lazar-gui 1.3.1 → 1.4.0.pre.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/.gitignore +3 -0
- data/FAQ.md +9 -6
- data/Gemfile +2 -2
- data/README.md +19 -8
- data/VERSION +1 -1
- data/api/api.json +1000 -0
- data/application.rb +269 -206
- data/config.ru +7 -2
- data/docker/Dockerfile +73 -0
- data/docker/start.sh +12 -0
- data/docker/swagger.html +107 -0
- data/helper.rb +46 -1
- data/lazar-gui.gemspec +6 -6
- data/lib/api.rb +29 -0
- data/lib/compound.rb +68 -0
- data/lib/dataset.rb +33 -0
- data/lib/endpoint.rb +23 -0
- data/lib/feature.rb +29 -0
- data/lib/model.rb +152 -0
- data/lib/report.rb +29 -0
- data/lib/substance.rb +34 -0
- data/lib/swagger.rb +3 -0
- data/lib/validation.rb +67 -0
- data/public/fonts/FontAwesome.otf +0 -0
- data/public/fonts/fontawesome-webfont.eot +0 -0
- data/public/fonts/fontawesome-webfont.svg +2671 -0
- data/public/fonts/fontawesome-webfont.ttf +0 -0
- data/public/fonts/fontawesome-webfont.woff +0 -0
- data/public/fonts/fontawesome-webfont.woff2 +0 -0
- data/public/images/orn-logo.jpg +0 -0
- data/public/javascripts/bootstrap.js +3944 -0
- data/public/javascripts/google_analytics_lazar.js +2 -2
- data/public/javascripts/jquery.min.js +2 -0
- data/public/javascripts/lazar-gui.js +313 -0
- data/public/javascripts/pagination.min.js +11 -0
- data/public/javascripts/popper.min.js +5 -0
- data/public/stylesheets/bootstrap.min.css +7 -0
- data/public/stylesheets/bootstrap.min.css.map +1 -0
- data/public/stylesheets/font-awesome.min.css +4 -0
- data/public/stylesheets/pagination.css +1 -0
- data/qmrf_report.rb +64 -14
- data/task.rb +68 -0
- data/unicorn.rb +0 -1
- data/views/batch.haml +48 -107
- data/views/details.haml +10 -2
- data/views/error.haml +4 -5
- data/views/faq.haml +6 -2
- data/views/help.haml +68 -0
- data/views/info.haml +3 -2
- data/views/layout.haml +68 -78
- data/views/model_details.haml +179 -144
- data/views/neighbors.haml +98 -80
- data/views/predict.haml +43 -178
- data/views/prediction.haml +109 -102
- data/views/style.scss +44 -37
- data/views/upload.haml +28 -0
- metadata +51 -105
- data/public/css/bootstrap-theme.min.css +0 -5
- data/public/css/bootstrap.min.css +0 -5
- data/public/css/bootstrap.vertical-tabs.min.css +0 -1
- data/public/css/images/black-asc.gif +0 -0
- data/public/css/images/black-desc.gif +0 -0
- data/public/css/images/black-unsorted.gif +0 -0
- data/public/css/images/bootstrap-black-unsorted.png +0 -0
- data/public/css/images/bootstrap-white-unsorted.png +0 -0
- data/public/css/images/dragtable-handle.png +0 -0
- data/public/css/images/dragtable-handle.svg +0 -7
- data/public/css/images/dropbox-asc-hovered.png +0 -0
- data/public/css/images/dropbox-asc.png +0 -0
- data/public/css/images/dropbox-desc-hovered.png +0 -0
- data/public/css/images/dropbox-desc.png +0 -0
- data/public/css/images/first.png +0 -0
- data/public/css/images/green-asc.gif +0 -0
- data/public/css/images/green-desc.gif +0 -0
- data/public/css/images/green-header.gif +0 -0
- data/public/css/images/green-unsorted.gif +0 -0
- data/public/css/images/ice-asc.gif +0 -0
- data/public/css/images/ice-desc.gif +0 -0
- data/public/css/images/ice-unsorted.gif +0 -0
- data/public/css/images/last.png +0 -0
- data/public/css/images/loading.gif +0 -0
- data/public/css/images/metro-black-asc.png +0 -0
- data/public/css/images/metro-black-desc.png +0 -0
- data/public/css/images/metro-loading.gif +0 -0
- data/public/css/images/metro-unsorted.png +0 -0
- data/public/css/images/metro-white-asc.png +0 -0
- data/public/css/images/metro-white-desc.png +0 -0
- data/public/css/images/next.png +0 -0
- data/public/css/images/prev.png +0 -0
- data/public/css/images/white-asc.gif +0 -0
- data/public/css/images/white-desc.gif +0 -0
- data/public/css/images/white-unsorted.gif +0 -0
- data/public/css/jquery-ui.css +0 -1225
- data/public/css/jquery-ui.theme.min.css +0 -5
- data/public/css/theme.bootstrap.css +0 -158
- data/public/css/theme.bootstrap.min.css +0 -1
- data/public/css/theme.default.min.css +0 -1
- data/public/fonts/glyphicons-halflings-regular.eot +0 -0
- data/public/fonts/glyphicons-halflings-regular.svg +0 -288
- data/public/fonts/glyphicons-halflings-regular.ttf +0 -0
- data/public/fonts/glyphicons-halflings-regular.woff +0 -0
- data/public/fonts/glyphicons-halflings-regular.woff2 +0 -0
- data/public/images/Email.png +0 -0
