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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)
(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 (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-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=>
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 .
}"
)
;; 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 (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-found request)
(values (build-response #:code 404)
(string-append "Resource not found: "
(uri->string (request-uri request)))))
(define (render-json json)
(list '((content-type . (application/json)))
(lambda (port)
(scm->json json port))))
(define (controller request body)
(match-lambda
(('GET)
(render-json info))
(('GET "meta")
(render-json info-meta))
(('GET "version")
(render-json (get-version)))
(('GET "species")
(render-json (get-species)))
))
(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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