diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..5073443 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,9 @@ +language: node_js +node_js: + - "6.1" + +before_script: + - npm install phantomjs + +script: + - phantomjs runner_test.js diff --git a/README.md b/README.md index daa0242..3a8769b 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # YPet +[![Build Status](https://travis-ci.org/AnoXDD/YPet.svg?branch=master)](https://travis-ci.org/AnoXDD/YPet) + [YPet](https://github.com/SuLab/YPet) is a Javascript library built in [Marionette.js](http://marionettejs.com/) to rapidly annotate paragraphs of text on websites. The project aims to rethink HTML text annotation, primarily focused on biocuration and adheres to the following rules: * Limit the possibility for damaged annotations, individual letters are not desired. @@ -17,8 +19,49 @@ Example of behavior: ## How to Use +The latest version of YPet (`ypet-new.js`) is built based on Marionette V3, but a older version of YPet (`ypet.js`) supports V2. + +The build badge at the beginning of this file indicates the status of the **latest** version. + +We recommend working with Marionette V3, because the older version of YPet does not process special characters like &, <, > properly. You will get `&`, `<`, `>` instead of the characters. + ### Setup +For Marionette V3: + +```javascript +/* Setup the paragraphs with a string to tokenize */ +var p1 = new Paragraph({'text': $('p#some-paragraph').html()}); +var p2 = new Paragraph({'text': 'Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tincidunt tempus lorem, quis sollicitudin lectus pretium nec. Ut non enim.'}); + +/* Configure the # and colors of Annotation types (minimum 1 required) */ +YPet.AnnotationTypes = new AnnotationTypeList([ +{name: 'Person', color: '#A4DEAB'}, +{name: 'Place', color: 'PowderBlue'}, +{name: 'Thing', color: 'rgb(0, 180, 200)'} +]); + +YPet = new Backbone.Marionette.Application({ + region: "#doc" // where p1 and p2 are placed +}); + +/* Assign views to Region */ +YPet.showView(new (Mn.View.extend({ + el: ".container-to-hold-p1p2", + regions: { + 'p1': '#container-to-place-p1', + 'p2': '#container-to-place-p2' + } +}))()); + +/* Put the new Annotation views on the page */ +YPet.getView().getRegion(1).show( new WordCollectionView({collection: p1.get('words')}) ); +YPet.getView().getRegion(2).show( new WordCollectionView({collection: p2.get('words')}) ); + +YPet.start(); +``` +For Marionette V2: + ```javascript YPet.addInitializer(function(options) { /* Setup the paragraphs with a string to tokenize */ @@ -47,12 +90,29 @@ YPet.start(); ``` -### Events +#### Events If you want to live track annotations as they're put on the paragraph (to save, send to a server, or do something else with) the following callbacks and serialization methods are available. Each annotation is returned as an object with a `start` and `text` attribute, as well as an array of children words. +For Marionette V3: + +```javascript +YPet.getView().getRegion(1).currentView.collection.parentDocument.get('annotations').on('add', function(model, collection) { + console.log('Add:', model.toJSON(), collection.toJSON()); +}); + +YPet.getView().getRegion(1).currentView.collection.parentDocument.get('annotations').on('remove', function(model, collection) { + console.log('Remove:', model.toJSON(), collection.toJSON()); +}); + +YPet.getView().getRegion(1).currentView.collection.parentDocument.get('annotations').on('change', function(model) { + console.log('Change:', model.toJSON()); +}); +``` + +For Marionette V2: ```javascript YPet['p1'].currentView.collection.parentDocument.get('annotations').on('add', function(model, collection) { @@ -70,7 +130,7 @@ YPet['p1'].currentView.collection.parentDocument.get('annotations').on('change', ## About -[YPet](https://github.com/SuLab/YPet) was developed to rapidly annotate bio-medical literature for [Mark2Cure](http://mark2cure.org) at [The Su Lab](http://sulab.org/) by [Max Nanis](http://twitter.com/x0xMaximus). +[YPet](https://github.com/SuLab/YPet) was developed to rapidly annotate bio-medical literature for [Mark2Cure](http://mark2cure.org) at [The Su Lab](http://sulab.org/) by [Max