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srouseTxbiomedsrouseTxbiomed
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Fb snprc tcruzi report update (#366)
* Adding reports for T Cruzi new positives and T Cruzi summary Added new surveillance section of More reports srr * Working To Add to new fb Adding reports for T Cruzi new positives and T Cruzi summary Added new surveillance section of More reports srr * Adding reports for T Cruzi new positives and T Cruzi summary Added new surveillance section of More reports srr * T cruzi report updates Moved queries to study schema Added AtCenter views Added FK to animal id 05.11.2021
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‎snprc_ehr/resources/queries/study/ReportTcruziNewPositives.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="ReportTcruziNewPositives" tableDbType="NOT_IN_DB">
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<tableTitle>T cruzi New Positives</tableTitle>
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<columns>
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<column columnName="Species">
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<columnTitle>Species</columnTitle>
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</column>
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<column columnName="CurrentLocation">
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<columnTitle>Current Location</columnTitle>
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</column>
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<column columnName="Id">
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<columnTitle>Animal Id</columnTitle>
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<fk>
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<fkTable>animal</fkTable>
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<fkColumnName>id</fkColumnName>
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</fk>
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</column>
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<column columnName="status">
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<columnTitle>Status</columnTitle>
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</column>
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<column columnName="TcruziResult">
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<columnTitle>T cruzi result</columnTitle>
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</column>
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<column columnName="MinDate">
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<columnTitle>First Date</columnTitle>
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</column>
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</columns>
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<sorts>
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<sort column="MinDate" descending="true"/>
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</sorts>
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</table>
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</tables>
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</metadata>
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</query>

‎snprc_ehr/resources/queries/study/ReportTcruziNewPositives.sql‎

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/**************************************************************
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Sourced from ReportTcruziPositiveSummary
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Purpose is to report all summary data on T. cruzi tests.
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Changed to CASE to report single value for result (i.e. combining seroPos and Positive)
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Runs as expected in SQLdbx.
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srr 04.16.2021
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Added IND and INDETERMINATE
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to results CASE
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srr 04.20.21
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Dr. Elmore request
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This report is for positive only, therefore restricting
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in each subquery and not the unioned result. Did not remove
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negative or indeterminate from case, but will never be used.
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Hope is to one day drive all TC reports from same SQL.
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No longer reporting NumTests. Purpose of this report is to
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only report first positive.
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srr 04.23.21
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**************************************************************/
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SELECT d.SpeciesCode AS Species, d.CurrentLocation,d.id, d.status, d.result AS "TcruziResult",
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min(d.TestDate) AS FirstDate /*, count(*) AS NumTests*/
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FROM
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(SELECT 'LabResults',
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b.id.demographics.species.arc_species_code.code AS SpeciesCode,
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b.id.curlocation.Room AS CurrentLocation,
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b.id,
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b.id.demographics.calculated_status AS status,
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b.date AS TestDate,
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b.runId.serviceRequested as panelName,
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b.serviceTestId.testName AS TestName,
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coalesce(b.runId, b.objectid) as runId,
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/*b.resultoorindicator,*/
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CASE b.qualresult
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WHEN 'NEGATIVE' THEN 'NEGATIVE'
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WHEN 'SERONEG' THEN 'NEGATIVE'
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WHEN 'POSITIVE' THEN 'POSITIVE'
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WHEN 'SEROPOS' THEN 'POSITIVE'
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WHEN 'IND' THEN 'INDETERMINATE'
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WHEN 'INDETERMINATE' THEN 'INDETERMINATE'
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END AS result
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FROM study.labworkResults b
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WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'
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AND b.serviceTestId.testName LIKE '%CRUZI%'
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AND b.qualresult IN ('SEROPOS','POSITIVE')
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-- AND b.id.demographics.calculated_status = 'Alive'
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union
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SELECT 'AssayResults',
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b.id.demographics.species.arc_species_code.code AS SpeciesCode,
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b.id.curlocation.Room AS CurrentLocation,
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b.id,
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b.id.demographics.calculated_status AS status,
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b.date AS TestDate,
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b.runId.serviceRequested as panelName,
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b.serviceTestId.testName AS TestName,
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coalesce(b.runId, b.objectid) as runId,
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/*b.resultoorindicator,*/
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CASE b.qualresult
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WHEN 'NEGATIVE' THEN 'NEGATIVE'
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WHEN 'SERONEG' THEN 'NEGATIVE'
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WHEN 'POSITIVE' THEN 'POSITIVE'
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WHEN 'SEROPOS' THEN 'POSITIVE'
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WHEN 'IND' THEN 'INDETERMINATE'
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WHEN 'INDETERMINATE' THEN 'INDETERMINATE'
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END AS result
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FROM study.assay_labworkResults b
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WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'
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AND b.serviceTestId.testName LIKE '%CRUZI%'
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AND b.qualresult IN ('SEROPOS','POSITIVE')
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--AND b.id.demographics.calculated_status = 'Alive'
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) AS d
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--WHERE result IN ('SEROPOS','POSITIVE')
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/* d.SpeciesCode AS Species,d.CurrentLocation,d.id, d.status,'T cruzi', d.result*/
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GROUP BY d.SpeciesCode,d.CurrentLocation, d.id,d.status, d.result
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/* Look at last 12 month per Dr. Elmore */
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HAVING min(d.TestDate) > timestampadd('SQL_TSI_MONTH', -12, now())
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AND d.result = 'POSITIVE'
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ORDER BY min(d.TestDate) desc --, min(d.TestDate)
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‎snprc_ehr/resources/queries/study/ReportTcruziNewPositives/.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="Species">
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<properties>
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<property name="columnTitle" value="Species"/>
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</properties>
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</column>
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<column name="Id">
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<properties>
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<property name="columnTitle" value="Id"/>
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</properties>
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</column>
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<column name="CurrentLocation">
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<properties>
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<property name="columnTitle" value="Current Location"/>
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</properties>
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</column>
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<column name="status">
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<properties>
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<property name="columnTitle" value="Status"/>
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</properties>
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</column>
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<column name="TcruziResult">
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<properties>
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<property name="columnTitle" value="T cruzi result"/>
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</properties>
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</column>
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<column name="FirstDate">
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<properties>
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<property name="columnTitle" value="First Positive Date"/>
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</properties>
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</column>
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</columns>
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<sorts>
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<sort column="FirstDate" descending="true"/>
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</sorts>
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</customView>

