diff options
Diffstat (limited to 'gn3-guile')
| -rwxr-xr-x | gn3-guile/web/webserver.scm | 69 |
1 files changed, 56 insertions, 13 deletions
diff --git a/gn3-guile/web/webserver.scm b/gn3-guile/web/webserver.scm index d86fdc2..123abf5 100755 --- a/gn3-guile/web/webserver.scm +++ b/gn3-guile/web/webserver.scm @@ -52,6 +52,8 @@ "Adds /meta to the URL" (string-append url "/meta")) +(define (wdt-taxon-name) "wdt:P225") + (define info `( ("name" . "GeneNetwork REST API") ("version" . ,get-version) @@ -75,12 +77,14 @@ response-body) "UTF-8")) -(define (sparql-exec2 endpoint-url query) - "Execute raw SPARQL query returning response as a UTF8 string" +(define (sparql-tsv endpoint-url query) + "Execute raw SPARQL query returning response as a UTF8 string, e.g. +(tsv->scm (sparql-tsv (wd-sparql-endpoint-url) \"wd:Q158695\")) +" ; GET /sparql?query=SELECT%20DISTINCT%20%2A%20where%20%7B%0A%20%20wd%3AQ158695%20wdt%3AP225%20%3Fo%20.%0A%7D%20limit%205 HTTP/2 - (bytevector->string (receive (response-status response-body) - (http-request (pk (string-append endpoint-url "?query=" (uri-encode query) ""))) - response-body) "UTF-8")) + (receive (response-status response-body) + (http-get (pk (string-append endpoint-url "?query=" (uri-encode query))) #:headers '((Accept . "text/tab-separated-values")(user-agent . "curl/7.74.0"))) + response-body)) (define (unpack field response) "Helper to get nested JSON field from SPARQL response" @@ -99,6 +103,11 @@ (let ((response (json-string->scm (sparql-exec endpoint-url query)))) (values (sparql-names response) (sparql-results response)))) +(define (tsv->scm text) + "Split a TSV string into a list of fields. Returns list of names header) and rows" + (let ([lst (map (lambda (f) (string-split f #\tab) ) (delete "" (string-split text #\newline)))]) + (values (car lst) (cdr lst)) + )) #! (define-values (names res) (sparql-species-meta)) @@ -139,13 +148,22 @@ curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset= !# (define (sparql-wd-species-info species) - (sparql-exec2 (wd-sparql-endpoint-url) " -SELECT DISTINCT * where { - wd:Q158695 wdt:P225 ?o . -} limit 100 + "Returns wikidata entry for species, e.g.: + + (sparql-wd-species-info \"Q158695\") generates something like + +SELECT DISTINCT * where { wd:Q158695 wdt:P225 ?o . } limit 10 " - )) + (sparql-tsv (wd-sparql-endpoint-url) (string-append " +SELECT DISTINCT * where { + wd:" species " " (wdt-taxon-name) " ?taxon ; + wdt:P685 ?ncbi ; + schema:description ?descr . + FILTER (lang(?descr)='en') +} limit 5 + +"))) (define (sparql-species) (sparql-scm (gn-sparql-endpoint-url) " @@ -205,8 +223,8 @@ SELECT ?species ?p ?o WHERE { (map (lambda (r) (let* ([k (car r)] [v (cdr r)]) - ; (cons k (map (lambda (i) (cons (car i) (car (cdr i)))) v)) - (map (lambda (i) (cons (car i) (car (cdr i)))) v) + ; with key use (cons k (map (lambda (i) (cons (car i) (car (cdr i)))) v)) + (map (lambda (i) (cons (url-parse-id (car i)) (car (cdr i)))) v) )) recs ) ) @@ -222,6 +240,31 @@ SELECT ?species ?p ?o WHERE { ; (define (wd-species-info wd) ; ) +(define (url-parse-id uri) + (if uri + (car (reverse (string-split uri #\057))) + "unknown" + )) + +(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"))]) + (if (string=? wd-id "unknown") + rec + ; wikidata query: + (receive (names row) (tsv->scm (sparql-wd-species-info wd-id)) + (display wd-id) + (display row) + (let ([ncbi (car (cdr (car row)) )]) + (cons `("wikidata" . ,wd-id) + (cons `("ncbi" . ,ncbi) + (cons `("taxonomy-name" . ,(car (car row))) rec)) + )) + ))) + ) (get-species) +)) + (define (get-species-api-str) (scm->json-string #("https://genenetwork.org/api/v2/mouse/" "https://genenetwork.org/api/v2/rat/"))) @@ -262,7 +305,7 @@ SELECT ?species ?p ?o WHERE { (('GET "version") (render-json get-version)) (('GET "species") - (render-json (list->vector (get-species)))) + (render-json (list->vector (get-expanded-species)))) (_ (not-found (request-uri request))) )) |