- data/public/images/Facebook.png +0 -0
- data/public/images/Google+.png +0 -0
- data/public/images/LinkedIn.png +0 -0
- data/public/images/OpenToxEuro2013_small.png +0 -0
- data/public/images/Twitter.png +0 -0
- data/public/images/arrow_down_float.png +0 -0
- data/public/images/arrow_left_float.png +0 -0
- data/public/images/arrow_right_float.png +0 -0
- data/public/images/arrow_up_float.png +0 -0
- data/public/images/asc.gif +0 -0
- data/public/images/bg.gif +0 -0
- data/public/images/desc.gif +0 -0
- data/public/images/gray_jean.png +0 -0
- data/public/images/info_white.png +0 -0
- data/public/javascripts/bootstrap.min.js +0 -7
- data/public/javascripts/jquery-1.11.2.min.js +0 -4
- data/public/javascripts/jquery-1.8.3.min.js +0 -2
- data/public/javascripts/jquery-ui-1.10.3.custom.min.js +0 -6
- data/public/javascripts/jquery.bpopup.min.js +0 -7
- data/public/javascripts/jquery.tablesorter.min.js +0 -2
- data/public/javascripts/jquery.tablesorter.widgets.js +0 -2678
- data/public/javascripts/jquery.tools.min.js +0 -5
- data/public/rect.png +0 -0
- data/test/lazarweb.rb +0 -193
- data/test/setup.rb +0 -7
- data/views/significant_fragments.haml +0 -66
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: b62bd400db67c63890b87da66fd39a5c409ae608
|
4
|
+
data.tar.gz: 846c1c3f564c6591b82ccede408f211a7ca66aaf
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 7d0b13b9618aa506941ea3a99ee59ee4e70ff7e539c3936562ae5b5ea23d4f68221bd41109947dd5b1b3255d6134abe21e227729632c0ae92afe914be1bf6ec7
|
7
|
+
data.tar.gz: 8d75947e07ef2754bcdd9d318212f4696e1a6b6ec87cc6d330cb333dbb0c253399b84c6518fa704a8c729ce4f7dd97592ae75cf601b69046023fe54c2ba89f1a
|
data/.gitignore
CHANGED
data/FAQ.md
CHANGED
@@ -19,20 +19,23 @@ inconsistencies that might affect the prediction.
|
|
19
19
|
|
20
20
|
#### How can I use *lazar* locally on my computer
|
21
21
|
If you are familiar with docker, you can use one of our docker images to run lazar locally:
|
22
|
-
|
23
|
-
https://hub.docker.com/r/insilicotox/
|
22
|
+
|
23
|
+
[lazar docker image](https://hub.docker.com/r/insilicotox/lazar)
|
24
|
+
|
25
|
+
[nano-lazar docker image](https://hub.docker.com/r/insilicotox/nano-lazar)
|
24
26
|
|
25
27
|
If you want to install lazar/nano-lazar without docker you should know how to use UNIX/Linux and the Ruby programming language. Source code and brief installation instructions for the GUIs is available at:
|
26
28
|
|
27
|
-
https://github.com/opentox/lazar-gui
|
28
|
-
|
29
|
+
[lazar gui source code](https://github.com/opentox/lazar-gui)
|
30
|
+
|
31
|
+
[nano-lazar gui source code](https://github.com/opentox/nano-lazar)
|
29
32
|
|
30
33
|
You can also use just the libraries from the command line:
|
31
34
|
|
32
|
-
https://github.com/opentox/lazar
|
35
|
+
[lazar|nano-lazar lib](https://github.com/opentox/lazar)
|
33
36
|
|
34
37
|
Documentation is available at:
|
35
38
|
|
36
|
-
http://www.rubydoc.info/gems/lazar
|
39
|
+
[gem](http://www.rubydoc.info/gems/lazar)
|
37
40
|
|
38
41
|
lazar depends on a couple of external libraries and programs, that could be difficult to install. Due to limited resources we cannot provide support, please use the docker version if you cannot manage it on your own.
|
data/Gemfile
CHANGED
data/README.md
CHANGED
@@ -1,16 +1,27 @@
|
|
1
|
-
|
2
|
-
|
1
|
+
*lazar* GUI
|
2
|
+
===========
|
3
|
+
lazar ( Lazy Structure- Activity Relationships ) takes a chemical structure as input and provides predictions for a variety of toxic properties. lazar uses an automated and reproducible read across procedure to calculate predictions. Rationales for predictions, applicability domain estimations and validation results are presented in a clear graphical interface for the critical examination by toxicological experts.
|
3
4
|
|
4
5
|
Installation:
|
5
6
|
-------------
|
6
|
-
|
7
|
+
|
8
|
+
```
|
9
|
+
bundle install
|
10
|
+
```
|
7
11
|
|
8
12
|
Service start:
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
+
--------------
|
14
|
+
|
15
|
+
```
|
16
|
+
sudo mongod &
|
17
|
+
R CMD Rserve --vanilla &
|
18
|
+
unicorn -p 8088 -c unicorn.rb -E production
|
19
|
+
```
|
13
20
|
|
14
21
|
Visit:
|
15
22
|
------
|
16
|
-
|
23
|
+
|
24
|
+
```
|
25
|
+
http://localhost:8088
|
26
|
+
```
|
27
|
+
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
1.
