broadinstitute · preetisi · May 21, 2019 · May 28, 2019 · May 30, 2019 · Jun 3, 2019
diff --git a/grails-app/conf/Config.groovy b/grails-app/conf/Config.groovy
@@ -316,9 +316,9 @@ environments {
 
 //        grails.serverURL = "http://demo52k.us-east-1.elasticbeanstalk.com"
 //      grails.serverURL = "http://ci-env.elasticbeanstalk.com"
-//      grails.serverURL = "http://type2diabetes-dev.elasticbeanstalk.com"
+      grails.serverURL = "http://type2diabetes-dev.elasticbeanstalk.com"
 
-     grails.serverURL = "http://type2diabetesgen-qasrvr.elasticbeanstalk.com"
+//     grails.serverURL = "http://type2diabetesgen-qasrvr.elasticbeanstalk.com"
 
 
 //      grails.serverURL = "http://ec2-54-175-211-21.compute-1.amazonaws.com/"              // temp for now, will house new prdsrv1 URL
@@ -465,6 +465,7 @@ grails.plugin.springsecurity.interceptUrlMap = [
         '/variant/**':          ['ROLE_USER'],
         '/variantInfo/**':      ['ROLE_USER'],
         '/grs/**':              ['ROLE_USER'],
+        '/gait/**':              ['ROLE_USER'],
         '/variantSearch/retrieveGwasSpecificPhenotypesAjax':    ['permitAll'],
         '/variantSearch/**':    ['ROLE_USER'],
         '/beacon/*':          ['permitAll'],
@@ -974,4 +975,6 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d",      // label for
 
 
 
-
+// Here the secret authentication strings
+auth.providers.twitter.secret = 'l3dJBs3w9QraAuivcfaqdjVGkJ4cxQSMMNNkZ6v9bwz8nXBCXQ'
+oauth.providers.google.secret = 'HKIxi3AOLAgyFV6lDJQCfEgY'
diff --git a/grails-app/conf/portalResources.groovy b/grails-app/conf/portalResources.groovy
@@ -32,6 +32,13 @@ modules = {
         resource url: 'css/dport/grsInfo.css'
     }
 
+    gaitInfo {
+        dependsOn "core", "mbar", "bootstrapMultiselect", "burdenTest","boxwhisker"
+
+        resource url: 'js/lib/dport/gaitInfo.js'
+        resource url: 'css/dport/grsInfo.css'
+    }
+
     regionInfo {
         resource url: 'js/lib/dport/regionInfo.js'
         resource url: 'css/dport/regionInfo.css'

diff --git a/grails-app/controllers/org/broadinstitute/mpg/GaitController.groovy b/grails-app/controllers/org/broadinstitute/mpg/GaitController.groovy
@@ -0,0 +1,60 @@
+package org.broadinstitute.mpg
+
+
+import groovy.json.JsonSlurper
+import org.broadinstitute.mpg.diabetes.util.PortalConstants
+import org.broadinstitute.mpg.meta.UserQueryContext
+import org.codehaus.groovy.grails.web.json.JSONObject
+
+class GaitController {
+    RestServerService  restServerService
+    WidgetService widgetService
+
+    def index() {
+        forward gaitInfo()
+    }
+
+    def gaitInfo(){
+        String uncharacterizedString = params.id
+        UserQueryContext userQueryContext = widgetService.generateUserQueryContext(uncharacterizedString)
+        if (userQueryContext.gene){
+            render (view: 'gaitInfo', model:[geneName: userQueryContext.originalRequest,allowExperimentChoice: false, allowPhenotypeChoice: true, allowStratificationChoice: true ])
+        }
+        if (userQueryContext.variant){
+            render (view: 'gaitInfo', model:[variantIdentifier: userQueryContext.originalRequest, variantSetId: userQueryContext.originalRequest,allowExperimentChoice: true, allowPhenotypeChoice: true, allowStratificationChoice: false])
+        }
+
+
+    }
+
+    def getGRSListOfVariantsAjax() {
+        String grsName = params.grsName
+
+        // TODO - eventually create new bean to hold all the options and have smarts for double checking validity
+        List <String> variantList = restServerService.getGrsVariants()//grsName should be passed in
+
+        if (variantList == null) {
+            render(status: 200, contentType: "application/json"){variantInfo:{results:[]}}
+            return
+        }
+
+        StringBuilder sb = new StringBuilder()
+        List <String> recordPerVariants = []
+        for (String varId in variantList){
+            List <String> idPieces = varId.split("_")
+            recordPerVariants << "{\"d\":1,\"dataset\":1,\"pVals\":[{\"count\":\"${idPieces[0]}\",\"level\":\"CHROM\"},"+
+                    "{\"count\":\"${idPieces[1]}\",\"level\":\"POS\"},"+
+                    "{\"count\":\"${idPieces[2]}\",\"level\":\"Reference_Allele\"},"+
+                    "{\"count\":\"${varId}\",\"level\":\"VAR_ID\"},"+
+                    "{\"count\":\"${idPieces[3]}\",\"level\":\"Effect_Allele\"}]}".toString()
+        }
+
+        JsonSlurper slurper = new JsonSlurper()
+        String codedVariantList = """{"results":[${recordPerVariants.join(",")}]}""".toString()
+        JSONObject sampleCallSpecifics = slurper.parseText(codedVariantList)
+
+        // send json response back
+        render(status: 200, contentType: "application/json") {sampleCallSpecifics}
+    }
+
+}
diff --git a/grails-app/controllers/org/broadinstitute/mpg/GrsController.groovy b/grails-app/controllers/org/broadinstitute/mpg/GrsController.groovy
@@ -16,6 +16,10 @@ class GrsController {
         render (view: 'grsInfo', model:[])
     }
 
