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
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
|
#!/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)
"https://sparql.genenetwork.org/sparql")
(define (wd-sparql-endpoint-url)
"https://query.wikidata.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 (sparql-exec2 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 "?query=" (uri-encode query) ""))
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"}
curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="SELECT DISTINCT * where {
wd:Q158695 wdt:P225 ?o .
} limit 5"
{
"head" : {
"vars" : [ "o" ]
},
"results" : {
"bindings" : [ {
"o" : {
"type" : "literal",
"value" : "Arabidopsis thaliana"
}
} ]
}
}
!#
(define (sparql-wd-species-info species)
(sparql-exec2 (wd-sparql-endpoint-url) "
SELECT DISTINCT * where {
wd:Q158695 wdt:P225 ?o .
} limit 100
"
))
(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)))
|
