rbbt-rest 1.6.2 → 1.6.3

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Files changed (46) hide show
  1. checksums.yaml +4 -4
  2. data/lib/rbbt/rest/common/misc.rb +10 -0
  3. data/lib/rbbt/rest/workflow/jobs.rb +8 -7
  4. data/share/views/compass/app.sass +278 -3
  5. data/share/views/compass/base/color.sass +66 -0
  6. data/share/views/compass/blocks.sass +0 -0
  7. data/share/views/compass/mixins/_blocks.sass +76 -80
  8. data/share/views/compass/mixins/_compass.sass +0 -0
  9. data/share/views/compass/mixins/_hide.sass +76 -1
  10. data/share/views/compass/table.sass +142 -0
  11. data/share/views/compass/variables/colors.sass +7 -0
  12. data/share/views/compass/variables/sizes.sass +5 -0
  13. data/share/views/entity_partials/action_card.haml +5 -5
  14. data/share/views/entity_partials/action_controller.haml +31 -33
  15. data/share/views/entity_partials/entity_card.haml +28 -27
  16. data/share/views/entity_partials/entity_list_card.haml +30 -42
  17. data/share/views/entity_partials/entity_map_card.haml +35 -43
  18. data/share/views/entity_partials/list_container.haml +6 -6
  19. data/share/views/layout.haml +53 -59
  20. data/share/views/layout/coda.haml +1 -0
  21. data/share/views/layout/doctype.haml +8 -0
  22. data/share/views/layout/footer.haml +36 -10
  23. data/share/views/layout/header.haml +47 -0
  24. data/share/views/layout/top_menu.haml +27 -13
  25. data/share/views/partials/form.haml +4 -4
  26. data/share/views/partials/table.haml +2 -1
  27. data/share/views/partials/table/column.haml +8 -9
  28. data/share/views/partials/table/files.haml +2 -2
  29. data/share/views/partials/table/filters.haml +16 -16
  30. data/share/views/partials/table/page.haml +9 -15
  31. data/share/views/public/js/ng-favourites.js +13 -0
  32. data/share/views/public/js/rbbt.aesthetics.js +51 -0
  33. data/share/views/public/js/rbbt.entity.js +62 -0
  34. data/share/views/public/js/rbbt.entity_list.js +54 -0
  35. data/share/views/public/js/rbbt.entity_map.js +52 -0
  36. data/share/views/public/js/rbbt.favourites.js +286 -0
  37. data/share/views/public/js/rbbt.favourites.js.old +195 -0
  38. data/share/views/public/js/rbbt.js +40 -0
  39. data/share/views/public/js/rbbt.knowledge_base.js +24 -0
  40. data/share/views/public/js/rbbt.page.js +32 -0
  41. data/share/views/public/js/rbbt/actions.js +15 -14
  42. data/share/views/public/js/rbbt/table.js +6 -4
  43. data/share/views/tools/cytoscape.haml +310 -0
  44. data/share/views/tools/protein_tool.haml +383 -0
  45. data/share/views/tools/protein_tool/controls.haml +315 -0
  46. metadata +23 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: 4befe1d0698694deab3648f0ccd4e7f0ef524934
4
- data.tar.gz: 7b24e154d080dc4546c7229f40c3779a3ce395d5
3
+ metadata.gz: adfb3bb568b61a43b82dab68a49bb59b059a5dec
4
+ data.tar.gz: 88b212ef91fa81098b35268b365006aa7ffd2bab
5
5
  SHA512:
6
- metadata.gz: 6a243e00d987137dcbe21c2d8257624b5681ed96a21bf9376cf13c8a4012c8d79bba63bf335b5004dcdded3f4f01fe6696e1b7e72aa9e308aeaae8c79960d042
7
- data.tar.gz: b6bf748fe63f4534f27fb4f8b3bf2c4114316ba87a6b0fe46d9fc9101dad584c4fb25a41cc53f45967b144ee91f3f7123e9b56d5a2e6799f9bdcb24dc1978273
6
+ metadata.gz: 13ca0d58a8b9f7b07028699348e5a4f00a8e10e29a2ced1b3e986fb0b10629cc96843af1045c799a330d7af5278a983e2e5d6d8b523c7897188ea731db029fed
7
+ data.tar.gz: 2e7d6741d5cd079dee1791739abdaaeb37fd766089faf6f5af07740de0ebf82c1d1d01a8431d38a7e0ffed54b53af16d66f787eb1addd5cbb3eae7617b3235f1
@@ -174,6 +174,16 @@ module RbbtRESTHelpers
174
174
  end
175
175
  end
176
176
 
177
+ def prepare_input(params, input, type)
178
+ value = consume_parameter(input, params)
179
+ param_file = consume_parameter(input.to_s + '__param_file', params)
180
+ return nil if value.nil? and param_file.nil?
