Merge discvr-23.7 to discvr-23.11

MccColony/resources/queries/study/demographics/.qview.xml

@@ -17,7 +17,9 @@
             </properties>
         </column>
         <column name="dam"/>
+        <column name="damMccAlias"/>
         <column name="sire"/>
+        <column name="sireMccAlias"/>
         <column name="birth"/>
         <column name="death"/>
         <column name="species"/>

PMR/resources/data/calculated_status_codes.tsv

@@ -0,0 +1,9 @@
+code    meaning
+Alive
+Dead
+ERROR
+No Record
+Shipped
+u   Unknown
+Unknown
+Fetus

PMR/resources/queries/study/pedigree.sql

@@ -26,4 +26,4 @@ d.id.demographics.species,
 'Demographics' as source
 
 FROM study.demographicsParents d
-WHERE d.numParents > 0
+WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL

PMR/resources/views/populateData.html

@@ -169,7 +169,7 @@
         },{
             label: 'Calculated Status Code',
             populateFn: 'populateFromFile',
-            moduleName: 'ehr',
+            moduleName: 'pmr',
             schemaName: 'ehr_lookups',
             queryName: 'calculated_status_codes',
             pk: 'rowid'

mGAP/resources/etls/prime-seq.xml

@@ -108,6 +108,8 @@
                     <column>sitesOnlyVcfId/name</column>
                     <column>novelSitesVcfId/dataid/DataFileUrl</column>
                     <column>novelSitesVcfId/name</column>
+                    <column>luceneIndex/dataid/DataFileUrl</column>
+                    <column>luceneIndex/name</column>
                     <column>humanJbrowseId</column>
                     <column>objectId</column>
                 </sourceColumns>
@@ -119,6 +121,7 @@
                     <column source="variantTable/dataid/DataFileUrl" target="variantTable" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
                     <column source="sitesOnlyVcfId/dataid/DataFileUrl" target="sitesOnlyVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
                     <column source="novelSitesVcfId/dataid/DataFileUrl" target="novelSitesVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
+                    <column source="luceneIndex/dataid/DataFileUrl" target="luceneIndex" transformClass="org.labkey.mgap.columnTransforms.LuceneIndexTransform" />
                     <column source="jbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseSessionTransform"/>
                     <column source="liftedVcfId/dataid/DataFileUrl" target="liftedVcfId" transformClass="org.labkey.mgap.columnTransforms.LiftedVcfTransform" />
                     <column source="humanJbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseHumanSessionTransform"/>

mGAP/resources/queries/mGAP/userRequests/.qview.xml

@@ -5,6 +5,8 @@
         <column name="lastName"/>
         <column name="title"/>
         <column name="institution"/>
+        <column name="category"/>
+        <column name="country"/>
         <column name="reason"/>
         <column name="userId"/>
         <column name="hasAccess"/>

mGAP/resources/schemas/dbscripts/postgresql/mgap-16.68-16.69.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.userRequests ADD country varchar(1000);

mGAP/resources/schemas/dbscripts/postgresql/mgap-16.69-16.70.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD luceneIndex int;

mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.68-16.69.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.userRequests ADD country varchar(1000);

mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.69-16.70.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD luceneIndex int;

mGAP/resources/schemas/mgap.xml

@@ -188,6 +188,15 @@
                     <fkColumnName>RowId</fkColumnName>
                 </fk>
             </column>
+            <column columnName="luceneIndex">
+                <columnTitle>Lucene Index File</columnTitle>
+                <nullable>true</nullable>
+                <fk>
+                    <fkDbSchema>sequenceanalysis</fkDbSchema>
+                    <fkTable>outputfiles</fkTable>
+                    <fkColumnName>rowid</fkColumnName>
+                </fk>
+            </column>
             <column columnName="totalSubjects">
                 <columnTitle>Total Subjects</columnTitle>
             </column>
@@ -366,6 +375,10 @@
                 <columnTitle>Category</columnTitle>
                 <nullable>true</nullable>
             </column>
+            <column columnName="country">
+                <columnTitle>Country</columnTitle>
+                <nullable>true</nullable>
+            </column>
             <column columnName="reason">
                 <columnTitle>Reason For Request</columnTitle>
                 <nullable>false</nullable>
@@ -1173,20 +1186,16 @@
             <column columnName="infoKey">
                 <columnTitle>INFO Key</columnTitle>
                 <nullable>true</nullable>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="sourceField">
                 <columnTitle>Source Field</columnTitle>
                 <nullable>true</nullable>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="dataType">
                 <columnTitle>Data Type</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="dataNumber">
                 <columnTitle>Data Number</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="url">
                 <columnTitle>Website URL</columnTitle>
@@ -1202,23 +1211,18 @@
             </column>
             <column columnName="toolName">
                 <columnTitle>Tool Name</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="formatString">
                 <columnTitle>Format String</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="hidden">
                 <columnTitle>Hidden?</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="isIndexed">
                 <columnTitle>Is Indexed?</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="allowableValues">
                 <columnTitle>Allowable Values</columnTitle>
-                <isHidden>true</isHidden>
             </column>
             <column columnName="container">
                 <isHidden>true</isHidden>

