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Merged
bbimber merged 4 commits into from
May 5, 2023
Merged

Add ONPRC parentage validation queries #688

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e578db9
Add parentage validation queries
bbimber Mar 2, 2023
37504d2
Updates to SQL queries
bbimber Mar 10, 2023
696daf2
Fix query name
bbimber May 4, 2023
dfb9d38
Update message in notification
bbimber May 4, 2023
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28 changes: 28 additions & 0 deletions onprc_ehr/resources/queries/study/parentsWrongGenderOrSpecies.query.xml
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@@ -0,0 +1,28 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="parentsWrongGenderOrSpecies" tableDbType="NOT_IN_DB">
<tableTitle>Parentage Records With Mismatched Gender or Species</tableTitle>
<pkColumnName>lsid</pkColumnName>
<updateUrl>/ehr/manageRecord.view?schemaName=study&amp;queryName=${queryName}&amp;keyField=lsid&amp;key=${lsid}&amp;update=1</updateUrl>
<columns>
<column columnName="Id">

</column>
<column columnName="parentGender">
<columnTitle>Parent Gender</columnTitle>
</column>
<column columnName="parentSpecies">
<columnTitle>Parent Species</columnTitle>
</column>
<column columnName="lsid">
<isHidden>true</isHidden>
</column>
<column columnName="queryName">
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
59 changes: 59 additions & 0 deletions onprc_ehr/resources/queries/study/parentsWrongGenderOrSpecies.sql
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SELECT
p.Id,
p.date,
p.Id.demographics.species,
p.relationship,
p.parent,
p.parent.demographics.gender as parentGender,
p.parent.demographics.species as parentSpecies,
p.lsid,
'Parentage' as queryName
FROM study.parentage p

WHERE p.qcstate.publicdata = true AND (
-- Gender:
(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Sire' AND p.parent.demographics.gender.origgender != 'm') OR
(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Dam' AND p.parent.demographics.gender.origgender != 'f') OR
(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Foster Dam' AND p.parent.demographics.gender.origgender != 'f') OR

-- Species
(p.Id.demographics.species IS NOT NULL AND p.parent.demographics.species IS NOT NULL AND p.Id.demographics.species != p.parent.demographics.species)
)

UNION ALL

SELECT
p.Id,
p.date,
p.Id.demographics.species,
'dam' as relationship,
p.dam as parent,
d.gender as parentGender,
d.species as parentSpecies,
p.lsid,
'Birth' as queryName
FROM study.birth p
JOIN study.demographics d on (p.dam = d.Id)
WHERE p.qcstate.publicdata = true AND (
(d.gender.origgender IS NOT NULL AND d.gender.origgender != 'f') OR
(p.Id.demographics.species IS NOT NULL AND d.species IS NOT NULL AND p.Id.demographics.species != d.species)
) AND p.date >= '2000-01-01'

UNION ALL

SELECT
p.Id,
p.date,
p.Id.demographics.species,
'sire' as relationship,
p.sire as parent,
d.gender as parentGender,
d.species as parentSpecies,
p.lsid,
'Birth' as queryName
FROM study.birth p
JOIN study.demographics d on (p.sire = d.Id)
WHERE p.qcstate.publicdata = true AND (
(d.gender.origgender IS NOT NULL AND d.gender.origgender != 'm') OR
(p.Id.demographics.species IS NOT NULL AND d.species IS NOT NULL AND p.Id.demographics.species != d.species)
) AND p.date >= '2000-01-01'
25 changes: 25 additions & 0 deletions onprc_ehr/resources/queries/study/parentsYoungerThanOffspring.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="parentsYoungerThanOffspring" tableDbType="NOT_IN_DB">
<tableTitle>Parentage Records With Parents Younger Than Offspring</tableTitle>
<pkColumnName>lsid</pkColumnName>
<updateUrl>/ehr/manageRecord.view?schemaName=study&amp;queryName=${queryName}&amp;keyField=lsid&amp;key=${lsid}&amp;update=1</updateUrl>
<columns>
<column columnName="Id">

