sequenceserver 0.7.4 → 0.7.5
Sign up to get free protection for your applications and to get access to all the features.
- data/LICENSE.Apache.txt +176 -0
- data/LICENSE.txt +6 -1
- data/lib/sequenceserver.rb +5 -2
- data/lib/sequenceserver/helpers.rb +7 -0
- data/public/js/liveclip.jquery.js +246 -0
- data/sequenceserver.gemspec +2 -2
- data/tests/ui.specs.todo +10 -0
- data/views/search.erb +1 -1
- metadata +7 -4
data/LICENSE.Apache.txt
ADDED
@@ -0,0 +1,176 @@
|
|
1
|
+
Apache License
|
2
|
+
Version 2.0, January 2004
|
3
|
+
http://www.apache.org/licenses/
|
4
|
+
|
5
|
+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
|
6
|
+
|
7
|
+
1. Definitions.
|
8
|
+
|
9
|
+
"License" shall mean the terms and conditions for use, reproduction,
|
10
|
+
and distribution as defined by Sections 1 through 9 of this document.
|
11
|
+
|
12
|
+
"Licensor" shall mean the copyright owner or entity authorized by
|
13
|
+
the copyright owner that is granting the License.
|
14
|
+
|
15
|
+
"Legal Entity" shall mean the union of the acting entity and all
|
16
|
+
other entities that control, are controlled by, or are under common
|
17
|
+
control with that entity. For the purposes of this definition,
|
18
|
+
"control" means (i) the power, direct or indirect, to cause the
|
19
|
+
direction or management of such entity, whether by contract or
|
20
|
+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
|
21
|
+
outstanding shares, or (iii) beneficial ownership of such entity.
|
22
|
+
|
23
|
+
"You" (or "Your") shall mean an individual or Legal Entity
|
24
|
+
exercising permissions granted by this License.
|
25
|
+
|
26
|
+
"Source" form shall mean the preferred form for making modifications,
|
27
|
+
including but not limited to software source code, documentation
|
28
|
+
source, and configuration files.
|
29
|
+
|
30
|
+
"Object" form shall mean any form resulting from mechanical
|
31
|
+
transformation or translation of a Source form, including but
|
32
|
+
not limited to compiled object code, generated documentation,
|
33
|
+
and conversions to other media types.
|
34
|
+
|
35
|
+
"Work" shall mean the work of authorship, whether in Source or
|
36
|
+
Object form, made available under the License, as indicated by a
|
37
|
+
copyright notice that is included in or attached to the work
|
38
|
+
(an example is provided in the Appendix below).
|
39
|
+
|
40
|
+
"Derivative Works" shall mean any work, whether in Source or Object
|
41
|
+
form, that is based on (or derived from) the Work and for which the
|
42
|
+
editorial revisions, annotations, elaborations, or other modifications
|
43
|
+
represent, as a whole, an original work of authorship. For the purposes
|
44
|
+
of this License, Derivative Works shall not include works that remain
|
45
|
+
separable from, or merely link (or bind by name) to the interfaces of,
|
46
|
+
the Work and Derivative Works thereof.
|
47
|
+
|
48
|
+
"Contribution" shall mean any work of authorship, including
|
49
|
+
the original version of the Work and any modifications or additions
|
50
|
+
to that Work or Derivative Works thereof, that is intentionally
|
51
|
+
submitted to Licensor for inclusion in the Work by the copyright owner
|
52
|
+
or by an individual or Legal Entity authorized to submit on behalf of
|
53
|
+
the copyright owner. For the purposes of this definition, "submitted"
|
54
|
+
means any form of electronic, verbal, or written communication sent
|
55
|
+
to the Licensor or its representatives, including but not limited to
|
56
|
+
communication on electronic mailing lists, source code control systems,
|
57
|
+
and issue tracking systems that are managed by, or on behalf of, the
|
58
|
+
Licensor for the purpose of discussing and improving the Work, but
|
59
|
+
excluding communication that is conspicuously marked or otherwise
|
60
|
+
designated in writing by the copyright owner as "Not a Contribution."
