compile-species recs table))
 (assoc "http://genenetwork.org/species_drosophila_melanogaster" h)
-(assoc-ref h "http://genenetwork.org/species_drosophila_melanogaster") ;; note switch!
+(assoc-ref h "http://genenetwork.org/id/Drosophila_melanogaster")
 (define d (car h))
 (assoc-ref (list d) "http://genenetwork.org/species_drosophila_melanogaster")
 
diff --git a/test/runner.scm b/test/runner.scm
index 5555dc2..da42235 100644
--- a/test/runner.scm
+++ b/test/runner.scm
@@ -10,6 +10,12 @@
 
 (test-begin "runner")
 
+(test-equal "species short names"
+  (get-species-shortnames (get-species)) #f)
+
+(test-equal "species binominal identifiers"
+  (get-species-binominal-names (get-species)) '("Solanum_lycopersicum" "Rattus_norvegicus" "Populus_trichocarpa" "Mus_musculus" "Hordeum_vulgare" "Homo_sapiens" "Glycine_max" "Arabidopsis_thaliana" "Oryzias_latipes" "Macaca_nemestrina" "Glossophaga_soricina" "Drosophila_melanogaster"))
+
 (test-assert "species-meta is expected contain a link to tomato"
   (assoc "tomato" (cdr (assoc "links" (get-species-meta)))))
 
diff --git a/web/gn-uri.scm b/web/gn-uri.scm
index f275bcd..5d95cd8 100644
--- a/web/gn-uri.scm
+++ b/web/gn-uri.scm
@@ -22,11 +22,12 @@
             ))
 
 
-
 (define (normalize-id str)
   ;; (string-replace-substring (string-downcase str) " " "_")
-  (string-replace-substring str " " "_")
-  )
+  (match str
+    (#f "unknown")
+    (_ (string-replace-substring str " " "_"))
+  ))
 
 (define (url-parse-id uri)
   (if uri
-- 
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