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Merge pull request #315 from zhx828/hotfix
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Fix issues in milestone 1.0.3
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@zhx828
zhx828 authored Oct 21, 2016
2 parents 01d8d57 + 247c220 commit 6c5fabc
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Showing 15 changed files with 407 additions and 218 deletions.
9 changes: 6 additions & 3 deletions Gruntfile.js
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Expand Up @@ -43,9 +43,6 @@ module.exports = function(grunt) {
files: ['test/spec/{,*/}*.js'],
tasks: ['babel:test', 'test:watch']
},
gruntfile: {
files: ['Gruntfile.js']
},
sass: {
files: ['<%= config.app %>/styles/{,*/}*.{scss,sass}'],
tasks: ['sass', 'postcss']
Expand All @@ -57,6 +54,12 @@ module.exports = function(grunt) {
json_to_sass: {
files: ['<%= config.app %>/resources/vars.json'],
tasks: ['json_to_sass', 'newer:copy:styles', 'postcss']
},
configFiles: {
files: ['<%= config.app %>/resources/attributes.json', 'Gruntfile.js'],
options: {
reload: true
}
}
},

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2 changes: 1 addition & 1 deletion app/_components/cbioportal-client.js
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Expand Up @@ -10,7 +10,7 @@ window.cbioportal_client = (function() {
var arg_string = arg_strings.join("&") || "?";
return $.ajax({
type: "POST",
url: window.cbioURL + '/' + endpt,
url: window.cbioURL + endpt,
data: arg_string,
dataType: "json"
});
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161 changes: 50 additions & 111 deletions app/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -68,18 +68,20 @@
<script src="_components/FileSaver.min.js"></script>
<script src="_components/cbio-util.js"></script>
<script src="_components/download-util.js"></script>
<script src="_components/Notification.js"></script>
<script src="_components/GeneValidator.js"></script>
<script src="_components/QueryByGeneUtil.js"></script>
<script src="_components/QueryByGeneTextArea.js"></script>
<script src="_components/MutatedGeneCNATable.js"></script>
<script src="scripts/model/dataProxy.js"></script>
<script src="_components/cbioportal-client.js"></script>
<!-- endbuild -->

<!-- build:js scripts/vc-session.js -->
<script src="_components/vc-session.js"></script>
<!-- endbuild -->

<!-- build:js scripts/iviz.js -->
<script src="_components/Notification.js"></script>
<script src="_components/GeneValidator.js"></script>
<script src="_components/QueryByGeneUtil.js"></script>
<script src="_components/QueryByGeneTextArea.js"></script>
<script src="scripts/main.js"></script>
<script src="scripts/vueCore.js"></script>
<script src="scripts/controller/util.js"></script>
Expand All @@ -106,16 +108,12 @@
<script src="scripts/views/components/dataTable/tableViewTemplate.js"></script>
<script src="scripts/views/components/customPlots/CaseDialogBox.js"></script>
<!-- endbuild -->

<script src="scripts/model/dataProxy.js"></script>
<script src="_components/cbioportal-client.js"></script>

</head>
<body>

<div class="container-fluid" id="complete-screen">
<div id="complete-screen-loader"
:class="{'show-loading': showScreenLoad}"
<div id="complete-screen-loader"
:class="{'show-loading': showScreenLoad}"
class="chart-loader" style="top: 30%; left: 30%; display: none;"><img
src="images/ajax-loader.gif" alt="loading"></div>
<nav class="navbar navbar-default navbar-fixed-top">
Expand All @@ -136,62 +134,67 @@
<span id="iviz-header-left-patient-select" class="iviz-header-button"
@click="openCases('patient')" class="number"
role="button" tabindex="0" style="display: block;"><i class="fa fa-user" aria-hidden="true"></i></span>
<span id="iviz-header-left-case-download" class="iviz-header-button" @click="downloadCaseData()"
role="button"
<span id="iviz-header-left-case-download" class="iviz-header-button" @click="downloadCaseData()"
role="button"
tabindex="0"><i class="fa fa-download" alt="download"></i></span>
<span id="query-by-gene-span">