|
1
|
+
1.4.0.pre.0
|
data/api/api.json
ADDED
@@ -0,0 +1,1000 @@
|
|
1
|
+
{
|
2
|
+
"openapi": "3.0.0",
|
3
|
+
"servers": [
|
4
|
+
{
|
5
|
+
"url": "https://SERVER_URI/api"
|
6
|
+
}
|
7
|
+
],
|
8
|
+
"info": {
|
9
|
+
"description": "REST API webservice for lazar. \n\n*lazar* (lazy structure–activity relationships) is a modular framework for\npredictive toxicology.",
|
10
|
+
"version": "1.4.0",
|
11
|
+
"title": "Lazar REST Service",
|
12
|
+
"contact": {
|
13
|
+
"name": "in silico toxicology gmbh",
|
14
|
+
"email": "info@in-silico.ch",
|
15
|
+
"url": "https://in-silico.ch"
|
16
|
+
},
|
17
|
+
"license": {
|
18
|
+
"name": "GNU GENERAL PUBLIC LICENSE",
|
19
|
+
"url": "https://github.com/opentox/lazar-rest/blob/master/LICENSE"
|
20
|
+
}
|
21
|
+
},
|
22
|
+
"externalDocs": {
|
23
|
+
"description": "See also documentation\n",
|
24
|
+
"url": "https://github.com/OpenRiskNet/home/blob/master/openshift/deployments/lazar/README.md"
|
25
|
+
},
|
26
|
+
"paths": {
|
27
|
+
"/api.json": {
|
28
|
+
"get": {
|
29
|
+
"tags": [
|
30
|
+
"api"
|
31
|
+
],
|
32
|
+
"description": "Get swagger api in JSON",
|
33
|
+
"responses": {
|
34
|
+
"200": {
|
35
|
+
"$ref": "#/components/responses/200"
|
36
|
+
},
|
37
|
+
"400": {
|
38
|
+
"$ref": "#/components/responses/400"
|
39
|
+
},
|
40
|
+
"500": {
|
41
|
+
"$ref": "#/components/responses/500"
|
42
|
+
}
|
43
|
+
}
|
44
|
+
}
|
45
|
+
},
|
46
|
+
"/compound/descriptor": {
|
47
|
+
"get": {
|
48
|
+
"tags": [
|
49
|
+
"compound",
|
50
|
+
"descriptor"
|
51
|
+
],
|
52
|
+
"description": "Get a list of all descriptors",
|
53
|
+
"parameters": [
|
54
|
+
{
|
55
|
+
"$ref": "#/components/parameters/subjectid"
|
56
|
+
}
|
57
|
+
],
|
58
|
+
"responses": {
|
59
|
+
"200": {
|
60
|
+
"$ref": "#/components/responses/200"
|
61
|
+
},
|
62
|
+
"400": {
|
63
|
+
"$ref": "#/components/responses/400"
|
64
|
+
},
|
65
|
+
"401": {
|
66
|
+
"$ref": "#/components/responses/401"
|
67
|
+
},
|
68
|
+
"404": {
|
69
|
+
"$ref": "#/components/responses/404"
|
70
|
+
},
|
71
|
+
"500": {
|
72
|
+
"$ref": "#/components/responses/500"
|
73
|
+
}
|
74
|
+
}
|
75
|
+
},
|
76
|
+
"post": {
|
77
|
+
"tags": [
|
78
|
+
"compound",
|
79
|
+
"descriptor"
|
80
|
+
],
|
81
|
+
"summary": "Descriptor calculation",
|
82
|
+
"description": "Calculate descriptors for a single compound as SMILES string",
|
83
|
+
"parameters": [
|
84
|
+
{
|
85
|
+
"$ref": "#/components/parameters/subjectid"
|
86
|
+
}
|
87
|
+
],
|
88
|
+
"responses": {
|
89
|
+
"202": {
|
90
|
+
"$ref": "#/components/responses/202"
|
91
|
+
},
|
92
|
+
"400": {
|
93
|
+
"$ref": "#/components/responses/400"
|
94
|
+
},
|
95
|
+
"401": {
|
96
|
+
"$ref": "#/components/responses/401"
|
97
|
+
},
|
98
|
+
"404": {
|
99
|
+
"$ref": "#/components/responses/404"
|
100
|
+
},
|
101
|
+
"500": {
|
102
|
+
"$ref": "#/components/responses/500"
|
103
|
+
}
|
104
|
+
},
|
105
|
+
"requestBody": {
|
106
|
+
"description": "identifier and descriptor/s",
|
107
|
+
"required": true,
|
108
|
+
"content": {
|
109
|
+
"application/x-www-form-urlencoded": {
|
110
|
+
"schema": {
|
111
|
+
"$ref": "#/components/schemas/postdescriptor"
|
112
|
+
}
|
113
|
+
}
|
114
|
+
}
|
115
|
+
}
|
116
|
+
}
|
117
|
+
},
|
118
|
+
"/compound/descriptor/{descriptor}": {
|
119
|
+
"get": {
|
120
|
+
"tags": [
|
121
|
+
"compound",
|
122
|
+
"descriptor"
|
123
|
+
],
|
124
|
+
"description": "Get informations about a single descriptor",
|
125
|
+
"parameters": [
|
126
|
+
{
|
127
|
+
"name": "descriptor",
|
128
|
+
"in": "path",
|
129
|
+
"description": "descriptor name or ID",
|
130
|
+
"required": true,
|
131
|
+
"schema": {
|
132
|
+
"type": "string"
|
133
|
+
}
|
134
|
+
},
|
135
|
+
{
|
136
|
+
"$ref": "#/components/parameters/subjectid"
|
137
|
+
}
|
138
|
+
],
|
139
|
+
"responses": {
|
140
|
+
"200": {
|
141
|
+
"$ref": "#/components/responses/200"
|
142
|
+
},
|
143
|
+
"400": {
|
144
|
+
"$ref": "#/components/responses/400"
|
145
|
+
},
|
146
|
+
"401": {
|
147
|
+
"$ref": "#/components/responses/401"
|
148
|
+
},
|
149
|
+
"404": {
|
150
|
+
"$ref": "#/components/responses/404"
|
151
|