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+
182
+ fixed_value = fix_input(type, value, param_file)
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+
184
+ fixed_value
185
+ end
186
+
177
187
 
178
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  def param2boolean(value)
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189
  case value
@@ -51,13 +51,14 @@ module WorkflowRESTHelpers
51
51
 
52
52
  task_inputs = {}
53
53
  inputs.each do |input|
54
- value = consume_parameter(input, params)
55
- param_file = consume_parameter(input.to_s + '__param_file', params)
56
- next if value.nil? and param_file.nil?
57
- type = input_types[input]
58
-
59
- fixed_value = fix_input(type, value, param_file)
60
- task_inputs[input] = fixed_value
54
+ #value = consume_parameter(input, params)
55
+ #param_file = consume_parameter(input.to_s + '__param_file', params)
56
+ #next if value.nil? and param_file.nil?
57
+ #type = input_types[input]
58
+
59
+ #fixed_value = fix_input(type, value, param_file)
60
+ #task_inputs[input] = fixed_value
61
+ task_inputs[input] = prepare_input(params, input, input_types[input])
61
62
  end
62
63
 
63
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  task_inputs
@@ -1,3 +1,278 @@
1
- @charset "UTF-8"
2
- @import "init"
3
- //@import "CSS:semantic-ui"
1
+ @import 'screen_sizes'
2
+
3
+ @import 'compass/css3/animation'
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+ .preload *
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+ +animation-duration(0s !important)
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+
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+ .clean_list
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+ list-style: none
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+ padding-left: 0
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+
11
+ $subtle-font: rgba(0,0,0,0.30)
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+
13
+ #content
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+ padding: 64px 16px 0 32px
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+
16
+ #top_menu
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+ z-index: 100
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+
19
+ .pointer
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+ cursor: pointer
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+
22
+ .title.header
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+ & > .name
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+ font-size: 1.3em
25
+ & > :not(.name)
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+ color: $subtle-font
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+
28
+ .name
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+ ~ .hash
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+ color: $subtle-font
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+ margin-left: 1em
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+
33
+ .main.menu
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+ .finder
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+ padding: 4px
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+ padding-top: 8px
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+
38
+ @media #{$only-large}
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+ #content
