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Merge pull request #54 from agduncan94/develop
Release 0.1.8
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| .DS_Store | ||
| node_modules/ | ||
| docker/data/ | ||
| cypress/data/ | ||
| cypress/screenshots/ | ||
| cypress/videos/ |
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@@ -2,8 +2,10 @@ FROM node:latest | |
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| LABEL maintainer="[email protected]" | ||
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| ARG plugin_version=master | ||
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| ENV JBROWSE_VERSION 1.16.6 | ||
| ENV PLUGIN_VERSION=0.1.7 | ||
| ENV PLUGIN_VERSION=$plugin_version | ||
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| # Install dependencies | ||
| RUN apt-get -qq update --fix-missing | ||
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| define( | ||
| [ | ||
| "dojo/_base/declare", | ||
| "JBrowse/View/Track/HTMLFeatures", | ||
| 'JBrowse/View/Track/_ExportMixin', | ||
| 'dojo/dom-construct', | ||
| 'dijit/form/Button', | ||
| 'dijit/form/NumberSpinner', | ||
| 'dijit/form/ValidationTextBox', | ||
| './ValidationTextArea' | ||
| ], | ||
| function( | ||
| declare, | ||
| HTMLFeatures, | ||
| ExportMixin, | ||
| domConstruct, | ||
| Button, | ||
| NumberSpinner, | ||
| ValidationTextBox, | ||
| ValidationTextArea) { | ||
| return declare([ HTMLFeatures, ExportMixin ], { | ||
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| _exportFormats: function() { | ||
| return [ | ||
| {name: 'icgc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'}, | ||
| {name: 'icgc-viewer/View/Export/BED', label: 'BED', fileExt: 'bed'}, | ||
| {name: 'icgc-viewer/View/Export/CSV', label: 'CSV', fileExt: 'csv'}, | ||
| {name: 'icgc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'}, | ||
| {name: 'icgc-viewer/View/Export/TrackConfig', label: 'Track Config', fileExt: 'conf'}, | ||
| {name: 'icgc-viewer/View/Export/TrackConfigJson', label: 'Track Config JSON', fileExt: 'json'} | ||
| ]; | ||
| }, | ||
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| _trackMenuOptions: function () { | ||
| var track = this; | ||
| var options = this.inherited(arguments); | ||
| options.push({ | ||
| label: 'Share Track as URL', | ||
| action: "contentDialog", | ||
| title: 'Share Track as URL', | ||
| content: dojo.hitch(this,'_shareableLinkContent') | ||
| }); | ||
| options.push({ | ||
| label: 'View Applied Filters', | ||
| action: "contentDialog", | ||
| title: 'View Applied Filters', | ||
| content: dojo.hitch(this,'_appliedFilters') | ||
| }); | ||
| return options; | ||
| }, | ||
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| /** | ||
| * Create dialog showing applied filters for the given track. | ||
| * User can apply new filters here too. | ||
| */ | ||
| _appliedFilters: function() { | ||
| var track = this; | ||
| var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' }); | ||
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| var headerString = '<h1 style="width: 80%">Track Filters</h1>'; | ||
| var headerElement = domConstruct.toDom(headerString); | ||
| domConstruct.place(headerElement, details); | ||
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| // Create help text | ||
| var helpString = '<span style="width: 80%">The following filters have been applied to the track. You can update the filters here, though no validation is done on the input.</span>'; | ||
| var helpElement = domConstruct.toDom(helpString); | ||
| domConstruct.place(helpElement, details); | ||
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| var filterString = '<div style="width: 80%"><h3>Filters</h3></div>'; | ||
| var filterElement = domConstruct.toDom(filterString); | ||
| domConstruct.place(filterElement, details); | ||
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| // Get filtered text | ||
| var filteredText = JSON.stringify(track.store.filters, null, 2) | ||
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| var textArea = new ValidationTextArea({ | ||
| rows: 20, | ||
| value: filteredText, | ||
| style: "width: 80%", | ||
| readOnly: false, | ||
| id: "filterTextArea", | ||
| invalidMessage: "Invalid JSON filter - must be a valid JSON", | ||
| isValid: function() { | ||
| var value = this.attr('value') | ||
| try { | ||
| JSON.parse(value) | ||
| } catch (e) { | ||
| return false; | ||
| } | ||
| return true; | ||
| } | ||
| }).placeAt(details); | ||
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| var donorString = '<div style="width: 80%"><h3>Donor UUID</h3></div>'; | ||
| var donorElement = domConstruct.toDom(donorString); | ||
| domConstruct.place(donorElement, details); | ||
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| var donorIdTextBox = new ValidationTextBox({ | ||
| value: track.store.config.donor, | ||
| style: "width: 80%", | ||
