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Use age_in_days for age calculations #1119

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b2845cf
Use age_in_days instead of timestampdiff
labkey-martyp Apr 15, 2026
e516b6c
age at time and demographicsAge
labkey-martyp Apr 22, 2026
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6 changes: 3 additions & 3 deletions ehr/resources/queries/study/demographicsAge.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,15 @@ ROUND(CONVERT(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())), DOUBLE

ROUND(CONVERT(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())), DOUBLE) / 12, 1) AS ageInYears,

TIMESTAMPDIFF('SQL_TSI_DAY', d.birth, COALESCE(d.lastDayAtCenter, now())) as ageInDays,
age_in_days(d.birth, COALESCE(d.lastDayAtCenter, now())) as ageInDays,

case
when (age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now()))) < 1
then (CONVERT(CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY', d.birth, COALESCE(d.lastDayAtCenter, now())), float), VARCHAR) || ' days')
then (CONVERT(CONVERT(age_in_days(d.birth, COALESCE(d.lastDayAtCenter, now())), float), VARCHAR) || ' days')
when (age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now()))) < 12
then (CONVERT(CONVERT(ROUND(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())), 1), float), VARCHAR) || ' months')
else
(CONVERT(CONVERT(FLOOR(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())) / 12), SQL_INTEGER), VARCHAR) || '.' || CONVERT(MOD(CONVERT(ROUND(age_in_months(d.birth, COALESCE(d.death, now())) / 12.0 * 10.0, 0), SQL_INTEGER), 10), VARCHAR) || ' years')
(CONVERT(CONVERT(FLOOR(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())) / 12), SQL_INTEGER), VARCHAR) || '.' || CONVERT(MOD(CONVERT(ROUND(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())) / 12.0 * 10.0, 0), SQL_INTEGER), 10), VARCHAR) || ' years')
end as ageFriendly

FROM study.Demographics d
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117 changes: 47 additions & 70 deletions ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1796,75 +1796,47 @@ private void appendAgeAtTimeCol(UserSchema ehrSchema, AbstractTableInfo ds, fina
@Override
public TableInfo getLookupTableInfo()
{
String name = queryName + "_ageAtTime";
String lookupQueryName = queryName + "_ageAtTime";
String dateSql = "c." + FieldKey.fromString(dateColName).toSQLString();
String pkSql = "c." + pkCol.getFieldKey().toSQLString();
UserSchema targetSchema = ds.getUserSchema().getDefaultSchema().getUserSchema(targetSchemaName);
QueryDefinition qd = QueryService.get().createQueryDef(u, targetSchemaContainer, targetSchema, name);
QueryDefinition qd = QueryService.get().createQueryDef(u, targetSchemaContainer, targetSchema, lookupQueryName);
// Compute the "as-of" date once: clamp to lastDayAtCenter when the record is after the animal left the center.
// All downstream age expressions reference x.effDate, so the clamp lives in one place.
//NOTE: do not need to account for QCstate b/c study.demographics only allows 1 row per subject
qd.setSql("SELECT\n" +
"c." + pkCol.getFieldKey().toSQLString() + ",\n" +
"\n" +
"CAST(\n" +
"CASE\n" +
"WHEN d.birth is null or c." + dateColName + " is null\n" +
" THEN null\n" +
"WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" +
" ROUND(CONVERT(age_in_months(d.birth, d.lastDayAtCenter), DOUBLE) / 12, 1)\n" +
"ELSE\n" +
" ROUND(CONVERT(age_in_months(d.birth, CAST(c." + dateColName + " as DATE)), DOUBLE) / 12, 1)\n" +
"END AS float) as AgeAtTime,\n" +
"\n" +

