diff options
| -rwxr-xr-x | gn/db/sparql.scm | 42 | ||||
| -rw-r--r-- | web/webserver.scm | 25 |
2 files changed, 61 insertions, 6 deletions
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm index c38b961..8722966 100755 --- a/gn/db/sparql.scm +++ b/gn/db/sparql.scm @@ -18,10 +18,11 @@ the case. #:use-module (json) #:use-module (srfi srfi-1) #:use-module (web client) + #:use-module (web http) #:use-module (web gn-uri) #:use-module (web request) + #:use-module (web response) #:use-module (web uri) - #:export (memo-sparql-species memo-sparql-species-meta sparql-species-meta @@ -37,9 +38,11 @@ the case. strip-lang make-table make-pairs - ) -) + sparql-http-get + sparql-by-term)) +(define virtuoso-endpoint + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/")) (define (strip-lang s) "Strip quotes and language tag (@en) from RDF entries" @@ -58,9 +61,9 @@ the case. (define (gn-sparql-prefix query) (string-append " -PREFIX gn: <http://genenetwork.org/id/> -PREFIX gnt: <http://genenetwork.org/term/> -PREFIX gnc: <http://genenetwork.org/category/> +PREFIX gn: <http://rdf.genenetwork.org/v1/id/> +PREFIX gnt: <http://rdf.genenetwork.org/v1/term/> +PREFIX gnc: <http://rdf.genenetwork.org/v1/category/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " query)) @@ -287,3 +290,30 @@ dump-species-metadata.ttl:gn:Axbxa gnt:belongsToSpecies gn:Mus_musculus . " gnid " ?key ?value . # FILTER ( !EXISTS{ " gnid " gnt:hasTissue ?value }) }"))) + + +(define* (sparql-http-get endpoint-url query #:optional (mime-type "text/microdata+html")) + (receive (response-status response-body) + (http-request + (format #f "~a?default-graph-uri=&query=~a&format=~a" + endpoint-url (uri-encode query) (uri-encode mime-type)) + #:method 'GET) + (values + (build-response + #:code (response-code response-status) + #:headers `((content-type . ,(parse-header 'content-type mime-type)))) + response-body))) + +(define (sparql-by-term prefix val) + (let ((url-alist '((gn . "<http://rdf.genenetwork.org/v1/id/>") + (gnc . "<http://rdf.genenetwork.org/v1/category/>") + (gnt . "<http://rdf.genenetwork.org/v1/term/>")))) + (format #f "PREFIX ~a: ~a + +CONSTRUCT { + ~a:~a ?p ?o . +} FROM <http://rdf.genenetwork.org/v1> +WHERE { + ~a:~a ?p ?o . + ?s ?p ?o . +}" prefix (assoc-ref url-alist prefix) prefix val prefix val))) diff --git a/web/webserver.scm b/web/webserver.scm index 0c0bdd1..e2412d2 100644 --- a/web/webserver.scm +++ b/web/webserver.scm @@ -327,6 +327,31 @@ otherwise search for set/group data" #\n) (render-json (get-id-data (list->string name)))) (rest (render-json "NOP"))))) + ;; RDF End-points + (('GET "v1" "id" id) + (receive (sparql-header sparql-resp) + (sparql-http-get + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/") + (sparql-by-term 'gn id)) + (list '((content-type text/html)) + (lambda (port) + (put-string port sparql-resp))))) + (('GET "v1" "category" category) + (receive (sparql-header sparql-resp) + (sparql-http-get + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/") + (sparql-by-term 'gnc category)) + (list '((content-type text/html)) + (lambda (port) + (put-string port sparql-resp))))) + (('GET "v1" "term" term) + (receive (sparql-header sparql-resp) + (sparql-http-get + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/") + (sparql-by-term 'gnt term)) + (list '((content-type text/html)) + (lambda (port) + (put-string port sparql-resp))))) (_ (not-found (request-uri request))))) (define (request-path-components request) |