rbbt-rest 1.6.2 → 1.6.3
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- checksums.yaml +4 -4
- data/lib/rbbt/rest/common/misc.rb +10 -0
- data/lib/rbbt/rest/workflow/jobs.rb +8 -7
- data/share/views/compass/app.sass +278 -3
- data/share/views/compass/base/color.sass +66 -0
- data/share/views/compass/blocks.sass +0 -0
- data/share/views/compass/mixins/_blocks.sass +76 -80
- data/share/views/compass/mixins/_compass.sass +0 -0
- data/share/views/compass/mixins/_hide.sass +76 -1
- data/share/views/compass/table.sass +142 -0
- data/share/views/compass/variables/colors.sass +7 -0
- data/share/views/compass/variables/sizes.sass +5 -0
- data/share/views/entity_partials/action_card.haml +5 -5
- data/share/views/entity_partials/action_controller.haml +31 -33
- data/share/views/entity_partials/entity_card.haml +28 -27
- data/share/views/entity_partials/entity_list_card.haml +30 -42
- data/share/views/entity_partials/entity_map_card.haml +35 -43
- data/share/views/entity_partials/list_container.haml +6 -6
- data/share/views/layout.haml +53 -59
- data/share/views/layout/coda.haml +1 -0
- data/share/views/layout/doctype.haml +8 -0
- data/share/views/layout/footer.haml +36 -10
- data/share/views/layout/header.haml +47 -0
- data/share/views/layout/top_menu.haml +27 -13
- data/share/views/partials/form.haml +4 -4
- data/share/views/partials/table.haml +2 -1
- data/share/views/partials/table/column.haml +8 -9
- data/share/views/partials/table/files.haml +2 -2
- data/share/views/partials/table/filters.haml +16 -16
- data/share/views/partials/table/page.haml +9 -15
- data/share/views/public/js/ng-favourites.js +13 -0
- data/share/views/public/js/rbbt.aesthetics.js +51 -0
- data/share/views/public/js/rbbt.entity.js +62 -0
- data/share/views/public/js/rbbt.entity_list.js +54 -0
- data/share/views/public/js/rbbt.entity_map.js +52 -0
- data/share/views/public/js/rbbt.favourites.js +286 -0
- data/share/views/public/js/rbbt.favourites.js.old +195 -0
- data/share/views/public/js/rbbt.js +40 -0
- data/share/views/public/js/rbbt.knowledge_base.js +24 -0
- data/share/views/public/js/rbbt.page.js +32 -0
- data/share/views/public/js/rbbt/actions.js +15 -14
- data/share/views/public/js/rbbt/table.js +6 -4
- data/share/views/tools/cytoscape.haml +310 -0
- data/share/views/tools/protein_tool.haml +383 -0
- data/share/views/tools/protein_tool/controls.haml +315 -0
- metadata +23 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: adfb3bb568b61a43b82dab68a49bb59b059a5dec
|
4
|
+
data.tar.gz: 88b212ef91fa81098b35268b365006aa7ffd2bab
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
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
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+
|
182
|
+
fixed_value = fix_input(type, value, param_file)
|
183
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+
|
184
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+
fixed_value
|
185
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+
end
|
186
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+
|
177
187
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|
178
188
|
def param2boolean(value)
|
179
189
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case value
|
@@ -51,13 +51,14 @@ module WorkflowRESTHelpers
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|
51
51
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|
52
52
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task_inputs = {}
|
53
53
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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
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-
type = input_types[input]
|
58
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-
|
59
|
-
fixed_value = fix_input(type, value, param_file)
|
60
|
-
task_inputs[input] = fixed_value
|
54
|
+
#value = consume_parameter(input, params)
|
55
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+
#param_file = consume_parameter(input.to_s + '__param_file', params)
|
56
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+
#next if value.nil? and param_file.nil?