</column>
<column columnName="parentBirth">
<columnTitle>Parent Birth</columnTitle>
</column>
<column columnName="lsid">
<isHidden>true</isHidden>
</column>
<column columnName="queryName">
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
50 changes: 50 additions & 0 deletions onprc_ehr/resources/queries/study/parentsYoungerThanOffspring.sql
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@@ -0,0 +1,50 @@
SELECT
p.Id,
p.parent,
p.relationship,
p.method,
p.Id.demographics.birth,
p.parent.demographics.birth as parentBirth,
p.lsid,
'Parentage' as queryName

FROM study.parentage p
WHERE
p.qcstate.publicdata = true AND
(p.Id.demographics.birth IS NOT NULL AND p.parent.demographics.birth IS NOT NULL AND p.Id.demographics.birth <= p.parent.demographics.birth)

UNION ALL

SELECT
p.Id,
p.dam as parent,
'Dam' as relationship,
'Observed' as method,
p.Id.demographics.birth,
d.birth as parentBirth,
p.lsid,
'Birth' as queryName

FROM study.birth p
JOIN study.demographics d on (p.dam = d.Id)
WHERE
p.qcstate.publicdata = true AND
(p.Id.demographics.birth IS NOT NULL AND d.birth IS NOT NULL AND p.Id.demographics.birth <= d.birth)

UNION ALL

SELECT
p.Id,
p.sire as parent,
'Sire' as relationship,
'Observed' as method,
p.Id.demographics.birth,
d.birth as parentBirth,
p.lsid,
'Birth' as queryName

FROM study.birth p
JOIN study.demographics d on (p.sire = d.Id)
WHERE
p.qcstate.publicdata = true AND
(p.Id.demographics.birth IS NOT NULL AND d.birth IS NOT NULL AND p.Id.demographics.birth <= d.birth)
21 changes: 21 additions & 0 deletions onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyAlertsNotification.java
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Expand Up @@ -957,6 +957,27 @@ protected void birthRecordsWithoutDemographics(final Container c, User u, final
}
}

protected void pedigreeIssues(final Container c, User u, final StringBuilder msg)
{
TableSelector ts = new TableSelector(getStudySchema(c, u).getTable("parentsYoungerThanOffspring"), Collections.singleton(getStudy(c).getSubjectColumnName()));
long count = ts.getRowCount();
if (count > 0)
{
msg.append("<b>WARNING: There are " + count + " parentage records where the parent is younger than the offspring.</b><br>\n");
msg.append("<p><a href='" + getExecuteQueryUrl(c, "study", "parentsYoungerThanOffspring", null) + "'>Click here to view them</a><br>\n\n");
msg.append("<hr>\n\n");
}

ts = new TableSelector(getStudySchema(c, u).getTable("parentsWrongGenderOrSpecies"), Collections.singleton(getStudy(c).getSubjectColumnName()));
count = ts.getRowCount();
if (count > 0)
{
msg.append("<b>WARNING: There are " + count + " parentage records listed with the wrong gender or species.</b><br>\n");
msg.append("<p><a href='" + getExecuteQueryUrl(c, "study", "parentsWrongGenderOrSpecies", null) + "'>Click here to view them</a><br>\n\n");
msg.append("<hr>\n\n");
}
}

protected void incompleteBirthRecords(final Container c, User u, final StringBuilder msg)
{
SimpleFilter filter = new SimpleFilter(new SimpleFilter.OrClause(
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1 change: 1 addition & 0 deletions onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyMgmtNotification.java
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Expand Up @@ -82,6 +82,7 @@ public String getMessageBodyHTML(Container c, User u)
offspringWithMother(c, u, msg, 250);
offspringWithMother(c, u, msg, 365);
incompleteBirthRecords(c, u, msg);
pedigreeIssues(c, u, msg);

//only send if there are alerts
if (msg.length() > 0)
Expand Down