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hmskleehmsklee
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add parser for ann
1 parent 0288d68 commit f18c5c0

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9 files changed

+286
-31
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9 files changed

+286
-31
lines changed

‎css/style.css‎

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@@ -63,6 +63,19 @@ header > button:hover {
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border-bottom:1px solid grey;
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}
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/* input */
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#brat-input {
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}
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#brat-input textarea {
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width:100%;
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height:300px;
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padding:5px;
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font-size:15px;
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}
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/* modal */
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.modal {
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color:#222;
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background:rgba(0,0,0,0.3);

‎data/example.ann‎

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un lock able
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T1 BOUND 0 2 un
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T2 FREE 4 7 lock
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T3 BOUND 8 12 able
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R1 unlock controlled:T1 controller:T2
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R2 unlockable controller:R1 controlled:T3

‎data/example2.ann‎

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Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities
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T1 Gene_or_gene_product 13 16 p21
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T2 Gene_or_gene_product 20 23 p53
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T3 BioProcess 34 44 DNA damage
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T4 Gene_or_gene_product 59 63 Cdk4
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T5 Gene_or_gene_product 68 72 Cdk2
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T6 Positive_activation 0 9 Induction
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T7 Negative_regulation 45 53 inhibits
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E1 Positive_activation:T6 Controller:T2 Controlled:T1
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E2 Negative_regulation::T7 Controller:E1 Controlled:T4
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E3 Negative_regulation::T7 Controller:E1 Controlled:T5

‎index.html‎

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@@ -10,6 +10,7 @@
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<body>
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<header id="header">
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Examples:
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<select id="dataset">
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<option>-- select dataset --</option>
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<option>data1</option>
@@ -21,10 +22,28 @@
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<option>morpheme2</option>
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<option>event annotation</option>
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</select>
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<button id="custom-annotation">Custom annotation</button>
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<button id="taxonomy-toggle">Taxonomy</button>
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<button id="options-toggle">Options</button>
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</header>
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<div id="brat-input" class="modal">
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<div>
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<header>
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<span class="tab active">Custom input in .ann format</span>
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</header>
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<div class="page active">
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<div>
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<button><label for="file-input">Load .ann file</label></button>
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<input type="file" id="file-input" style="display:none;">
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</div>
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<textarea></textarea>
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<div id="error-message"></div>
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</div>
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</div>
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</div>
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<div id="main">
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<div id="tooltip">
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</div>
@@ -47,14 +66,17 @@
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<p><input type="checkbox" data-option="tree"> Open tree view in modal</p>
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</div>
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</div>
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</div>
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<script src="libs/svg.js"></script>
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<script src="libs/svg.draggable.js"></script>
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<script src="libs/jscolor.min.js"></script>
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<script src="libs/d3.min.js"></script>
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<script src="js/xhr.js"></script>
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<script src="js/ymljson.js"></script>
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<script src="js/ann-parser.js"></script>
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<script src="js/parser.js"></script>
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<script src="js/treelayout.js"></script>
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<script src="js/main.js"></script>
@@ -69,6 +91,11 @@
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<script src="js/components/link.js"></script>
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<script type="text/javascript">
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// page setup
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// manage input
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// manage visualization
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Main.init();
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</script>
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‎js/ann-parser.js‎

