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Merged
github-actions merged 7 commits into from
Aug 19, 2026
Merged

[bot] Fast-forward for 26.8.0 #745

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55a3895
Scope cage lookups to the EHR study container in housing tables (#734)
labkey-martyp Jul 29, 2026
7fd8527
Fix Record Treatment link to pass schedule slot date as scheduledDate…
labkey-martyp Jul 29, 2026
16deb1b
Merge 26.7 to 26.8
labkey-teamcity Aug 4, 2026
44b1091
Use shared treatment link display column factory (#736)
labkey-martyp Aug 6, 2026
86290dc
Remove stray quote from NIRC study.aliases query (#740)
labkey-bpatel Aug 6, 2026
687e792
Merge 26.3 to 26.7
labkey-teamcity Aug 10, 2026
5f7857c
Merge 26.7 to 26.8
labkey-teamcity Aug 11, 2026
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2 changes: 1 addition & 1 deletion nirc_ehr/resources/data/editable_lookups.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ ehr_lookups observation_areas Clinical Observation Areas Clinical observation ar
ehr_lookups obstetric_observations Clinical Obstetric Observations Obstetric Observations Fixed Values.
ehr_lookups ocular_observations Clinical Ocular Observations Ocular Observations Fixed Values.
ehr_lookups ocular_problem Clinical Ocular Problem Clinical observation fixed values.
ehr_lookups pairing_formation_types Pairing Formation Type value
ehr_lookups pairing_formation_types Behavior Pairing Formation Type Pairing formation values.
ehr_lookups pairing_goal Behavior Pairing Goal Used in pairing dataset.
ehr_lookups pairing_reason Behavior Introduction Reason Used in pairing dataset.
ehr_lookups pairing_observation Behavior Interaction Summary Used in pairing dataset.
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1 change: 0 additions & 1 deletion nirc_ehr/resources/queries/study/aliases.sql
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Expand Up @@ -16,4 +16,3 @@ UNION
SELECT Id,
Alias as alias
FROM study.alias where Id.demographics.calculated_status != 'Alive - In Progress'
'
1 change: 1 addition & 0 deletions nirc_ehr/resources/queries/study/treatmentSchedule.query.xml
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Expand Up @@ -2,6 +2,7 @@
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="treatmentSchedule" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.nirc_ehr.table.NIRC_EHRCustomizer" />
<tableTitle>Treatment Schedule</tableTitle>
<tableUrl>/EHR/treatmentDetails.view?key=${lsid}</tableUrl>
<pkColumnName>primaryKey</pkColumnName>
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1 change: 0 additions & 1 deletion nirc_ehr/resources/queries/study/treatmentSchedule.sql
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Expand Up @@ -38,7 +38,6 @@ JOIN(
timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly AS timestamp), dr.dateOnly) + 1 AS daysElapsed,
t1.enddate,
t1.code,
t1.treatmentRecord,
t1.volume,
t1.vol_units,
t1.concentration,
Expand Down
123 changes: 33 additions & 90 deletions nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@
import org.labkey.api.ehr.security.EHRDataEntryPermission;
import org.labkey.api.ehr.security.EHRVeterinarianPermission;
import org.labkey.api.ehr.table.FixedWidthDisplayColumn;
import org.labkey.api.ehr.table.TreatmentLinkConfig;
import org.labkey.api.ehr.table.TreatmentLinkDisplayColumnFactory;
import org.labkey.api.exp.api.StorageProvisioner;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.gwt.client.FacetingBehaviorType;
Expand Down Expand Up @@ -67,6 +69,10 @@

public class NIRC_EHRCustomizer extends AbstractTableCustomizer
{
private static final TreatmentLinkConfig RECORD_TREATMENT = TreatmentLinkConfig.builder()
.formTypes("Behavior", "Behavioral Rounds", "Bulk Behavior Entry")
.build();

public UserSchema getEHRUserSchema(AbstractTableInfo ds, String name)
{
Container ehrContainer = EHRService.get().getEHRStudyContainer(ds.getUserSchema().getContainer());
Expand Down Expand Up @@ -131,6 +137,11 @@ public void customize(TableInfo table)
customizeTreatmentOrder(ti);
}

if (matches(ti, "study", "treatmentSchedule"))
{
customizeTreatmentSchedule(ti);
}

if (matches(ti, "study", "prc_order"))
{
customizeProcedureOrder(ti);
Expand Down Expand Up @@ -896,15 +907,17 @@ private void ensureSortColumn(AbstractTableInfo ti, ColumnInfo baseColumn)

private void customizeHousingTable(AbstractTableInfo ti)
{
// ehr_lookups.cage is unique on (Container, Location), so the cage subqueries below must be container-scoped;
// a second EHR folder defining the same location would otherwise make them return multiple rows.
Container lookupContainer = EHRService.get().getEHRStudyContainer(ti.getUserSchema().getContainer());
if (lookupContainer == null)
lookupContainer = ti.getUserSchema().getContainer(); // as DefaultEHRCustomizer does

if (ti.getColumn("room") == null && ti.getColumn("cage") != null)
{
UserSchema us = getUserSchema(ti, "ehr_lookups");
if (us != null)
{
SQLFragment roomSql = new SQLFragment("(SELECT room FROM ehr_lookups.cage WHERE location = " + ExprColumn.STR_TABLE_ALIAS + ".cage)");
ExprColumn roomCol = new ExprColumn(ti, "room", roomSql, JdbcType.VARCHAR, ti.getColumn("cage"));
ti.addColumn(roomCol);
}
SQLFragment roomSql = new SQLFragment("(SELECT room FROM ehr_lookups.cage WHERE Container = ? AND location = " + ExprColumn.STR_TABLE_ALIAS + ".cage)", lookupContainer);
ExprColumn roomCol = new ExprColumn(ti, "room", roomSql, JdbcType.VARCHAR, ti.getColumn("cage"));
ti.addColumn(roomCol);

