blob: d7687a0dcf7e4baca58cd50e6bf6af1118d10ba3 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
|
#!/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-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-names response)
(cdr (assoc "vars" (cdr (assoc "head" response))))
)
(define (sparql-results response)
(cdr (assoc "bindings" (cdr (assoc "results" response
)))))
(define (sparql-exec query)
"Return list of varnames and list of results"
(let ([response (sparql-scm query)])
(values (sparql-names response) (sparql-results response))
))
(define (sparql-species)
(sparql-exec "
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 (get-species-uris)
(map (lambda (m) (cdr (assoc "value"(cdr (car m))))) (array->list (sparql-species)))
)
(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 (get-species)
(receive (names results) (sparql-species))
results)
(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/"
"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 (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)))
(('GET "species-all")
(render-json (triples)))
(_ (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)))
|