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const parseAnn = (function() {
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class TextBoundMention {
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constructor(id, label, charStart, charEnd) {
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this.id = id;
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this.label = label;
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this.charStart = charStart;
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this.charEnd = charEnd;
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}
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}
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class EventMention {
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constructor(id, label, trigger, args) {
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this.id = id;
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this.label = label;
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this.trigger = trigger;
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this.arguments = args;
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}
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}
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class RelationMention {
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constructor(id, label, arg1, arg2) {
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this.id = id;
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this.label = label;
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this.arguments = [arg1, arg2];
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}
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}
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class Attribute {
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constructor(id, target, attribute, value) {
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this.id = id;
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this.target = target;
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this.attribute = attribute;
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this.value = value;
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}
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}
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const re = /:+(?=[TER]\d+$)/;
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function parseTextBoundMention(tokens, text) {
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const id = +tokens[0].slice(1),
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label = tokens[1],
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charStart = +tokens[2],
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charEnd = +tokens[3];
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if (id > 0 && charStart >= 0 && charStart < charEnd && charEnd < text.length) {
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return new TextBoundMention('T' + id, label, charStart, charEnd);
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}
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}
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function parseEventMention(tokens, mentions) {
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const id = +tokens[0].slice(1),
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trigger = tokens[1],
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arguments = tokens.slice(2);
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if (id > 0 && trigger) {
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let split = trigger.split(re);
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if (split[0].length > 0 && mentions[split[1]]) {
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const em = new EventMention('E' + id, split[0], split[1], []);
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arguments.forEach(argument => {
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let splitArgument = argument.split(re);
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if (splitArgument[0].length > 0 && mentions[splitArgument[1]]) {
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em.arguments.push({
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type: splitArgument[0],
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id: splitArgument[1]
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});
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}
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});
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return em;
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}
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}
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}
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function parseRelationMention(tokens, mentions) {
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const id = +tokens[0].slice(1),
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label = tokens[1],
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arg1 = tokens[2],
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arg2 = tokens[3];
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if (id > 0 && arg2) {
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const split1 = arg1.split(re),
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split2 = arg2.split(re);
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if (mentions[split1[1]] && mentions[split2[1]]) {
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return new RelationMention('R' + id, label, {
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type: split1[0],
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id: split1[1]
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}, {
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type: split2[0],
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id: split2[1]
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});
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}
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}
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}
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function parseAttributes(tokens, mentions) {
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const id = +tokens[0].slice(1),
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attr = tokens[1],
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target = tokens[2];
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if (id > 0 && mentions[target]) {
104+
return new Attribute(id, target, attr, tokens.slice(3).join(' '));
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}
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}
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function parse(input) {
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var output = {
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texts: [],
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events: [],
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relations: [],
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attributes: [],
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unparsedLines: [],
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mentions: {}
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}
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let lines = input.split('\n');
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let text = lines[0];
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if (!text) {
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output.unparsedLines = lines;
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return output;
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}
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let unparsedLines = [];
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let mentions = {};
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for (let i = 1; i < lines.length; ++i) {
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const line = lines[i].trim();
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if (!line) { continue; }
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let tokens = line.split(/\s+/);
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let parseIsSuccessful = false;
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/** The following IDs are currently supported:
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T: text-bound annotation
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E: event
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R: relation
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A: attribute
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Normalizations, notes, and equivalence relations are not currently supported
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*/
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switch (tokens[0].charAt(0)) {
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case 'T':
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let tbm = parseTextBoundMention(tokens, text);
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if (tbm) {
152+
output.texts.push(tbm);
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mentions[tbm.id] = tbm;
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}
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break;
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case 'E':
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let em = parseEventMention(tokens, mentions);
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if (em) {
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output.events.push(em);
160+
mentions[em.id] = em;
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}
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break;
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case 'R':
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let rm = parseRelationMention(tokens, mentions);
165+
if (rm) {
166+
output.relations.push(rm);
167+
mentions[rm.id] = rm;
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}
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break;
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case 'A':
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let a = parseAttribute(tokens, mentions);
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if (a) {
173+
output.attributes.push(a);
174+
mentions[a.id] = a;
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}
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break;
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}
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179+
if (!parseIsSuccessful) {
180+
unparsedLines.push(line);
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}
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}
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output.mentions = mentions;
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output.unparsedLines = unparsedLines;
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return output;
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}
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return parse;
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})();

‎js/main.js‎

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@@ -25,8 +25,11 @@ const Main = (function() {
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/**
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* init: set up singleton classes and create initial drawing
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*/
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let _initialized = false;
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function init() {
2930
// setup
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if (_initialized) { return; }
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_initialized = true;
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body = document.body.getBoundingClientRect();
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svg = SVG('main')
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.size(body.width, window.innerHeight - body.top - 10);
@@ -38,8 +41,13 @@ const Main = (function() {
3841
tm = new Taxonomy('taxonomy');
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tree = new TreeLayout('#tree', svg);
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44+
load('data/example2.ann').then(text => {
45+
console.log(text);
46+
console.log(parseAnn(text));
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});
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return;
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// load and render initial dataset by default
42-
changeDataset(6);
50+
// changeDataset(6);
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// svg event listeners
4553
svg.on('row-resize', function(e) {
@@ -198,6 +206,9 @@ const Main = (function() {
198206
}
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});
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document.getElementById('custom-annotation').onclick = function() {
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document.getElementById('brat-input').classList.add('open');
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}
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document.getElementById('options-toggle').onclick = function() {
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setActiveTab('options');
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}

‎js/parser.js‎

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@@ -103,28 +103,12 @@ const Parser = (function() {
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/* load a json from a path */
104104
readJson(path, callback) {
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106-
var json = path || './data/data1.json';
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function loadJSON(path) {
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var httpRequest = new XMLHttpRequest();
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httpRequest.onreadystatechange = function() {
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if (httpRequest.readyState === 4) {
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if (httpRequest.status === 200) {
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var data = JSON.parse(httpRequest.responseText);
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parseData(data);
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if (callback) {
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callback();
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}
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}
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}
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};
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httpRequest.open('GET', path);
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httpRequest.send();
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}
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/* parse json file*/
127-
loadJSON(json);
106+
load(path).then((data) => {
107+
parseData(data);
108+
if (callback) {
109+
callback();
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}
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})
128112
}
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130114
get tokens() { return _tokens; }

‎js/xhr.js‎

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function load(url) {
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var xhr = new XMLHttpRequest();
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xhr.open("GET", url);
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xhr.send();
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return new Promise((res, err) => {
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xhr.onreadystatechange = function() {
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if (xhr.readyState === 4) {
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if (xhr.status === 200) {
10+
res(xhr.responseText);
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}
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else {
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err(xhr);
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}
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}
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}
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});
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}

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