mGAP/resources/views/overview.html

@@ -14,31 +14,24 @@
 <script>
     $( function() {
         $( "i.mgap-video-icon" ).on("click", function(e){
-            const el = $(e.target);
-            const videoName = el.attr('data-video');
-            const title = el.attr('data-video-title');
-
-            LDK.Assert.assertNotEmpty('Missing data-video attribute.', videoName);
-
-            mGAP.Utils.showVideoDialog(videoName, title);
+            mGAP.Utils.showVideoDialog(e);
         });
     } );
 </script>
 <div class="colDiv">
     <div style="flex: 1;margin-right: 20px;">
         Non-human primates, such as Rhesus macaques, are a powerful genetic model of human disease.  mGAP seeks to fill several major voids to promote genomic analyses and the study of human genetic disease in this key pre-clinical model.
-        The database provides open access to rhesus macaque genomic and phenotypic data.  Our dataset was originally generated using animals from the large, pedigreed colony of Indian-origin rhesus macaques housed at the Oregon National Primate Research Center (ONPRC); however, it has
-        since <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-externalData.view">been expanded to include data from other National Primate Research Centers and NHP colonies.</a>.
+        The database provides open access to rhesus macaque genomic and phenotypic data, with data primarily generated using subjects from <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-externalData.view">the National Primate Research Center system and other captive NHP colonies.</a>.
         <br><br>
-        <span style="font-weight: bold">NEW: Click the video icons (<i class="fa-solid fa-video mgap-video-icon"></i>) load help videos, or <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-tutorials.view">view our tutorials page</a> for more detail.</span>
+        <span style="font-weight: bold">NEW: Click the video icon (<i class="fa-solid fa-video mgap-video-icon" data-video="overview" data-video-title="mGAP Overview"></i>) to load an overview video describing mGAP's features. There are additional icons/videos below, or <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-tutorials.view">view our tutorials page</a> for more detail.</span>
         <br>
         <h4><span style="text-decoration: underline">Short Variant Catalog:</span> <img style="vertical-align: sub" width="40px" src="<%=contextPath%>/mgap/images/SNV.png" alt="SNV"></h4>
         The primary dataset generated by mGAP is a catalog of short variants (summarized to the right). Raw sequence data are <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-dataProcessing.view">analyzed using a vetted pipeline</a> designed to produce high-confidence genotype calls.
         The resulting variants are <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">annotated using a wide range of data sources</a>, including predicted function, overlap with regulatory elements and association with phenotypes and diseases.
         <br>
         <ul style="padding-top: 10px;">
             <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?">Genome Browser</a> to view and search data. <i class="fa-solid fa-video mgap-video-icon" data-video="genome-browser" data-video-title="Genome Browser Overview"></i></li>
-            <li>Use our new <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?target=variantSearch">Full-text Search</a> tool to query variants based on gene, or using our <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">extensive annotations</a> <i class="fa-solid fa-video mgap-video-icon" data-video="variant-search" data-video-title="Variant Full-text Search (BETA)"></i></li>
+<!--            <li>Use our new <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?target=variantSearch">Full-text Search</a> tool to query variants based on gene, or using our <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">extensive annotations</a> &lt;!&ndash;<i class="fa-solid fa-video mgap-video-icon" data-video="variant-search" data-video-title="Variant Full-text Search (BETA)"></i>&ndash;&gt;</li>-->
             <li>View our list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-variantList.view">Predicted Damaging Variants</a>, which is a list of predicted high-impact or disease associated variants, generated from each release <i class="fa-solid fa-video mgap-video-icon" data-video="predicted-damaging-variants" data-video-title="Predicted Damaging Variants"></i></li>
             <li>Unlike many datasets, mGAP has genotype-level data, <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=clinical">often connected to living animals from pedigreed breeding colonies</a></li>
             <li>Download raw data, including <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=datasets">sequence data</a> and <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=variants">variant data</a></li>
@@ -49,7 +42,7 @@ <h4><span style="text-decoration: underline;">Structural Variant Catalog:</span>
         We have released a draft dataset with structural variants generated from PacBio sequencing of 44 Rhesus macaques. These data complement the short variant catalog by detecting categories of variants not readily accomplished with short read Illumina data.
         <br>
         <ul style="padding-top: 10px;">
-            <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?activeTracks=mGAP Structural Variants 1.0&loc=4:137,917,074..137,937,929">Genome Browser</a> to view and search structural variant data</li>
+            <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?activeTracks=mGAP Structural Variants 1.0&location=11:6,936,982..7,002,783">Genome Browser</a> to view and search structural variant data</li>
         </ul>
 