+
},
|
152
|
+
"500": {
|
153
|
+
"$ref": "#/components/responses/500"
|
154
|
+
}
|
155
|
+
}
|
156
|
+
}
|
157
|
+
},
|
158
|
+
"/compound/{InChI}": {
|
159
|
+
"get": {
|
160
|
+
"tags": [
|
161
|
+
"compound"
|
162
|
+
],
|
163
|
+
"description": "Get compound representation",
|
164
|
+
"parameters": [
|
165
|
+
{
|
166
|
+
"$ref": "#/components/parameters/InChI"
|
167
|
+
},
|
168
|
+
{
|
169
|
+
"$ref": "#/components/parameters/subjectid"
|
170
|
+
}
|
171
|
+
],
|
172
|
+
"responses": {
|
173
|
+
"200": {
|
174
|
+
"description": "OK",
|
175
|
+
"content": {
|
176
|
+
"application/json": {
|
177
|
+
"schema": {
|
178
|
+
"type": "string",
|
179
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
180
|
+
}
|
181
|
+
},
|
182
|
+
"chemical/x-daylight-smiles": {
|
183
|
+
"schema": {
|
184
|
+
"type": "string",
|
185
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
186
|
+
}
|
187
|
+
},
|
188
|
+
"chemical/x-inchi": {
|
189
|
+
"schema": {
|
190
|
+
"type": "string",
|
191
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
192
|
+
}
|
193
|
+
},
|
194
|
+
"chemical/x-mdl-sdfile": {
|
195
|
+
"schema": {
|
196
|
+
"type": "string",
|
197
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
198
|
+
}
|
199
|
+
},
|
200
|
+
"image/png": {
|
201
|
+
"schema": {
|
202
|
+
"type": "string",
|
203
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
204
|
+
}
|
205
|
+
},
|
206
|
+
"image/svg+xml": {
|
207
|
+
"schema": {
|
208
|
+
"type": "string",
|
209
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
210
|
+
}
|
211
|
+
},
|
212
|
+
"text/plain": {
|
213
|
+
"schema": {
|
214
|
+
"type": "string",
|
215
|
+
"example": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
216
|
+
}
|
217
|
+
}
|
218
|
+
}
|
219
|
+
},
|
220
|
+
"400": {
|
221
|
+
"$ref": "#/components/responses/400"
|
222
|
+
},
|
223
|
+
"500": {
|
224
|
+
"$ref": "#/components/responses/500"
|
225
|
+
}
|
226
|
+
}
|
227
|
+
}
|
228
|
+
},
|
229
|
+
"/dataset": {
|
230
|
+
"get": {
|
231
|
+
"tags": [
|
232
|
+
"dataset"
|
233
|
+
],
|
234
|
+
"description": "Get a list of all datasets",
|
235
|
+
"parameters": [
|
236
|
+
{
|
237
|
+
"$ref": "#/components/parameters/subjectid"
|
238
|
+
}
|
239
|
+
],
|
240
|
+
"responses": {
|
241
|
+
"200": {
|
242
|
+
"$ref": "#/components/responses/200"
|
243
|
+
},
|
244
|
+
"400": {
|
245
|
+
"$ref": "#/components/responses/400"
|
246
|
+
},
|
247
|
+
"401": {
|
248
|
+
"$ref": "#/components/responses/401"
|
249
|
+
},
|
250
|
+
"404": {
|
251
|
+
"$ref": "#/components/responses/404"
|
252
|
+
},
|
253
|
+
"500": {
|
254
|
+
"$ref": "#/components/responses/500"
|
255
|
+
}
|
256
|
+
}
|
257
|
+
}
|
258
|
+
},
|
259
|
+
"/dataset/{id}": {
|
260
|
+
"get": {
|
261
|
+
"tags": [
|
262
|
+
"dataset"
|
263
|
+
],
|
264
|
+
"description": "Get dataset representation",
|
265
|
+
"parameters": [
|
266
|
+
{
|
267
|
+
"$ref": "#/components/parameters/id"
|
268
|
+
},
|
269
|
+
{
|
270
|
+
"$ref": "#/components/parameters/subjectid"
|
271
|
+
}
|
272
|
+
],
|
273
|
+
"responses": {
|
274
|
+
"200": {
|
275
|
+
"description": "OK",
|
276
|
+
"content": {
|
277
|
+
"text/csv": {
|
278
|
+
},
|
279
|
+
"application/csv": {
|
280
|
+
}
|
281
|
+
}
|
282
|
+
},
|
283
|
+
"400": {
|
284
|
+
"$ref": "#/components/responses/400"
|
285
|
+
},
|
286
|
+
"401": {
|
287
|
+
"$ref": "#/components/responses/401"
|
288
|
+
},
|
289
|
+
"403": {
|
290
|
+
"$ref": "#/components/responses/403"
|
291
|
+
},
|
292
|
+
"404": {
|
293
|
+
"$ref": "#/components/responses/404"
|
294
|
+
},
|
295
|
+
"500": {
|
296
|
+
"$ref": "#/components/responses/500"
|
297
|
+
}
|
298
|
+
}
|
299
|
+
}
|
300
|
+
},
|
301
|
+
"/dataset/{id}/{attribute}": {
|
302
|
+
"get": {
|
303
|
+
"tags": [
|
304
|
+
"dataset"
|
305
|
+
],
|
306
|
+
"description": "Get dataset representation",
|
307
|
+
"parameters": [
|
308
|
+
{
|
309
|
+
"name": "attribute",
|
310
|
+
"in": "path",
|
311
|
+
"description": "requested attribute",
|
312
|
+
"required": true,
|
313
|
+
"schema": {
|
314
|
+
"type": "string",
|
315
|
+
"enum": [
|
316
|
+
"compounds",
|
317
|
+
"substances",
