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Merge pull request #226 from LabKey/fb_merge_24.7_to_develop
Merge discvr-24.7 to develop
2 parents f446861 + 1a4f414 commit 6cf88f6

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-24
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18 files changed

+470
-24
lines changed

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

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<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="true">
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<columns>
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<column name="Id"/>
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<column name="gender"/>
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<column name="species"/>
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<column name="geographic_origin"/>
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<column name="calculated_status"/>
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<column name="birth"/>
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<column name="Id/age/yearAndDays">
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<properties>
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<property name="columnTitle" value="Age"/>
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</properties>
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</column>
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<column name="death"/>
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<column name="Id/MostRecentWeight/MostRecentWeight">
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<properties>
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<property name="columnTitle" value="Current Weight (kg)"/>
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</properties>
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</column>
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<column name="Id/parents/dam"/>
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<column name="Id/parents/damType"/>
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<column name="Id/parents/sire"/>
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<column name="Id/parents/sireType"/>
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<column name="Id/MostRecentWeight/MostRecentWeightDate">
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<properties>
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<property name="columnTitle" value="Weight Date"/>
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</properties>
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</column>
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<column name="history"/>
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>
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</sorts>
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<!--<filters>-->
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<!--<filter column="qcstate/publicdata" operator="eq" value="true"/>-->
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<!--</filters>-->
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</customView>

‎PMR/resources/views/pmrAnimalHistory.html‎

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inputValue: LDK.panel.SingleSubjectFilterType.filterName,
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label:'Single Animal'
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},{
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xtype: 'onprc_ehr-multianimalfiltertype',
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xtype: 'ehr-multianimalfiltertype',
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inputValue: EHR.panel.MultiAnimalFilterType.filterName,
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label: EHR.panel.MultiAnimalFilterType.label
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},{

‎PMR/resources/views/pmrAnimalHistory.view.xml‎

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</permissionClasses>
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<dependencies>
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<dependency path="ehr.context" />
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<dependency path="onprc_ehr/panel/MultiAnimalFilterType.js"/>
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<dependency path="ehr/panel/AnimalHistoryPanel.js"/>
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</dependencies>
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</view>

‎mGAP/resources/queries/mGAP/duplicateGvcfs.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="" useColumnOrder="false" tableDbType="TABLE">
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<tableTitle>Duplicated gVCFs</tableTitle>
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<columns>
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<column columnName="readset">
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<columnTitle>Readset Id</columnTitle>
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</column>
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<column columnName="minRowId">
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<columnTitle>First Row Id</columnTitle>
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</column>
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<column columnName="minAnalysisId">
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<columnTitle>First Analysis Id</columnTitle>
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</column>
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<column columnName="totalOutputs">
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<columnTitle>Total gVCFs</columnTitle>
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</column>
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</columns>
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</table>
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</tables>
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</metadata>
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</query>

‎mGAP/resources/queries/mGAP/duplicateGvcfs.sql‎

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SELECT
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o.readset,
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min(o.rowId) as minRowId,
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min(o.analysis_id) as minAnalysisId,
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count(*) as totalPrototypes
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FROM sequenceanalysis.outputfiles o
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WHERE o.category = 'Seurat Object Prototype'
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GROUP BY o.readset
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HAVING COUNT(*) > 1

‎mGAP/resources/queries/mGAP/releaseTracks/.qview.xml‎

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<column name="label"/>
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<column name="source"/>
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<column name="category"/>
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<column name="totalSamples"/>
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<column name="url"/>
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<column name="vcfId"/>
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<column name="description"/>

‎mGAP/resources/queries/mGAP/sampleSummary.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="" tableDbType="TABLE">
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<pkColumnName>subjectName</pkColumnName>
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<tableTitle>mGAP Subject/gVCF Summary</tableTitle>
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</table>
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</tables>
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</metadata>
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</query>

‎mGAP/resources/queries/mGAP/sampleSummary.sql‎

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SELECT
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t.subjectId,
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am.externalAlias,
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t.readset,
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ss.gender,
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ss.species,
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ss.geographic_origin,
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ss.center,
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t.tracks,
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t.total,
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CASE WHEN ss.originalId IS NULL OR ss.gender IS NULL or ss.species IS NULL or ss.center IS NULL THEN true ELSE false END as missingDemographics
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FROM (SELECT
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COALESCE(o.readset.subjectId, rt.subjectId) as subjectId,
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o.readset,
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group_concat(rt.trackName, chr(10)) as tracks,
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count(distinct o.rowid) as total
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FROM sequenceanalysis.outputfiles o
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FULL JOIN mgap.releaseTrackSubsets rt ON (o.readset.subjectId = rt.subjectId)
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WHERE o.fileSets like '%mGAP%'
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GROUP BY o.readset, rt.subjectId, o.readset.subjectId
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) t
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LEFT JOIN mgap.subjectsSource ss on (t.subjectId = ss.originalId)
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LEFT JOIN mgap.animalMapping am on (t.subjectId = am.subjectname)

