diff options
Diffstat (limited to 'gn3-guile')
| -rwxr-xr-x | gn3-guile/web/webserver.scm | 60 |
1 files changed, 45 insertions, 15 deletions
diff --git a/gn3-guile/web/webserver.scm b/gn3-guile/web/webserver.scm index 648ea6a..a1db6ad 100755 --- a/gn3-guile/web/webserver.scm +++ b/gn3-guile/web/webserver.scm @@ -12,6 +12,7 @@ (ice-9 format) (ice-9 iconv) (ice-9 receive) + (ice-9 string-fun) ;; (ice-9 debugger) ;; (ice-9 breakpoints) ;; (ice-9 source) @@ -44,13 +45,22 @@ "Add the path to the API URL" (string-append (prefix) "/" postfix)) -(define (mk-doc postfix) +(define (mk-html postfix) "Create a pointer to HTML documentation" (string-append (base-url) "/" postfix ".html")) -(define (meta url) - "Adds /meta to the URL" - (string-append url "/meta")) +(define (mk-meta path) + "Create a meta URL for the API path" + (mk-url (string-append path ".meta.json"))) + +(define (mk-term postfix) + (mk-html (string-append "term" "/" postfix))) + +(define (mk-id postfix) + (mk-html (string-append "id" "/" postfix))) + +(define (mk-predicate postfix) + (mk-html (string-append "predicate" "/" postfix))) (define (wdt-taxon-name) "wdt:P225") @@ -60,10 +70,10 @@ ("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". ,(meta (prefix))))) + ("see also". ,(mk-meta (prefix))))) (define info-meta `( - ("doc" . ,(mk-doc "info")) + ("doc" . ,(mk-html "info")) ("API" . ((,(mk-url "species")."Get a list of all species") (,(mk-url "mouse")."Get information on mouse") @@ -254,25 +264,33 @@ SELECT ?species ?p ?o WHERE { [rest rest])) ) +(define (normalize-id str) + ;; (string-replace-substring (string-downcase str) " " "_") + (string-replace-substring str " " "_") + ) + (define (get-expanded-species) "Here we add information related to each species" (map (lambda (rec) - (let ([wd-id (url-parse-id (assoc-ref rec "22-rdf-syntax-ns#isDefinedBy"))]) + (let ([wd-id (url-parse-id (assoc-ref rec "22-rdf-syntax-ns#isDefinedBy"))] + [short-name (normalize-id (assoc-ref rec "name"))]) (if (string=? wd-id "unknown") rec ; wikidata query: (receive (names row) (tsv->scm (sparql-wd-species-info wd-id)) (match (pk (car row)) ((taxonomy-name ncbi descr) - (cons `("wikidata" . ,wd-id) - (cons `("ncbi" . ,(strip-lang ncbi)) - (cons `("ncbi-url" . ,(string-append "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" (strip-lang ncbi))) - (cons `("uniprot-url" . ,(string-append "https://www.uniprot.org/taxonomy/" (strip-lang ncbi))) - + (let ([ncbi-id (strip-lang ncbi)]) + (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 `("taxonomy-name" . ,(strip-lang taxonomy-name)) - ; (cons `("shortname" . ,shortname) + ; (cons `("shortname" . ,shortname) - problematic (cons `("description" . ,(strip-lang descr)) - rec))))))) + rec)))))))))) ) ))) ) (get-species) @@ -282,6 +300,18 @@ 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-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)) + )))) + ;; ---- REST API web server handler (define (not-found2 request) @@ -318,7 +348,7 @@ SELECT ?species ?p ?o WHERE { (('GET "version") (render-json get-version)) (('GET "species") - (render-json (list->vector (get-expanded-species)))) + (render-json (get-species-rec))) (_ (not-found (request-uri request))) )) |