<span id="query-by-gene-span">
<textarea id="query-by-gene-textarea" class="expand expandFocusOut" rows="1" cols="10"></textarea>
</span>
<span class="iviz-header-arrow">
<i class="fa fa-arrow-right fa-lg" aria-hidden="true"></i>
<i class="fa fa-arrow-right fa-lg" aria-hidden="true"></i>
</span>
<form id="iviz-form" v-on:submit.prevent="submitForm" method="post" target="_blank" style="float: left;">
<form id="iviz-form" v-on:submit.prevent="submitForm" method="post" target="_blank" style="float: left;">
<input type="submit" id="iviz-header-left-1" value="Query" class="iviz-header-button" style="display: block;">
</form>

</div>

<div id="iviz-header-right">
<custom-case-input></custom-case-input>

<select id="iviz-add-chart" class="chosen-select"
v-select :charts="charts" v-if="showDropDown">
<option id='' value="">Add Chart</option>
<option id="{{data.attr_id}}" v-if="!data.show" value="{{data.attr_id}}" v-for="(index,data) in charts">{{data.display_name}}</option>
<option id="{{data.attr_id}}" v-if="!data.show" value="{{data.attr_id}}" v-for="(index,data) in charts">
{{data.display_name}}
</option>
</select>
</div>

<div id="breadcrumbs_container" v-if="hasfilters">
<div style="float:left;" >
<div style="float:left;">
<span class="breadcrumb_container">Your selections: </span>
</div>

<span class="breadcrumb_container" v-if="customfilter.patientIds.length>0||customfilter.sampleIds.length>0">
<span>{{customfilter.display_name}}</span>
<i class="fa fa-times breadcrumb_remove"
<i class="fa fa-times breadcrumb_remove"
@click="clearAllCharts(true)"></i>
</span>
<div style="float:left" v-for="group in groups">
<bread-crumb :attributes.sync="item"
:filters.sync="item.filter" v-for="(index1, item) in group.attributes"
v-if="item.filter.length>0" ></bread-crumb>
v-if="item.filter.length>0"></bread-crumb>
</div>
<div style="float:left">
<button type='button' @click="clearAllCharts(true)"
class="btn btn-default btn-xs">Clear All
</button>
</div>
<div style="float:left"><button type='button' @click="clearAllCharts(true)"
class="btn btn-default btn-xs">Clear All</button></div>
</div>
</div>
</nav>
<div :class="{'start-loading': showScreenLoad}">
<div class="grid" id="main-grid"
:class="{loading:isloading}">
<main-template :groups.sync="groups" :redrawgroups.sync="redrawgroups"
:selectedpatients.sync="selectedpatients"
:selectedsamples.sync="selectedsamples"
:hasfilters.sync="hasfilters"
:customfilter.sync="customfilter"
:clear-all="clearAll"></main-template>
</div>
<div class="grid" id="main-grid"
:class="{loading:isloading}">
<main-template :groups.sync="groups" :redrawgroups.sync="redrawgroups"
:selectedpatients.sync="selectedpatients"
:selectedsamples.sync="selectedsamples"
:hasfilters.sync="hasfilters"
:customfilter.sync="customfilter"
:clear-all="clearAll"></main-template>
</div>
</div>

</div>
Expand All @@ -200,95 +203,31 @@
<script>
$(document).ready(function() {
//Include style variables
window.style = {
vars: {}
};
iViz.vue.manage.init();

// This is used to indicate how to disable two buttons. By default, they are set to true.
iViz.vue.manage.getInstance().showManageButton = true;
iViz.vue.manage.getInstance().showSaveButton = true;

