diff options
| -rw-r--r-- | gn/data/group.scm | 23 | ||||
| -rw-r--r-- | gn/data/species.scm | 10 | ||||
| -rw-r--r-- | gn/db/sparql.scm | 22 | ||||
| -rw-r--r-- | web/gn-uri.scm | 13 |
4 files changed, 64 insertions, 4 deletions
diff --git a/gn/data/group.scm b/gn/data/group.scm new file mode 100644 index 0000000..003ac11 --- /dev/null +++ b/gn/data/group.scm @@ -0,0 +1,23 @@ +(define-module (gn data group) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:use-module (ice-9 format) + #:use-module (ice-9 iconv) + #:use-module (ice-9 receive) + #:use-module (ice-9 string-fun) + #:use-module (gn db sparql) + #:use-module (web gn-uri) + + #:export ( + get-group-links + )) + +(define (get-group-links gnid) + "Return all the URIs that link to group info, e.g. for Mus_musculus" + (let ([recs (car (cdr (compile-groups-meta)))] + [uri (mk-gnid gnid)]) + (filter-map + (lambda (r) (if (string=? (second r) uri) + (list ("ref" . (car r))) + #f)) recs) + )) diff --git a/gn/data/species.scm b/gn/data/species.scm index 72ab7cf..ca3bb05 100644 --- a/gn/data/species.scm +++ b/gn/data/species.scm @@ -6,9 +6,11 @@ #:use-module (ice-9 receive) #:use-module (ice-9 string-fun) #:use-module (gn db sparql) + #:use-module (gn data group) #:use-module (web gn-uri) #:export ( + gnid-species get-species-meta get-species-data get-species-shortnames @@ -17,10 +19,10 @@ get-expanded-taxon-data )) -(define (gn-species short-name) - "Find the GN identifier from shortname" +(define (gnid-species short-name) + "Find the GN identifier from shortname, e.g. Mus_musculus" (let ([rec (get-expanded-taxon-data short-name)]) - rec + (url-parse-id (assoc-ref rec "gnid")) )) (define (get-species) @@ -128,5 +130,5 @@ ("meta" . ,(mk-meta id)) ("data" . ,(mk-data id)) ("up" . ,(mk-meta "species")) - ("links" . "test") ; ,(get-group-links (gn-species id))) + ("links" . ,(list->vector (get-group-links (gnid-species id)))) )) diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm index fd779c6..2665235 100644 --- a/gn/db/sparql.scm +++ b/gn/db/sparql.scm @@ -14,8 +14,10 @@ #:export (memo-sparql-species memo-sparql-species-meta sparql-species-meta + sparql-groups-meta memo-sparql-wd-species-info compile-species + compile-groups-meta get-rows tsv->scm strip-lang @@ -218,3 +220,23 @@ dump-species-metadata.ttl:gn:Axbxa gnt:belongsToSpecies gn:Mus_musculus . )) rows) recs) + +;; ------------------------------------------------------------------------------ + +(define (sparql-groups-meta) + "Return values names recs" + (sparql-scm (gn-sparql-endpoint-url) " + SELECT DISTINCT ?set ?species ?descr WHERE { + ?set rdf:type gnc:inbredSet ; + gnt:belongsToSpecies ?species . + OPTIONAL {?set rdfs:label ?descr } . + }")) + +(define memo-sparql-groups-meta + (memoize2 sparql-groups-meta)) + +(define (compile-groups-meta) + "Return tuple of names and rows containing #(set species descr)" + (receive (names res) (memo-sparql-groups-meta) + (let ([rows (get-rows names res)]) + (list names rows)))) diff --git a/web/gn-uri.scm b/web/gn-uri.scm index c52066d..c0a440a 100644 --- a/web/gn-uri.scm +++ b/web/gn-uri.scm @@ -11,6 +11,9 @@ mk-doc mk-html mk-url + mk-id + mk-gnid + mk-predicate prefix url-parse-id normalize-id @@ -43,6 +46,9 @@ (define (base-url) "http://localhost:8091") +(define uri-base-url + "http://genenetwork.org") + (define (prefix) "Build the API URL including version" (base-url)) @@ -51,6 +57,10 @@ "Add the path to the API URL" (string-append (prefix) "/" postfix ext)) +(define* (mk-uri postfix) + "Add the path to the GN URI" + (string-append uri-base-url "/" postfix)) + (define (mk-html path) "Create a pointer to HTML documentation" (string-append (base-url) "/" path ".html")) @@ -73,5 +83,8 @@ (define (mk-id postfix) (mk-html (string-append "id" "/" postfix))) +(define (mk-gnid postfix) + (mk-uri (string-append "id" "/" postfix))) + (define (mk-predicate postfix) (mk-html (string-append "predicate" "/" postfix))) |