LoadApplication.xml

<?xml version="1.0" encoding="UTF-8"?>
<etl xmlns="http://labkey.org/etl/xml">
    <name>Load CDS Application Tables</name>
    <description>Populate tables used to drive the Dataspace application</description>
    <transforms>
        <transform id="ClearMappingTables" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ClearMappingTask">
            </taskref>
        </transform>
        <transform id="PopulateStudies" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateStudiesTask">
            </taskref>
        </transform>
        <transform id="PopulateVisits" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateStudyVisitTask">
            </taskref>
        </transform>
        <transform id="PopulateLab" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_lab" />
            <destination schemaName="cds" queryName="lab" targetOption="truncate"/>
        </transform>
        <transform id="PopulateMAbMixMetadata" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_MAbMixMetadata" />
            <destination schemaName="cds" queryName="MAbMixMetadata" targetOption="truncate" />
        </transform>
        <transform id="PopulateMAbMix" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_MAbMix" />
            <destination schemaName="cds" queryName="MAbMix" targetOption="truncate" />
        </transform>
        <transform id="PopulateMAbMetaGridBase" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_mabmetasummary" />
            <destination schemaName="cds" queryName="mAbMetaGridBase" targetOption="truncate" />
        </transform>
        <transform id="PopulateDemographics" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_demographics"/>
                    <setting name="targetDataset" value="Demographics" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateMAb" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_nabmab"/>
                    <setting name="targetDataset" value="NABMAb" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateMAbGridBase" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateGridBaseTask">
                <settings>
                    <setting name="sourceSchema" value="study"/>
                    <setting name="sourceQuery" value="ds_mabgridbase"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="mAbGridBase"/>
                    <!-- ds_mabgridbase joins cds.mabmixmetadata, which is project instead of study scoped -->
                    <setting name="bypassContainerFilter" value="true"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateICS" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_ics"/>
                    <setting name="targetDataset" value="ICS" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateNAB" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_nab"/>
                    <setting name="targetDataset" value="NAb" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateELISpot" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_elispot"/>
                    <setting name="targetDataset" value="ELISPOT" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateBAMA" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_bama"/>
                    <setting name="targetDataset" value="BAMA" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulatePKMAB" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_pkmab"/>
                    <setting name="targetDataset" value="PKMAB" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateBCRsequence" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateDatasetTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_bcr_sequence_study"/>
                    <setting name="targetDataset" value="BCR_sequence" />
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateAssay" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateAssayTask">
            </taskref>
        </transform>
        <transform id="PopulateStudyAssay" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ContainerSensitivePopulateTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_studyassay"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="studyassay"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateRelationship" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateRelationshipTask">
            </taskref>
        </transform>
        <transform id="PopulateICSAntigen" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_icsantigen" />
            <destination schemaName="cds" queryName="ICSAntigen" targetOption="truncate" />
        </transform>
        <transform id="PopulateNAbAntigen" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_nabantigen" />
            <destination schemaName="cds" queryName="NAbAntigen" targetOption="truncate" />
        </transform>
        <transform id="PopulateELISpotAntigen" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_elispotantigen" />
            <destination schemaName="cds" queryName="ELISpotantigen" targetOption="truncate" />
        </transform>
        <transform id="PopulateBAMAAntigen" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_bamaantigen" />
            <destination schemaName="cds" queryName="BAMAAntigen" targetOption="truncate" />
        </transform>
        <transform id="PopulateAntigenPanelMetadata" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_antigenPanelMeta" />
            <destination schemaName="cds" queryName="antigenPanelMeta" targetOption="truncate" />
        </transform>
        <transform id="PopulateVirusPanel" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_virusPanel" />
            <destination schemaName="cds" queryName="virusPanel" targetOption="truncate" />
        </transform>
        <transform id="PopulateAntigenPanel" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_antigenPanel" />
            <destination schemaName="cds" queryName="antigenPanel" targetOption="truncate" />
        </transform>
