diff options
Diffstat (limited to 'gn3-guile/web')
| -rwxr-xr-x | gn3-guile/web/webserver.scm | 58 |
1 files changed, 36 insertions, 22 deletions
diff --git a/gn3-guile/web/webserver.scm b/gn3-guile/web/webserver.scm index 30f8e64..5dc0038 100755 --- a/gn3-guile/web/webserver.scm +++ b/gn3-guile/web/webserver.scm @@ -45,14 +45,22 @@ "Add the path to the API URL" (string-append (prefix) "/" postfix)) -(define (mk-html postfix) +(define (mk-html path) "Create a pointer to HTML documentation" - (string-append (base-url) "/" postfix ".html")) + (string-append (base-url) "/" path ".html")) + +(define (mk-doc path) + "Create a pointer to HTML documentation" + (mk-html (string-append "doc/" path))) (define (mk-meta path) "Create a meta URL for the API path" (mk-url (string-append path ".meta.json"))) +(define (mk-rec path) + "Create a JSON URL for the API path" + (mk-url (string-append path ".json"))) + (define (mk-term postfix) (mk-html (string-append "term" "/" postfix))) @@ -70,7 +78,8 @@ ("comment" . "This is the official REST API for the GeneNetwork service hosted at https://genenetwork.org/") ("license" . (("source code" . "AGPL"))) ("note" . "work in progress (WIP)") - ("see also". ,(mk-meta (prefix))))) + ("prefix" . ,(prefix)) + ("links". (("species" . ,(mk-meta "species")))))) (define info-meta `( ("doc" . ,(mk-html "info")) @@ -187,7 +196,8 @@ gn:Mus_musculus gnt:organism taxon:10090 . (define (sparql-species) (sparql-scm (gn-sparql-endpoint-url) " -PREFIX gn: <http://genenetwork.org/> +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 { @@ -198,7 +208,7 @@ SELECT DISTINCT ?species WHERE { (sparql-scm (gn-sparql-endpoint-url) " PREFIX gn: <http://genenetwork.org/id/> PREFIX gnc: <http://genenetwork.org/category/> -PREFIX gnterm: <http://genenetwork.org/term/> +PREFIX gnt: <http://genenetwork.org/term/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?species ?p ?o WHERE { @@ -268,6 +278,7 @@ SELECT ?species ?p ?o WHERE { )) (define (strip-lang s) + "Strip quotes and language tag (@en) from RDF entries" (list->string (match (string->list s) [(#\"rest ... #\") rest] [(#\"rest ... #\" #\@ #\e #\n) rest] @@ -290,14 +301,15 @@ SELECT ?species ?p ?o WHERE { (receive (names row) (tsv->scm (sparql-wd-species-info wd-id)) (match (pk (car row)) ((taxonomy-name ncbi descr) - (let ([ncbi-id (strip-lang ncbi)]) + (let ([ncbi-id (strip-lang ncbi)] + [taxonomy-lnk (string-replace-substring (strip-lang taxonomy-name) " " "_")]) (cons `("id" . ,short-name) (cons `("wikidata" . ,wd-id) (cons `("taxonomy-id" . ,ncbi-id) (cons `("ncbi-url" . ,(string-append "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" ncbi-id)) (cons `("uniprot-url" . ,(string-append "https://www.uniprot.org/taxonomy/" ncbi-id)) (cons `("wikidata-url" . ,(string-append "http://www.wikidata.org/entity/" wd-id)) - (cons `("wikispecies-url" . ,(string-append "https://species.wikimedia.org/wiki/" (strip-lang taxonomy-name)) + (cons `("wikispecies-url" . ,(string-append "https://species.wikimedia.org/wiki/" taxonomy-lnk)) (cons `("taxonomy-name" . ,(strip-lang taxonomy-name)) ; (cons `("shortname" . ,shortname) - problematic (cons `("description" . ,(strip-lang descr)) @@ -311,17 +323,21 @@ SELECT ?species ?p ?o WHERE { (scm->json-string #("https://genenetwork.org/api/v2/mouse/" "https://genenetwork.org/api/v2/rat/"))) -(define (get-species-links recs) - recs +(define (get-species-links) + '(("description" . "URI")) ) (define (get-species-rec) - (let ([recs (get-expanded-species)]) - `(("items" . ,(list->vector recs)) - ("doc" . ,(mk-term "species")) - ("meta" . ,(mk-meta "species")) - ("links" . ,(list->vector (get-species-links recs)) - )))) + (list->vector (get-expanded-species))) + +(define (get-species-meta) + `( + ("comment" . "Get information on species") + ("doc" . ,(mk-doc "species")) + ("meta" . ,(mk-meta "species")) + ("rec" . ,(mk-rec "species")) + ("links" . ,(get-species-links) + ))) ;; ---- REST API web server handler @@ -350,16 +366,14 @@ SELECT ?species ?p ?o WHERE { (match-lambda (('GET) (render-json info)) - (('GET "meh") - (render-json-string2 "ITEST")) - (('HEAD "meh") - (render-json-string2 "ITEST")) - (('GET "meta") - (render-json info-meta)) (('GET "version") (render-json get-version)) - (('GET "species") + (('GET "species.json") (render-json (get-species-rec))) + (('GET "species.meta.json") + (render-json (get-species-meta))) + (('GET "species") + (render-json (get-species-meta))) (_ (not-found (request-uri request))) )) |