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@imedina
imedina committed Apr 5, 2019
2 parents fb4235b + 80c2837 commit 1a76365
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Showing 6 changed files with 31 additions and 24 deletions.
2 changes: 1 addition & 1 deletion lib/jsorolla
Submodule jsorolla updated 28 files
+2 −2 package.json
+4 −0 src/core/clients/opencga-client.js
+13 −8 src/core/data-adapter/opencga-adapter.js
+69 −3 src/core/tracks/renderers/CoverageRenderer.js
+1 −1 src/core/utilsNew.js
+8 −0 src/core/webcomponents/cellbase/variation/cellbase-variant-annotation-summary.html
+435 −6 src/core/webcomponents/opencga/alignment/opencga-panel-transcript-view.html
+1 −1 src/core/webcomponents/opencga/catalog/opencga-login.html
+5 −5 src/core/webcomponents/opencga/clinical/opencga-clinical-portal.html
+2 −0 src/core/webcomponents/opencga/opencga-active-filters.html
+78 −10 src/core/webcomponents/opencga/variant/VariantGridFormatter.js
+98 −0 src/core/webcomponents/opencga/variant/opencga-interpretation-variant-review.html
+3 −15 src/core/webcomponents/opencga/variant/opencga-variant-browser.html
+1 −1 src/core/webcomponents/opencga/variant/opencga-variant-cohort-stats.html
+17 −4 src/core/webcomponents/opencga/variant/opencga-variant-filter-clinical.html
+101 −92 src/core/webcomponents/opencga/variant/opencga-variant-filter.html
+39 −61 src/core/webcomponents/opencga/variant/opencga-variant-grid.html
+12 −1 src/core/webcomponents/opencga/variant/opencga-variant-interpretation-detail.html
+220 −410 src/core/webcomponents/opencga/variant/opencga-variant-interpretation-editor.html
+80 −11 src/core/webcomponents/opencga/variant/opencga-variant-interpretation-grid.html
+223 −143 src/core/webcomponents/opencga/variant/opencga-variant-interpretation.html
+13 −11 src/core/webcomponents/opencga/variant/opencga-variant-interpreter-genome-browser.html
+170 −183 src/core/webcomponents/opencga/variant/opencga-variant-samples.html
+116 −0 src/genome-browser/test/gb-variant-component-demo.html
+186 −0 src/genome-browser/test/gb-variant-demo.html
+1 −1 src/genome-browser/test/genome-browser-variants.html
+8 −8 src/genome-browser/tracks/variant-track.js
+5 −15 src/genome-browser/webcomponent/genome-browser.html
2 changes: 1 addition & 1 deletion package.json
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@@ -1,6 +1,6 @@
{
"name": "iva",
"version": "1.0.0-rc4",
"version": "1.0.1",
"description": "IVA description",
"repository": {
"type": "git",
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2 changes: 1 addition & 1 deletion src/conf/config.js
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Expand Up @@ -77,7 +77,7 @@ const opencga = {

const application = {
title: "IVA",
version: "v1.0.0-rc4",
version: "v1.0.1",
logo: "img/opencb-logo.png",
// The order, title and nested submenus are respected
menu: [
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22 changes: 14 additions & 8 deletions src/conf/tools.js
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Expand Up @@ -30,6 +30,11 @@ const filterMenu = {
title: "Study and Cohorts",
collapsed: false,
subsections: [
{
id: "study",
title: "Studies Filter",
tooltip: "Only considers variants from the selected studies"
},
{
id: "cohort",
title: "Cohort Stats (MAF)",
Expand All @@ -42,18 +47,13 @@ const filterMenu = {
{id: "ALL", name: "All"}
]
},
platinum: {
illumina_platinum: [
{id: "ALL", name: "All"}
GRCH37: {
platinum: [
{id: "ALL", name: "ALL"}
]
}
},
tooltip: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined"
},
{
id: "study",
title: "Studies Filter",
tooltip: "Only considers variants from the selected studies"
}
]
},
Expand Down Expand Up @@ -378,6 +378,12 @@ const tools = {
}
},
detail: [
// {
// id: "variantReview",
// component: "opencga-interpretation-variant-review",
// title: "Review",
// active: false
// },
{
id: "annotation",
component: "cellbase-variantannotation-view",
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15 changes: 8 additions & 7 deletions src/prod/index.html
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Expand Up @@ -67,13 +67,14 @@
<!-- others-->
<link rel="stylesheet" href="../../node_modules/bootstrap-colorpicker/dist/css/bootstrap-colorpicker.min.css">
<link rel="stylesheet" href="../../node_modules/eonasdan-bootstrap-datetimepicker/build/css/bootstrap-datetimepicker.min.css">
<link rel="stylesheet" href="../../node_modules/font-awesome/css/font-awesome.min.css">
<link href="../../node_modules/font-awesome/fonts/FontAwesome.otf">
<link href="../../node_modules/font-awesome/fonts/fontawesome-webfont.eot">
<link href="../../node_modules/font-awesome/fonts/fontawesome-webfont.svg">
<link href="../../node_modules/font-awesome/fonts/fontawesome-webfont.ttf">
<link href="../../node_modules/font-awesome/fonts/fontawesome-webfont.woff">
<link href="../../node_modules/font-awesome/fonts/fontawesome-webfont.woff2">
<!-- <link rel="stylesheet" href="../../node_modules/font-awesome/css/font-awesome.min.css">-->
<link rel="stylesheet" href="../../node_modules/@fortawesome/fontawesome-free/css/all.min.css">
<!-- <link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/FontAwesome.otf">-->
<link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.eot">
<link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.svg">
<link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.ttf">
<link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.woff">
<link href="../../node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.woff2">
<link rel="stylesheet" href="../../node_modules/qtip2/dist/jquery.qtip.min.css">
<link rel="stylesheet" href="../../lib/jsorolla/dist/css/style.css">
<link rel="stylesheet" href="../../node_modules/animate.css/animate.min.css">
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12 changes: 6 additions & 6 deletions src/welcome.html
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Expand Up @@ -50,11 +50,11 @@ <h2>Overview</h2>
<datalist id="FeatureDatalist"></datalist>
<!-- Examples -->
<span style="font-size: 0.8em; padding-left: 10px">
Examples - Gene: <a on-click="onExampleClick" data-type="gene" style="cursor: pointer">BRCA2</a>,
Region: <a on-click="onExampleClick" data-type="region" style="cursor: pointer">3</a>, <a on-click="onExampleClick" data-type="region" style="cursor: pointer">3:113000-1150000</a>,
SNP: <a on-click="onExampleClick" data-type="snp" style="cursor: pointer">rs445909</a>
Variant: <a on-click="onExampleClick" data-type="variant" style="cursor: pointer">13:32962274:G:T</a>
</span>
Examples - Gene: <a on-click="onExampleClick" data-type="gene" style="cursor: pointer">BRCA2</a>,
Region: <a on-click="onExampleClick" data-type="region" style="cursor: pointer">3</a>, <a on-click="onExampleClick" data-type="region" style="cursor: pointer">3:113000-1150000</a>,
SNP: <a on-click="onExampleClick" data-type="snp" style="cursor: pointer">rs445909</a>
Variant: <a on-click="onExampleClick" data-type="variant" style="cursor: pointer">13:32962274:G:T</a>
</span>
</div>
</template>
<br>
Expand Down Expand Up @@ -122,7 +122,7 @@ <h4>Note:</h4>
}

onExampleClick(e) {
let query = {};
let query = {study: this.opencgaSession.study.fqn};
switch (e.currentTarget.dataset.type) {
case "gene":
query.gene = e.currentTarget.text;
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