        <transform id="product" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_product" />
            <destination schemaName="cds" queryName="product" targetOption="truncate" />
        </transform>
        <transform id="PopulateStudyProduct" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ContainerSensitivePopulateTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_studyproduct"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="studyproductmap"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateTreatmentArms" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateTreatmentArmTask">
            </taskref>
        </transform>
        <transform id="PopulateGridBase" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateGridBaseTask">
                <settings>
                    <setting name="sourceSchema" value="study"/>
                    <setting name="sourceQuery" value="ds_gridbase"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="GridBase"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateFacts" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateFactsTask"/>
        </transform>
        <transform id="PopulateProperties" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_properties"/>
            <destination schemaName="cds" queryName="properties" targetOption="truncate" />
        </transform>
        <transform id="document" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_document" />
            <destination schemaName="cds" queryName="document" targetOption="truncate" />
        </transform>
        <transform id="PopulateStudyDocument" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ContainerSensitivePopulateTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_studydocument"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="studydocument"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateAssayDocument"  type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_assaydocument" />
            <destination schemaName="cds" queryName="assaydocument" targetOption="truncate" />
        </transform>
        <transform id="PopulatePublication" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_publication" />
            <destination schemaName="cds" queryName="publication" targetOption="truncate" />
        </transform>
        <transform id="PopulatePublicationDocument" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_publicationDocument" />
            <destination schemaName="cds" queryName="publicationDocument" targetOption="truncate" />
        </transform>
        <transform id="PopulateStudyPublication" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ContainerSensitivePopulateTask">
                <settings>
                    <setting name="sourceSchema" value="cds"/>
                    <setting name="sourceQuery" value="ds_studypublication"/>
                    <setting name="targetSchema" value="cds"/>
                    <setting name="targetQuery" value="studypublication"/>
                </settings>
            </taskref>
        </transform>
        <transform id="PopulateStudyMab" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="ds_studymab"/>
            <destination schemaName="cds" queryName="studymab" targetOption="truncate"/>
        </transform>
        <transform id="PopulateStudyReport" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.PopulateStudyReportTask"/>
        </transform>
        <transform id="PopulateStudyCuratedGroup" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_studyCuratedGroup"/>
            <destination schemaName="cds" queryName="studyCuratedGroup" targetOption="truncate"/>
        </transform>
        <transform id="PopulatePublicationReport" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_publicationReport"/>
            <destination schemaName="cds" queryName="publicationReport" targetOption="truncate"/>
        </transform>
        <transform id="PopulatePublicationCuratedGroup" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_publicationCuratedGroup"/>
            <destination schemaName="cds" queryName="publicationCuratedGroup" targetOption="truncate"/>
        </transform>
        <transform id="PopulateAssayReport" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_assayReport"/>
            <destination schemaName="cds" queryName="assayReport" targetOption="truncate"/>
        </transform>
        <transform id="TruncateVirusLabId" type="org.labkey.di.pipeline.TransformTask">
            <destination schemaName="cds" queryName="virus_lab_id" targetOption="truncate"/>
        </transform>
        <transform id="TruncateVirusSynonym" type="org.labkey.di.pipeline.TransformTask">
            <destination schemaName="cds" queryName="virus_synonym" targetOption="truncate"/>
        </transform>
        <transform id="PopulateVirusMetadataAll" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_virus_metadata_all"/>
            <destination schemaName="cds" queryName="virus_metadata_all" targetOption="truncate"/>
        </transform>
        <transform id="PopulateAssayCombinedAntigenMetadata" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_assay_combined_antigen_metadata"/>
            <destination schemaName="cds" queryName="assay_combined_antigen_metadata" targetOption="truncate"/>
        </transform>
        <transform id="PopulateVirusLabId" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_virus_lab_id"/>
            <destination schemaName="cds" queryName="virus_lab_id"/>
        </transform>
        <transform id="PopulateVirusSynonym" type="org.labkey.di.pipeline.TransformTask">
            <source schemaName="cds" queryName="import_virus_synonym"/>
            <destination schemaName="cds" queryName="virus_synonym"/>
        </transform>
        <!--Should occur last-->
        <transform id="ClearAndWarmCube" type="TaskrefTransformStep">
            <taskref ref="org.labkey.cds.data.steps.ClearAndWarmCube">
            </taskref>
        </transform>
    </transforms>
</etl>