"CAST(\n" +
"CASE\n" +
"WHEN d.birth is null or c." + dateColName + " is null\n" +
" THEN null\n" +
"WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" +
" ROUND(CONVERT(timestampdiff('SQL_TSI_DAY', d.birth, d.lastDayAtCenter), DOUBLE) / 365.25, 2)\n" +
"ELSE\n" +
" ROUND(CONVERT(timestampdiff('SQL_TSI_DAY', d.birth, CAST(c." + dateColName + " as DATE)), DOUBLE) / 365.25, 2)\n" +
"END AS float) as AgeAtTimeYears,\n" +
"\n" +
"CAST(\n" +
"CASE\n" +
"WHEN d.birth is null or c." + dateColName + " is null\n" +
" THEN null\n" +
"WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" +
" floor(age(d.birth, d.lastDayAtCenter))\n" +
"ELSE\n" +
" floor(age(d.birth, CAST(c." + dateColName + " as DATE)))\n" +
"END AS float) as AgeAtTimeYearsRounded,\n" +
"\n" +
//Added 'Age at time Days' by kollil on 02/15/2019
"CAST(\n" +
"CASE\n" +
"WHEN d.birth is null or c." + dateColName + " is null\n" +
" THEN null\n" +
"WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" +
" CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY',d.birth, d.lastDayAtCenter), INTEGER)\n" +
"ELSE\n" +
" CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY',d.birth, CAST(c." + dateColName + " AS DATE)), INTEGER)\n" +
"END AS float) as AgeAtTimeDays,\n" +
"\n" +
//
"CAST(\n" +
"CASE\n" +
"WHEN d.birth is null or c." + dateColName + " is null\n" +
" THEN null\n" +
"WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < c." + dateColName + ") THEN\n" +
" CONVERT(age_in_months(d.birth, d.lastDayAtCenter), INTEGER)\n" +
"ELSE\n" +
" CONVERT(age_in_months(d.birth, CAST(c." + dateColName + " AS DATE)), INTEGER)\n" +
"END AS float) as AgeAtTimeMonths,\n" +
//NOTE: written as subselect so we ensure a single row returned in case data in ehr_lookups.ageclass has rows that allow dupes
"(SELECT ac.ageclass FROM ehr_lookups.ageclass ac\n" +
" WHERE " +
" (CONVERT(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())), DOUBLE) / 12) >= ac.\"min\" AND\n" +
" ((CONVERT(age_in_months(d.birth, COALESCE(d.lastDayAtCenter, now())), DOUBLE) / 12) < ac.\"max\" OR ac.\"max\" is null) AND\n" +
" d.species = ac.species AND\n" +
" (d.gender = ac.gender OR ac.gender IS NULL)\n" +
") AS AgeClassAtTime \n" +
"FROM \"" + schemaName + "\".\"" + queryName + "\" c " +
"LEFT JOIN \"" + ehrPath + "\".study.demographics d ON (d.Id = c." + idCol.getFieldKey().toSQLString() + ")"
String pkAlias = pkCol.getFieldKey().toSQLString();
qd.setSql(
"SELECT\n" +
" x." + pkAlias + ",\n" +
" CAST(CASE WHEN x.birth IS NULL OR x.effDate IS NULL THEN NULL\n" +
" ELSE ROUND(CONVERT(age_in_months(x.birth, x.effDate), DOUBLE) / 12, 1) END AS float) AS AgeAtTime,\n" +
" CAST(CASE WHEN x.birth IS NULL OR x.effDate IS NULL THEN NULL\n" +
" ELSE ROUND(CONVERT(age_in_days(x.birth, x.effDate), DOUBLE) / 365.25, 2) END AS float) AS AgeAtTimeYears,\n" +
" CAST(CASE WHEN x.birth IS NULL OR x.effDate IS NULL THEN NULL\n" +
" ELSE floor(age(x.birth, x.effDate)) END AS INTEGER) AS AgeAtTimeYearsRounded,\n" +
" CAST(CASE WHEN x.birth IS NULL OR x.effDate IS NULL THEN NULL\n" +
" ELSE age_in_days(x.birth, x.effDate) END AS INTEGER) AS AgeAtTimeDays,\n" +
" CAST(CASE WHEN x.birth IS NULL OR x.effDate IS NULL THEN NULL\n" +
" ELSE CONVERT(age_in_months(x.birth, x.effDate), INTEGER) END AS INTEGER) AS AgeAtTimeMonths,\n" +
//NOTE: written as subselect so we ensure a single row returned in case data in ehr_lookups.ageclass has rows that allow dupes
" (SELECT ac.ageclass FROM ehr_lookups.ageclass ac\n" +
" WHERE (CONVERT(age_in_months(x.birth, x.effDate), DOUBLE) / 12) >= ac.\"min\"\n" +
" AND ((CONVERT(age_in_months(x.birth, x.effDate), DOUBLE) / 12) < ac.\"max\" OR ac.\"max\" IS NULL)\n" +
" AND x.species = ac.species\n" +
" AND (x.gender = ac.gender OR ac.gender IS NULL)\n" +
" ) AS AgeClassAtTime\n" +
"FROM (\n" +
" SELECT\n" +
" " + pkSql + " AS " + pkAlias + ",\n" +
" d.birth AS birth,\n" +
" d.species AS species,\n" +
" d.gender AS gender,\n" +
" CASE WHEN (d.lastDayAtCenter IS NOT NULL AND d.lastDayAtCenter < " + dateSql + ")\n" +
" THEN d.lastDayAtCenter\n" +
" ELSE CAST(" + dateSql + " AS DATE) END AS effDate\n" +
" FROM \"" + schemaName + "\".\"" + queryName + "\" c\n" +
" LEFT JOIN \"" + ehrPath + "\".study.demographics d ON (d.Id = c." + idCol.getFieldKey().toSQLString() + ")\n" +
") x"
);
qd.setIsTemporary(true);

Expand All @@ -1877,12 +1849,17 @@ public TableInfo getLookupTableInfo()
{
_log.warn(e.getMessage(), e);
}
return null;
}

if (ti != null)
{
((BaseColumnInfo)ti.getColumn(pkCol.getName())).setHidden(true);
((BaseColumnInfo)ti.getColumn(pkCol.getName())).setKeyField(true);
ColumnInfo pk = ti.getColumn(pkCol.getName());
if (pk instanceof BaseColumnInfo basePk)
{
basePk.setHidden(true);
basePk.setKeyField(true);
}
}
else
{
Expand All @@ -1891,7 +1868,7 @@ public TableInfo getLookupTableInfo()
if (demographics != null)
{
_log.warn("Demographics table columns: ");
_log.warn(targetSchema.getTable("demographics").getColumnNameSet());
_log.warn(demographics.getColumnNameSet());
}
}

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