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srouseTxbiomedsrouseTxbiomed
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Adding T cruzi reports (#360)
* 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
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‎snprc_ehr/resources/queries/snprc_ehr/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 "T cruzi result",
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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)

‎snprc_ehr/resources/queries/snprc_ehr/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.
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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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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 "T cruzi result",
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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/src/org/labkey/snprc_ehr/SNPRC_EHRModule.java‎

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EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Search Apath History", this, DetailsURL.fromString("/query/executeQuery.view?schemaName=study&query.queryName=apathHistoryReport"), "Pathololgy");
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EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Overall Behavior Report", this, DetailsURL.fromString("/query/executeQuery.view?schemaName=study&query.queryName=BehaviorReport"), "Behavior");
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EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Birth Record Report", this, DetailsURL.fromString("/snprc_ehr/BirthReport.view?"), "Colony Management");
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EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "T cruzi New Positives Report",this,DetailsURL.fromString("/query/executeQuery.view?schemaName=snprc_ehr&query.queryName=ReportTcruziNewPositives"),"Surveillance");
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EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "T cruzi Summary Report",this,DetailsURL.fromString("/query/executeQuery.view?schemaName=snprc_ehr&query.queryName=ReportTcruziSummaryAll"),"Surveillance");
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// Add the current date to the chimp observation report
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SimpleDateFormat format = new SimpleDateFormat("MM-dd-yyyy");

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