sequenceserver 3.0.1 → 3.1.0
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- checksums.yaml +4 -4
- data/bin/sequenceserver +2 -2
- data/lib/sequenceserver/api_errors.rb +1 -1
- data/lib/sequenceserver/blast/job.rb +20 -3
- data/lib/sequenceserver/blast/report.rb +74 -86
- data/lib/sequenceserver/blast/tasks.rb +38 -0
- data/lib/sequenceserver/config.rb +54 -20
- data/lib/sequenceserver/makeblastdb.rb +16 -2
- data/lib/sequenceserver/report.rb +0 -6
- data/lib/sequenceserver/routes.rb +32 -21
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver.rb +1 -1
- data/public/css/app.css +121 -0
- data/public/css/app.min.css +1 -0
- data/public/css/sequenceserver.css +0 -148
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/circos.js +2 -2
- data/public/js/collapse_preferences.js +37 -0
- data/public/js/databases.js +65 -37
- data/public/js/databases_tree.js +2 -1
- data/public/js/dnd.js +37 -50
- data/public/js/form.js +78 -50
- data/public/js/grapher.js +23 -37
- data/public/js/hits_overview.js +2 -2
- data/public/js/kablammo.js +2 -2
- data/public/js/length_distribution.js +3 -3
- data/public/js/null_plugins/grapher/histogram.js +25 -0
- data/public/js/null_plugins/options.js +3 -0
- data/public/js/null_plugins/query_stats.js +11 -0
- data/public/js/null_plugins/report_plugins.js +6 -1
- data/public/js/null_plugins/search_header_plugin.js +4 -0
- data/public/js/options.js +161 -56
- data/public/js/query.js +85 -59
- data/public/js/report.js +1 -1
- data/public/js/search.js +2 -0
- data/public/js/search_button.js +67 -56
- data/public/js/sidebar.js +1 -1
- data/public/js/tests/database.spec.js +5 -5
- data/public/js/tests/{advanced_parameters.spec.js → form.spec.js} +35 -1
- data/public/js/tests/mock_data/databases.json +5 -5
- data/public/js/tests/mocks/circos.js +6 -0
- data/public/js/tests/report.spec.js +4 -3
- data/public/js/tests/search_query.spec.js +5 -6
- data/public/sequenceserver-report.min.js +45 -23
- data/public/sequenceserver-search.min.js +57 -13
- data/public/sequenceserver_logo.webp +0 -0
- data/views/blastn_options.erb +66 -66
- data/views/blastp_options.erb +59 -59
- data/views/blastx_options.erb +68 -68
- data/views/layout.erb +60 -3
- data/views/search.erb +33 -38
- data/views/search_layout.erb +152 -0
- data/views/tblastn_options.erb +57 -57
- data/views/tblastx_options.erb +64 -64
- metadata +31 -22
- data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +0 -345
- data/public/SequenceServer_logo.png +0 -0
data/public/css/app.css
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@tailwind base;
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@tailwind components;
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@tailwind utilities;
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/* Backported bootstrap tooltip styles */
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.tooltip {
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position: absolute;
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z-index: 1070;
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display: block;
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font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
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font-style: normal;
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font-weight: 400;
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line-height: 1.42857143;
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line-break: auto;
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text-align: left;
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text-decoration: none;
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text-transform: none;
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letter-spacing: normal;
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word-spacing: normal;
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font-size: 12px;
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opacity: 0;
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}
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}