|
318
|
+
"features"
|
319
|
+
]
|
320
|
+
}
|
321
|
+
},
|
322
|
+
{
|
323
|
+
"$ref": "#/components/parameters/id"
|
324
|
+
},
|
325
|
+
{
|
326
|
+
"$ref": "#/components/parameters/subjectid"
|
327
|
+
}
|
328
|
+
],
|
329
|
+
"responses": {
|
330
|
+
"200": {
|
331
|
+
"$ref": "#/components/responses/200"
|
332
|
+
},
|
333
|
+
"400": {
|
334
|
+
"$ref": "#/components/responses/400"
|
335
|
+
},
|
336
|
+
"401": {
|
337
|
+
"$ref": "#/components/responses/401"
|
338
|
+
},
|
339
|
+
"403": {
|
340
|
+
"$ref": "#/components/responses/403"
|
341
|
+
},
|
342
|
+
"404": {
|
343
|
+
"$ref": "#/components/responses/404"
|
344
|
+
},
|
345
|
+
"500": {
|
346
|
+
"$ref": "#/components/responses/500"
|
347
|
+
}
|
348
|
+
}
|
349
|
+
}
|
350
|
+
},
|
351
|
+
"/endpoint": {
|
352
|
+
"get": {
|
353
|
+
"tags": [
|
354
|
+
"endpoint"
|
355
|
+
],
|
356
|
+
"description": "Get a list of all available endpoints",
|
357
|
+
"parameters": [
|
358
|
+
{
|
359
|
+
"$ref": "#/components/parameters/subjectid"
|
360
|
+
}
|
361
|
+
],
|
362
|
+
"responses": {
|
363
|
+
"200": {
|
364
|
+
"$ref": "#/components/responses/200"
|
365
|
+
},
|
366
|
+
"400": {
|
367
|
+
"$ref": "#/components/responses/400"
|
368
|
+
},
|
369
|
+
"401": {
|
370
|
+
"$ref": "#/components/responses/401"
|
371
|
+
},
|
372
|
+
"404": {
|
373
|
+
"$ref": "#/components/responses/404"
|
374
|
+
},
|
375
|
+
"500": {
|
376
|
+
"$ref": "#/components/responses/500"
|
377
|
+
}
|
378
|
+
}
|
379
|
+
}
|
380
|
+
},
|
381
|
+
"/endpoint/{endpoint}": {
|
382
|
+
"get": {
|
383
|
+
"tags": [
|
384
|
+
"endpoint"
|
385
|
+
],
|
386
|
+
"description": "Get a list of all available models for an endpoint",
|
387
|
+
"parameters": [
|
388
|
+
{
|
389
|
+
"$ref": "#/components/parameters/endpoint"
|
390
|
+
},
|
391
|
+
{
|
392
|
+
"$ref": "#/components/parameters/subjectid"
|
393
|
+
}
|
394
|
+
],
|
395
|
+
"responses": {
|
396
|
+
"200": {
|
397
|
+
"$ref": "#/components/responses/200"
|
398
|
+
},
|
399
|
+
"400": {
|
400
|
+
"$ref": "#/components/responses/400"
|
401
|
+
},
|
402
|
+
"401": {
|
403
|
+
"$ref": "#/components/responses/401"
|
404
|
+
},
|
405
|
+
"404": {
|
406
|
+
"$ref": "#/components/responses/404"
|
407
|
+
},
|
408
|
+
"500": {
|
409
|
+
"$ref": "#/components/responses/500"
|
410
|
+
}
|
411
|
+
}
|
412
|
+
}
|
413
|
+
},
|
414
|
+
"/feature": {
|
415
|
+
"get": {
|
416
|
+
"tags": [
|
417
|
+
"feature"
|
418
|
+
],
|
419
|
+
"description": "Get a list of ids for all features",
|
420
|
+
"parameters": [
|
421
|
+
{
|
422
|
+
"$ref": "#/components/parameters/subjectid"
|
423
|
+
}
|
424
|
+
],
|
425
|
+
"responses": {
|
426
|
+
"200": {
|
427
|
+
"$ref": "#/components/responses/200"
|
428
|
+
},
|
429
|
+
"400": {
|
430
|
+
"$ref": "#/components/responses/400"
|
431
|
+
},
|
432
|
+
"401": {
|
433
|
+
"$ref": "#/components/responses/401"
|
434
|
+
},
|
435
|
+
"404": {
|
436
|
+
"$ref": "#/components/responses/404"
|
437
|
+
},
|
438
|
+
"500": {
|
439
|
+
"$ref": "#/components/responses/500"
|
440
|
+
}
|
441
|
+
}
|
442
|
+
}
|
443
|
+
},
|
444
|
+
"/feature/{id}": {
|
445
|
+
"get": {
|
446
|
+
"tags": [
|
447
|
+
"feature"
|
448
|
+
],
|
449
|
+
"description": "Get feature representation",
|
450
|
+
"parameters": [
|
451
|
+
{
|
452
|
+
"$ref": "#/components/parameters/id"
|
453
|
+
},
|
454
|
+
{
|
455
|
+
"$ref": "#/components/parameters/subjectid"
|
456
|
+
}
|
457
|
+
],
|
458
|
+
"responses": {
|
459
|
+
"200": {
|
460
|
+
"$ref": "#/components/responses/200"
|
461
|
+
},
|
462
|
+
"400": {
|
463
|
+
"$ref": "#/components/responses/400"
|
464
|
+
},
|
465
|
+
"401": {
|
466
|
+
"$ref": "#/components/responses/401"
|
467
|
+
},
|
468
|
+
"403": {
|
469
|
+
"$ref": "#/components/responses/403"
|
470
|
+
},
|
471
|
+
"404": {
|
472
|
+
"$ref": "#/components/responses/404"
|
473
|
+
},
|
474
|
+
"500": {
|
475
|
+
"$ref": "#/components/responses/500"
|
476
|
+
}
|
477
|
+
}
|
478
|
+
}
|
479
|
+
},
|
480
|
+
"/model": {
|
481
|
+
"get": {
|
482
|
+
"tags": [
|
483
|
+
"model"
|
484
|
+
],
|
485
|
+
"description": "Get a list of all prediction models",
|
486
|
+
