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Merge 25.11 to 26.3
2 parents 482c895 + 543577d commit f744bfe

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Lines changed: 332 additions & 60 deletions

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‎onprc_ehr/resources/queries/study/Demographics_NotInMMA,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="Demographics_NotInMMA" tableDbType="NOT_IN_DB">
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<tableTitle>Demographics (Excluding animals in Weight MMA regimen)</tableTitle>
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</table>
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</tables>
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</metadata>
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</query>

‎onprc_ehr/resources/queries/study/Demographics_NotInMMA.sql‎

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/*
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Created by Kollil in Dec 2025
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Tkt # 13461
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Added two filters to the Demographics dataset:
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1. Filter out any animal with the following SNOMED Codes:
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Begin active weight management regimen (P-YY961)
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However, we would need to include animals that have this additional SNOMED Code if it's entered AFTER the one above
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Release from active weight management regimen (P-YY960)
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2. Remove Shelters, Corral and Hospital locations from the lists
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*/
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SELECT
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d.Id.curlocation.area AS Area,
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d.Id.curlocation.room AS Room,
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d.Id.curlocation.cage AS Cage,
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d.Id,
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d.Id.utilization.use AS ProjectsAndGroups,
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d.species,
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d.geographic_origin,
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d.gender AS Sex,
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d.calculated_status,
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d.birth,
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d.Id.Age.YearAndDays,
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d.Id.MostRecentWeight.MostRecentWeight,
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d.Id.MostRecentWeight.MostRecentWeightDate,
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d.Id.viral_status.viralStatus,
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d.history
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FROM Demographics d
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WHERE d.Id.curlocation.area NOT IN ('Shelters', 'Corral', 'Hospital', 'Catch Area')-- Exclude animals from these locations
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AND NOT (-- Exclude females under 5yrs, males under 7yrs
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(d.gender.code = 'f' AND d.Id.age.ageInYears < 5)
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OR (d.gender.code = 'm' AND d.Id.age.ageInYears < 7)
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)
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AND NOT EXISTS (
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-- -- Find animals whose latest 'Weight MMA BEGIN' has no later 'Weight MMA RELEASE'
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SELECT 1
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FROM study.WeightMMA b
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WHERE b.Id = d.Id
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AND b.code = 'P-YY961'
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AND b.date = (
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SELECT MAX(b2.date)
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FROM study.WeightMMA b2
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WHERE b2.Id = d.Id
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AND b2.code = 'P-YY961'
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)
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AND NOT EXISTS (
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SELECT 1
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FROM study.WeightMMA r
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WHERE r.Id = d.Id
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AND r.code = 'P-YY960'
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AND r.date > b.date
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)
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)

‎onprc_ehr/resources/queries/study/WeightMMA.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="WeightMMA" tableDbType="NOT_IN_DB">
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<tableTitle>Animals in weight management regimen</tableTitle>
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<columns>
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<column columnName="Id">
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<isHidden>false</isHidden>
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<fk>
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<fkDbSchema>study</fkDbSchema>
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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="date">
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<isHidden>false</isHidden>
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<columnTitle>Prev Weight Date</columnTitle>
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</column>
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<column columnName="set_number">
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<columnTitle>Set Number</columnTitle>
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</column>
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<column columnName="code">
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<columnTitle>Snomed Code</columnTitle>
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</column>
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<column columnName="qualifier">
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<columnTitle>Qualifier</columnTitle>
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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>
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</query>

‎onprc_ehr/resources/queries/study/WeightMMA.sql‎

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-- Created by Kolli, March 2026
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--New query created in the code base as the automated tests are failing.
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SELECT s.Id,
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s.date,
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s.set_number,
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s.code,
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s.qualifier
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FROM ehr.snomed_tags s
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where s.code like 'P-YY961'
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Union
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SELECT s.Id,
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s.date,
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s.set_number,
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s.code,
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s.qualifier
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FROM ehr.snomed_tags s
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where s.code like 'P-YY960'