ensureSortColumn(ti, ti.getColumn("room"));
}
Expand All @@ -913,8 +926,8 @@ private void customizeHousingTable(AbstractTableInfo ti)
TableInfo realTable = getRealTable(ti);
if (realTable != null && realTable.getColumn("participantid") != null && realTable.getColumn("date") != null && realTable.getColumn("enddate") != null)
{
SQLFragment roomSql = new SQLFragment(realTable.getSqlDialect().getDateDiff(Calendar.DATE, "{fn curdate()}", "COALESCE((SELECT max(h2.enddate) as d FROM " + realTable.getSelectName() + " h2 LEFT JOIN ehr_lookups.cage cg ON h2.cage = cg.location " +
"WHERE h2.enddate IS NOT NULL AND h2.enddate <= " + ExprColumn.STR_TABLE_ALIAS + ".date AND h2.participantid = " + ExprColumn.STR_TABLE_ALIAS + ".participantid AND cg.room != (SELECT room FROM ehr_lookups.cage WHERE location = " + ExprColumn.STR_TABLE_ALIAS + ".cage)), " + ExprColumn.STR_TABLE_ALIAS + ".date)"));
SQLFragment roomSql = new SQLFragment(realTable.getSqlDialect().getDateDiff(Calendar.DATE, "{fn curdate()}", "COALESCE((SELECT max(h2.enddate) as d FROM " + realTable.getSelectName() + " h2 LEFT JOIN ehr_lookups.cage cg ON h2.cage = cg.location AND cg.Container = ? " +
"WHERE h2.enddate IS NOT NULL AND h2.enddate <= " + ExprColumn.STR_TABLE_ALIAS + ".date AND h2.participantid = " + ExprColumn.STR_TABLE_ALIAS + ".participantid AND cg.room != (SELECT room FROM ehr_lookups.cage WHERE Container = ? AND location = " + ExprColumn.STR_TABLE_ALIAS + ".cage)), " + ExprColumn.STR_TABLE_ALIAS + ".date)"), lookupContainer, lookupContainer);
ExprColumn roomCol = new ExprColumn(ti, "daysInRoom", roomSql, JdbcType.INTEGER, realTable.getColumn("participantid"), realTable.getColumn("date"), realTable.getColumn("enddate"));
roomCol.setLabel("Days In Room");
ti.addColumn(roomCol);
Expand Down Expand Up @@ -1065,88 +1078,18 @@ private void customizeTreatmentOrder(AbstractTableInfo ti)
{
WrappedColumn col = new WrappedColumn(ti.getColumn("objectid"), "treatmentRecord");
col.setLabel("Record Treatment");
col.setDisplayColumnFactory(new DisplayColumnFactory() {

@Override
public DisplayColumn createRenderer(final ColumnInfo colInfo)
{
return new DataColumn(colInfo){

@Override
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String objectid = (String)getBoundColumn().getValue(ctx);
Date date = (Date)ctx.get("date");
String caseid = (String)ctx.get("caseid");
String category = (String)ctx.get("category");
ActionURL url = new ActionURL("ehr", "dataEntryForm", ti.getUserSchema().getContainer());
if (!ti.getUserSchema().getContainer().hasPermission(ti.getUserSchema().getUser(), EHRClinicalEntryPermission.class))
return;

if (category.equals("Behavior"))
{
if (caseid != null)
{
url.addParameter("formType", "Behavioral Rounds");
url.addParameter("caseid", caseid);
}
else
{
url.addParameter("formType", "Bulk Behavior Entry");
}
}
else
{
if (caseid != null)
{
url.addParameter("formType", "Clinical Rounds");
url.addParameter("caseid", caseid);
}
else
{
url.addParameter("formType", "medicationTreatment");
}
}

url.addParameter("treatmentid", objectid);
url.addParameter("scheduledDate", date.toString());

String returnUrl = new ActionURL("ehr", "animalHistory", ti.getUserSchema().getContainer()) + "#inputType:none&showReport:0&activeReport:clinMedicationSchedule";
url.addParameter("returnUrl", returnUrl);

out.write(LinkBuilder.labkeyLink("Record Treatment", url).target("_blank"));
}

@Override
public void addQueryFieldKeys(Set<FieldKey> keys)
{
super.addQueryFieldKeys(keys);
keys.add(getBoundColumn().getFieldKey());
keys.add(FieldKey.fromString("date"));
keys.add(FieldKey.fromString("caseid"));
keys.add(FieldKey.fromString("category"));
}

@Override
public boolean isSortable()
{
return false;
}

@Override
public boolean isFilterable()
{
return false;
}
col.setDisplayColumnFactory(TreatmentLinkDisplayColumnFactory.forOrder(RECORD_TREATMENT));
ti.addColumn(col);
}
}

@Override
public boolean isEditable()
{
return false;
}
};
}
});
private void customizeTreatmentSchedule(AbstractTableInfo ti)
{
if (ti.getColumn("treatmentRecord") == null && ti.getColumn("objectid") != null)
{
WrappedColumn col = new WrappedColumn(ti.getColumn("objectid"), "treatmentRecord");
col.setLabel("Record Treatment");
col.setDisplayColumnFactory(TreatmentLinkDisplayColumnFactory.forSchedule(RECORD_TREATMENT));
ti.addColumn(col);
}
}
Expand Down
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