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Add ONPRC parentage validation queries (#688)
* Add parentage validation queries
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‎onprc_ehr/resources/queries/study/parentsWrongGenderOrSpecies.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="parentsWrongGenderOrSpecies" tableDbType="NOT_IN_DB">
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<tableTitle>Parentage Records With Mismatched Gender or Species</tableTitle>
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<pkColumnName>lsid</pkColumnName>
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<updateUrl>/ehr/manageRecord.view?schemaName=study&amp;queryName=${queryName}&amp;keyField=lsid&amp;key=${lsid}&amp;update=1</updateUrl>
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<columns>
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<column columnName="Id">
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</column>
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<column columnName="parentGender">
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<columnTitle>Parent Gender</columnTitle>
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</column>
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<column columnName="parentSpecies">
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<columnTitle>Parent Species</columnTitle>
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</column>
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<column columnName="lsid">
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<isHidden>true</isHidden>
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</column>
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<column columnName="queryName">
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<isHidden>true</isHidden>
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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/parentsWrongGenderOrSpecies.sql‎

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SELECT
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p.Id,
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p.date,
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p.Id.demographics.species,
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p.relationship,
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p.parent,
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p.parent.demographics.gender as parentGender,
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p.parent.demographics.species as parentSpecies,
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p.lsid,
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'Parentage' as queryName
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FROM study.parentage p
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WHERE p.qcstate.publicdata = true AND (
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-- Gender:
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(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Sire' AND p.parent.demographics.gender.origgender != 'm') OR
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(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Dam' AND p.parent.demographics.gender.origgender != 'f') OR
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(p.parent.demographics.gender.origgender IS NOT NULL AND p.relationship = 'Foster Dam' AND p.parent.demographics.gender.origgender != 'f') OR
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-- Species
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(p.Id.demographics.species IS NOT NULL AND p.parent.demographics.species IS NOT NULL AND p.Id.demographics.species != p.parent.demographics.species)
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)
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UNION ALL
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SELECT
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p.Id,
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p.date,
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p.Id.demographics.species,
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'dam' as relationship,
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p.dam as parent,
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d.gender as parentGender,
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d.species as parentSpecies,
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p.lsid,
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'Birth' as queryName
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FROM study.birth p
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JOIN study.demographics d on (p.dam = d.Id)
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WHERE p.qcstate.publicdata = true AND (
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(d.gender.origgender IS NOT NULL AND d.gender.origgender != 'f') OR
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(p.Id.demographics.species IS NOT NULL AND d.species IS NOT NULL AND p.Id.demographics.species != d.species)
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) AND p.date >= '2000-01-01'
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UNION ALL
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SELECT
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p.Id,
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p.date,
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p.Id.demographics.species,
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'sire' as relationship,
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p.sire as parent,
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d.gender as parentGender,
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d.species as parentSpecies,
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p.lsid,
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'Birth' as queryName
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FROM study.birth p
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JOIN study.demographics d on (p.sire = d.Id)
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WHERE p.qcstate.publicdata = true AND (
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(d.gender.origgender IS NOT NULL AND d.gender.origgender != 'm') OR
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(p.Id.demographics.species IS NOT NULL AND d.species IS NOT NULL AND p.Id.demographics.species != d.species)
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) AND p.date >= '2000-01-01'

‎onprc_ehr/resources/queries/study/parentsYoungerThanOffspring.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="parentsYoungerThanOffspring" tableDbType="NOT_IN_DB">
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<tableTitle>Parentage Records With Parents Younger Than Offspring</tableTitle>
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<pkColumnName>lsid</pkColumnName>
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<updateUrl>/ehr/manageRecord.view?schemaName=study&amp;queryName=${queryName}&amp;keyField=lsid&amp;key=${lsid}&amp;update=1</updateUrl>
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<columns>
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<column columnName="Id">
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</column>
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<column columnName="parentBirth">
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<columnTitle>Parent Birth</columnTitle>
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</column>
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<column columnName="lsid">
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<isHidden>true</isHidden>
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</column>
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<column columnName="queryName">
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<isHidden>true</isHidden>
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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/parentsYoungerThanOffspring.sql‎

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SELECT
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p.Id,
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p.parent,
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p.relationship,
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p.method,
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p.Id.demographics.birth,
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p.parent.demographics.birth as parentBirth,
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p.lsid,
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'Parentage' as queryName
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FROM study.parentage p
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WHERE
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p.qcstate.publicdata = true AND
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(p.Id.demographics.birth IS NOT NULL AND p.parent.demographics.birth IS NOT NULL AND p.Id.demographics.birth <= p.parent.demographics.birth)
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UNION ALL
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SELECT
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p.Id,
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p.dam as parent,
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'Dam' as relationship,
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'Observed' as method,
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p.Id.demographics.birth,
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d.birth as parentBirth,
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p.lsid,
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'Birth' as queryName
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FROM study.birth p
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JOIN study.demographics d on (p.dam = d.Id)
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WHERE
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p.qcstate.publicdata = true AND
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(p.Id.demographics.birth IS NOT NULL AND d.birth IS NOT NULL AND p.Id.demographics.birth <= d.birth)
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UNION ALL
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SELECT
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p.Id,
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p.sire as parent,
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'Sire' as relationship,
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'Observed' as method,
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p.Id.demographics.birth,
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d.birth as parentBirth,
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p.lsid,
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'Birth' as queryName
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FROM study.birth p
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JOIN study.demographics d on (p.sire = d.Id)
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WHERE
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p.qcstate.publicdata = true AND
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(p.Id.demographics.birth IS NOT NULL AND d.birth IS NOT NULL AND p.Id.demographics.birth <= d.birth)

‎onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyAlertsNotification.java‎

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

‎onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyMgmtNotification.java‎

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offspringWithMother(c, u, msg, 250);
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offspringWithMother(c, u, msg, 365);
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incompleteBirthRecords(c, u, msg);
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pedigreeIssues(c, u, msg);
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//only send if there are alerts
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if (msg.length() > 0)

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