‎onprc_ehr/resources/queries/study/weightRelChange_NotInMMA.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="weightRelChange_NotInMMA" tableDbType="NOT_IN_DB">
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<tableTitle>Weight Change, Relative to Current Weight (Excluding the animals enrolled in MMA)</tableTitle>
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<description>This query shows the percent change of each weight, relative to the current weight</description>
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<columns>
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<column columnName="lsid">
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<isKeyField>true</isKeyField>
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<isHidden>true</isHidden>
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</column>
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<column columnName="Id">
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<isHidden>false</isHidden>
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<fk>
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<fkDbSchema>study</fkDbSchema>
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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="date">
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<isHidden>false</isHidden>
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<columnTitle>Prev Weight Date</columnTitle>
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</column>
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<column columnName="weight">
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<columnTitle>Prev Weight (kg)</columnTitle>
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</column>
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<column columnName="PctChange">
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<columnTitle>% Change Relative To Current</columnTitle>
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</column>
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<column columnName="AbsPctChange">
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<columnTitle>Abs Pct Change</columnTitle>
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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>
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</query>

‎onprc_ehr/resources/queries/study/weightRelChange_NotInMMA.sql‎

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/*
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Created by Kollil in Dec 2025
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Tkt # 13461
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Added two filters to the Demographics dataset:
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1. Filter out any animal with the following SNOMED Codes:
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Begin active weight management regimen (P-YY961)
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However, we would need to include animals that have this additional SNOMED Code if it's entered AFTER the one above
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Release from active weight management regimen (P-YY960)
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2. Remove Shelters, Corral and Hospital locations from the lists
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*/
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SELECT DISTINCT
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l.lsid,
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l.Id,
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l.date AS LatestWeightDate,
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l.weight AS LatestWeight,
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p.date, -- AS PrevWeightDate
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p.weight, -- AS PrevWeight
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timestampdiff('SQL_TSI_DAY', p.date, l.date) AS IntervalInDays,
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age_in_months(p.date, l.date) AS IntervalInMonths,
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CASE
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WHEN p.weight IS NOT NULL AND p.weight > 0 THEN
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ROUND(((l.weight - p.weight) * 100 / p.weight), 1)
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ELSE NULL
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END AS PctChange,
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CASE
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WHEN p.weight IS NOT NULL AND p.weight > 0 THEN
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ABS(ROUND(((l.weight - p.weight) * 100 / p.weight), 1))
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ELSE NULL
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END AS AbsPctChange,
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l.qcstate AS LatestQcState,
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p.qcstate AS PrevQcState
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FROM
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(SELECT Id, MAX(date) AS LatestDate
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FROM study.weight
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GROUP BY Id) lw
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JOIN study.weight l
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ON l.Id = lw.Id
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AND l.date = lw.LatestDate
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LEFT JOIN study.weight p
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ON p.Id = lw.Id
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AND p.date = (
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SELECT MAX(w2.date)
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FROM study.weight w2
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WHERE w2.Id = lw.Id
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AND w2.date <= timestampadd('SQL_TSI_DAY', -30, lw.LatestDate)
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AND w2.date >= timestampadd('SQL_TSI_DAY', -100, lw.LatestDate)
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)
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WHERE l.Id.curlocation.area NOT IN ('Shelters', 'Corral', 'Hospital', 'Catch Area')-- Exclude animals from these locations
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AND NOT (-- Exclude females under 5yrs, males under 7yrs
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(l.Id.demographics.gender.code = 'f' AND l.Id.age.ageInYears < 5)
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OR (l.Id.demographics.gender.code = 'm' AND l.Id.age.ageInYears < 7)
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)
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AND l.qcstate.publicdata = true
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AND NOT EXISTS (
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-- -- Find animals whose latest 'Weight MMA BEGIN' has no later 'Weight MMA RELEASE'
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SELECT 1
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FROM study.WeightMMA b
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WHERE b.Id = l.Id
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AND b.code = 'P-YY961'
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AND b.date = (
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SELECT MAX(b2.date)
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FROM study.WeightMMA b2
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WHERE b2.Id = l.Id
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AND b2.code = 'P-YY961'
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)
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AND NOT EXISTS (
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SELECT 1
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FROM study.WeightMMA r
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WHERE r.Id = l.Id
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AND r.code = 'P-YY960'
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AND r.date > b.date
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)
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)

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