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-rw-r--r--gn/data/species.scm5
-rw-r--r--gn/db/sparql.scm2
-rw-r--r--test/runner.scm6
-rw-r--r--web/gn-uri.scm7
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