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New,monospace}.text-2xl{font-size:1.5rem;line-height:2rem}.text-base{font-size:1rem;line-height:1.5rem}.text-lg{font-size:1.125rem;line-height:1.75rem}.text-sm{font-size:.875rem;line-height:1.25rem}.text-xl{font-size:1.25rem;line-height:1.75rem}.font-bold{font-weight:700}.font-medium{font-weight:500}.uppercase{text-transform:uppercase}.lowercase{text-transform:lowercase}.capitalize{text-transform:capitalize}.italic{font-style:italic}.ordinal{--tw-ordinal:ordinal;font-variant-numeric:var(--tw-ordinal) var(--tw-slashed-zero) var(--tw-numeric-figure) var(--tw-numeric-spacing) var(--tw-numeric-fraction)}.leading-6{line-height:1.5rem}.text-gray-400{--tw-text-opacity:1;color:rgb(156 163 175/var(--tw-text-opacity))}.text-gray-600{--tw-text-opacity:1;color:rgb(75 85 99/var(--tw-text-opacity))}.text-gray-700{--tw-text-opacity:1;color:rgb(55 65 81/var(--tw-text-opacity))}.text-gray-800{--tw-text-opacity:1;color:rgb(31 41 55/var(--tw-text-opacity))}.text-gray-900{--tw-text-opacity:1;color:rgb(17 24 39/var(--tw-text-opacity))}.text-red-700{--tw-text-opacity:1;color:rgb(185 28 28/var(--tw-text-opacity))}.text-red-800{--tw-text-opacity:1;color:rgb(153 27 27/var(--tw-text-opacity))}.text-seqblue{--tw-text-opacity:1;color:rgb(27 85 122/var(--tw-text-opacity))}.text-white{--tw-text-opacity:1;color:rgb(255 255 255/var(--tw-text-opacity))}.underline{-webkit-text-decoration-line:underline;text-decoration-line:underline}.\!shadow{--tw-shadow:0 1px 3px 0 #0000001a,0 1px 2px -1px #0000001a!important;--tw-shadow-colored:0 1px 3px 0 var(--tw-shadow-color),0 1px 2px -1px var(--tw-shadow-color)!important;box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)!important}.shadow{--tw-shadow:0 1px 3px 0 #0000001a,0 1px 2px -1px #0000001a;--tw-shadow-colored:0 1px 3px 0 var(--tw-shadow-color),0 1px 2px -1px var(--tw-shadow-color)}.shadow,.shadow-2xl{box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)}.shadow-2xl{--tw-shadow:0 25px 50px -12px #00000040;--tw-shadow-colored:0 25px 50px -12px var(--tw-shadow-color)}.shadow-lg{--tw-shadow:0 10px 15px -3px #0000001a,0 4px 6px -4px #0000001a;--tw-shadow-colored:0 10px 15px -3px var(--tw-shadow-color),0 4px 6px -4px var(--tw-shadow-color)}.shadow-lg,.shadow-sm{box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)}.shadow-sm{--tw-shadow:0 1px 2px 0 #0000000d;--tw-shadow-colored:0 1px 2px 0 var(--tw-shadow-color)}.shadow-xl{--tw-shadow:0 20px 25px -5px #0000001a,0 8px 10px -6px #0000001a;--tw-shadow-colored:0 20px 25px -5px var(--tw-shadow-color),0 8px 10px -6px var(--tw-shadow-color);box-shadow:var(--tw-ring-offset-shadow,0 0 #0000),var(--tw-ring-shadow,0 0 #0000),var(--tw-shadow)}.outline-none{outline:2px solid #0000;outline-offset:2px}.outline{outline-style:solid}.ring{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(3px + var(--tw-ring-offset-width)) var(--tw-ring-color);box-shadow:var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow,0 0 #0000)}.blur{--tw-blur:blur(8px);filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!invert{--tw-invert:invert(100%)!important;filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)!important}.invert{--tw-invert:invert(100%);filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!filter{filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)!important}.filter{filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}.\!transition{transition-property:color,background-color,border-color,fill,stroke,opacity,box-shadow,transform,filter,-webkit-text-decoration-color,-webkit-backdrop-filter!important;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter!important;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter,-webkit-text-decoration-color,-webkit-backdrop-filter!important;transition-timing-function:cubic-bezier(.4,0,.2,1)!important;transition-duration:.15s!important}.transition{transition-property:color,background-color,border-color,fill,stroke,opacity,box-shadow,transform,filter,-webkit-text-decoration-color,-webkit-backdrop-filter;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter;transition-property:color,background-color,border-color,text-decoration-color,fill,stroke,opacity,box-shadow,transform,filter,backdrop-filter,-webkit-text-decoration-color,-webkit-backdrop-filter;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.transition-all{transition-property:all;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.transition-opacity{transition-property:opacity;transition-timing-function:cubic-bezier(.4,0,.2,1);transition-duration:.15s}.tooltip{position:absolute;z-index:1070;display:block;font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-style:normal;font-weight:400;line-height:1.42857143;line-break:auto;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;word-spacing:normal;word-wrap:normal;white-space:normal;font-size:12px;filter:alpha(opacity=0);opacity:0}.tooltip.in{filter:alpha(opacity=90);opacity:.9}.tooltip.top{padding:5px 0;margin-top:-3px}.tooltip.right{padding:0 5px;margin-left:3px}.tooltip.bottom{padding:5px 0;margin-top:3px}.tooltip.left{padding:0 5px;margin-left:-3px}.