Nanis](http://twitter.com/x0xMaximus). The testing script is written by [Runjie Guan](http://anoxic.me). ![The Scripps Research Institute](http://www.scripps.edu/files/images/logo120.png "The Scripps Research Institute") diff --git a/runner_test.js b/runner_test.js new file mode 100644 index 0000000..21c286b --- /dev/null +++ b/runner_test.js @@ -0,0 +1,96 @@ +/* phantomjs page setup */ + +var page = require('webpage').create(); + +page.onConsoleMessage = function(msg) { + console.log(msg); +}; + +page.viewportSize = { + width: 800, + height: 800 +}; + +var test_suites = { + "./test/test_page.html": [ + "_testClickOnValidWords", + "_testClickOnInvalidWords", + + "_testDragSameLine", + "_testDragDifferentLine", + "_testDragOverSelectedWord", + "_testDragFromSelectedWord", + "_testDragToSelectedWord", + + "_testDragInvalidWord", + "_testSubmitResults" + ], + "./test/test_page_special_char.html": [ + "_testClickOnInvalidWords", + + "_testSelectAll", + "_testClickOnEachValidWord", + ], + "./test/test_page_fixed.html": [ + "_testClickOnValidWordsFixed", + + "_testDragFixed", + "_testDragSelectedFixed", + + "_testDragInvalidWordFixed" + ] +}; + +/* test runner */ +var htmls = Object.keys(test_suites); +var running_html = ""; +for (var i = 0; i < htmls.length; ++i) { + (function(i) { + var interval = setInterval(function() { + if (running_html === htmls[i]) { + clearInterval(interval); + page.open(running_html, function(status) { + if (status !== "success") { + console.log("Error loading page"); + phantom.exit(1); + } else { + console.log("\n===========Page loaded: " + running_html + "==========="); + } + + page.evaluate(function() { + return document.testInit(); + }); + + test_suites[running_html].forEach(function(test_function) { + var msg = page.evaluate("document." + test_function); + if (msg && msg != "") { + throw new Error("Error: " + msg); + } + }); + + console.log(test_suites[running_html].length + " tests PASSED"); + // Pass to the next test suite + if (!(running_html = htmls[++i])) { + phantom.exit(0); + } + }); + + } + }, 1000); + })(i); +} +running_html = htmls[0]; + + +page.onError = function(msg, trace) { + console.error("An error occured"); + console.error(JSON.stringify(trace)); + /* inject a line number into the error message raised by assert() */ + if (trace.length > 1) { + console.log(msg.replace(/: in /, + " in line " + (parseInt(trace[1].line) - 1) + " of ")); + } else { + console.log("line " + (parseInt(trace[0].line) - 1) + ": " + msg); + } + phantom.exit(1); +}; diff --git a/src/backbone.marionette_v3.min.js b/src/backbone.marionette_v3.min.js new file mode 100644 index 0000000..7186b31 --- /dev/null +++ b/src/backbone.marionette_v3.min.js @@ -0,0 +1,11 @@ +// MarionetteJS (Backbone.Marionette) +// ---------------------------------- +// v3.1.0 +// +// Copyright (c)2016 Derick Bailey, Muted Solutions, LLC. +// Distributed under MIT license +// +// http://marionettejs.com +!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t(require("backbone"),require("underscore"),require("backbone.radio")):"function"==typeof define&&define.amd?define(["backbone","underscore","backbone.radio"],t):e.Marionette=e.Mn=t(e.Backbone,e._,e.Backbone.Radio)}(this,function(e,t,i){"use strict";function n(e,t,i){return i.toUpperCase()}function r(e){for(var i=arguments.length,n=Array(i>1?i-1:0),r=1;r1?i-1:0),s=1;s1?i-1:0),r=1;r0)for(e=0;e1?n-1:0),s=1;s1&&void 0!==arguments[1]?arguments[1]:{},n=!e._isAttached&&P(this.el),r="undefined"==typeof i.replaceElement?!!t.result(this,"replaceElement"):!!i.replaceElement;n&&s(e,"before:attach",e),r?this._replaceEl(e):this.attachHtml(e),n&&(e._isAttached=!0,s(e,"attach",e)),this.currentView=e},_ensureElement:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};if(t.isObject(this.el)||(this.$el=this.getEl(this.el),this.el=this.$el[0]),!this.$el||0===this.$el.length){var i="undefined"==typeof e.allowMissingEl?!!t.result(this,"allowMissingEl"):!!e.allowMissingEl;if(i)return!1;throw new Y('An "el" must exist in DOM for this region '+this.cid)}return!0},_ensureView:function(e){if(!e)throw new Y({name:"ViewNotValid",message:"The view passed is undefined and therefore invalid. 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