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|
#!/usr/bin/env guile \
-e main -s
!#
;; Minimal web server can be started from command line. Current example routes:
;;
;; localhost:8080/
;;
(use-modules
(json)
(ice-9 match)
(ice-9 format)
(ice-9 iconv)
(ice-9 receive)
;; (ice-9 debugger)
;; (ice-9 breakpoints)
;; (ice-9 source)
(srfi srfi-1)
(srfi srfi-26)
(web http)
(web client)
(web request)
(web response)
(web uri)
(fibers web server))
(define get-version
"2.0")
(define (base-url)
"https://genenetwork.org")
(define (gn-sparql-endpoint-url)
(string-append "https://sparql.genenetwork.org/sparql"))
(define (prefix)
"Build the API URL including version"
(string-append (base-url) "/api/" get-version))
(define (mk-url postfix)
"Add the path to the API URL"
(string-append (prefix) "/" postfix))
(define (mk-doc 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 info `(
("name" . "GeneNetwork REST API")
("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)")
("see also". ,(meta (prefix)))))
(define info-meta `(
("doc" . ,(mk-doc "info"))
("API" .
((,(mk-url "species")."Get a list of all species")
(,(mk-url "mouse")."Get information on mouse")
(,(mk-url "datasets")."Get a list of datasets")))))
(define (sparql-exec endpoint-url query)
"Execute raw SPARQL query returning response as a UTF8 string"
(bytevector->string (receive (response-status response-body)
(http-request (string-append endpoint-url "?default-graph-uri=&query=" (uri-encode query) "&format=application%2Fsparql-results%2Bjson"))
response-body) "UTF-8"))
(define (unpack field response)
"Helper to get nested JSON field from SPARQL response"
(cdr (assoc field response)))
(define (sparql-names response)
"Helper to get the names part of a SPARQL query"
(unpack "vars" (unpack "head" response)))
(define (sparql-results response)
"Helper to get the results part of a SPARQL query"
(unpack "bindings" (unpack "results" response)))
(define (sparql-scm endpoint-url query)
"Return dual S-exp 'resultset' of varnames and results"
(let ((response (json-string->scm (sparql-exec endpoint-url query))))
(values (sparql-names response) (sparql-results response))))
#!
(define-values (names res) (sparql-species-meta))
(define table (get-rows names res))
(define recs '())
(define h (compile-species recs table))
(assoc "http://genenetwork.org/species_drosophila_melanogaster" h)
(assoc-ref h "http://genenetwork.org/species_drosophila_melanogaster") ;; note switch!
(define d (car h))
(assoc-ref (list d) "http://genenetwork.org/species_drosophila_melanogaster")
(scm->json #(1 (("2" . 3))))
;; [1,{"2":3}]
(scm->json #("http://genenetwork.org/species_drosophila_melanogaster" (("http://genenetwork.org/menuName" . "Drosophila") ("http://genenetwork.org/binomialName" . "Drosophila melanogaster") )))
;; ["http://genenetwork.org/species_drosophila_melanogaster",{"http://genenetwork.org/menuName":"Drosophila","http://genenetwork.org/binomialName":"Drosophila melanogaster"}]
l
;; (("http://genenetwork.org/menuName" "Drosophila") ("http://genenetwork.org/name" "Drosophila") ("http://genenetwork.org/binomialName" "Drosophila melanogaster"))
(scm->json (map (lambda (i) (cons (car i) (car (cdr i)))) l))
;; {"http://genenetwork.org/menuName":"Drosophila","http://genenetwork.org/name":"Drosophila","http://genenetwork.org/binomialName":"Drosophila melanogaster"}
!#
(define (sparql-species)
(sparql-scm (gn-sparql-endpoint-url) "
PREFIX gn: <http://genenetwork.org/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT DISTINCT ?species WHERE {
?species rdf:type gn:species .
}"))
(define (sparql-species-meta)
(sparql-scm (gn-sparql-endpoint-url) "
PREFIX gn: <http://genenetwork.org/id/>
PREFIX gnterm: <http://genenetwork.org/term/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT ?species ?p ?o WHERE {
MINUS { ?species rdf:type ?o . }
{
SELECT DISTINCT ?species ?p ?o WHERE {
?species rdf:type gn:species .
?species ?p ?o .
}}}"))
(define (get-values names row)
"Get values by name from a resultset row"
(map (lambda (n) (unpack "value" (unpack n row))) (array->list names)))
(define (get-rows names results)
"Format results as a list of values ordered by names"
(map (lambda (row) (get-values names row)) (array->list results)))
;; from the triples first harvest the species URIs, followed by creating records of information
(define (compile-species recs rows)
"Compile a matrix of species triples into records"
(for-each (lambda (r)
(let* ([s (car r)]
[v (cdr (cdr r))]
[p (car (cdr r))]
[nrec '()]
[kv (assoc s recs)]) ; find record to fill based on subject
(if (not kv)
(set! nrec '())
(set! nrec (cdr kv))
)
(set! nrec (assoc-set! nrec p v))
(set! recs (assoc-set! recs s nrec))
))
rows)
recs)
;; result should be a vector of list of pair
(define (species-digest recs)
(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)
))
recs )
)
(define (get-species)
(receive (names res) (sparql-species-meta)
(let* ([table (get-rows names res)]
[recs '()]
[h (compile-species recs table)])
(species-digest h))
))
; (define (wd-species-info wd)
; )
(define (get-species-api-str)
(scm->json-string #("https://genenetwork.org/api/v2/mouse/"
"https://genenetwork.org/api/v2/rat/")))
;; ---- REST API web server handler
(define (not-found2 request)
(values (build-response #:code 404)
(string-append "Resource X not found: "
(uri->string (request-uri request)))))
(define (not-found uri)
(list (build-response #:code 404)
(string-append "Resource not found: " (uri->string uri))))
(define (render-json json)
(list '((content-type . (application/json)))
(lambda (port)
(scm->json json port))))
(define (render-json-string2 json)
(list '((content-type . (text/plain)))
(lambda (port)
;; (display "ThthxST" port)
(format port "~a" "foo")
)))
(define (controller request body)
(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")
(render-json (list->vector (get-species))))
(_ (not-found (request-uri request)))
))
(define (request-path-components request)
(split-and-decode-uri-path (uri-path (request-uri request))))
(define (handler request body)
(format #t "~a ~a\n"
(request-method request)
(uri-path (request-uri request)))
(apply values
((controller request body)
(cons (request-method request)
(request-path-components request)))))
(define (start-web-server address port)
(format (current-error-port)
"GN REST API web server listening on http://~a:~a/~%"
address port)
;; Wrap handler in another function to support live hacking via the
;; REPL. If handler is passed as is and is then redefined via the
;; REPL, the web server will still be using the old handler. The
;; only way to update the handler reference held by the web server
;; would be to restart the web server.
(run-server (cut handler <> <>)
#:addr (inet-pton AF_INET address)
#:port port))
(define (main args)
(write (string-append "Starting Guile REST API " get-version " server!"))
(write args)
(newline)
(let ((listen (inexact->exact (string->number (car (cdr args))))))
(display `("listening on" ,listen))
;; (write listen)
;; (run-server hello-world-handler 'http `(#:port ,listen))))
(start-web-server "127.0.0.1" listen)))
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