‎mGAP/resources/queries/mGAP/subjectsSource.sql‎

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CASE
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WHEN d.center IS NOT NULL THEN d.center
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WHEN s.subjectname IS NOT NULL THEN 'ONPRC'
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WHEN s.Id IS NOT NULL THEN 'ONPRC'
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ELSE NULL END as center,
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d.status as status,
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m.subjectname as originalId
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FROM mgap.animalMapping m
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LEFT JOIN laboratory.subjects s ON (m.subjectname = s.subjectname)
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LEFT JOIN "/Internal/PMR/".study.demographics s ON (m.subjectname = s.Id)
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LEFT JOIN mgap.demographics d ON (m.subjectname = d.subjectname)
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WHERE (s.subjectname IS NOT NULL OR d.subjectname IS NOT NULL)
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WHERE (s.Id IS NOT NULL OR d.subjectname IS NOT NULL)

‎mGAP/resources/views/mgapDataDashboard.html‎

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<script type="text/javascript" nonce="<%=scriptNonce%>">
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Ext4.onReady(function (){
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var webpart = <%=webpartContext%>;
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Ext4.create('Ext.panel.Panel', {
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renderTo: webpart.wrapperDivId,
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border: false,
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items: [{
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xtype: 'panel',
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border: false,
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defaults: {
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border: false
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},
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items: [{
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html: 'This page contains links and reports designed to help manage mGAP data.'
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}]
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},{
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xtype: 'ldk-navpanel',
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style: 'padding-top: 20px;',
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border: false,
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sections: [{
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header: 'Upcoming Release',
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items: [{
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name: 'Release Instructions',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'wiki',
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queryName: 'page',
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name: 'mgapRelease'
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})
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},{
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name: 'gVCF/Track Summary',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'sampleSummary'
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})
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},{
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name: 'Tracks',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'releaseTracks'
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})
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},{
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name: 'Subjects Per Track',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'releaseTrackSubsets'
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})
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},{
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name: 'gVCFs',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'sequenceanalysis',
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queryName: 'outputfiles',
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'query.fileSets~contains': 'mgap'
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})
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},{
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name: 'mGAP Alias to True ID',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'animalMapping'
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})
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}]
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},{
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header: 'Release QC',
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items: [{
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name: 'gVCFs Missing Demographics',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'sampleSummary',
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'query.missingDemographics~eq': '1'
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})
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},{
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name: 'gVCFs Missing mGAP Alias',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'sampleSummary',
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'query.externalAlias~isblank': ''
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})
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}]
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},{
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header: 'Prior Releases',
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items: [{
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name: 'Releases',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'variantCatalogReleases'
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})
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}, {
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name: 'Tracks In Each Release',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'tracksPerRelease'
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})
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}, {
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name: 'Subject Information Synced to mGAP',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'subjectDatasetsSource'
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})
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}]
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},{
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header: 'Data and Processing',
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items: [{
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name: 'Readsets Without Alignments',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'sequenceanalysis',
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queryName: 'sequence_readsets',
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'query.totalAlignments~eq': 0,
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'query.totalForwardReads~isnonblank': null,
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'query.status~isblank': null,
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'query.isArchived~eq': 0,
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'query.sort': 'name',
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'query.maxRows': 250
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})
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},{
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name: 'Supplemental Pedigree (for non-ONPRC animals)',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'demographics'
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})
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}]
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},{
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header: 'Data Archival',
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items: [{
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name: 'Readsets Not Archived to SRA',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'sequenceanalysis',
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queryName: 'sequence_readsets',
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'query.totalForwardReads~isnonblank': null,
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'query.isArchived~eq': 0
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}
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)
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},{
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name: 'BAM (not CRAM) Files',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'sequenceanalysis',
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queryName: 'outputfiles',
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'query.dataid/DataFileUrl~contains': '.bam'
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}
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)
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},{
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name: 'Analyses Using Non-Passing Readsets',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'sequenceanalysis',
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queryName: 'sequence_analyses',
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'query.readset/status~isnonblank': null
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})
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},{
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name: 'Duplicate gVCFs',
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url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
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schemaName: 'mgap',
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queryName: 'duplicategvcfs'
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})
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}]
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}]
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}]
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});
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});
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</script>

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