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-width:5px 5px 0;border-top-color:#000}.tooltip.top-left .tooltip-arrow{right:5px}.tooltip.top-left .tooltip-arrow,.tooltip.top-right .tooltip-arrow{bottom:0;margin-bottom:-5px;border-width:5px 5px 0;border-top-color:#000}.tooltip.top-right .tooltip-arrow{left:5px}.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-width:5px 5px 5px 0;border-right-color:#000}.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-width:5px 0 5px 5px;border-left-color:#000}.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-left .tooltip-arrow{top:0;right:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-right .tooltip-arrow{top:0;left:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip-inner{max-width:200px;padding:3px 8px;color:#fff;text-align:center;background-color:#000;border-radius:4px}.tooltip-arrow{position:absolute;width:0;height:0;border-color:#0000;border-style:solid}.hover\:bg-blue-400:hover{--tw-bg-opacity:1;background-color:rgb(96 165 250/var(--tw-bg-opacity))}.hover\:bg-gray-200:hover{--tw-bg-opacity:1;background-color:rgb(229 231 235/var(--tw-bg-opacity))}.hover\:bg-gray-300:hover{--tw-bg-opacity:1;background-color:rgb(209 213 219/var(--tw-bg-opacity))}.hover\:bg-red-600:hover{--tw-bg-opacity:1;background-color:rgb(220 38 38/var(--tw-bg-opacity))}.hover\:bg-seqorange:hover{--tw-bg-opacity:1;background-color:rgb(199 79 19/var(--tw-bg-opacity))}.hover\:bg-sky-400:hover{--tw-bg-opacity:1;background-color:rgb(56 189 248/var(--tw-bg-opacity))}.hover\:bg-sky-500:hover{--tw-bg-opacity:1;background-color:rgb(14 165 233/var(--tw-bg-opacity))}.hover\:bg-yellow-100:hover{--tw-bg-opacity:1;background-color:rgb(254 249 195/var(--tw-bg-opacity))}.hover\:font-bold:hover{font-weight:700}.hover\:text-white:hover{--tw-text-opacity:1;color:rgb(255 255 255/var(--tw-text-opacity))}.focus\:outline-none:focus{outline:2px solid #0000;outline-offset:2px}.focus\:ring-1:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(1px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-1:focus,.focus\:ring-2:focus{box-shadow:var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow,0 0 #0000)}.focus\:ring-2:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(2px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-seqorange:focus{--tw-ring-opacity:1;--tw-ring-color:rgb(199 79 19/var(--tw-ring-opacity))}.focus\:ring-offset-2:focus{--tw-ring-offset-width:2px}.group:hover .group-hover\:visible{visibility:visible}@media (min-width:640px){.sm\:my-8{margin-top:2rem;margin-bottom:2rem}.sm\:ml-3{margin-left:.75rem}.sm\:block{display:block}.sm\:inline-block{display:inline-block}.sm\:flex{display:flex}.sm\:h-screen{height:100vh}.sm\:w-auto{width:auto}.sm\:w-full{width:100%}.sm\:max-w-screen-md{max-width:768px}.sm\:flex-row-reverse{flex-direction:row-reverse}.sm\:items-center{align-items:center}.sm\:p-0{padding:0}.sm\:p-6{padding:1.5rem}.sm\:px-6{padding-left:1.5rem;padding-right:1.5rem}.sm\:pb-4{padding-bottom:1rem}.sm\:align-middle{vertical-align:middle}.sm\:text-sm{font-size:.875rem;line-height:1.25rem}}@media (min-width:768px){.md\:my-2{margin-top:.5rem;margin-bottom:.5rem}.md\:flex{display:flex}.md\:w-auto{width:auto}.md\:grid-cols-2{grid-template-columns:repeat(2,minmax(0,1fr))}.md\:space-x-4>:not([hidden])~:not([hidden]){--tw-space-x-reverse:0;margin-right:calc(1rem*var(--tw-space-x-reverse));margin-left:calc(1rem*(1 - var(--tw-space-x-reverse)))}}@media 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-
|
|
596
|
-
.dnd-overlay-container p {
|
|
597
|
-
font-size: 48px;
|
|
598
|
-
}
|
|
599
|
-
|
|
600
466
|
/* higlight when hit is selected */
|
|
601
467
|
.glow {
|
|
602
468
|
border-left: 2px solid #c74f14;
|
|
@@ -649,20 +515,6 @@ input[type=checkbox] {
|
|
|
649
515
|
display: table-cell;
|
|
650
516
|
}
|
|
651
517
|
|
|
652
|
-
|
|
653
|
-
/** For advanced params dropdown **/
|
|
654
|
-
.input-group-btn {
|
|
655
|
-
vertical-align: top;
|
|
656
|
-
}
|
|
657
|
-
#advanced-params-dropdown {
|
|
658
|
-
padding: 0;
|
|
659
|
-
}
|
|
660
|
-
#advanced-params-dropdown li {
|
|
661
|
-
padding: 10px;
|
|
662
|
-
cursor: pointer;
|
|
663
|
-
letter-spacing: 1px;
|
|
664
|
-
}
|
|
665
|
-
|
|
666
518
|
.share-url-component input[type="text"] {
|
|
667
519
|
width: 100%;
|
|
668
520
|
}
|