|
61
|
+
|
62
|
+
"Contributor" shall mean Licensor and any individual or Legal Entity
|
63
|
+
on behalf of whom a Contribution has been received by Licensor and
|
64
|
+
subsequently incorporated within the Work.
|
65
|
+
|
66
|
+
2. Grant of Copyright License. Subject to the terms and conditions of
|
67
|
+
this License, each Contributor hereby grants to You a perpetual,
|
68
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
69
|
+
copyright license to reproduce, prepare Derivative Works of,
|
70
|
+
publicly display, publicly perform, sublicense, and distribute the
|
71
|
+
Work and such Derivative Works in Source or Object form.
|
72
|
+
|
73
|
+
3. Grant of Patent License. Subject to the terms and conditions of
|
74
|
+
this License, each Contributor hereby grants to You a perpetual,
|
75
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
76
|
+
(except as stated in this section) patent license to make, have made,
|
77
|
+
use, offer to sell, sell, import, and otherwise transfer the Work,
|
78
|
+
where such license applies only to those patent claims licensable
|
79
|
+
by such Contributor that are necessarily infringed by their
|
80
|
+
Contribution(s) alone or by combination of their Contribution(s)
|
81
|
+
with the Work to which such Contribution(s) was submitted. If You
|
82
|
+
institute patent litigation against any entity (including a
|
83
|
+
cross-claim or counterclaim in a lawsuit) alleging that the Work
|
84
|
+
or a Contribution incorporated within the Work constitutes direct
|
85
|
+
or contributory patent infringement, then any patent licenses
|
86
|
+
granted to You under this License for that Work shall terminate
|
87
|
+
as of the date such litigation is filed.
|
88
|
+
|
89
|
+
4. Redistribution. You may reproduce and distribute copies of the
|
90
|
+
Work or Derivative Works thereof in any medium, with or without
|
91
|
+
modifications, and in Source or Object form, provided that You
|
92
|
+
meet the following conditions:
|
93
|
+
|
94
|
+
(a) You must give any other recipients of the Work or
|
95
|
+
Derivative Works a copy of this License; and
|
96
|
+
|
97
|
+
(b) You must cause any modified files to carry prominent notices
|
98
|
+
stating that You changed the files; and
|
99
|
+
|
100
|
+
(c) You must retain, in the Source form of any Derivative Works
|
101
|
+
that You distribute, all copyright, patent, trademark, and
|
102
|
+
attribution notices from the Source form of the Work,
|
103
|
+
excluding those notices that do not pertain to any part of
|
104
|
+
the Derivative Works; and
|
105
|
+
|
106
|
+
(d) If the Work includes a "NOTICE" text file as part of its
|
107
|
+
distribution, then any Derivative Works that You distribute must
|
108
|
+
include a readable copy of the attribution notices contained
|
109
|
+
within such NOTICE file, excluding those notices that do not
|
110
|
+
pertain to any part of the Derivative Works, in at least one
|
111
|
+
of the following places: within a NOTICE text file distributed
|
112
|
+
as part of the Derivative Works; within the Source form or
|
113
|
+
documentation, if provided along with the Derivative Works; or,
|
114
|
+
within a display generated by the Derivative Works, if and
|
115
|
+
wherever such third-party notices normally appear. The contents
|
116
|
+
of the NOTICE file are for informational purposes only and
|
117
|
+
do not modify the License. You may add Your own attribution
|
118
|
+
notices within Derivative Works that You distribute, alongside
|
119
|
+
or as an addendum to the NOTICE text from the Work, provided
|
120
|
+
that such additional attribution notices cannot be construed
|
121
|
+
as modifying the License.
|
122
|
+
|
123
|
+
You may add Your own copyright statement to Your modifications and
|
124
|
+
may provide additional or different license terms and conditions
|
125
|
+
for use, reproduction, or distribution of Your modifications, or
|
126
|
+
for any such Derivative Works as a whole, provided Your use,
|
127
|
+
reproduction, and distribution of the Work otherwise complies with
|
128
|
+
the conditions stated in this License.
