sequenceserver 2.0.0.rc8 → 2.0.0
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- checksums.yaml +4 -4
- data/bin/sequenceserver +22 -30
- data/lib/sequenceserver/api_errors.rb +5 -1
- data/lib/sequenceserver/blast/constants.rb +1 -1
- data/lib/sequenceserver/blast/hit.rb +5 -16
- data/lib/sequenceserver/blast/job.rb +9 -18
- data/lib/sequenceserver/blast/report.rb +5 -3
- data/lib/sequenceserver/config.rb +4 -1
- data/lib/sequenceserver/database.rb +69 -9
- data/lib/sequenceserver/job.rb +1 -1
- data/lib/sequenceserver/makeblastdb.rb +40 -45
- data/lib/sequenceserver/routes.rb +4 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver.rb +15 -11
- data/public/config.js +143 -142
- data/public/css/fonts.css +23 -22
- data/public/css/grapher.css +598 -594
- data/public/css/sequenceserver.css +86 -24
- data/public/css/sequenceserver.min.css +2 -2
- data/public/js/alignment_exporter.js +14 -14
- data/public/js/databases_tree.js +215 -0
- data/public/js/download_fasta.js +1 -1
- data/public/js/hit.js +6 -2
- data/public/js/hits_overview.js +1 -1
- data/public/js/length_distribution.js +5 -5
- data/public/js/query.js +4 -7
- data/public/js/report.js +12 -24
- data/public/js/search.js +21 -2
- data/public/js/sidebar.js +4 -4
- data/public/js/svgExporter.js +12 -12
- data/public/js/visualisation_helpers.js +4 -5
- data/public/sequenceserver-report.min.js +11 -11
- data/public/sequenceserver-search.min.js +15 -11
- data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
- data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
- data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
- data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
- data/public/vendor/system-csp-production.js +3 -3
- data/public/vendor/system-csp-production.js.map +1 -1
- data/public/vendor/system-csp-production.src.js +146 -140
- data/public/vendor/system-polyfills.js.map +1 -1
- data/public/vendor/system-polyfills.src.js +1 -0
- data/public/vendor/system.js +3 -3
- data/public/vendor/system.js.map +1 -1
- data/public/vendor/system.src.js +4771 -2383
- data/views/_options.erb +21 -0
- data/views/layout.erb +17 -18
- metadata +102 -43
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/public/shims/form-core.js +0 -3
- data/public/shims/form-validation.js +0 -3
- data/public/shims/plugins/jquery.ui.position.js +0 -13
- data/public/shims/styles/shim.css +0 -1
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test('basic test', function() {
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expect(1);
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ok(true, 'this had better work.');
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test('can access the DOM', function() {
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expect(1);
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var fixture = document.getElementById('qunit-fixture');
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equal(fixture.innerText || fixture.textContent, 'this had better work.', 'should be able to access the DOM.');
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});
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<!DOCTYPE html>
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<title>Light theme visual tests</title>
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<link rel="stylesheet" href="./../../../dist/themes/default/style.min.css">
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<link rel="stylesheet" href="./../../../dist/themes/default-dark/style.min.css">
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<style>.tree { border:1px solid black; padding:10px; width:300px; margin:20px; float:left; min-height:200px; }</style>
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<div class="tree" id="full"><ul><li data-jstree='{ "selected" : true, "type" : "file" }'>full</li><li>asdf</li></ul></div>
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<div class="tree" id="dark"><ul><li data-jstree='{ "selected" : true, "type" : "file"}'>full</li><li>asdf</li></ul></div>
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<script>
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$('#tree, #core').jstree();
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$('#full').jstree({ plugins : ["checkbox","sort","types","wholerow"], "types" : { "file" : { "icon" : "jstree-file" } } });
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$('#dark').jstree({ plugins : ["checkbox","sort","types","wholerow"], "core" : { "themes" : { "name" : "default-dark" } }, "types" : { "file" : { "icon" : "jstree-file" } } });
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<link rel="stylesheet" href="./../../../dist/themes/default-dark/style.min.css">
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<style>.tree { border:1px solid black; padding:10px; width:300px; margin:20px; float:left; min-height:200px; }</style>
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</div>
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<div class="tree" id="full"><ul><li data-jstree='{ "selected" : true, "type" : "file" }'>full</li><li>asdf</li></ul></div>
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<div class="tree" id="dark"><ul><li data-jstree='{ "selected" : true, "type" : "file"}'>full</li><li>asdf</li></ul></div>
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<script>
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$('#tree').jstree();
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$('#full').jstree({ plugins : ["checkbox","sort","types","wholerow"], "types" : { "file" : { "icon" : "jstree-file" } } });
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$('#dark').jstree({ plugins : ["checkbox","sort","types","wholerow"], "core" : { "themes" : { "name" : "default-dark" } }, "types" : { "file" : { "icon" : "jstree-file" } } });
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/*
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* SystemJS v0.19.
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* SystemJS v0.19.46
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