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+ padding: 64px 16px 0 32px
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+
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+
43
+ .entity_card, .entity_list_card
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+ > .content
45
+ > .info
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+ float: right
47
+ width: 35%
48
+ display: block
49
+ > .description, > .actions, > .card_actions
50
+ float: left
51
+ width: calc(65% - 16px)
52
+ display: block
53
+
54
+ .action_parameters, .filter_controls
55
+ .input.field
56
+ width: calc(50% - 32px)
57
+ float: left
58
+ margin-right: 32px !important
59
+ &:not(.submit)
60
+ clear: none !important
61
+
62
+ .responsive_column
63
+ width: 40%
64
+ margin-right: 10%
65
+ float: left
66
+
67
+ =small_screen
68
+ #content
69
+ padding: 64px 4px
70
+
71
+ .entity_card, .entity_list_card
72
+ > .content
73
+ > .info
74
+ width: 100%
75
+ > .description, > .actions, > .card_actions
76
+ width: 100%
77
+
78
+ .main.menu
79
+ .finder
80
+ padding: 4px
81
+ padding-top: 8px
82
+ form input
83
+ width: 5em
84
+
85
+ .row
86
+ clear: both
87
+
88
+ @media #{$not-large}
89
+ +small_screen
90
+
91
+ #modal
92
+ +small_screen
93
+
94
+ .action_parameters, .filter_controls
95
+ form
96
+ &:after
97
+ content: ''
98
+ clear: both
99
+ display: block
100
+
101
+ .action_content
102
+ clear: both
103
+
104
+
105
+ .entity_card, .entity_list_card, .action_card
106
+ > .content > .ui.basic.segment, > .action_content > .ui.basic.segment
107
+ padding: 0px
108
+
109
+ .fragment.loading
110
+ &:after
111
+ content: " loading page fragment... "
112
+ display: inline-block
113
+ margin: 0em 1em
114
+
115
+ table, table.responsive
116
+ //tfoot
117
+ display: none !important
118
+
119
+ .action_loader
120
+ min-height: 48px
121
+ border-top: none !important
122
+
123
+ .action_content
124
+ > .action_card > .action_parameters, > .action_card > .title, > .action_card > .action_description
125
+ display: none
126
+
127
+ body
128
+ margin: 0 !important
129
+
130
+ .rbbt_reveal_content
131
+ display: none
132
+
133
+ .button.wrap
134
+ padding: 0px !important
135
+ > a
136
+ display: inline-block
137
+ padding: .5892825em 1.125em
138
+
139
+ #modal
140
+ top: 5em
141
+ left: 50%
142
+ max-height: calc(100% - 10em)
143
+ overflow: auto
144
+
145
+ .table_column_selector
146
+ span.field
147
+ font-size: 1.2em
148
+ width: 10em
149
+ display: inline-block
150
+
151
+ .figure.float
152
+ float: left
153
+ margin-right: 32px
154
+ background: white
155
+ border: 1px solid rgba(0,0,0,0.12)
156
+ padding: 4px
157
+ .title
158
+ color: $subtle-font
159
+
160
+ .tool_menu
161
+ margin-bottom: 0px
162
+ > dd
163
+ overflow: auto !important
164
+
165
+ .entity_list
166
+ width: auto !important
167
+ clear: both
168
+ span.title
169
+ border: none !important
170
+
171
+ table
172
+ .caption, .title
173
+ color: $subtle-font
174
+
175
+ .info > .meta dt
176
+ font-weight: bold
177
+
178
+ dd > ul
179
+ margin-top: 0px
180
+
181
+ .segment[class*='very basic']
182
+ padding: 0px !important
183
+
184
+ .icon.star.favourite
185
+ color: gold !important
186
+
187
+ .workflow_task
188
+ .field.submit
189
+ .jobname
190
+ float: left
191
+ width: 13em !important
192
+ .format
193
+ float: left
194