|
129
|
+
|
130
|
+
5. Submission of Contributions. Unless You explicitly state otherwise,
|
131
|
+
any Contribution intentionally submitted for inclusion in the Work
|
132
|
+
by You to the Licensor shall be under the terms and conditions of
|
133
|
+
this License, without any additional terms or conditions.
|
134
|
+
Notwithstanding the above, nothing herein shall supersede or modify
|
135
|
+
the terms of any separate license agreement you may have executed
|
136
|
+
with Licensor regarding such Contributions.
|
137
|
+
|
138
|
+
6. Trademarks. This License does not grant permission to use the trade
|
139
|
+
names, trademarks, service marks, or product names of the Licensor,
|
140
|
+
except as required for reasonable and customary use in describing the
|
141
|
+
origin of the Work and reproducing the content of the NOTICE file.
|
142
|
+
|
143
|
+
7. Disclaimer of Warranty. Unless required by applicable law or
|
144
|
+
agreed to in writing, Licensor provides the Work (and each
|
145
|
+
Contributor provides its Contributions) on an "AS IS" BASIS,
|
146
|
+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
|
147
|
+
implied, including, without limitation, any warranties or conditions
|
148
|
+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
|
149
|
+
PARTICULAR PURPOSE. You are solely responsible for determining the
|
150
|
+
appropriateness of using or redistributing the Work and assume any
|
151
|
+
risks associated with Your exercise of permissions under this License.
|
152
|
+
|
153
|
+
8. Limitation of Liability. In no event and under no legal theory,
|
154
|
+
whether in tort (including negligence), contract, or otherwise,
|
155
|
+
unless required by applicable law (such as deliberate and grossly
|
156
|
+
negligent acts) or agreed to in writing, shall any Contributor be
|
157
|
+
liable to You for damages, including any direct, indirect, special,
|
158
|
+
incidental, or consequential damages of any character arising as a
|
159
|
+
result of this License or out of the use or inability to use the
|
160
|
+
Work (including but not limited to damages for loss of goodwill,
|
161
|
+
work stoppage, computer failure or malfunction, or any and all
|
162
|
+
other commercial damages or losses), even if such Contributor
|
163
|
+
has been advised of the possibility of such damages.
|
164
|
+
|
165
|
+
9. Accepting Warranty or Additional Liability. While redistributing
|
166
|
+
the Work or Derivative Works thereof, You may choose to offer,
|
167
|
+
and charge a fee for, acceptance of support, warranty, indemnity,
|
168
|
+
or other liability obligations and/or rights consistent with this
|
169
|
+
License. However, in accepting such obligations, You may act only
|
170
|
+
on Your own behalf and on Your sole responsibility, not on behalf
|
171
|
+
of any other Contributor, and only if You agree to indemnify,
|
172
|
+
defend, and hold each Contributor harmless for any liability
|
173
|
+
incurred by, or claims asserted against, such Contributor by reason
|
174
|
+
of your accepting any such warranty or additional liability.
|
175
|
+
|
176
|
+
END OF TERMS AND CONDITIONS
|
data/LICENSE.txt
CHANGED
@@ -4,7 +4,12 @@ Copyright (c) 2010-2011 Yannick Wurm, Benjamin J. Woodcroft, Anurag Priyam.
|
|
4
4
|
|
5
5
|
1. Definitions
|
6
6
|
|
7
|
-
The software: the SequenceServer software and associated documentation.
|
7
|
+
The software: the SequenceServer software and associated documentation. The
|
8
|
+
term does not extend to unmodified open source software components used within
|
9
|
+
SequenceServer which are governed by their own license agreements. However,
|
10
|
+
modfications to such components shall be deemed a part of the SequenceServer
|
11
|
+
software.
|
12
|
+
|
8
13
|
The authors: Yannick Wurm, Anurag Priyam, Benjamin J. Woodcroft.