$.getJSON('resources/vars.json')
.then(function(data) {
window.style.vars.width = {
one: iViz.util.pxStringToNumber(data['grid-w-1']) || 195,
two: iViz.util.pxStringToNumber(data['grid-w-2']) || 400
};
window.style.vars.height = {
one: iViz.util.pxStringToNumber(data['grid-h-1']) || 170,
two: iViz.util.pxStringToNumber(data['grid-h-2']) || 350
};
window.style.vars.chartHeader = 17;
window.style.vars.borderWidth = 2;
Window
window.style.vars.scatter = {
width: (window.style.vars.width.two - window.style.vars.borderWidth) || 400,
height: (window.style.vars.height.two - window.style.vars.chartHeader
- window.style.vars.borderWidth) || 350
};
window.style.vars.survival = {
width: window.style.vars.scatter.width,
height: window.style.vars.scatter.height
};
window.style.vars.specialTables = {
width: window.style.vars.scatter.width,
height: window.style.vars.scatter.height - 25
};
window.style.vars.piechart = {
width: 140,
height: 140
};
window.style.vars.barchart = {
width: (window.style.vars.width.two - window.style.vars.borderWidth) || 400,
height: (window.style.vars.height.one - window.style.vars.chartHeader * 2
- window.style.vars.borderWidth) || 130
};
})
.fail(function() {
window.style.vars = {
width: {
one: 195,
two: 400
},
height: {
one: 170,
two: 350
},
chartHeader: 15,
borderWidth: 2,
scatter: {
width: 400,
height: 350
},
survival: {
width: 400,
height: 350
},
specialTables: {
width: 400,
height:350
},
piechart: {
width: 180,
height: 140
},
barchart: {
width: 400,
height: 30
}
}
});
window.cbioURL = 'http://www.cbioportal.org/';
window.mutationProfileId ='hnsc_tcga_mutations';
window.cbioResourceURL = 'resources/';
window.mutationProfileId = 'hnsc_tcga_mutations';
window.cnaProfileId = 'hnsc_tcga_gistic';
window.case_set_id = '-1';
var studyCasesMap = {};
studyCasesMap['hnsc_tcga']={};
studyCasesMap['hnsc_tcga'] = {};
window.iviz = {};
window.iviz.datamanager = new DataManagerForIviz.init(window.cbioURL, studyCasesMap);
$.when(window.iviz.datamanager.initialSetup()).then(function(_data) {
iViz.init(_data);
$.when(
window.iviz.datamanager.initialSetup(),
window.iviz.datamanager.getStyleVars()
).then(function(_data, styles) {
var opts = {};

if(_.isObject(styles)) {
opts.styles = styles;
}
iViz.init(_data, opts);
});

QueryByGeneTextArea.init('#query-by-gene-textarea', function(genes) {
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36 changes: 36 additions & 0 deletions app/resources/attributes.json
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@@ -0,0 +1,36 @@
{
"clinicalAttrs": {
"general": {
"priority": [
"CANCER_TYPE",
"CANCER_TYPE_DETAILED",
"GENDER",
"SEX",
"AGE",
"sequenced",
"has_cna_data",
"sample_count_patient"
],
"hidden": []
},
"studies": {
"mskimpact": {
"priority":[
"DARWIN_PATIENT_AGE",
"OS_STATUS",
"SAMPLE_TYPE",
"DARWIN_VITAL_STATUS"
],
"hidden": [
"OS_SURVIVAL",
"DFS_SURVIVAL",
"AGE"
]
}
}
},
"tableAttrs": [
"CANCER_TYPE",
"CANCER_TYPE_DETAILED"
]
}
11 changes: 0 additions & 11 deletions app/scripts/controller/util.js
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Expand Up @@ -653,17 +653,6 @@
return string.join('<br/>');
};

content.pxStringToNumber = function(_str) {
var result;
if (_.isString(_str)) {
var tmp = _str.split('px');
if (tmp.length > 0) {
result = Number(tmp[0]);
}
}
return result;
};

return content;
})();
})(window.iViz,
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