+ width: 7em !important
195
+ form
196
+ .field
197
+ max-width: 500px
198
+
199
+ .job_control > ul
200
+ @extend .clean_list
201
+ > li
202
+ display: inline-block
203
+
204
+ .selection.dropdown > .menu > .item:not([data-value])
205
+ font-style: italic
206
+ color: grey
207
+
208
+ option[disabled]
209
+ opacity: 1 !important
210
+ font-weight: bold
211
+ &:before
212
+ content: "\00A7 "
213
+ display: inline
214
+
215
+ .finder
216
+ padding: 0 !important
217
+ input
218
+ line-height: 1.32em
219
+ font-size: 1.32em
220
+ padding: 4px
221
+
222
+ .bulleted
223
+ white-space: nowrap
224
+ &:before
225
+ content: "\2022"
226
+ display: inline-block
227
+ text-align: center
228
+
229
+ a.entity.highlight
230
+ @extend .bulleted
231
+ font-weight: bold
232
+
233
+ .figure
234
+ margin-bottom: 1em
235
+ margin-top: 1em
236
+
237
+
238
+ a.entity[data-aes-color]:not([data-aes-color=none])
239
+ @extend .bulleted
240
+ &[data-aes-color=gold]
241
+ &:before
242
+ color: gold
243
+ &[data-aes-color=red]
244
+ &:before
245
+ color: red
246
+ &[data-aes-color=yellow]
247
+ &:before
248
+ color: yellow
249
+ &[data-aes-color=blue]
250
+ &:before
251
+ color: blue
252
+ &[data-aes-color=green]
253
+ &:before
254
+ color: green
255
+
256
+ span.bullet
257
+ @extend .bulleted
258
+ @extend .pointer
259
+ &:hover
260
+ border: 1px solid rgba(0,0,0,0.12)
261
+ width: 1.5em
262
+ height: 1.5em
263
+ margin-top: 0.5em
264
+ text-align: center
265
+ position: absolute
266
+ left: 0
267
+ &.red
268
+ color: red
269
+ &.green
270
+ color: green
271
+
272
+ label[title]
273
+ cursor: help
274
+
275
+ .progress.ui.message
276
+ margin-top: 8px
277
+ .progress.ui.message:empty
278
+ display: none
@@ -0,0 +1,66 @@
1
+ @import "base/variables/color"
2
+
3
+ =subtle_color
4
+ color: $subtle_color
5
+
6
+ =gold
7
+ color: gold
8
+
9
+ =error
10
+ color: red
11
+
12
+ $background-transparent: 0.15
13
+
14
+ $color-background-main: $color-one
15
+ $color-background-alt: $color-one
16
+
17
+ $color-background-subtle: tint($color-background-alt, 40)
18
+ $color-background-glassy: transparentize($color-background-subtle, 0.18)
19
+
20
+ $color-background-button: #c9c9c9
21
+ $color-background-active: shade($color-background-button, 40)
22
+ $color-background-hover: shade($color-background-button, 20)
23
+ $color-background-inactive: transparentize($color-background-button, 0.80)
24
+ $color-background-error: $color-accent
25
+
26
+ %background-white
27
+ background: white
28
+ a:not([href="#"])
29
+ color: $color-link
30
+
31
+ %background-main
32
+ background: $color-background-main
33
+ a:not([href="#"])
34
+ color: $color-link-alt
35
+
36
+ %background-subtle
37
+ background: $color-background-subtle
38
+ a:not([href="#"])
39
+ color: $color-link-alt
40
+
41
+ %background-glassy
42
+ background: $color-background-glassy
43
+
44
+ %background-hover
45
+ background: $color-background-hover
46
+ a:not([href="#"])
47
+ color: $color-link-alt
48
+
49
+ %background-active
50
+ background: $color-background-active
51
+ &, a:not([href="#"])
52
+ color: white
53
+
54
+ %background-error
55
+ background: $color-background-error
56
+ color: $color-accent
57
+ & > a
58
+ color: $color-accent
59
+
60
+ =subtle_background
61
+ @extend %background-subtle
62
+
63
+ =white_background
64
+ @extend %background-white
