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Merge discvr-24.11 to develop
2 parents 2f085d8 + 459e008 commit 7c504f9

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-641
lines changed

‎PMR/resources/etls/pmr-datasets.xml‎

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@@ -141,6 +141,8 @@
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<column>relationship</column>
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<column>method</column>
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<column>objectid</column>
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<column>created</column>
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<column>modified</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="QCState/Label" operator="eq" value="Completed"/>
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<column>conception</column>
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<column>conceptualDay</column>
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<column>objectid</column>
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<column>created</column>
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<column>modified</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="QCState/Label" operator="eq" value="Completed"/>

‎PMR/resources/etls/pmr-demographics.xml‎

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<column>calculated_status</column>
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<column>QCState/Label</column>
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<column>objectid</column>
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<column>created</column>
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<column>modified</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="demographics" targetOption="truncate" bulkLoad="true" batchSize="2500">

‎mGAP/resources/data/species.tsv‎

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common_name scientific_name mhc_prefix
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Cotton-top Tamarin Saguinus oedipus Saoe
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Cynomolgus macaque Macaca fascicularis Mafa
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Marmoset Callithrix jacchus Caja
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Pigtail macaque Macaca nemestrina Mane
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Rhesus macaque Macaca mulatta Mamu
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Sooty Mangabey Cercocebus atys Ceat
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Stump Tailed Macaca Arctoides Maar
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Vervet Chlorocebus sabaeus Chsa
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Japanese macaque Macaca fuscata Mafu

‎mGAP/resources/etls/prime-seq.xml‎

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@@ -53,19 +53,24 @@
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<column>releaseId</column>
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<column>trackName</column>
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<column>label</column>
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<column>species</column>
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<column>totalSamples</column>
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<column>category</column>
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<column>url</column>
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<column>source</column>
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<column>description</column>
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<column>isprimarytrack</column>
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<column>shouldindex</column>
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<column>vcfIndexId/dataid/DataFileUrl</column>
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<column>vcfIndexId/library_id/name</column>
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<column>vcfId/dataid/DataFileUrl</column>
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<column>vcfId/library_id/name</column>
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</sourceColumns>
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</source>
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<destination schemaName="mGAP" queryName="tracksPerRelease" bulkLoad="true" targetOption="truncate">
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<columnTransforms>
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<column source="vcfId/dataid/DataFileUrl" target="vcfId" transformClass="org.labkey.mgap.columnTransforms.TrackOutputFileTransform" />
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<column source="vcfIndexId/dataid/DataFileUrl" target="vcfIndexId" transformClass="org.labkey.mgap.columnTransforms.TrackOutputFileTransform" />
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</columnTransforms>
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</destination>
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</transform>
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<column>releaseDate</column>
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<column>vcfId/dataid/DataFileUrl</column>
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<column>genomeId/name</column>
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<column>species</column>
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<column>totalSubjects</column>
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<column>totalVariants</column>
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<column>dbSnpId</column>

‎mGAP/resources/queries/mGAP/combinedPedigree.sql‎

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SELECT
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s.subjectname,
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s.Id as subjectname,
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s.gender,
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s.mother as dam,
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s.father as sire,
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s.Id.parents.dam as dam,
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s.Id.parents.sire as sire,
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s.species,
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s.geographic_origin,
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s.geographic_origin
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FROM laboratory.subjects s
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FROM "/Internal/PMR/".study.demographics s
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UNION ALL
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@@ -19,4 +19,4 @@ SELECT
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null as geographic_origin
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FROM mgap.demographics d
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WHERE d.subjectname NOT IN (SELECT DISTINCT s.subjectname FROM laboratory.subjects s)
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WHERE d.subjectname NOT IN (SELECT DISTINCT s.Id FROM "/Internal/PMR/".study.demographics s)

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

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<column name="rowid"/>
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<column name="trackName"/>
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<column name="label"/>
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<column name="species"/>
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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"/>
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<column name="isprimarytrack"/>
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<column name="mergepriority"/>
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<column name="skipvalidation"/>
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<column name="vcfId/container/Name">
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<properties>

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

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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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<javaCustomizer class="org.labkey.mgap.query.SampleSummaryCustomizer"/>
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<pkColumnName>subjectName</pkColumnName>
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<tableTitle>mGAP Subject/gVCF Summary</tableTitle>
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<columns>
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<column columnName="aliasSubjectName">
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<columnTitle>SubjectId Listed In Alias Table</columnTitle>
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<isHidden>true</isHidden>
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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>

‎mGAP/resources/queries/mGAP/sampleSummary.sql‎

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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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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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am.subjectname as aliasSubjectName
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FROM (SELECT
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COALESCE(o.readset.subjectId, rt.subjectId) as subjectId,

‎mGAP/resources/queries/mGAP/sampleSummary/.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView">
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<sorts>
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<sort column="subjectId" descending="false"/>
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</sorts>
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</customView>

‎mGAP/resources/queries/mGAP/variantCatalogReleases/.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView">
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<columns>
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<column name="version"/>
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<column name="species"/>
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<column name="releaseDate"/>
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<column name="totalSubjects"/>
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<column name="totalVariants"/>

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