‎snprc_ehr/resources/queries/study/ReportTcruziNewPositives/AtCenter.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="Species">
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<properties>
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<property name="columnTitle" value="Species"/>
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</properties>
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</column>
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<column name="Id">
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<properties>
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<property name="columnTitle" value="Id"/>
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</properties>
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</column>
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<column name="CurrentLocation">
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<properties>
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<property name="columnTitle" value="Current Location"/>
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</properties>
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</column>
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<column name="status">
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<properties>
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<property name="columnTitle" value="Status"/>
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</properties>
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</column>
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<column name="TcruziResult">
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<properties>
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<property name="columnTitle" value="T cruzi result"/>
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</properties>
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</column>
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<column name="FirstDate">
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<properties>
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<property name="columnTitle" value="First Positive Date"/>
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</properties>
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</column>
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</columns>
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<filters>
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<filter column="Id/Demographics/calculated_status" operator="eq" value="Alive"/>
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</filters>
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<sorts>
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<sort column="FirstDate" descending="true"/>
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</sorts>
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</customView>
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‎snprc_ehr/resources/queries/study/ReportTcruziSummaryAll.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="ReportTcruziSummaryAll" tableDbType="NOT_IN_DB">
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<tableTitle>T cruzi Summary</tableTitle>
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<columns>
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<column columnName="Species">
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<columnTitle>Species</columnTitle>
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</column>
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<column columnName="Id">
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<columnTitle>Animal Id</columnTitle>
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<fk>
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<fkTable>animal</fkTable>
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<fkColumnName>id</fkColumnName>
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</fk>
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</column>
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<column columnName="status">
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<columnTitle>Status</columnTitle>
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</column>
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<column columnName="TcruziResult">
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<columnTitle>T cruzi result</columnTitle>
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</column>
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<column columnName="MinDate">
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<columnTitle>MinDate</columnTitle>
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</column>
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<column columnName="MaxDate">
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<columnTitle>MaxDate</columnTitle>
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</column>
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<column columnName="TestCount">
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<columnTitle>Test Count</columnTitle>
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</column>
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</columns>
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<sorts>
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<sort column="MinDate" descending="true"/>
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</sorts>
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</table>
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</tables>
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</metadata>
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</query>