+    def gaitInfo(){
+        render (view: 'gaitInfo', model:[])
+    }
+
     def getGRSListOfVariantsAjax() {
         String grsName = params.grsName
 

diff --git a/grails-app/i18n/informational.properties b/grails-app/i18n/informational.properties
@@ -2720,6 +2720,7 @@ informational.modules.VariantFinder.title=Variant Finder
 informational.modules.VariantFinder.description=<p>This versatile tool lets you specify multiple search criteria to find genetic variants \
   whose associations meet those criteria.
 informational.modules.GAIT.title=GAIT
+informational.modules.geneGAIT.title=Gene GAIT
 informational.modules.GAIT.description=<p>The Genetic Association Interactive Tool allows you to compute custom association statistics by specifying the phenotype to test for association, a subset of samples to analyze based on specific phenotypic criteria, and a set of covariates to control for in the analysis. In order to protect patient privacy, GAIT will only allow visualization or analysis of data from more than 100 individuals.</p><div style="float: left; margin-top: 5px;" class="btn dk-t2d-green dk-reference-button dk-right-column-buttons-compact "><a href="https://s3.amazonaws.com/broad-portal-resources/tutorials/KP_GAIT_guide.pdf" target="_blank">GAIT guide</a></div>
 informational.modules.GRS.title=Genetic Risk Score
 informational.modules.GRS.description=The Genetic Risk Score (GRS) tool takes a defined set of T2D risk-associated variants and allows you \

diff --git a/grails-app/i18n/portalHome.properties b/grails-app/i18n/portalHome.properties
@@ -14,6 +14,8 @@ portal.header.nav.blog=blog
 portal.header.nav.login=log in
 portal.header.nav.downloads=downloads
 portal.header.nav.grs=Genetic Risk Score
+portal.header.nav.geneGait=Custom burden test
+portal.header.nav.variantGait=Genetic Association Interactive Tool
 portal.header.data_portal=Data portal
 portal.header.tagline=Providing data and tools to promote understanding and treatment of type 2 diabetes and its complications
 portal.home.collaborate=Click here to learn more

