diff options
| -rwxr-xr-x | gn3-guile/web/webserver.scm | 87 |
1 files changed, 49 insertions, 38 deletions
diff --git a/gn3-guile/web/webserver.scm b/gn3-guile/web/webserver.scm index e72eba9..1219f52 100755 --- a/gn3-guile/web/webserver.scm +++ b/gn3-guile/web/webserver.scm @@ -21,7 +21,7 @@ (web uri) (fibers web server)) -(define (get-version) +(define get-version "2.0") (define (base-url) @@ -29,7 +29,7 @@ (define (prefix) "Build the API URL including version" - (string-append (base-url) "/api/" (get-version))) + (string-append (base-url) "/api/" get-version)) (define (mk-url postfix) "Add the path to the API URL" @@ -45,7 +45,7 @@ (define info `( ("name" . "GeneNetwork REST API") - ("version" . ,(get-version)) + ("version" . ,get-version) ("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)") @@ -59,45 +59,54 @@ (,(mk-url "mouse")."Get information on mouse") (,(mk-url "datasets")."Get a list of datasets"))))) + +(define (sparql-scm query) + (json-string->scm + (bytevector->string (receive (response-status response-body) + (http-request (string-append "https://sparql.genenetwork.org/sparql?default-graph-uri=&query=" (uri-encode query) "&format=application%2Fsparql-results%2Bjson")) + + response-body) "UTF-8" + ))) + +(define (sparql-exec query) + (sparql-scm query)) + +(define (sparql-results query) + (cdr (assoc "bindings" (cdr (assoc "results" (sparql-exec query) + ))))) + (define (sparql-species) - " -PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> -PREFIX dct: <http://purl.org/dc/terms/> -PREFIX foaf: <http://xmlns.com/foaf/0.1/> -PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> + (sparql-results " PREFIX gn: <http://genenetwork.org/> -PREFIX hgnc: <http://bio2rdf.org/hgnc:> -PREFIX homologene: <https://bio2rdf.org/homologene:> -PREFIX kegg: <http://bio2rdf.org/ns/kegg#> -PREFIX molecularTrait: <http://genenetwork.org/molecular-trait/> -PREFIX nuccore: <https://www.ncbi.nlm.nih.gov/nuccore/> -PREFIX omim: <https://www.omim.org/entry/> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX phenotype: <http://genenetwork.org/phenotype/> -PREFIX pubchem: <https://pubchem.ncbi.nlm.nih.gov/> -PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX taxon: <http://purl.uniprot.org/taxonomy/> -PREFIX uniprot: <http://purl.uniprot.org/uniprot/> -PREFIX up: <http://purl.uniprot.org/core/> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> - -CONSTRUCT { - ?s ?p ?o -} WHERE { - ?s rdf:type gn:species . - ?s ?p ?o . + +SELECT DISTINCT ?species WHERE { + ?species rdf:type gn:species . }" + )) + +(define (get-species-uris) + (map (lambda (m) (cdr (assoc "value"(cdr (car m))))) (array->list (sparql-species))) ) -;; curl "https://sparql.genenetwork.org/sparql?default-graph-uri=&query=prefix+gn%3A+%3Chttp%3A%2F%2Fgenenetwork.org%2F%3E+%0D%0A%0D%0ASELECT+distinct+*+WHERE+%7B%3Fu++gn%3AbinomialName+%3Fo%7D&format=application%2Fsparql-results%2Bjson"|jq -(define (get-species) - (bytevector->string (receive (response-status response-body) - (http-request "https://sparql.genenetwork.org/sparql?default-graph-uri=&query=prefix+gn%3A+%3Chttp%3A%2F%2Fgenenetwork.org%2F%3E+%0D%0A%0D%0ASELECT+distinct+*+WHERE+%7B%3Fu++gn%3AbinomialName+%3Fo%7D&format=application%2Fsparql-results%2Bjson") - - response-body) "UTF-8" - )) +(define (sparql-species-meta) + (sparql-results " +PREFIX gn: <http://genenetwork.org/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> + +SELECT DISTINCT ?species ?p ?o WHERE { + ?species rdf:type gn:species . + ?species ?p ?o . +}" + )) + +(define (get-species-all) + (sparql-species-meta)) + +(define (triples) + (array->list (get-species-all))) + +;; from the triples first harvest the species URIs, followed by creating records of information (define (get-species-api-str) (scm->json-string #("https://genenetwork.org/api/v2/mouse/" @@ -122,9 +131,11 @@ CONSTRUCT { (('GET "meta") (render-json info-meta)) (('GET "version") - (render-json (get-version))) + (render-json get-version)) (('GET "species") (render-json (get-species))) + (('GET "species-all") + (render-json (triples))) )) (define (request-path-components request) @@ -153,7 +164,7 @@ CONSTRUCT { #:port port)) (define (main args) - (write (string-append "Starting Guile REST API " (get-version) " server!")) + (write (string-append "Starting Guile REST API " get-version " server!")) (write args) (newline) (let ((listen (inexact->exact (string->number (car (cdr args)))))) |