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mgapDataDashboard.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 mGAP data.'
}]
},{
xtype: 'ldk-navpanel',
style: 'padding-top: 20px;',
border: false,
sections: [{
header: 'Upcoming Release',
items: [{
name: 'Release Instructions',
url: LABKEY.ActionURL.buildURL('wiki', 'page.view', null, {
name: 'mgapRelease'
})
},{
name: 'gVCF/Track Summary',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'sampleSummary'
})
},{
name: 'Tracks',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'releaseTracks'
})
},{
name: 'Subjects Per Track',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'releaseTrackSubsets'
})
},{
name: 'gVCFs',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'outputfiles',
'query.fileSets~contains': 'mgap'
})
},{
name: 'mGAP Alias to True ID',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'animalMapping'
})
}]
},{
header: 'Release QC',
items: [{
name: 'gVCFs Missing Demographics',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'sampleSummary',
'query.missingDemographics~eq': '1'
})
},{
name: 'gVCFs Missing mGAP Alias',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'sampleSummary',
'query.externalAlias~isblank': ''
})
},{
name: 'gVCFs With SubjectId / Case-sensitive Difference',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'subjectCaseMismatch',
'query.externalAlias~isnonblank': ''
})
}]
},{
header: 'Prior Releases',
items: [{
name: 'Releases',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'variantCatalogReleases'
})
}, {
name: 'Tracks In Each Release',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'tracksPerRelease'
})
}, {
name: 'Subject Information Synced to mGAP',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'subjectDatasetsSource'
})
}]
},{
header: 'Data and Processing',
items: [{
name: 'WGS/WXS Readsets Without BAM/CRAM',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_readsets',
'query.outputFileTypes~doesnotcontain': 'Alignment',
'query.totalForwardReads~isnonblank': null,
'query.application~in' :'Whole Exome;Whole Genome: Deep Coverage',
'query.status~isblank': null,
'query.sort': 'name',
'query.maxRows': 250
})
},{
name: 'WGS/WXS Readsets Without A gVCF File',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_readsets',
'query.outputFileTypes~doesnotcontain': 'gVCF File',
'query.totalForwardReads~isnonblank': null,
'query.application~in' :'Whole Exome;Whole Genome: Deep Coverage',
'query.status~isblank': null,
'query.sort': 'name',
'query.maxRows': 250
})
},{
name: 'Supplemental Pedigree (for non-ONPRC animals)',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'demographics'
})
}]
},{
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'
}
)
},{
name: 'Analyses Using Non-Passing Readsets',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'sequenceanalysis',
queryName: 'sequence_analyses',
'query.readset/status~isnonblank': null
})
},{
name: 'Duplicate gVCFs',
url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
schemaName: 'mgap',
queryName: 'duplicategvcfs'
})
}]
}]
}]
});
});
</script>