65
+
66
+
File without changes
@@ -1,83 +1,79 @@
1
- @import "mixins/deps"
2
- @import "base/icons"
3
-
4
- $tile: 8px
5
- $delta: $tile / 2
6
-
7
- %height-8
8
- height: 8 * $tile
9
-
10
- %width-8
11
- width: 8 * $tile
12
-
13
- %width-full
14
- width: 100%
15
-
16
- %text-valign-center
17
- +vertical-center(calc(50% - 0.5em))
18
- & > *
19
- +vertical-center(calc(50% - 0.5em))
20
-
21
- %top_bar_size
22
- @extend %height-8
23
- @extend %width-full
24
-
25
- %top_bar_position
26
- position: fixed
27
- top: 0
28
- left: 0
29
-
30
- %top_bar_layout
31
- display: flex
32
- flex-direction: row-reverse
33
-
34
- %top_bar_style
35
- background: darken(#FFF, 20)
36
-
37
- %nodisplay
38
- display: none
39
-
40
- %reload_button_order
41
- order: 0
42
-
43
- %reload_button_style
44
- border: 1px solid black
45
-
46
- %text-font-8
47
- @extend %height-8
48
- line-height: 8 * $tile
49
- font-size: 8 * $tile * 1.5
50
- @extend %text-valign-center
51
-
52
- %text-box-8-8
53
- @extend %text-font-8
54
- @extend %width-8
55
- text-align: center
1
+ @import "variables/sizes"
2
+ @import "variables/colors"
3
+ @import "mixins/hide"
4
+
5
+ @import "compass/css3/opacity"
6
+ @import "compass/css3/transition"
7
+ @import "compass/css3/box-shadow"
8
+
9
+ =background-glassy
10
+ background: transparentize(tint($color-one, 40), 0.70)
11
+
12
+ =border-glassy
13
+ border: 1px solid transparentize($color-one, 0.20)
14
+
15
+ =background-main
16
+ background: $color-one
17
+
18
+ =background-subtle
19
+ background: tint($color-one, 50)
20
+
21
+ =background-white
22
+ background: white
23
+
24
+ =padded_block
25
+ padding: $tile
26
+
27
+ =background-material
28
+ background: $color-two
29
+
30
+ =top_shadow($depth: 1)
31
+
32
+ $z1 : 0
33
+ $z2 : 0
34
+ $z3 : 0
35
+ $z4 : 0
36
+ $z5 : 0
37
+
38
+ @if $depth == 1
39
+ $z1 : 1
40
+ @if $depth == 2
41
+ $z2 : 1
42
+ @if $depth == 3
43
+ $z3 : 1
44
+ @if $depth == 4
45
+ $z4 : 1
46
+ @if $depth == 5
47
+ $z5 : 1
48
+
49
+ @include box-shadow( 0px 1px 1.5px rgba(#000, $z1), 0px 3px 3px rgba(#000, $z2), 0px 10px 10px rgba(#000, $z3), 0px 14px 14px rgba(#000, $z4), 0px 19px 19px rgba(#000, $z5))
50
+
51
+ =bottom_shadow($depth: 1)
52
+ $z1 : 0
53
+ $z2 : 0
54
+ $z3 : 0
55
+ $z4 : 0
56
+ $z5 : 0
57
+ @if $depth == 1
58
+ $z1 : 1
59
+ @if $depth == 2
60
+ $z2 : 1
61
+ @if $depth == 3
62
+ $z3 : 1
63
+ @if $depth == 4
64
+ $z4 : 1
65
+ @if $depth == 5
66
+ $z5 : 1
67
+
68
+ @include box-shadow( 0px 1px 1px rgba(#000, $z1), 0px 3px 3px rgba(#000, $z2), 0px 6px 3px rgba(#000, $z3), 0px 10px 5px rgba(#000, $z4), 0px 15px 6px rgba(#000, $z5))
56
69
 
57
- %horizontal-item-8
58
- @extend %text-font-8
59
- @extend %stack-left
60
-
61
- %reload_button_layout
62
- display: inline-block
63
- @extend %text-box-8-8
64
-
65
- %float-left
66
- float: left
67
-
68
- %stack-left
69
- @extend %float-left
70
- &:not(:first-of-type)
71
- margin-left: $delta
72
-
73
70
 
74
- %top_bar_button_set
75
- +clearfix
76
- & > *
77
- @extend %horizontal-item-8
71
+ =material($depth: 1)
72
+ +top_shadow($depth)
73
+ +bottom_shadow($depth)
74
+ z-index: $depth * 2
78
75
 
79
- %rail_items
80
- position: absolute
81
- @extend %width-full
82
- right: -100%
83
- top: 8 * $tile
76
+ =material_block($depth: 1)
77
+ +padded_block
78
+ +background-material
79
+ +material($depth)