|
57
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+
#type = input_types[input]
|
58
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+
|
59
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+
#fixed_value = fix_input(type, value, param_file)
|
60
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+
#task_inputs[input] = fixed_value
|
61
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+
task_inputs[input] = prepare_input(params, input, input_types[input])
|
61
62
|
end
|
62
63
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|
63
64
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task_inputs
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@@ -1,3 +1,278 @@
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1
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-
@
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2
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-
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3
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-
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1
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+
@import 'screen_sizes'
|
2
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+
|
3
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+
@import 'compass/css3/animation'
|
4
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+
.preload *
|
5
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+
+animation-duration(0s !important)
|
6
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+
|
7
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+
.clean_list
|
8
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+
list-style: none
|
9
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+
padding-left: 0
|
10
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+
|
11
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+
$subtle-font: rgba(0,0,0,0.30)
|
12
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+
|
13
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+
#content
|
14
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+
padding: 64px 16px 0 32px
|
15
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+
|
16
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+
#top_menu
|
17
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+
z-index: 100
|
18
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+
|
19
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+
.pointer
|
20
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+
cursor: pointer
|
21
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+
|
22
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+
.title.header
|
23
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+
& > .name
|
24
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+
font-size: 1.3em
|
25
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+
& > :not(.name)
|
26
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+
color: $subtle-font
|
27
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+
|
28
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+
.name
|
29
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+
~ .hash
|
30
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+
color: $subtle-font
|
31
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+
margin-left: 1em
|
32
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+
|
33
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+
.main.menu
|
34
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+
.finder
|
35
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+
padding: 4px
|
36
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+
padding-top: 8px
|
37
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+
|
38
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+
@media #{$only-large}
|
39
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+
#content
|
40
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+
padding: 64px 16px 0 32px
|
41
|
+
|
42
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+
|
43
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+
.entity_card, .entity_list_card
|
44
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+
> .content
|
45
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+
> .info
|
46
|
+
float: right
|
47
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+
width: 35%
|
48
|
+
display: block
|
49
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+
> .description, > .actions, > .card_actions
|
50
|
+
float: left
|
51
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+
width: calc(65% - 16px)
|
52
|
+
display: block
|
53
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+
|
54
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+
.action_parameters, .filter_controls
|
55
|
+
.input.field
|
56
|
+
width: calc(50% - 32px)
|
57
|
+
float: left
|
58
|
+
margin-right: 32px !important
|
59
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+
&:not(.submit)
|
60
|
+
clear: none !important
|
61
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+
|
62
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+
.responsive_column
|
63
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+
width: 40%
|
64
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+
margin-right: 10%
|
65
|
+
float: left
|
66
|
+
|
67
|
+
=small_screen
|
68
|
+
#content
|
69
|
+
padding: 64px 4px
|
70
|
+
|
71
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+
.entity_card, .entity_list_card
|
72
|
+
> .content
|
73
|
+
> .info
|
74
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+
width: 100%
|
75
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+
> .description, > .actions, > .card_actions
|
76
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+
width: 100%
|
77
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+
|
78
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+
.main.menu
|
79
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+
.finder
|
80
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+
padding: 4px
|
81
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+
padding-top: 8px
|
82
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+
form input
|
83
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+
width: 5em
|
84
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+
|
85
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+
.row
|
86
|
+
clear: both
|
87
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+
|
88
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+
@media #{$not-large}
|
89
|
+
+small_screen
|
90
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+
|
91
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+
#modal
|
92
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+
+small_screen
|
93
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+
|
94
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+
.action_parameters, .filter_controls
|
95
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+
form
|
96
|
+
&:after
|
97
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+
content: ''
|
98
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+
clear: both
|
99
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+
display: block
|
100
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+
|
101
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+
.action_content
|
102
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+
clear: both
|
103
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+
|
104
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+
|
105
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+
.entity_card, .entity_list_card, .action_card
|
106
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+
> .content > .ui.basic.segment, > .action_content > .ui.basic.segment
|
107
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+
padding: 0px
|
108
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+
|
109
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+
.fragment.loading
|
110
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+
&:after
|
111
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+
content: " loading page fragment... "
|
112
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+
display: inline-block
|
113
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+
margin: 0em 1em
|
114
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+
|
115
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+
table, table.responsive
|
116
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+
//tfoot
|
117
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+
display: none !important
|
118
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+
|
119
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+
.action_loader
|
120
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+
min-height: 48px
|
121
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+
border-top: none !important
|
122
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+
|
123
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+
.action_content
|
124
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+
> .action_card > .action_parameters, > .action_card > .title, > .action_card > .action_description
|
125
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+
display: none
|
126
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+
|
127
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+
