rbbt-rest 1.6.2 → 1.6.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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?
181
+
182
+ fixed_value = fix_input(type, value, param_file)
183
+
184
+ fixed_value
185
+ end
186
+
177
187
 
178
188
  def param2boolean(value)
179
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
64
  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'
4
+ .preload *
5
+ +animation-duration(0s !important)
6
+
7
+ .clean_list
8
+ list-style: none
9
+ padding-left: 0
10
+
11
+ $subtle-font: rgba(0,0,0,0.30)
12
+
13
+ #content
14
+ padding: 64px 16px 0 32px
15
+
16
+ #top_menu
17
+ z-index: 100
18
+
19
+ .pointer
20
+ cursor: pointer
21
+
22
+ .title.header
23
+ & > .name
24
+ font-size: 1.3em
25
+ & > :not(.name)
26
+ color: $subtle-font
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+
28
+ .name
29
+ ~ .hash
30
+ color: $subtle-font
31
+ margin-left: 1em
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+
33
+ .main.menu
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+ .finder
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+ padding: 4px
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+ padding-top: 8px
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+
38
+ @media #{$only-large}
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+ #content
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+ padding: 64px 16px 0 32px
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+
42
+
43
+ .entity_card, .entity_list_card
44
+ > .content
45
+ > .info
46
+ 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)