"parameters": [
|
487
|
+
{
|
488
|
+
"$ref": "#/components/parameters/subjectid"
|
489
|
+
}
|
490
|
+
],
|
491
|
+
"responses": {
|
492
|
+
"200": {
|
493
|
+
"$ref": "#/components/responses/200"
|
494
|
+
},
|
495
|
+
"400": {
|
496
|
+
"$ref": "#/components/responses/400"
|
497
|
+
},
|
498
|
+
"401": {
|
499
|
+
"$ref": "#/components/responses/401"
|
500
|
+
},
|
501
|
+
"404": {
|
502
|
+
"$ref": "#/components/responses/404"
|
503
|
+
},
|
504
|
+
"500": {
|
505
|
+
"$ref": "#/components/responses/500"
|
506
|
+
}
|
507
|
+
}
|
508
|
+
}
|
509
|
+
},
|
510
|
+
"/model/{id}": {
|
511
|
+
"get": {
|
512
|
+
"tags": [
|
513
|
+
"model"
|
514
|
+
],
|
515
|
+
"description": "Get model representation",
|
516
|
+
"parameters": [
|
517
|
+
{
|
518
|
+
"$ref": "#/components/parameters/id"
|
519
|
+
},
|
520
|
+
{
|
521
|
+
"$ref": "#/components/parameters/subjectid"
|
522
|
+
}
|
523
|
+
],
|
524
|
+
"responses": {
|
525
|
+
"200": {
|
526
|
+
"$ref": "#/components/responses/200"
|
527
|
+
},
|
528
|
+
"400": {
|
529
|
+
"$ref": "#/components/responses/400"
|
530
|
+
},
|
531
|
+
"401": {
|
532
|
+
"$ref": "#/components/responses/401"
|
533
|
+
},
|
534
|
+
"403": {
|
535
|
+
"$ref": "#/components/responses/403"
|
536
|
+
},
|
537
|
+
"404": {
|
538
|
+
"$ref": "#/components/responses/404"
|
539
|
+
}
|
540
|
+
}
|
541
|
+
},
|
542
|
+
"post": {
|
543
|
+
"tags": [
|
544
|
+
"model"
|
545
|
+
],
|
546
|
+
"description": "Predict a compound.",
|
547
|
+
"parameters": [
|
548
|
+
{
|
549
|
+
"$ref": "#/components/parameters/id"
|
550
|
+
},
|
551
|
+
{
|
552
|
+
"$ref": "#/components/parameters/subjectid"
|
553
|
+
}
|
554
|
+
],
|
555
|
+
"responses": {
|
556
|
+
"202": {
|
557
|
+
"$ref": "#/components/responses/202"
|
558
|
+
},
|
559
|
+
"400": {
|
560
|
+
"$ref": "#/components/responses/400"
|
561
|
+
},
|
562
|
+
"401": {
|
563
|
+
"$ref": "#/components/responses/401"
|
564
|
+
},
|
565
|
+
"403": {
|
566
|
+
"$ref": "#/components/responses/403"
|
567
|
+
},
|
568
|
+
"404": {
|
569
|
+
"$ref": "#/components/responses/404"
|
570
|
+
}
|
571
|
+
},
|
572
|
+
"requestBody": {
|
573
|
+
"description": "SMILES identifier.\n",
|
574
|
+
"required": true,
|
575
|
+
"content": {
|
576
|
+
"application/x-www-form-urlencoded": {
|
577
|
+
"schema": {
|
578
|
+
"$ref": "#/components/schemas/postmodel"
|
579
|
+
}
|
580
|
+
}
|
581
|
+
}
|
582
|
+
}
|
583
|
+
}
|
584
|
+
},
|
585
|
+
"/report": {
|
586
|
+
"get": {
|
587
|
+
"tags": [
|
588
|
+
"report"
|
589
|
+
],
|
590
|
+
"description": "Get a list of QMRF reports",
|
591
|
+
"parameters": [
|
592
|
+
{
|
593
|
+
"$ref": "#/components/parameters/subjectid"
|
594
|
+
}
|
595
|
+
],
|
596
|
+
"responses": {
|
597
|
+
"200": {
|
598
|
+
"$ref": "#/components/responses/200"
|
599
|
+
},
|
600
|
+
"400": {
|
601
|
+
"$ref": "#/components/responses/400"
|
602
|
+
},
|
603
|
+
"401": {
|
604
|
+
"$ref": "#/components/responses/401"
|
605
|
+
},
|
606
|
+
"404": {
|
607
|
+
"$ref": "#/components/responses/404"
|
608
|
+
},
|
609
|
+
"500": {
|
610
|
+
"$ref": "#/components/responses/500"
|
611
|
+
}
|
612
|
+
}
|
613
|
+
}
|
614
|
+
},
|
615
|
+
"/report/{id}": {
|
616
|
+
"get": {
|
617
|
+
"tags": [
|
618
|
+
"report"
|
619
|
+
],
|
620
|
+
"description": "Get QMRF for prediction model",
|
621
|
+
"parameters": [
|
622
|
+
{
|
623
|
+
"$ref": "#/components/parameters/id"
|
624
|
+
},
|
625
|
+
{
|
626
|
+
"$ref": "#/components/parameters/subjectid"
|
627
|
+
}
|
628
|
+
],
|
629
|
+
"responses": {
|
630
|
+
"200": {
|
631
|
+
"description": "OK",
|
632
|
+
"content": {
|
633
|
+
"application/xml": {
|
634
|
+
"schema": {
|
635
|
+
"type": "object"
|
636
|
+
}
|
637
|
+
}
|
638
|
+
}
|
639
|
+
},
|
640
|
+
"400": {
|
641
|
+
"$ref": "#/components/responses/400"
|
642
|
+
},
|
643
|
+
"401": {
|
644
|
+
"$ref": "#/components/responses/401"
|
645
|
+
},
|
646
|
+
"403": {
|
647
|
+
"$ref": "#/components/responses/403"
|
648
|
+
},
|
649
|
+
"404": {
|
650
|
+
"$ref": "#/components/responses/404"
|
651
|
+
}
|
652
|
+
}
|
653
|
+
}
|
654
|
+
},
|
655
|
+
"/substance": {
|
656
|
+
"get": {
|
657
|
+
"tags": [