diff --git a/grails-app/views/gait/gaitInfo.gsp b/grails-app/views/gait/gaitInfo.gsp
@@ -0,0 +1,152 @@
+<%--
+  Created by IntelliJ IDEA.
+  User: psingh
+  Date: 5/21/19
+  Time: 1:44 AM
+--%>
+
+<!DOCTYPE html>
+<html>
+<head>
+    <meta name="layout" content="t2dGenesCore"/>
+    <r:require modules="core"/>
+    <r:require modules="datatables"/>
+    <r:require modules="gaitInfo"/>
+    <r:require modules="geneInfo"/>
+    <r:require modules="burdenTest"/>
+    <r:layoutResources/>
+
+
+    <link type="application/font-woff">
+    <link type="application/vnd.ms-fontobject">
+    <link type="application/x-font-ttf">
+    <link type="font/opentype">
+
+</head>
+
+<body>
+
+<div id="rSpinner" class="dk-loading-wheel center-block" style="display:none">
+    <img src="${resource(dir: 'images', file: 'ajax-loader.gif')}" alt="Loading"/>
+</div>
+<script>
+
+    $( document ).ready(function() {
+        "use strict";
+
+        var drivingVariables = {
+            geneName: "${geneName}",
+            variantIdentifier: "${variantIdentifier}",
+            allowExperimentChoice:"${allowExperimentChoice}",
+            allowPhenotypeChoice:"${allowPhenotypeChoice}",
+            allowStratificationChoice:"${allowStratificationChoice}"
+
+        };
+
+        mpgSoftware.gaitInfo.setGaitInfoData(drivingVariables);
+        mpgSoftware.gaitInfo.buildGaitDisplay();
+
+
+        var pageTitle = $(".accordion-toggle").find("h2").text();
+        var textUnderTitle = $(".accordion-inner").find("h5").text();
+        $(".accordion-toggle").remove();
+        $(".accordion-inner").find("h5").remove();
+
+        var PageTitleDiv = '<div class="row">\n'+
+            '<div class="col-md-12">\n'+
+            '<h1 class="dk-page-title">' + pageTitle + '</h1>\n'+
+            '<div class="col-md-12">\n'+
+            '<h5 class="dk-under-header">' + textUnderTitle + '</h5>\n'+
+            '</div></div>';
+
+        $(PageTitleDiv).insertBefore(".gene-info-container");
+        $(".user-interaction").addClass("col-md-12");
+
+
+        /* end of DK's script */
+
+    });
+
+
+
+</script>
+
+<style>
+ul.nav-tabs > li > a { background: none !important; }
+ul.nav-tabs > li.active > a { background-color: #fff !important; }
+#modeledPhenotypeTabs li.active > a { background-color: #9fd3df !important; }
+</style>
+
+<div id="main">
+
+    <div class="container">
+
+        <div class="gene-info-container row">
+
+            <em style="font-weight: 900;"><%=geneName%></em>
+
+
+            <em style="font-weight: 900;"><%=variantIdentifier%></em>
+
+
+            %{--If its gene Gait page then allowExperimentChoice = 0 and 'geneName':'geneName'--}%
+            %{--<g:if test="${geneName?.equals('')}">--}%
+
+                %{--<g:render template="/templates/burdenTestSharedTemplate" model="['variantIdentifier': variantIdentifier, 'accordionHeaderClass': 'accordion-heading']" />--}%
+
+                %{--<g:render template="/widgets/burdenTestShared" model="['variantIdentifier': variantIdentifier,--}%
+                                                                       %{--'accordionHeaderClass': 'accordion-heading',--}%
+                                                                       %{--'modifiedTitle': 'Variant Interactive burden test',--}%
+                                                                       %{--'modifiedGaitSummary': 'The Genetic Association Interactive Tool (GAIT) allows you to compute the disease or phenotype burden for this gene, using custom sets of variants, samples, and covariates. In order to protect patient privacy, GAIT will only allow visualization or analysis of data from more than 100 individuals.',--}%
+                                                                       %{--'allowExperimentChoice': 1,--}%
+                                                                       %{--'allowPhenotypeChoice': 1,--}%
+                                                                       %{--'allowStratificationChoice': 0,--}%
+                                                                       %{--'grsVariantSet':'',--}%
+                                                                       %{--'geneName':'']"/>--}%
+            %{--</g:if>--}%
+
+            %{--<g:else>--}%
+                %{--<g:render template="/templates/burdenTestSharedTemplate" model="['variantIdentifier': '', 'accordionHeaderClass': 'accordion-heading']" />--}%
+
+                %{--<g:render template="/widgets/burdenTestShared" model="['variantIdentifier': '',--}%
+                                                                       %{--'accordionHeaderClass': 'accordion-heading',--}%
+                                                                       %{--'modifiedTitle': 'Gene Interactive burden test',--}%
+                                                                       %{--'modifiedGaitSummary': 'The Genetic Association Interactive Tool (GAIT) allows you to compute the disease or phenotype burden for this gene, using custom sets of variants, samples, and covariates. In order to protect patient privacy, GAIT will only allow visualization or analysis of data from more than 100 individuals.',--}%
+                                                                       %{--'allowExperimentChoice': 1,--}%
+                                                                       %{--'allowPhenotypeChoice': 1,--}%
+                                                                       %{--'allowStratificationChoice': 1,--}%
+                                                                       %{--'grsVariantSet':'',--}%
+                                                                       %{--'geneName':geneName]"/>--}%
+
+            %{--</g:else>--}%
+
+
+            <g:render template="/templates/burdenTestSharedTemplate" model="['variantIdentifier': variantIdentifier, 'accordionHeaderClass': 'accordion-heading']" />
+
+
+
+            %{--If its gene Gait page then allowExperimentChoice = 0 and 'geneName':'geneName'--}%
+            <g:render template="/widgets/burdenTestShared" model="['variantIdentifier': '',
+                                                                   'accordionHeaderClass': 'accordion-heading',
+                                                                   'modifiedTitle': 'Genetic Association Interactive Tool',
+                                                                   'modifiedGaitSummary': 'The Genetic Association Interactive Tool (GAIT) allows you to compute the disease or phenotype burden for this gene, using custom sets of variants, samples, and covariates. In order to protect patient privacy, GAIT will only allow visualization or analysis of data from more than 100 individuals.',
+                                                                   'allowExperimentChoice': allowExperimentChoice,
+                                                                   'allowPhenotypeChoice': allowPhenotypeChoice,
+                                                                   'allowStratificationChoice': allowStratificationChoice,
+                                                                   'grsVariantSet':'',
+                                                                   'geneName':geneName]"/>
+
+
+
+
+
+
+
+        </div>
+    </div>
+
+</div>
+
+</body>
+</html>
+
diff --git a/grails-app/views/gene/geneInfo.gsp b/grails-app/views/gene/geneInfo.gsp
@@ -105,6 +105,7 @@
                 data: {geneName: '${geneName}'},
                 async: true
             }).done(function (data) {
+                console.log(geneName);
                 mpgSoftware.geneInfo.fillTheGeneFields(data); // fills the uniprot summary
                 $('[data-toggle="popover"]').popover({
                     animation: true,