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Add MHC data dashboard and validation queries #1160

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Oct 24, 2024
Merged

Add MHC data dashboard and validation queries #1160

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29 changes: 29 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantCachedResults.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="" tableDbType="TABLE">
<tableTitle>Cached Genotyping Results Discordant With Data</tableTitle>
<columns>
<column columnName="totalTestsCached">
<columnTitle>Total Tests (Cached)</columnTitle>
</column>
<column columnName="resultCached">
<columnTitle>Result (Cached)</columnTitle>
</column>
<column columnName="scoreCached">
<columnTitle>Score (Cached)</columnTitle>
</column>
<column columnName="totalTestsSource">
<columnTitle>Total Tests (Source)</columnTitle>
</column>
<column columnName="resultSource">
<columnTitle>Result (Source)</columnTitle>
</column>
<column columnName="scoreSource">
<columnTitle>Score (Source)</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
19 changes: 19 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantCachedResults.sql
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SELECT
COALESCE(t1.subjectId, t2.marker) as subjectId,
COALESCE(t1.marker, t2.marker) as marker,
COALESCE(t1.assaytype, t2.assaytype) as assaytype,

t1.totalTests as totalTestsCached,
t1.result as resultCached,
t1.score as scoreCached,

t2.totalTests as totalTestsSource,
t2.result as resultSource,
t2.score as scoreSource

FROM geneticscore.mhc_data t1
FULL JOIN geneticscore.mhc_data_source t2 ON (t1.subjectId = t2.subjectId AND t1.marker = t2.marker AND t1.assaytype = t2.assaytype)

WHERE
NOT ISEQUAL(t1.totalTests, t2.totalTests) OR
NOT ISEQUAL(t1.result, t2.result)
22 changes: 22 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="" tableDbType="TABLE">
<tableTitle>Subjects Discordant Between Genotyping Results and Readsets</tableTitle>
<columns>
<column columnName="readsetSubjectId">
<columnTitle>Readset Subject Id</columnTitle>
</column>
<column columnName="folder">
<columnTitle>Genotype Folder</columnTitle>
<!-- <isHidden>true</isHidden>-->
</column>
<column columnName="container">
<columnTitle>Analysis Folder</columnTitle>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
10 changes: 10 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.sql
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SELECT
a.rowId,
a.subjectId,
a.analysisId.readset.subjectId as readsetSubjectId,
a.analysisId,
a.folder,
a.analysisId.container

FROM assay.GenotypeAssay.Genotype.Data a
WHERE a.run.assayType = 'SBT' AND a.analysisId.readset.subjectId != a.subjectId
12 changes: 12 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="" tableDbType="TABLE">
<tableTitle>Subjects Discordant Between Genotyping Results and Readsets</tableTitle>
<columns>

</columns>
</table>
</tables>
</metadata>
</query>
8 changes: 8 additions & 0 deletions GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.sql
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SELECT
a.subjectId,
a.readsetSubjectId,
a.analysisId,
a.folder

FROM geneticscore.discordantSubjectIds a
GROUP BY a.subjectId, a.readsetSubjectId, a.analysisId, a.folder
114 changes: 114 additions & 0 deletions GeneticsCore/resources/views/mhcDataDashboard.html
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<script type="text/javascript" nonce="<%=scriptNonce%>">

Ext4.onReady(function (){
var webpart = <%=webpartContext%>;

Ext4.create('Ext.panel.Panel', {
renderTo: webpart.wrapperDivId,
border: false,
items: [{
xtype: 'panel',
border: false,
defaults: {
border: false
},
items: [{
html: 'This page contains links and reports designed to help manage MHC data.'
}]
},{
xtype: 'ldk-navpanel',
style: 'padding-top: 20px;',
border: false,
sections: [{
header: 'Sample/Data QC',
items: [{
name: 'Subjects Discordant Between Genotyping Results and Readsets',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'geneticscore',
queryName: 'discordantSubjectIdsGrouped'
})
},{
name: 'Genotyping Results Not Connected to an Analysis',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'assay',
queryName: 'GenotypeAssay.Genotype.Data',
'query.analysisId/rowId~isblank': ''
})
},{
name: 'Discordant Cached Results',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'geneticscore',
queryName: 'discordantCachedResults'
})
},{
name: 'Analyses Using Non-Passing Readsets',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_analyses',
'query.readset/status~isnonblank': null
})
}]
},{
header: 'Data and Processing',
items: [{
name: 'All Analyses',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_analyses',
'query.viewName': 'SBT Information',
'query.readset~nonblank': null,
})
},{
name: 'Analyses without Cached Results',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_analyses',
'query.viewName': 'SBT Information',
'query.readset~nonblank': null,
'query.readset/status~isblank': null,
'query.numCachedResults~gt': 0,
})
},{
name: 'Readsets Without Alignments',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_readsets',
'query.totalAlignments~eq': 0,
'query.totalForwardReads~isnonblank': null,
'query.status~isblank': null,
'query.isArchived~eq': 0,
'query.sort': 'name',
'query.maxRows': 250
})
},{
name: 'Cached MHC Typing Results (source data for PRIMe)',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'geneticscore',
queryName: 'mhc_data'
})
}]
},{
header: 'Data Archival',
items: [{
name: 'Readsets Not Archived to SRA',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_readsets',
'query.totalForwardReads~isnonblank': null,
'query.isArchived~eq': 0
}
)
},{
name: 'BAM (not CRAM) Files',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'outputfiles',
'query.dataid/DataFileUrl~contains': '.bam'
}
)
}]
}]
}]
});
});
</script>
8 changes: 8 additions & 0 deletions GeneticsCore/resources/views/mhcDataDashboard.view.xml
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<view xmlns="http://labkey.org/data/xml/view" title="MHC Typing Dashboard">
<permissionClasses>
<permissionClass name="org.labkey.api.security.permissions.ReadPermission"/>
</permissionClasses>
<dependencies>

</dependencies>
</view>
6 changes: 6 additions & 0 deletions GeneticsCore/resources/views/mhcDataDashboard.webpart.xml
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<webpart xmlns="http://labkey.org/data/xml/webpart" title="MHC Typing Dashboard">
<view name="mhcDataDashboard"/>
<locations>
<location name="body"/>
</locations>
</webpart>
4 changes: 2 additions & 2 deletions GeneticsCore/src/org/labkey/GeneticsCore/mhc/MhcTaskRef.java
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Expand Up @@ -63,12 +63,12 @@ public RecordedActionSet run(@NotNull PipelineJob job) throws PipelineJobExcepti

for (String subject : subjects)
{
processSubject(job, subject);

if (job.isCancelled())
{
throw new CancelledException();
}

processSubject(job, subject);
}

job.getLogger().info("Done!");
Expand Down