| id: "donorTextBox", | ||
| regExp: "^DO[0-9]+$", | ||
| invalidMessage: "Invalid Donor ID - Must be of the form DOxxxx, where xxxx is some number greater than 0.", | ||
| trim: true | ||
| }).placeAt(details); | ||
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| var sizeHeader = '<div style="width: 80%"><h3>Size</h3></div>'; | ||
| var sizeElement = domConstruct.toDom(sizeHeader); | ||
| domConstruct.place(sizeElement, details); | ||
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| var sizeTextBox = new NumberSpinner({ | ||
| value: track.store.size, | ||
| style: "width: 80%", | ||
| id: "sizeTextBox", | ||
| constraints: { min: 1, max: 1000, places: 0 }, | ||
| smallDelta: 10 | ||
| }).placeAt(details); | ||
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| var updateTrackButton = new Button({ | ||
| label: 'Apply New Filters', | ||
| iconClass: 'dijitIconSave', | ||
| onClick: function() { | ||
| const trackString = document.getElementById("filterTextArea").value; | ||
| const donorString = document.getElementById("donorTextBox").value; | ||
| const sizeString = document.getElementById("sizeTextBox").value; | ||
| var storeConf = { | ||
| browser: track.browser, | ||
| refSeq: track.browser.refSeq, | ||
| type: track.store.config.type, | ||
| donor: donorString, | ||
| size: sizeString, | ||
| filters: trackString | ||
| }; | ||
| var storeName = track.browser.addStoreConfig(null, storeConf); | ||
| track.config.store = storeName; | ||
| track.browser.publish( '/jbrowse/v1/v/tracks/replace', [track.config] ); | ||
| } | ||
| }).placeAt(details); | ||
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| donorIdTextBox.on('change', function(e) { | ||
| updateTrackButton.set('disabled', !donorIdTextBox.validate() || !sizeTextBox.validate() || !textArea.validate()) | ||
| }); | ||
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| sizeTextBox.on('change', function(e) { | ||
| updateTrackButton.set('disabled', !donorIdTextBox.validate() || !sizeTextBox.validate() || !textArea.validate()) | ||
| }); | ||
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| textArea.on('change', function(e) { | ||
| updateTrackButton.set('disabled', !donorIdTextBox.validate() || !sizeTextBox.validate() || !textArea.validate()) | ||
| }); | ||
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| return details; | ||
| }, | ||
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| _shareableLinkContent: function() { | ||
| var track = this; | ||
| var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' }); | ||
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| var headerString = '<h1 style="width: 80%">Shareable Link</h1>'; | ||
| var headerElement = domConstruct.toDom(headerString); | ||
| domConstruct.place(headerElement, details); | ||
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| // Create addTracks value | ||
| var addTracksArray = []; | ||
| var addTrackConf = {}; | ||
| addTrackConf.label = track.config.label; | ||
| addTrackConf.storeClass = track.store.config.type; | ||
| addTrackConf.type = track.config.type; | ||
| addTrackConf.key = track.config.key; | ||
| addTrackConf.metadata = track.config.metadata; | ||
| addTrackConf.unsafePopup = true; | ||
| addTrackConf.filters = track.store.config.filters; | ||
| addTrackConf.donor = track.store.config.donor; | ||
| addTrackConf.size = track.config.size; | ||
| addTracksArray.push(addTrackConf); | ||
| addTracksArray = JSON.stringify(addTracksArray); | ||
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| // Create a shareable URL | ||
| var params = new URLSearchParams(window.location.search); | ||
| params.set("addTracks", addTracksArray); | ||
| var shareableLink = window.location.protocol + "//" + window.location.host + window.location.pathname + '?' + params.toString(); | ||
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| // Create help text | ||
| var helpString = '<span style="width: 80%">Use the following link to share the selected track at the current location.</span>'; | ||
| var helpElement = domConstruct.toDom(helpString); | ||
| domConstruct.place(helpElement, details); | ||
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| // Create text area with shareable link | ||
| var textArea = domConstruct.create( | ||
| 'textarea',{ | ||
| rows: 10, | ||
| value: shareableLink, | ||
| style: "width: 80%", | ||
| readOnly: true | ||
| }, details ); | ||
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| // Create a DOM element for the link | ||
| var linkString = '<a target="_blank" href="' + shareableLink + '">Open in New Tab</a>'; | ||
| var linkElement = domConstruct.toDom(linkString); | ||
| domConstruct.place(linkElement, details); | ||
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| return details; | ||
| } | ||
| }); | ||
| } | ||
| ); |
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