body
|
128
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+
margin: 0 !important
|
129
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+
|
130
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+
.rbbt_reveal_content
|
131
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+
display: none
|
132
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+
|
133
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+
.button.wrap
|
134
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+
padding: 0px !important
|
135
|
+
> a
|
136
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+
display: inline-block
|
137
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+
padding: .5892825em 1.125em
|
138
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+
|
139
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+
#modal
|
140
|
+
top: 5em
|
141
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+
left: 50%
|
142
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+
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
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+
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
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+
|
171
|
+
table
|
172
|
+
.caption, .title
|
173
|
+
color: $subtle-font
|
174
|
+
|
175
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+
.info > .meta dt
|
176
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+
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
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+
width: 7em !important
|
195
|
+
form
|
196
|
+
.field
|
197
|
+
max-width: 500px
|
198
|
+
|
199
|
+
.job_control > ul
|
200
|
+
@extend .clean_list
|
201
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+
> li
|
202
|
+
display: inline-block
|
203
|
+
|
204
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+
.selection.dropdown > .menu > .item:not([data-value])
|
205
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+
font-style: italic
|
206
|
+
color: grey
|
207
|
+
|
208
|
+
option[disabled]
|
209
|
+
opacity: 1 !important
|
210
|
+
font-weight: bold
|
211
|
+
&:before
|
212
|
+
content: "\00A7 "
|
213
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+
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
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background: $color-background-glassy
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%background-hover
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background: $color-background-hover
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a:not([href="#"])
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color: $color-link-alt
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%background-active
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background: $color-background-active
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&, a:not([href="#"])
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color: white
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%background-error
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background: $color-background-error
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color: $color-accent
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& > a
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color: $color-accent
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=subtle_background
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@extend %background-subtle
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=white_background
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@extend %background-white
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@@ -1,83 +1,79 @@
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@import "variables/sizes"
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@import "variables/colors"
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@import "mixins/hide"
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@import "compass/css3/opacity"
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@import "compass/css3/transition"
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@import "compass/css3/box-shadow"
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=background-glassy
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background: transparentize(tint($color-one, 40), 0.70)
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=border-glassy
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border: 1px solid transparentize($color-one, 0.20)
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=background-main
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background: $color-one
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=background-subtle
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background: tint($color-one, 50)
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=background-white
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background: white
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=padded_block
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padding: $tile
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=background-material
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background: $color-two
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=top_shadow($depth: 1)
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$z1 : 0
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$z2 : 0
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$z3 : 0
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$z4 : 0
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$z5 : 0
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@if $depth == 1
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$z1 : 1
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@if $depth == 2
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$z2 : 1
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@if $depth == 3
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$z3 : 1
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@if $depth == 4
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$z4 : 1
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@if $depth == 5
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$z5 : 1
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@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, $z5))
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=bottom_shadow($depth: 1)
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$z1 : 0
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$z2 : 0
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$z3 : 0
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$z4 : 0
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$z5 : 0
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@if $depth == 1
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$z1 : 1
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@if $depth == 2
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$z2 : 1
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@if $depth == 3
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$z3 : 1
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@if $depth == 4
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$z4 : 1
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@if $depth == 5
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$z5 : 1
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@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))
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%horizontal-item-8
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@extend %text-font-8
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@extend %stack-left
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%reload_button_layout
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display: inline-block
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@extend %text-box-8-8
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%float-left
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float: left
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-
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%stack-left
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@extend %float-left
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&:not(:first-of-type)
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margin-left: $delta
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-
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+
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=material($depth: 1)
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+top_shadow($depth)
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+
+bottom_shadow($depth)
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z-index: $depth * 2
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-
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-
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top: 8 * $tile
|
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+
=material_block($depth: 1)
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+
+padded_block
|
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+
+background-material
|
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+
+material($depth)
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