|
9
14
|
|
10
15
|
|
data/lib/sequenceserver.rb
CHANGED
@@ -270,8 +270,11 @@ module SequenceServer
|
|
270
270
|
advanced_opts = params['advanced']
|
271
271
|
validate_advanced_parameters(advanced_opts) #check the advanced options are sensible
|
272
272
|
|
273
|
-
# blastn implies blastn, not megablast
|
274
|
-
|
273
|
+
# blastn implies blastn, not megablast; but let's not interfere if a user
|
274
|
+
# specifies `task` herself
|
275
|
+
if method == 'blastn' and not advanced_opts =~ /task/
|
276
|
+
advanced_opts << ' -task blastn '
|
277
|
+
end
|
275
278
|
|
276
279
|
method = settings.binaries[ method ]
|
277
280
|
settings.log.debug('settings.databases: ' + settings.databases.inspect)
|
@@ -95,6 +95,13 @@ module SequenceServer
|
|
95
95
|
type = type.downcase
|
96
96
|
name = name.freeze
|
97
97
|
title = title.join(' ').freeze
|
98
|
+
|
99
|
+
# skip past all but alias file of a NCBI multi-part BLAST database
|
100
|
+
if name.match(/\/\w*[.]\d{2,}[.\w]*/)
|
101
|
+
log.info(%|Found a multi-part database volume at #{name} - ignoring it.|)
|
102
|
+
next
|
103
|
+
end
|
104
|
+
|
98
105
|
#LOG.info("Found #{type} database: #{title} at #{name}")
|
99
106
|
(db[type] ||= []) << Database.new(name, title)
|
100
107
|
end
|
@@ -0,0 +1,246 @@
|
|
1
|
+
/**
|
2
|
+
* jQuery Live Clipboard
|
3
|
+
*
|
4
|
+
* Copyright (c) 2009 Shinichi Tomita (shinichi.tomita@gmail.com)
|
5
|
+
*
|
6
|
+
* Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
+
* of this software and associated documentation files (the "Software"), to deal
|
8
|
+
* in the Software without restriction, including without limitation the rights
|
9
|
+
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
+
* copies of the Software, and to permit persons to whom the Software is
|
11
|
+
* furnished to do so, subject to the following conditions:
|
12
|
+
*
|
13
|
+
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
14
|
+
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
15
|
+
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
16
|
+
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
17
|
+
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
18
|
+
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
19
|
+
* SOFTWARE.
|
20
|
+
*/
|
21
|
+
(function($) {
|
22
|
+
|
23
|
+
var namespace = 'liveclip';
|
24
|
+
var relayEvents =
|
25
|
+
'click,dblclick,mousedown,mouseup,mousemove,mouseover,mouseout,keypress,keyup'.split(',');
|
26
|
+
|
27
|
+
/**
|
28
|
+
* Adjust clipboard textarea size to cover parent clippable element.
|
29
|
+
*/
|
30
|
+
function track() {
|
31
|
+
var target = $(this);
|
32
|
+
var clipboard = target.clipboard();
|
33
|
+
var w = target.outerWidth(), h = target.outerHeight(), offset = target.offset();
|
34
|
+
if (/^(auto|scroll)$/.test(target.css('overflow'))) w -= 20;
|
35
|
+
if (clipboard) clipboard.css({ width : w, height : h, top : offset.top, left : offset.left });
|
36
|
+
}
|
37
|
+
|
38
|
+
/**
|
39
|
+
* Finding and capture event target element, excluding clipboard textarea.
|
40
|
+
* This is "pseudo" capturing, assuming no layered elements covering over the target.
|
41
|
+
*/
|
42
|
+
function capture(el, e) {
|
43
|
+
var captured = _capture(el);
|
44
|
+
var clipboard = captured.clipboard();
|
45
|
+
// if captured element has clipboard, return it.