|
658
|
+
"substance"
|
659
|
+
],
|
660
|
+
"description": "Get a list of all substances",
|
661
|
+
"parameters": [
|
662
|
+
{
|
663
|
+
"$ref": "#/components/parameters/subjectid"
|
664
|
+
}
|
665
|
+
],
|
666
|
+
"responses": {
|
667
|
+
"200": {
|
668
|
+
"$ref": "#/components/responses/200"
|
669
|
+
},
|
670
|
+
"400": {
|
671
|
+
"$ref": "#/components/responses/400"
|
672
|
+
},
|
673
|
+
"401": {
|
674
|
+
"$ref": "#/components/responses/401"
|
675
|
+
},
|
676
|
+
"404": {
|
677
|
+
"$ref": "#/components/responses/404"
|
678
|
+
},
|
679
|
+
"500": {
|
680
|
+
"$ref": "#/components/responses/500"
|
681
|
+
}
|
682
|
+
}
|
683
|
+
}
|
684
|
+
},
|
685
|
+
"/substance/{id}": {
|
686
|
+
"get": {
|
687
|
+
"tags": [
|
688
|
+
"substance"
|
689
|
+
],
|
690
|
+
"description": "Get substance representation by ID",
|
691
|
+
"parameters": [
|
692
|
+
{
|
693
|
+
"$ref": "#/components/parameters/id"
|
694
|
+
},
|
695
|
+
{
|
696
|
+
"$ref": "#/components/parameters/subjectid"
|
697
|
+
}
|
698
|
+
],
|
699
|
+
"responses": {
|
700
|
+
"200": {
|
701
|
+
"$ref": "#/components/responses/200"
|
702
|
+
},
|
703
|
+
"400": {
|
704
|
+
"$ref": "#/components/responses/400"
|
705
|
+
},
|
706
|
+
"401": {
|
707
|
+
"$ref": "#/components/responses/401"
|
708
|
+
},
|
709
|
+
"403": {
|
710
|
+
"$ref": "#/components/responses/403"
|
711
|
+
},
|
712
|
+
"404": {
|
713
|
+
"$ref": "#/components/responses/404"
|
714
|
+
},
|
715
|
+
"500": {
|
716
|
+
"$ref": "#/components/responses/500"
|
717
|
+
}
|
718
|
+
}
|
719
|
+
}
|
720
|
+
},
|
721
|
+
"/validation": {
|
722
|
+
"get": {
|
723
|
+
"tags": [
|
724
|
+
"validation"
|
725
|
+
],
|
726
|
+
"description": "Get a list of all validation types",
|
727
|
+
"parameters": [
|
728
|
+
{
|
729
|
+
"$ref": "#/components/parameters/subjectid"
|
730
|
+
}
|
731
|
+
],
|
732
|
+
"responses": {
|
733
|
+
"200": {
|
734
|
+
"$ref": "#/components/responses/200"
|
735
|
+
},
|
736
|
+
"400": {
|
737
|
+
"$ref": "#/components/responses/400"
|
738
|
+
},
|
739
|
+
"401": {
|
740
|
+
"$ref": "#/components/responses/401"
|
741
|
+
},
|
742
|
+
"404": {
|
743
|
+
"$ref": "#/components/responses/404"
|
744
|
+
},
|
745
|
+
"500": {
|
746
|
+
"$ref": "#/components/responses/500"
|
747
|
+
}
|
748
|
+
}
|
749
|
+
}
|
750
|
+
},
|
751
|
+
"/validation/{validationtype}": {
|
752
|
+
"get": {
|
753
|
+
"tags": [
|
754
|
+
"validation"
|
755
|
+
],
|
756
|
+
"description": "Get all validations of a validation type",
|
757
|
+
"parameters": [
|
758
|
+
{
|
759
|
+
"$ref": "#/components/parameters/valtype"
|
760
|
+
},
|
761
|
+
{
|
762
|
+
"$ref": "#/components/parameters/subjectid"
|
763
|
+
}
|
764
|
+
],
|
765
|
+
"responses": {
|
766
|
+
"200": {
|
767
|
+
"$ref": "#/components/responses/200"
|
768
|
+
},
|
769
|
+
"400": {
|
770
|
+
"$ref": "#/components/responses/400"
|
771
|
+
},
|
772
|
+
"401": {
|
773
|
+
"$ref": "#/components/responses/401"
|
774
|
+
},
|
775
|
+
"403": {
|
776
|
+
"$ref": "#/components/responses/403"
|
777
|
+
},
|
778
|
+
"404": {
|
779
|
+
"$ref": "#/components/responses/404"
|
780
|
+
},
|
781
|
+
"500": {
|
782
|
+
"$ref": "#/components/responses/500"
|
783
|
+
}
|
784
|
+
}
|
785
|
+
}
|
786
|
+
},
|
787
|
+
"/validation/{validationtype}/{id}": {
|
788
|
+
"get": {
|
789
|
+
"tags": [
|
790
|
+
"validation"
|
791
|
+
],
|
792
|
+
"description": "Get validation representation",
|
793
|
+
"parameters": [
|
794
|
+
{
|
795
|
+
"$ref": "#/components/parameters/valtype"
|
796
|
+
},
|
797
|
+
{
|
798
|
+
"$ref": "#/components/parameters/id"
|
799
|
+
},
|
800
|
+
{
|
801
|
+
"$ref": "#/components/parameters/subjectid"
|
802
|
+
}
|
803
|
+
],
|
804
|
+
"responses": {
|
805
|
+
"200": {
|
806
|
+
"$ref": "#/components/responses/200"
|
807
|
+
},
|
808
|
+
"400": {
|
809
|
+
"$ref": "#/components/responses/400"
|
810
|
+
},
|
811
|
+
"401": {
|
812
|
+
"$ref": "#/components/responses/401"
|
813
|
+
},
|
814
|
+
"403": {
|
815
|
+
"$ref": "#/components/responses/403"
|
816
|
+
},
|
817
|
+
"404": {
|
818
|
+
"$ref": "#/components/responses/404"
|
819
|
+
},
|
820
|
+
"500": {
|
821
|
+
