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Merged
spamhurts merged 5 commits into from
Dec 23, 2025
Merged

Add earliest housing demographics provider #868

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5cfa757
Added earliest housing demographics provider and query.
spamhurts Dec 19, 2025
171ee7a
removed redundant column wrapping method and replaced "Id" strings wi…
spamhurts Dec 19, 2025
7c22bdf
actually removed the redundant column wrapping method that was missed…
spamhurts Dec 19, 2025
8431213
- Use the ID_COLUMN constant in QueryConstants.java.
spamhurts Dec 22, 2025
c6c0029
commented out earliest housing registration to sort out test issue
spamhurts Dec 23, 2025
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17 changes: 17 additions & 0 deletions snprc_ehr/resources/queries/study/demographicsEarliestHousing.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
/*
* Copyright (c) 2017-2018 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
d.Id AS Id,
h.date as FirstHousingDate,
h.room as FirstHousingRoom,
h.room.area.description as FirstHousingRoomDescription
FROM study.demographics d


--date of first housing
LEFT JOIN study.housing as h on h.id = d.id and h.qcstate.publicdata = true
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RameshRapa marked this conversation as resolved.
and h.date = (select min(c1.date) from study.housing as c1
where h.id = c1.id)
2 changes: 2 additions & 0 deletions snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRModule.java
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Expand Up @@ -65,6 +65,7 @@
import org.labkey.snprc_ehr.demographics.CurrentDietDemographicsProvider;
import org.labkey.snprc_ehr.demographics.CurrentPedigreeDemographicsProvider;
import org.labkey.snprc_ehr.demographics.DeathsDemographicsProvider;
import org.labkey.snprc_ehr.demographics.EarliestHousingDemographicsProvider;
import org.labkey.snprc_ehr.demographics.IdHistoryDemographicsProvider;
import org.labkey.snprc_ehr.demographics.LastBcsDemographicsProvider;
import org.labkey.snprc_ehr.demographics.LastHousingDemographicsProvider;
Expand Down Expand Up @@ -194,6 +195,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
EHRService.get().registerDemographicsProvider(new MhcSummaryDemographicsProvider(this));
EHRService.get().registerDemographicsProvider(new LastHousingDemographicsProvider(this));
EHRService.get().registerDemographicsProvider(new LastBcsDemographicsProvider(this));
EHRService.get().registerDemographicsProvider(new EarliestHousingDemographicsProvider(this));

EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.housing, "Find Animals Housed In A Given Room/Cage At A Specific Time", this, DetailsURL.fromString("/ehr-housingOverlaps.view?groupById=1"), "Commonly Used Queries");
EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.animalSearch, "Population Summary By Species, Gender and Age", this, DetailsURL.fromString("/query-executeQuery.view?schemaName=study&query.queryName=colonyPopulationByAge"), "Other Searches");
Expand Down
43 changes: 43 additions & 0 deletions snprc_ehr/src/org/labkey/snprc_ehr/demographics/EarliestHousingDemographicsProvider.java
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@@ -0,0 +1,43 @@
package org.labkey.snprc_ehr.demographics;

import org.labkey.api.ehr.demographics.AbstractListDemographicsProvider;
import org.labkey.api.module.Module;
import org.labkey.api.query.FieldKey;

import java.util.Collection;
import java.util.HashSet;
import java.util.Set;

public class EarliestHousingDemographicsProvider extends AbstractListDemographicsProvider

{

public EarliestHousingDemographicsProvider(Module owner)
{
super(owner, "study", "demographicsEarliestHousing", "earliestHousing");
_supportsQCState = false;
}

@Override
public String getName()
{
return "Earliest Housing";
}

@Override
protected Collection<FieldKey> getFieldKeys()
{
Set<FieldKey> keys = new HashSet<>();
keys.add(FieldKey.fromString("FirstHousingDate"));
keys.add(FieldKey.fromString("FirstHousingRoom"));
keys.add(FieldKey.fromString("FirstHousingRoomDescription"));

return keys;
}

@Override
public boolean requiresRecalc(String schema, String query)
{
return ("study".equalsIgnoreCase(schema) && "Housing".equalsIgnoreCase(query));
}
}
42 changes: 26 additions & 16 deletions snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java
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Expand Up @@ -19,6 +19,7 @@
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.BaseColumnInfo;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.Container;
import org.labkey.api.data.ForeignKey;
Expand All @@ -29,6 +30,7 @@
import org.labkey.api.data.WhitespacePreservingDisplayColumnFactory;
import org.labkey.api.data.WrappedColumn;

import org.labkey.api.data.WrappedColumnInfo;
import org.labkey.api.ehr.EHRService;
import org.labkey.api.ehr.security.EHRDataEntryPermission;
import org.labkey.api.exp.api.StorageProvisioner;
Expand Down Expand Up @@ -62,6 +64,8 @@ public class SNPRC_EHRCustomizer extends AbstractTableCustomizer

private Set<CalculatedColumn> calculatedColumns;

public static final String ID_COL = "Id";
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@jallentxbiomed jallentxbiomed Dec 22, 2025 •
edited
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In src/org/labkey/snrpc_ehr/constants/QueryConstants.java we have this string already as constant ID_COLUMN

