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imedina committed Mar 5, 2019
2 parents b418433 + afabba9 commit 8450a17
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Showing 9 changed files with 365 additions and 43 deletions.
2 changes: 1 addition & 1 deletion lib/jsorolla
Submodule jsorolla updated 22 files
+27 −76 src/core/clients/opencga-client.js
+17 −13 src/core/tracks/CoverageTrack.js
+31 −20 src/core/tracks/GeneTrack.js
+1 −1 src/core/tracks/renderers/CoverageRenderer.js
+124 −0 src/core/webcomponents/cellbase/core/cellbase-gene-filter.html
+402 −293 src/core/webcomponents/opencga/alignment/opencga-panel-transcript-view.html
+117 −60 src/core/webcomponents/opencga/catalog/clinical/opencga-clinical-analysis-editor.html
+6 −6 src/core/webcomponents/opencga/catalog/clinical/opencga-clinical-analysis-portal.html
+544 −0 src/core/webcomponents/opencga/catalog/clinical/opencga-clinical-analysis-view.html
+7 −7 src/core/webcomponents/opencga/catalog/clinical/opencga-clinical-portal.html
+50 −57 src/core/webcomponents/opencga/catalog/family/opencga-family-grid.html
+37 −41 src/core/webcomponents/opencga/catalog/individual/opencga-individual-grid.html
+0 −556 src/core/webcomponents/opencga/clinical/clinical-analysis-view.html
+1 −1 src/core/webcomponents/opencga/clinical/opencga-variant-clinical.html
+1 −1 src/core/webcomponents/opencga/clinical/test/clinical-analysis-view.html
+33 −0 src/core/webcomponents/opencga/commons/CatalogUIUtils.js
+4 −4 src/core/webcomponents/opencga/variant/VariantGridFormatter.js
+1 −1 src/core/webcomponents/opencga/variant/opencga-interpreted-variant-grid.html
+1 −1 src/core/webcomponents/opencga/variant/opencga-variant-interpretation-editor.html
+79 −37 src/core/webcomponents/opencga/variant/opencga-variant-interpretation.html
+436 −0 src/core/webcomponents/opencga/variant/opencga-variant-interpreter-genome-browser.html
+1 −1 src/core/webcomponents/reactome/reactome-variant-network.html
2 changes: 1 addition & 1 deletion package.json
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "iva",
"version": "1.0.0-rc2",
"version": "1.0.0-rc3",
"description": "IVA description",
"repository": {
"type": "git",
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66 changes: 66 additions & 0 deletions src/about.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
<!--
~ Copyright 2015-2016 OpenCB
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->

<dom-module id="about-web">
<template>
<!--<style include="jso-styles">-->
<style>
.about-center {
margin: auto;
width: 65%;
text-align: justify;
font-size: 16px;
color: #797979;
}
</style>

<!-- This is where main application is rendered -->
<div class="about-center">
<h1>About</h1>
<hr>

</div>
</template>

<script>

class About extends Polymer.Element {

constructor() {
super();
}

static get is() {
return 'about-web';
}

static get properties() {
return {
version: {
type: String
}
}
}

_attachDom(dom) {
this.appendChild(dom);
}

}

customElements.define(About.is, About);
</script>
</dom-module>
23 changes: 14 additions & 9 deletions src/conf/config.js
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ const opencga = {

const application = {
title: "IVA",
version: "v1.0.0-rc2",
version: "v1.0.0-rc3",
logo: "img/opencb-logo.png",
// The order, title and nested submenus are respected
menu: [
Expand Down Expand Up @@ -285,14 +285,19 @@ const application = {
settings: {
visibility: "public",
},
about: [
{name: "Documentation", url: "http://docs.opencb.org/display/iva/IVA+Home", icon: "fa fa-book"},
{name: "Tutorial", url: "http://docs.opencb.org/display/iva/Tutorials", icon: ""},
{name: "Source code", url: "https://github.com/opencb/iva", icon: "fa fa-github"},
{name: "Releases", url: "https://github.com/opencb/iva/releases", icon: ""},
{name: "Contact", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"},
{name: "FAQ", url: "", icon: ""},
],
about: {
dropdown: true,
links: [
{id: "documentation", name: "Documentation", url: "http://docs.opencb.org/display/iva/IVA+Home", icon: "fa fa-book"},
{id: "tutorial", name: "Tutorial", url: "http://docs.opencb.org/display/iva/Tutorials", icon: ""},
{id: "code", name: "Source code", url: "https://github.com/opencb/iva", icon: "fa fa-github"},
{id: "releases", name: "Releases", url: "https://github.com/opencb/iva/releases", icon: ""},
{id: "about", name: "About", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"},
{id: "terms", name: "Terms", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"},
{id: "contact", name: "Contact", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"},
{id: "faq", name: "FAQ", url: "", icon: ""},
]
},
login: {
visible: true,
},
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66 changes: 66 additions & 0 deletions src/contact.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
<!--
~ Copyright 2015-2016 OpenCB
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->

<dom-module id="contact-web">
<template>
<!--<style include="jso-styles">-->
<style>
.contact-center {
margin: auto;
width: 65%;
text-align: justify;
font-size: 16px;
color: #797979;
}
</style>

<!-- This is where main application is rendered -->
<div class="contact-center">
<h1>Contact</h1>
<hr>

</div>
</template>

<script>

class Contact extends Polymer.Element {

constructor() {
super();
}

static get is() {
return 'contact-web';
}

static get properties() {
return {
version: {
type: String
}
}
}

_attachDom(dom) {
this.appendChild(dom);
}

}

customElements.define(Contact.is, Contact);
</script>
</dom-module>
66 changes: 66 additions & 0 deletions src/faq.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
<!--
~ Copyright 2015-2016 OpenCB
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->

<dom-module id="faq-web">
<template>
<!--<style include="jso-styles">-->
<style>
.faq-center {
margin: auto;
width: 65%;
text-align: justify;
font-size: 16px;
color: #797979;
}
</style>

<!-- This is where main application is rendered -->
<div class="faq-center">
<h1>Frequently Asked Questions</h1>
<hr>

</div>
</template>

<script>

class Faq extends Polymer.Element {

constructor() {
super();
}

static get is() {
return 'faq-web';
}

static get properties() {
return {
version: {
type: String
}
}
}

_attachDom(dom) {
this.appendChild(dom);
}

}

customElements.define(Faq.is, Faq);
</script>
</dom-module>
6 changes: 6 additions & 0 deletions src/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,12 @@
<script type="text/javascript" src="../lib/jsorolla/src/core/svg.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/region.js"></script>

<script type="text/javascript" src="../lib/jsorolla/src/core/tracks/FeatureTrack.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/tracks/CoverageTrack.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/tracks/GeneTrack.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/tracks/renderers/CoverageRenderer.js"></script>
<!--<script type="text/javascript" src="../lib/jsorolla/src/core/tracks/renderers/GeneRenderer.js"></script>-->

<script type="text/javascript" src="../lib/jsorolla/src/core/cache/indexeddb-cache.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/cache/file-feature-cache.js"></script>
<script type="text/javascript" src="../lib/jsorolla/src/core/cache/feature-chunk-cache.js"></script>
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