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Merged
bbimber merged 3 commits into from
Jun 9, 2025
Merged

Add metadata for many SIV study queries #333

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ccfed34
Add metadata for many SIV study queries
bbimber Jun 9, 2025
e7e3309
Add genetics table
bbimber Jun 9, 2025
7ee526a
Add additional study tables
bbimber Jun 9, 2025
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28 changes: 28 additions & 0 deletions Studies/resources/queries/study/assignment.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="assignment" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date Added</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="enddate">
<columnTitle>End Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="study">
<columnTitle>Study</columnTitle>
</column>
<column columnName="subgroup">
<columnTitle>Sub-Group</columnTitle>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
28 changes: 28 additions & 0 deletions ...ources/query/study/demographics.query.xml → ...rces/queries/study/demographics.query.xml
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Expand Up @@ -28,6 +28,34 @@
query.Id~eq=${Id}
</url>
</column>
<column columnName="objectId">
<isHidden>true</isHidden>
<isKeyField>true</isKeyField>
</column>
<column columnName="sex">
<columnTitle>Sex</columnTitle>
</column>
<column columnName="geographic_origin">
<columnTitle>Geographic Origin</columnTitle>
</column>
<column columnName="birth">
<columnTitle>Birth</columnTitle>
</column>
<column columnName="death">
<columnTitle>Death</columnTitle>
</column>
<column columnName="species">
<columnTitle>Species</columnTitle>
</column>
<column columnName="mother">
<columnTitle>Mother</columnTitle>
</column>
<column columnName="father">
<columnTitle>Father</columnTitle>
</column>
<column columnName="calculated_status">
<columnTitle>Status</columnTitle>
</column>
</columns>
</table>
</tables>
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22 changes: 22 additions & 0 deletions Studies/resources/queries/study/flags.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="flags" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date Added</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="enddate">
<columnTitle>End Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="flag">
<columnTitle>Flag</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
30 changes: 30 additions & 0 deletions Studies/resources/queries/study/genetics.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="flags" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date Added</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
<column columnName="assayType">
<columnTitle>Assay Type</columnTitle>
</column>
<column columnName="marker">
<columnTitle>Marker/Allele</columnTitle>
</column>
<column columnName="result">
<columnTitle>Result</columnTitle>
</column>
<column columnName="score">
<columnTitle>Score</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
33 changes: 33 additions & 0 deletions Studies/resources/queries/study/immunizations.query.xml
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@@ -0,0 +1,33 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="immunizations" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date Added</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
<column columnName="treatment">
<columnTitle>Treatment</columnTitle>
</column>
<column columnName="route">
<columnTitle>Route</columnTitle>
</column>
<column columnName="quantity">
<columnTitle>Quantity</columnTitle>
</column>
<column columnName="quantity_units">
<columnTitle>Quantity Units</columnTitle>
</column>
<column columnName="reason">
<columnTitle>Reason</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
34 changes: 34 additions & 0 deletions Studies/resources/queries/study/labwork.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="labwork" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
<column columnName="test">
<columnTitle>Test</columnTitle>
</column>
<column columnName="result">
<columnTitle>Result</columnTitle>
</column>
<column columnName="units">
<columnTitle>Units</columnTitle>
</column>
<column columnName="qualResult">
<columnTitle>Qualitative Result</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="method">
<columnTitle>Method</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
22 changes: 22 additions & 0 deletions Studies/resources/queries/study/procedures.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="procedures" tableDbType="TABLE">
<columns>
<column columnName="Id">
<url />
</column>
<column columnName="date">
<isHidden>true</isHidden>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
<column columnName="procedure">
<columnTitle>Procedure</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
31 changes: 31 additions & 0 deletions Studies/resources/queries/study/samples.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="samples" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date Added</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="sampleid">
<columnTitle>Sample ID</columnTitle>
</column>
<column columnName="sampleType">
<columnTitle>Sample Type</columnTitle>
</column>
<column columnName="preservation">
<columnTitle>Preservation</columnTitle>
</column>
<column columnName="quantity">
<columnTitle>Quantity</columnTitle>
</column>
<column columnName="quantity_units">
<columnTitle>Quantity Units</columnTitle>
</column>

</columns>
</table>
</tables>
</metadata>
</query>
0 ...resources/query/study/studyData.query.xml → ...sources/queries/study/studyData.query.xml
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65 changes: 65 additions & 0 deletions Studies/resources/queries/study/treatments.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="treatments" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="enddate">
<columnTitle>End Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="category">
<columnTitle>Category</columnTitle>
</column>
<column columnName="treatment">
<columnTitle>Treatment</columnTitle>
</column>
<column columnName="route">
<columnTitle>Route</columnTitle>
</column>
<column columnName="frequency">
<columnTitle>Frequency</columnTitle>
</column>
<column columnName="amount">
<columnTitle>Amount</columnTitle>
</column>
<column columnName="amountUnits">
<columnTitle>Amount Units</columnTitle>
</column>
<column columnName="volume">
<columnTitle>Volume</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="vol_units">
<columnTitle>Volume Units</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="concentration">
<columnTitle>Concentration</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="conc_units">
<columnTitle>Conc. Units</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="dosage">
<columnTitle>Dosage</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="dosage_units">
<columnTitle>Dosage Units</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="reason">
<columnTitle>Reason</columnTitle>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
40 changes: 40 additions & 0 deletions Studies/resources/queries/study/viralloads.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="flags" tableDbType="TABLE" useColumnOrder="true">
<columns>
<column columnName="Id"/>
<column columnName="date">
<columnTitle>Date</columnTitle>
<formatString>Date</formatString>
</column>
<column columnName="sampleType">
<columnTitle>Sample Type</columnTitle>
</column>
<column columnName="assayType">
<columnTitle>Assay Type</columnTitle>
</column>
<column columnName="target">
<columnTitle>target</columnTitle>
</column>
<column columnName="lod">
<columnTitle>LOD</columnTitle>
</column>
<column columnName="result">
<columnTitle>Result</columnTitle>
</column>
<column columnName="units">
<columnTitle>Units</columnTitle>
</column>
<column columnName="qualResult">
<columnTitle>Qualitative Result</columnTitle>
<isHidden>true</isHidden>
</column>
<column columnName="resultOORIndicator">
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
6 changes: 6 additions & 0 deletions ...es/resources/query/study/weight.query.xml → .../resources/queries/study/weight.query.xml
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Expand Up @@ -3,6 +3,12 @@
<tables xmlns="http://labkey.org/data/xml">
<table tableName="weight" tableDbType="TABLE">
<columns>
<column columnName="Id">
<url />
</column>
<column columnName="date">
<isHidden>true</isHidden>
</column>
<column columnName="weight">
<columnTitle>Weight (kg)</columnTitle>
<formatString>0.####</formatString>
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