|
46
|
+
return captured !== el && clipboard ? clipboard : captured;
|
47
|
+
|
48
|
+
function _capture(el) {
|
49
|
+
var target = el;
|
50
|
+
el.children().each(function() {
|
51
|
+
var child = $(this);
|
52
|
+
var w = child.width(), h = child.innerHeight(), offset = child.offset();
|
53
|
+
if (e.pageX > offset.left && e.pageX < offset.left + w &&
|
54
|
+
e.pageY > offset.top && e.pageY < offset.top + h) {
|
55
|
+
target = _capture(child);
|
56
|
+
}
|
57
|
+
})
|
58
|
+
return target;
|
59
|
+
}
|
60
|
+
}
|
61
|
+
|
62
|
+
/**
|
63
|
+
* Context menu event handler
|
64
|
+
*/
|
65
|
+
function contextmenuHandler(e) {
|
66
|
+
var clipboard = $(this);
|
67
|
+
var target = clipboard.data(namespace + '-target');
|
68
|
+
var options = target.data(namespace + '-clipboard-options');
|
69
|
+
|
70
|
+
if (options.active && options.active.call(target) === false) {
|
71
|
+
clipboard.attr('readonly', 'readonly');
|
72
|
+
return;
|
73
|
+
}
|
74
|
+
|
75
|
+
if (options.paste || options.del) {
|
76
|
+
clipboard.removeAttr('readonly');
|
77
|
+
} else {
|
78
|
+
clipboard.attr('readonly', 'readonly');
|
79
|
+
}
|
80
|
+
|
81
|
+
var val = options.copy ? options.copy.call(target) : '';
|
82
|
+
clipboard.val(val);
|
83
|
+
clipboard.get(0).select();
|
84
|
+
if (options.paste || options.del) {
|
85
|
+
val = clipboard.val();
|
86
|
+
var watchPID = clipboard.data(namespace+'-watcher');
|
87
|
+
if (watchPID) {
|
88
|
+
clearInterval(watchPID);
|
89
|
+
clipboard.removeData(namespace+'-watcher');
|
90
|
+
}
|
91
|
+
watchPID = setInterval(function() {
|
92
|
+
var v = clipboard.val();
|
93
|
+
if (v !== val) {
|
94
|
+
try {
|
95
|
+
if (v === '') {
|
96
|
+
if (options.del) options.del.call(target)
|
97
|
+
} else {
|
98
|
+
if (options.paste) options.paste.call(target, v);
|
99
|
+
clipboard.val('');
|
100
|
+
}
|
101
|
+
} catch(e) {}
|
102
|
+
clearInterval(watchPID);
|
103
|
+
clipboard.removeData(namespace+'-watcher');
|
104
|
+
}
|
105
|
+
}, 100);
|
106
|
+
clipboard.data(namespace+'-watcher', watchPID);
|
107
|
+
}
|
108
|
+
}
|
109
|
+
|
110
|
+
|
111
|
+
/**
|
112
|
+
* Keyboard down event handler
|
113
|
+
*/
|
114
|
+
function keydownHandler(e) {
|
115
|
+
var clipboard = $(this);
|
116
|
+
var target = clipboard.data(namespace + '-target');
|
117
|
+
var options = target.data(namespace + '-clipboard-options');
|
118
|
+
|
119
|
+
if (e.metaKey) {
|
120
|
+
switch (e.keyCode) {
|
121
|
+
case 67 : // Command + C
|
122
|
+
var val = options.copy ? options.copy.call(target) : '';
|
123
|
+
clipboard.val(val)
|
124
|
+
clipboard.get(0).select();
|
125
|
+
break;
|
126
|
+
case 86 : // Command + V
|
127
|
+
if (options.paste) {
|
128
|
+
clipboard.get(0).select();
|
129
|
+
setTimeout(function() {
|
130
|
+
var data = clipboard.val();
|
131
|
+
options.paste.call(target, data);
|
132
|
+
clipboard.val('')
|
133
|
+
}, 10);
|
134
|
+
}
|
135
|
+
break;
|
136
|
+
case 88 : // Command + X
|
137
|
+
var val = options.copy ? options.copy.call(target) : '';
|
138
|
+
clipboard.val(val)
|
139
|
+
clipboard.get(0).select();
|
140
|
+
if (options.del) {
|
141
|
+
setTimeout(function() {
|
142
|
+
options.del.call(target)
|
143
|
+
}, 10);
|
144
|
+
}
|
145
|
+
break;
|
