From 66c26676c938e6ba35440bcb2e851fb025549ed0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 20 Aug 2023 13:09:03 +0200
Subject: Add gnid to species - still a bug

---
 gn/data/species.scm | 14 +++++++-------
 gn/db/sparql.scm    | 22 ++++++++++++++++------
 test/runner.scm     |  3 +++
 web/gn-uri.scm      |  2 ++
 web/webserver.scm   |  2 +-
 5 files changed, 29 insertions(+), 14 deletions(-)

diff --git a/gn/data/species.scm b/gn/data/species.scm
index 98ea1b1..e06931e 100644
--- a/gn/data/species.scm
+++ b/gn/data/species.scm
@@ -16,6 +16,12 @@
             get-expanded-taxon-data
             ))
 
+(define (gn-species short-name)
+  "Find the GN identifier from shortname"
+  (let ([rec (get-expanded-taxon-data short-name)])
+    rec
+  ))
+
 (define (get-species)
   (receive (names res) (memo-sparql-species-meta)
     (let* ([table (get-rows names res)]
@@ -62,13 +68,6 @@
   )
 
 
-(define (get-expanded-species)
-  "Here we add information related to each species"
-  (map (lambda (rec)
-         (expand-species rec)
-	 ) (get-species)
-))
-
 (define (get-expanded-taxon-data short-name)
   "Here we add information related to one taxonomy species"
   (call/cc (lambda (return)
@@ -121,4 +120,5 @@
     ("meta" . ,(mk-meta id))
     ("data" . ,(mk-data id))
     ("up" . ,(mk-meta "species"))
+    ("links" . ,(get-group-links (gn-species id)))
   ))
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm
index 0e8c938..fd779c6 100644
--- a/gn/db/sparql.scm
+++ b/gn/db/sparql.scm
@@ -13,6 +13,7 @@
 
   #:export (memo-sparql-species
             memo-sparql-species-meta
+            sparql-species-meta
             memo-sparql-wd-species-info
             compile-species
             get-rows
@@ -180,6 +181,14 @@ SELECT ?species ?p ?o WHERE {
 (define memo-sparql-species-meta
   (memoize2 sparql-species-meta))
 
+#!
+dump-species-metadata.ttl:gn:Axbxa rdf:type gnc:inbredSet .
+dump-species-metadata.ttl:gn:Axbxa rdfs:label "AXB/BXA Family" .
+dump-species-metadata.ttl:gn:Axbxa gnt:family "Reference Populations (replicate average, SE, N)" .
+dump-species-metadata.ttl:gn:Axbxa gnt:mappingMethod "AXBXA" .
+dump-species-metadata.ttl:gn:Axbxa gnt:code "AXB" .
+dump-species-metadata.ttl:gn:Axbxa gnt:belongsToSpecies gn:Mus_musculus .
+!#
 
 (define (get-values names row)
   "Get values by name from a resultset row"
@@ -194,17 +203,18 @@ SELECT ?species ?p ?o WHERE {
 (define (compile-species recs rows)
   "Compile a matrix of species triples into records"
   (for-each (lambda (r)
-		(let* ([s (car r)]
+		(let* ([species (car r)]
 		       [v (cdr (cdr r))]
 		       [p (car (cdr r))]
 		       [nrec '()]
-		       [kv (assoc s recs)]) ; find record to fill based on subject
-		  (if (not kv)
-		      (set! nrec '())
-		      (set! nrec (cdr kv))
+		       [kvs (assoc species recs)]) ; find record to fill based on subject
+                  ;; for each gnid add value pair
+		  (if (not kvs)
+		      (set! nrec `(("gnid" ,species)))
+		      (set! nrec (cdr kvs))
 		      )
 		  (set! nrec (assoc-set! nrec p v))
-		  (set! recs (assoc-set! recs s nrec))
+		  (set! recs (assoc-set! recs species nrec))
 		  ))
 		rows)
   recs)
diff --git a/test/runner.scm b/test/runner.scm
index 45f2b0c..5555dc2 100644
--- a/test/runner.scm
+++ b/test/runner.scm
@@ -19,4 +19,7 @@
 (test-equal "tomato-data should have a description"
   (assoc-ref (get-expanded-taxon-data "tomato") "description") "type of plant species with edible, often red, berry fruit")
 
+(test-assert "mouse-meta should list all groups/populations/cohorts"
+  (assoc "links" (get-expanded-taxon-meta "mouse")))
+
 (test-end "runner")
diff --git a/web/gn-uri.scm b/web/gn-uri.scm
index a4292f0..c52066d 100644
--- a/web/gn-uri.scm
+++ b/web/gn-uri.scm
@@ -9,6 +9,8 @@
             mk-meta
             mk-data
             mk-doc
+            mk-html
+            mk-url
             prefix
             url-parse-id
             normalize-id
diff --git a/web/webserver.scm b/web/webserver.scm
index 485d334..6be0890 100755
--- a/web/webserver.scm
+++ b/web/webserver.scm
@@ -23,7 +23,7 @@
  (web client)
  (web request)
  (web response)
-;  (web uri)
+ (web uri)
  (fibers web server)
  (gn cache memoize)
  (web gn-uri)
-- 
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