‎snprc_ehr/resources/queries/study/ReportTcruziSummaryAll.sql‎

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/**************************************************************
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Sourced from ReportTcruziPositiveSummary
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Purpose is to report all summary data on T. cruzi tests.
5+
6+
Changed to CASE to report single value for result (i.e. combining seroPos and Positive)
7+
Runs as expected in SQLdbx.
8+
srr 04.16.2021
9+
Added IND and INDETERMINATE
10+
to results CASE
11+
srr 04.20.21
12+
13+
This report is for positive only, therefore restricting
14+
in each subquery and not the unioned result. Did not remove
15+
negative or indeterminate from case, but will never be used.
16+
Hope is to one day drive all TC reports from same SQL.
17+
No longer reporting NumTests. Purpose of this report is to
18+
only report first positive.
19+
srr 04.23.21
20+
**************************************************************/
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SELECT d.SpeciesCode AS Species, d.CurrentLocation,d.id, d.status, d.result AS "TcruziResult",
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min(d.TestDate) AS MinDate,max(d.TestDate) AS MaxDate, count(*) TestCount
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FROM
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(SELECT 'LabResults',
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b.id.demographics.species.arc_species_code.code AS SpeciesCode,
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b.id.curlocation.Room AS CurrentLocation,
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b.id,
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b.id.demographics.calculated_status AS status,
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b.date AS TestDate,
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b.runId.serviceRequested as panelName,
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b.serviceTestId.testName AS TestName,
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coalesce(b.runId, b.objectid) as runId,
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/*b.resultoorindicator,*/
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CASE b.qualresult
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WHEN 'NEGATIVE' THEN 'NEGATIVE'
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WHEN 'SERONEG' THEN 'NEGATIVE'
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WHEN 'POSITIVE' THEN 'POSITIVE'
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WHEN 'SEROPOS' THEN 'POSITIVE'
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WHEN 'IND' THEN 'INDETERMINATE'
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WHEN 'INDETERMINATE' THEN 'INDETERMINATE'
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END AS result
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FROM study.labworkResults b
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WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'
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AND b.serviceTestId.testName LIKE '%CRUZI%'
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AND b.qualresult IN ('SEROPOS','POSITIVE')
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-- AND b.id.demographics.calculated_status = 'Alive'
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union
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SELECT 'AssayResults',
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b.id.demographics.species.arc_species_code.code AS SpeciesCode,
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b.id.curlocation.Room AS CurrentLocation,
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b.id,
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b.id.demographics.calculated_status AS status,
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b.date AS TestDate,
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b.runId.serviceRequested as panelName,
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b.serviceTestId.testName AS TestName,
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coalesce(b.runId, b.objectid) as runId,
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/*b.resultoorindicator,*/
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CASE b.qualresult
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WHEN 'NEGATIVE' THEN 'NEGATIVE'
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WHEN 'SERONEG' THEN 'NEGATIVE'
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WHEN 'POSITIVE' THEN 'POSITIVE'
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WHEN 'SEROPOS' THEN 'POSITIVE'
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WHEN 'IND' THEN 'INDETERMINATE'
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WHEN 'INDETERMINATE' THEN 'INDETERMINATE'
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END AS result
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FROM study.assay_labworkResults b
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WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'
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AND b.serviceTestId.testName LIKE '%CRUZI%'
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AND b.qualresult IN ('SEROPOS','POSITIVE')
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--AND b.id.demographics.calculated_status = 'Alive'
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) AS d
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--WHERE result IN ('SEROPOS','POSITIVE')
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/* d.SpeciesCode AS Species,d.CurrentLocation,d.id, d.status,'T cruzi', d.result*/
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GROUP BY d.SpeciesCode,d.CurrentLocation, d.id,d.status, d.result
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ORDER BY min(d.TestDate) desc --, min(d.TestDate)

‎snprc_ehr/resources/queries/study/ReportTcruziSummaryAll/.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="Species">
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<properties>
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<property name="columnTitle" value="Species"/>
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</properties>
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</column>
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<column name="Id">
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<properties>
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<property name="columnTitle" value="Id"/>
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</properties>
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</column>
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<column name="CurrentLocation">
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<properties>
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<property name="columnTitle" value="Current Location"/>
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</properties>
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</column>
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<column name="status">
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<properties>
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<property name="columnTitle" value="Status"/>
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</properties>
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</column>
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<column name="TcruziResult">
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<properties>
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<property name="columnTitle" value="T cruzi result"/>
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</properties>
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</column>
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<column name="MinDate">
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<properties>
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<property name="columnTitle" value="MinDate"/>
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</properties>
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</column>
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<column name="MaxDate">
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<properties>
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<property name="columnTitle" value="MaxDate"/>
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</properties>
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</column>
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<column name="TestCountZ">
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<properties>
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<property name="columnTitle" value="TestCount"/>
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</properties>
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</column>
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</columns>
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<sorts>
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<sort column="MinDate" descending="true"/>
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</sorts>
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</customView>
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