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
|
(define-module (gn packages ratspub)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system python)
#:use-module (gnu packages admin)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages javascript)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gn packages javascript)
#:use-module (gn packages machine-learning)
#:use-module (gn packages web))
(define-public ratspub
(package
(name "ratspub")
(version "0.4.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chen42/ratspub")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1daf0qd0lyvfp9ab1qvhj37xvrrzkwvsfnickls5i9lbpgisizm4"))
;(modules '((guix build utils)))
;(snippet
; '(begin (substitute* "server.py"
; ;; Keep the service running on port 4200
; (("4200") "4201"))
; #t))
))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(inetutils (assoc-ref inputs "inetutils")))
(substitute* '("templates/cytoscape.html"
"templates/tableview.html"
"templates/tableview0.html"
"templates/userarchive.html")
;(("https.*FileSaver.js.*>") "/static/FileSaver.js\">") ; Something about our copy is different
;(("https.*cytoscape-svg.js.*>") "/static/cytoscape-svg.js\">") ; TODO
(("https.*cytoscape.min.js.*>") "/static/cytoscape.min.js\">"))
(substitute* "templates/layout.html"
(("https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css.*")
"/static/bootstrap.min.css\">\n")
(("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
"/static/bootstrap.min.js\"></script>\n")
(("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css")
"/static/font-awesome.min.css")
(("https://code.jquery.com/jquery-3.2.1.slim.min.js.*")
"/static/jquery.slim.min.js\"></script>\n")
;(("https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js.*")
; "/static/popper.min.js\"></script>\n")
)
(substitute* "ratspub.py"
(("hostname") (string-append inetutils "/bin/hostname"))))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(copy-recursively "." out))
#t))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(awesome (assoc-ref inputs "font-awesome"))
(bootstrap (assoc-ref inputs "bootstrap"))
(cytoscape (assoc-ref inputs "cytoscape"))
(jquery (assoc-ref inputs "jquery"))
(js-filesaver (assoc-ref inputs "js-filesaver"))
;(js-popper (assoc-ref inputs "js-popper"))
)
(symlink (string-append awesome
"/share/web/font-awesomecss/font-awesome.min.css")
(string-append out "/static/font-awesome.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/css/bootstrap.min.css")
(string-append out "/static/bootstrap.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/js/bootstrap.min.js")
(string-append out "/static/bootstrap.min.js"))
(symlink (string-append cytoscape
"/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
(string-append out "/static/cytoscape.min.js"))
(symlink (string-append jquery
"/share/web/jquery/jquery.slim.min.js")
(string-append out "/static/jquery.slim.min.js"))
(symlink (string-append js-filesaver
"/share/javascript/FileSaver.js")
(string-append out "/static/FileSaver.js"))
;(symlink (string-append js-popper
; "/share/web/popper/popper.min.js")
; (string-append out "/static/popper.min.js"))
)
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/server.py")
`("PATH" ":" prefix (,(dirname (which "edirect.pl"))
,(dirname (which "dirname"))
,(dirname (which "grep"))
,(dirname (which "sed"))))
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("edirect" ,edirect)
("inetutils" ,inetutils)
("python-bcrypt" ,python-bcrypt)
("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
("python-keras" ,python-keras-for-ratspub)
("python-nltk" ,python-nltk)
("tensorflow" ,tensorflow)))
(native-inputs
`(("bootstrap" ,web-bootstrap)
("cytoscape" ,javascript-cytoscape)
("font-awesome" ,web-font-awesome)
("jquery" ,web-jquery)
("js-filesaver" ,js-filesaver-1.3.2)
;("js-popper" ,js-popper) ; empty output
))
(home-page "http://rats.pub/")
(synopsis "Relationship with Addiction Through Searches of PubMed")
(description
"RatsPub is a tool to efficiently and comprehensively answer the question
\"What do we know about these genes and addiction?\". RatsPub answers this
question by searching PubMed to find sentences containing the query terms (i.e.,
gene symbols) and over 300 drug addiction-related keywords that are organized
into six categories. Data from @url{https://www.ebi.ac.uk/gwas/,
@acronym{NHGRI-EBI GWAS, European Bioinformatics Institute Genome-Wide
Association Studies}} catalog are also included in the search. These
gene-keyword relationships are presented as an interactive graph and a table.")
(license license:expat)))
(define-public ratspub-with-tensorflow-native
(package
(inherit
(tensowflow-native-instead-of-tensorflow ratspub))
(name "ratspub-with-tensorflow-native")))
;; We want a copy of python-keras with the AUC optimizer backported.
;; We skip the tests because we "test in production".
;; That's a lie. The test suite just takes a long time to run.
(define-public python-keras-for-ratspub
(hidden-package
(package
(inherit python-keras)
(source
(origin
(inherit (package-source python-keras))
(patches (search-patches "keras-auc-optimizer.patch"))))
(arguments
(substitute-keyword-arguments (package-arguments python-keras)
((#:phases phases)
`(modify-phases ,phases
(delete 'check))))))))
(define-public hrdp-project
(package
(name "hrdp-project")
(version "0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/noderboarder/hrdp-project")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ag7jm43p35yh0cqcn53wg4iw7sgfypw10mxq5klxvhgj3r6cf7i"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(add-after 'unpack 'patch-sources
(lambda _
(substitute* "./app/templates/layout.html"
(("https://.*.bootstrapcdn.com/bootstrap/4.*/css/bootstrap.min.css.*")
"/static/bootstrap.min.css\">\n")
(("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
"/static/bootstrap.min.js\"></script>\n")
(("https://code.jquery.com/jquery-3.*.slim.min.js.*")
"/static/jquery.slim.min.js\"></script>\n")
;(("https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js.*")
; "/static/popper.min.js\"></script>\n")
)
#t))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(python (assoc-ref inputs "python")))
(delete-file "main.py")
(with-output-to-file "main.py"
(lambda ()
(format #t "#!~a/bin/python
from app import create_app
app = create_app()
if __name__ == '__main__':
app.run(debug=True, port=4222)~%"
python)))
(chmod "main.py" #o555)
(copy-recursively "." out))
#t))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(bootstrap (assoc-ref inputs "bootstrap"))
(jquery (assoc-ref inputs "jquery"))
;(js-popper (assoc-ref inputs "js-popper"))
)
(symlink (string-append bootstrap
"/share/web/bootstrap/css/bootstrap.min.css")
(string-append out "/app/static/bootstrap.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/js/bootstrap.min.js")
(string-append out "/app/static/bootstrap.min.js"))
(symlink (string-append jquery
"/share/web/jquery/jquery.slim.min.js")
(string-append out "/app/static/jquery.slim.min.js"))
;(symlink (string-append js-popper
; "/share/web/popper/popper.min.js")
; (string-append out "/static/popper.min.js"))
)
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/main.py")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("python" ,python)
("python-flask-sqlalchemy" ,python-flask-sqlalchemy)))
(native-inputs
`(("bootstrap" ,web-bootstrap)
("jquery" ,web-jquery)
;("js-popper" ,js-popper) ; empty output
))
(home-page "https://github.com/noderboarder/hrdp-project")
(synopsis "")
(description "")
(license license:expat)))
|