146
|
+
default :
|
147
|
+
break;
|
148
|
+
}
|
149
|
+
} else if (e.keyCode==46) { // delete
|
150
|
+
if (options.del) options.del.call(target);
|
151
|
+
}
|
152
|
+
|
153
|
+
}
|
154
|
+
|
155
|
+
|
156
|
+
$.fn.extend({
|
157
|
+
|
158
|
+
/**
|
159
|
+
* Attach clipboard feature to block element
|
160
|
+
* Get current clipboard proxy textarea
|
161
|
+
*/
|
162
|
+
clipboard : function(options) {
|
163
|
+
var elements = this;
|
164
|
+
|
165
|
+
if (options) { // setter
|
166
|
+
|
167
|
+
$(elements).each(function() {
|
168
|
+
var target = $(this);
|
169
|
+
var clipboard = target.data(namespace + '-clipboard');
|
170
|
+
if (!clipboard) {
|
171
|
+
clipboard = $('<textarea></textarea>')
|
172
|
+
.addClass(namespace+'-clipboard')
|
173
|
+
.addClass(options.cls ? options.cls : '')
|
174
|
+
.css({
|
175
|
+
cursor : 'default',
|
176
|
+
position : 'absolute',
|
177
|
+
fontSize : $.liveclip.debug ? '12px' : '1px',
|
178
|
+
opacity : $.liveclip.debug ? .5 : .01
|
179
|
+
})
|
180
|
+
.appendTo(document.body)
|
181
|
+
.bind('contextmenu', contextmenuHandler)
|
182
|
+
.bind('keydown', keydownHandler);
|
183
|
+
$.each(relayEvents, function(i, eventName) {
|
184
|
+
clipboard.bind(eventName+'.'+namespace, function(e) {
|
185
|
+
capture(target, e).trigger(e);
|
186
|
+
});
|
187
|
+
});
|
188
|
+
if ($.liveclip.autoTrack) { target.bind('mouseover.'+namespace, track) }
|
189
|
+
target.data(namespace+'-clipboard', clipboard);
|
190
|
+
clipboard.data(namespace+'-target', target);
|
191
|
+
}
|
192
|
+
target.data(namespace+'-clipboard-options', options);
|
193
|
+
track.call(target);
|
194
|
+
});
|
195
|
+
return this;
|
196
|
+
|
197
|
+
} else { // getter
|
198
|
+
return $(this).data(namespace + '-clipboard');
|
199
|
+
}
|
200
|
+
|
201
|
+
}
|
202
|
+
,
|
203
|
+
|
204
|
+
/**
|
205
|
+
* remove attached clipboard feature
|
206
|
+
*/
|
207
|
+
removeClipboard : function() {
|
208
|
+
$(this).each(function() {
|
209
|
+
$(this).clipboard().remove();
|
210
|
+
$(this).unbind('mouseover.'+namespace, track)
|
211
|
+
.removeData(namespace + '-clipboard')
|
212
|
+
.removeData(namespace + '-clipboard-options');
|
213
|
+
});
|
214
|
+
return this;
|
215
|
+
}
|
216
|
+
|
217
|
+
});
|
218
|
+
|
219
|
+
$.liveclip = {
|
220
|
+
debug : false,
|
221
|
+
autoTrack : false
|
222
|
+
}
|
223
|
+
|
224
|
+
/**
|
225
|
+
* Track all clipboard, aligning to target element position and size
|
226
|
+
* If no target element available in document, removing clipboard.
|
227
|
+
*/
|
228
|
+
$.trackClipboards = function() {
|
229
|
+
$('body > textarea.'+namespace+'-clipboard').each(function() {
|
230
|
+
var clipboard = $(this);
|
231
|
+
var target = clipboard.data(namespace + '-target');
|
232
|
+
if (target && target.parent()) {
|
233
|
+
track.call(target);
|
234
|
+
} else {
|
235
|
+
clipboard.remove();
|
236
|
+
}
|
237
|
+
});
|
238
|
+
}
|
239
|
+
|
240
|
+
$(function() {
|
241
|
+
if ($.liveclip.autoTrack) {
|
242
|
+
$(document).mousemove($.trackClipboards);
|
243
|
+
}
|
244
|
+
})
|
245
|
+
|
246
|
+
})(jQuery)
|
data/sequenceserver.gemspec
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
# meta
|
3
3
|
s.name = 'sequenceserver'
|
4
|
-
s.version = '0.7.