"$ref": "#/components/responses/500"
|
822
|
+
}
|
823
|
+
}
|
824
|
+
}
|
825
|
+
}
|
826
|
+
},
|
827
|
+
"tags": [
|
828
|
+
{
|
829
|
+
"name": "api",
|
830
|
+
"description": "Swagger API representation in JSON"
|
831
|
+
},
|
832
|
+
{
|
833
|
+
"name": "compound",
|
834
|
+
"description": "Compound"
|
835
|
+
},
|
836
|
+
{
|
837
|
+
"name": "dataset",
|
838
|
+
"description": "Dataset"
|
839
|
+
},
|
840
|
+
{
|
841
|
+
"name": "descriptor",
|
842
|
+
"description": "Descriptor"
|
843
|
+
},
|
844
|
+
{
|
845
|
+
"name": "endpoint",
|
846
|
+
"description": "Endpoint"
|
847
|
+
},
|
848
|
+
{
|
849
|
+
"name": "feature",
|
850
|
+
"description": "Feature"
|
851
|
+
},
|
852
|
+
{
|
853
|
+
"name": "model",
|
854
|
+
"description": "Lazar Model Service"
|
855
|
+
},
|
856
|
+
{
|
857
|
+
"name": "report",
|
858
|
+
"description": "QMRF Reporting"
|
859
|
+
},
|
860
|
+
{
|
861
|
+
"name": "substance",
|
862
|
+
"description": "Substance"
|
863
|
+
},
|
864
|
+
{
|
865
|
+
"name": "validation",
|
866
|
+
"description": "Validation"
|
867
|
+
}
|
868
|
+
],
|
869
|
+
"components": {
|
870
|
+
"schemas": {
|
871
|
+
"postmodel": {
|
872
|
+
"type": "object",
|
873
|
+
"properties": {
|
874
|
+
"identifier": {
|
875
|
+
"type": "string",
|
876
|
+
"example": "O=C1NC(=O)NC=C1"
|
877
|
+
}
|
878
|
+
}
|
879
|
+
},
|
880
|
+
"postdescriptor": {
|
881
|
+
"type": "object",
|
882
|
+
"properties": {
|
883
|
+
"identifier": {
|
884
|
+
"type": "string",
|
885
|
+
"example": "O=C1NC(=O)NC=C1"
|
886
|
+
},
|
887
|
+
"descriptor": {
|
888
|
+
"type": "string",
|
889
|
+
"example": "Openbabel.MW,Openbabel.atoms"
|
890
|
+
}
|
891
|
+
}
|
892
|
+
}
|
893
|
+
},
|
894
|
+
"parameters": {
|
895
|
+
"id": {
|
896
|
+
"name": "id",
|
897
|
+
"in": "path",
|
898
|
+
"description": "id",
|
899
|
+
"required": true,
|
900
|
+
"schema": {
|
901
|
+
"type": "string"
|
902
|
+
}
|
903
|
+
},
|
904
|
+
"endpoint": {
|
905
|
+
"name": "endpoint",
|
906
|
+
"in": "path",
|
907
|
+
"description": "type",
|
908
|
+
"required": true,
|
909
|
+
"schema": {
|
910
|
+
"type": "string"
|
911
|
+
}
|
912
|
+
},
|
913
|
+
"InChI": {
|
914
|
+
"name": "InChI",
|
915
|
+
"in": "path",
|
916
|
+
"description": "InChI String",
|
917
|
+
"required": true,
|
918
|
+
"schema": {
|
919
|
+
"type": "string"
|
920
|
+
}
|
921
|
+
},
|
922
|
+
"valtype": {
|
923
|
+
"name": "validationtype",
|
924
|
+
"in": "path",
|
925
|
+
"description": "validation type",
|
926
|
+
"required": true,
|
927
|
+
"schema": {
|
928
|
+
"type": "string",
|
929
|
+
"enum": [
|
930
|
+
"crossvalidation",
|
931
|
+
"leaveoneout",
|
932
|
+
"repeatedcrossvalidation",
|
933
|
+
"regressioncrossvalidation"
|
934
|
+
]
|
935
|
+
}
|
936
|
+
},
|
937
|
+
"subjectid": {
|
938
|
+
"in": "header",
|
939
|
+
"name": "subjectid",
|
940
|
+
"description": "authorization token",
|
941
|
+
"required": false,
|
942
|
+
"schema": {
|
943
|
+
"type": "string"
|
944
|
+
}
|
945
|
+
}
|
946
|
+
},
|
947
|
+
"responses": {
|
948
|
+
"200": {
|
949
|
+
"description": "OK",
|
950
|
+
"content": {
|
951
|
+
"application/json": {
|
952
|
+
"schema": {
|
953
|
+
"type": "object"
|
954
|
+
}
|
955
|
+
}
|
956
|
+
}
|
957
|
+
},
|
958
|
+
"201": {
|
959
|
+
"description": "Created",
|
960
|
+
"content": {
|
961
|
+
"application/json": {
|
962
|
+
"schema": {
|
963
|
+
"type": "object"
|
964
|
+
}
|
965
|
+
}
|
966
|
+
}
|
967
|
+
},
|
968
|
+
"202": {
|
969
|
+
"description": "Accepted",
|
970
|
+
"content": {
|
971
|
+
"application/json": {
|
972
|
+
"schema": {
|
973
|
+
"type": "object"
|
974
|
+
}
|
975
|
+
},
|
976
|
+
"text/plain": {
|
977
|
+
"schema": {
|
978
|
+
"type": "object"
|
979
|
+
}
|
980
|
+
}
|
981
|
+
}
|
982
|
+
},
|
983
|
+
"400": {
|
984
|
+
"description": "Bad Request"
|
985
|
+
},
|
986
|
+
"401": {
|
987
|
+
"description": "Unauthorized"
|
988
|
+
},
|
989
|
+
"403": {
|
990
|
+
"description": "Forbidden"
|
991
|
+
},
|
992
|
+
"404": {
|
993
|
+
"description": "Resource Not Found"
|
994
|
+
},
|
995
|
+
"500": {
|
996
|
+
"description": "Server Error"
|
997
|
+
}
|
998
|
+
}
|
999
|
+
}
|
1000
|
+
}
|