         <h4><span style="text-decoration: underline;">NHP Models of Human Disease:</span> <img style="vertical-align: sub" width="40px" src="<%=contextPath%>/mgap/images/phenotypes.png" alt="Phenotypes"></h4>

mGAP/resources/views/quickLinks.html

@@ -17,7 +17,7 @@
                     '<li><a href="' + LABKEY.ActionURL.buildURL('mgap', 'variantList', null) + '">Predicted Damaging Variants</a></li>' +
                     (jbrowseId ? '<li><a href="' + LABKEY.ActionURL.buildURL('jbrowse', 'browser', null, {database: jbrowseId}) + '">Genome Browser (Macaque)</a></li>' : '') +
                     (humanJbrowseId ? '<li><a href="' + LABKEY.ActionURL.buildURL('jbrowse', 'browser', null, {database: humanJbrowseId}) + '">Genome Browser (Human)</a></li>' : '') +
-                    '<li><a href="' + LABKEY.ActionURL.buildURL('mgap', 'genomeBrowser', null, {target: 'variantSearch'}) + '">Full-text Variant Search (BETA)</a></li>' +
+                    // '<li><a href="' + LABKEY.ActionURL.buildURL('mgap', 'genomeBrowser', null, {target: 'variantSearch'}) + '">Full-text Variant Search (BETA)</a></li>' +
                 '</ul>'
             );
         }

mGAP/resources/views/requestLogin.html

@@ -60,7 +60,15 @@
                 name: 'category',
                 width: 500,
                 allowBlank: false,
-                storeValues: ['Academic/NPRC', 'Academic/Non-NPRC', 'Foundation', 'Industry', 'Other']
+                storeValues: ['NPRC', 'Academic/Non-NPRC', 'Foundation', 'Industry', 'NIH', 'Other']
+            },{
+                xtype: 'ldk-simplecombo',
+                labelWidth: 130,
+                fieldLabel: 'Country',
+                name: 'country',
+                width: 500,
+                allowBlank: false,
+                storeValues: ['United States', 'International']
             },{
                 xtype: 'textarea',
                 labelAlign: 'top',
@@ -86,7 +94,7 @@
                     }
 
                     var values = form.getValues();
-                    if (values.email != values.emailConfirmation){
+                    if (values.email !== values.emailConfirmation){
                         Ext4.Msg.alert('Error', 'Emails do not match');
                         return;
                     }

mGAP/resources/views/tutorials.html

@@ -3,36 +3,49 @@
         $( document ).ready(function() {
             const videos = [{
                 Title: 'Overview',
-                src: 'overview',
+                name: 'overview',
             },{
                 Title: 'Genome Browser Overview',
-                src: 'genome-browser',
+                name: 'genome-browser',
             },{
                 Title: 'Phenotypes and Phenotype Searches',
-                src: 'phenotypes-and-models',
+                name: 'phenotypes-and-models',
+            },{
+                Title: 'Predicted Damaging Variant List',
+                name: 'predicted-damaging-variants',
             },{
                 Title: 'Using the Variant Table',
-                src: 'mgap-table-view-tutorial',
+                name: 'mgap-table-view-tutorial',
             }]
 
-            // $('#tileview').dxTileView({
-            //     items: videos,
-            //     height: 390,
-            //     baseItemHeight: 120,
-            //     baseItemWidth: 185,
-            //     itemMargin: 10,
-            //     itemTemplate(itemData, itemIndex, itemElement) {
-            //         const $image = $('<div>')
-            //                 .addClass('image')
-            //                 .css('background-image', `url(${itemData.src})`);
-            //
-            //         itemElement
-            //                 .append(`<div>${itemData.Title}</div>`)
-            //                 .append($image);
-            //     },
-            // });
+            videos.forEach(itemData => {
+                const videoURL = LABKEY.ActionURL.getContextPath() + '/mgap/videos/' + itemData.name + ".mp4";
+
+                const $video = $(`<video src="${videoURL}" type="video/mp4" alt="Overview" width="200"/>`)
+                        .css('background-image', `url(${videoURL})`)
+                        .attr('data-video', itemData.name)
+                        .attr('data-video-title', itemData.Title)
+                        .addClass('mgap-video-icon')
+                        .css('border', 'solid')
+                        .on("click", function(e){
+                            mGAP.Utils.showVideoDialog(e);
+                        });
+
+                const $div = $('<div>')
+                        .css('float', 'left')
+                        .css('text-align', 'center')
+                        .css('margin', '10px')
+                        .css('width', '245')
+                        .css('height', '175')
+                        .append(`<div>${itemData.Title}</div>`)
+                        .append($video)
+
+                $('div.thumbnail-panel').append($div)
+            })
         });
     })(jQuery);
 </script>
 
-<div id="tileview">Videos will be added shortly</div>
+Click any of the thumbnails below to view the help video. If you have additional questions, <a href="<%=contextPath%><%=containerPath%>/mgap-contact.view">click here</a> to send a help or feature request, or email <a href="mailto:mgap@ohsu.edu">mgap@ohsu.edu</a>.
+<br><br>
+<div class="thumbnail-panel" />