|
4
|
+
s.version = '0.7.5'
|
5
5
|
s.authors = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
|
6
6
|
s.email = 'anurag08priyam@gmail.com'
|
7
7
|
s.homepage = 'http://sequenceserver.com'
|
@@ -20,7 +20,7 @@ DESC
|
|
20
20
|
# gem
|
21
21
|
s.files = Dir['lib/**/*'] + Dir['views/**/*'] + Dir['public/**/*'] + Dir['tests/**/*']
|
22
22
|
s.files = s.files + ['config.ru', 'example.config.yml']
|
23
|
-
s.files = s.files + ['LICENSE.txt', 'README.txt']
|
23
|
+
s.files = s.files + ['LICENSE.txt', 'LICENSE.Apache.txt', 'README.txt']
|
24
24
|
s.files = s.files + ['Gemfile', 'sequenceserver.gemspec']
|
25
25
|
s.executables = ['sequenceserver']
|
26
26
|
s.require_paths = ['lib']
|
data/tests/ui.specs.todo
ADDED
@@ -0,0 +1,10 @@
|
|
1
|
+
it "should automatically focus sequence input box" do
|
2
|
+
# when the page loads, check that sequence input box is focussed
|
3
|
+
#
|
4
|
+
# NOTE: unless #75 is resolved, make sure to test this functionality only if
|
5
|
+
# HTML5 autofocus attribute is supported
|
6
|
+
end
|
7
|
+
|
8
|
+
it "should ensure spell checking is disabled for sequence input box" do
|
9
|
+
# NOTE: only if the browser supports it
|
10
|
+
end
|
data/views/search.erb
CHANGED
@@ -31,7 +31,7 @@
|
|
31
31
|
<div class="span12">
|
32
32
|
<div class="offset-left sequence">
|
33
33
|
<div class="clearfix">
|
34
|
-
<textarea name="sequence" id="sequence" rows="11" placeholder="Paste your sequence(s) here..." ></textarea>
|
34
|
+
<textarea name="sequence" id="sequence" rows="11" spellcheck="false" <%= 'autofocus="true"' unless @blast %> placeholder="Paste your sequence(s) here..." ></textarea>
|
35
35
|
</div>
|
36
36
|
</div>
|
37
37
|
</div>
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequenceserver
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 9
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 7
|
9
|
-
-
|
10
|
-
version: 0.7.
|
9
|
+
- 5
|
10
|
+
version: 0.7.5
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Anurag Priyam
|
@@ -17,7 +17,7 @@ autorequire:
|
|
17
17
|
bindir: bin
|
18
18
|
cert_chain: []
|
19
19
|
|
20
|
-
date:
|
20
|
+
date: 2012-02-09 00:00:00 Z
|
21
21
|
dependencies:
|
22
22
|
- !ruby/object:Gem::Dependency
|
23
23
|
name: bundler
|
@@ -89,6 +89,7 @@ files:
|
|
89
89
|
- public/css/custom.css
|
90
90
|
- public/js/jquery.js
|
91
91
|
- public/js/jquery.enablePlaceholder.min.js
|
92
|
+
- public/js/liveclip.jquery.js
|
92
93
|
- public/js/sequenceserver.js
|
93
94
|
- public/js/jquery.activity.js
|
94
95
|
- public/js/sequenceserver.blast.js
|
@@ -103,9 +104,11 @@ files:
|
|
103
104
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
|
104
105
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
|
105
106
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
|
107
|
+
- tests/ui.specs.todo
|
106
108
|
- config.ru
|
107
109
|
- example.config.yml
|
108
110
|
- LICENSE.txt
|
111
|
+
- LICENSE.Apache.txt
|
109
112
|
- README.txt
|
110
113
|
- Gemfile
|
111
114
|
- sequenceserver.gemspec
|