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@spamhurts spamhurts Dec 22, 2025

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Thanks. I'll make the change.


public SNPRC_EHRCustomizer()
{
_provider = new CustomizerQueryProvider();
Expand Down Expand Up @@ -161,8 +165,14 @@ public void doTableSpecificCustomizations(AbstractTableInfo ti)
*/
if (matches(ti, "study", "Animal"))
{
UserSchema us = getEHRUserSchema(ti, STUDY_SCHEMA);
customizeAnimalTable(ti);
var col42 = getWrappedCol(us, ti, "earliestHousing", "demographicsEarliestHousing",ID_COL,ID_COL);
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col42.setLabel("Housing - Earliest");
col42.setDescription("The calculates the earliest housing location for each living animal.");
ti.addColumn(col42);
}

if (matches(ti, "study", "Animal Events") || matches(ti, "study", "encounters"))
{
customizeEncounterTable(ti);
Expand Down Expand Up @@ -444,35 +454,35 @@ private void customizeAnimalTable(AbstractTableInfo ds)
}
if (ds.getColumn("flags") == null)
{
var col = getWrappedCol(us, ds, "Flags", "demographicsActiveFlags", "Id", "Id");
var col = getWrappedCol(us, ds, "Flags", "demographicsActiveFlags", ID_COL, ID_COL);
col.setLabel("ActiveFlags");
col.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=ehr_lookups&queryName=flag_values&query.Id~eq=${Id}", ds.getContainerContext()));
ds.addColumn(col);
}
if (ds.getColumn("parents") == null)
{
var col = getWrappedCol(us, ds, "parents", "demographicsParents", "Id", "Id");
var col = getWrappedCol(us, ds, "parents", "demographicsParents", ID_COL, ID_COL);
col.setLabel("Parents");
ds.addColumn(col);
}

if (ds.getColumn("mhcSummary") == null)
{
var col = getWrappedCol(us, ds, "mhcSummary", "mhcSummary", "Id", "Id");
var col = getWrappedCol(us, ds, "mhcSummary", "mhcSummary", ID_COL, ID_COL);
col.setLabel("mhcSummary");
ds.addColumn(col);
}
if (ds.getColumn("totalOffspring") == null)
{
var col15 = getWrappedCol(us, ds, "totalOffspring", "demographicsTotalOffspring", "Id", "Id");
var col15 = getWrappedCol(us, ds, "totalOffspring", "demographicsTotalOffspring", ID_COL, ID_COL);
col15.setLabel("Number of Offspring");
col15.setDescription("Shows the total offspring of each animal");
ds.addColumn(col15);
}

if (ds.getColumn("labworkHistory") == null)
{
var col = getWrappedCol(us, ds, "labworkHistory", "demographicsLabwork", "Id", "Id");
var col = getWrappedCol(us, ds, "labworkHistory", "demographicsLabwork", ID_COL, ID_COL);
col.setLabel("Labwork History");
col.setDescription("Shows the date of last labwork for a subsets of tests");
ds.addColumn(col);
Expand All @@ -481,15 +491,15 @@ private void customizeAnimalTable(AbstractTableInfo ds)
//do we have freezer samples?
if (ds.getColumn("freezerSamples") == null)
{
var col = getWrappedCol(us, ds, "freezerSamples", "demographicsFreezers", "Id", "Id");
var col = getWrappedCol(us, ds, "freezerSamples", "demographicsFreezers", ID_COL, ID_COL);
col.setLabel("Freezer Samples");
col.setDescription("Shows the number of archived freezer samples");
col.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=study&queryName=freezerWorks&query.Id~eq=${Id}", ds.getContainerContext()));
ds.addColumn(col);
}
if (ds.getColumn("idHistoryList") == null)
{
var col = getWrappedCol(us, ds, "idHistoryList", "demographicsIdHistory", "Id", "Id");
var col = getWrappedCol(us, ds, "idHistoryList", "demographicsIdHistory", ID_COL, ID_COL);
col.setLabel("Id Hx List");
col.setDescription("List of Ids assigned to animal");
col.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=study&queryName=idHistory&query.Id~eq=${Id}", ds.getContainerContext()));
Expand All @@ -498,46 +508,46 @@ private void customizeAnimalTable(AbstractTableInfo ds)

if (ds.getColumn("activeAccounts") == null)
{
var col = getWrappedCol(us, ds, "activeAccounts", "demographicsActiveAccount", "Id", "Id");
var col = getWrappedCol(us, ds, "activeAccounts", "demographicsActiveAccount", ID_COL, ID_COL);
col.setLabel("Accounts - Active");
col.setDescription("Shows all accounts to which the animal is actively assigned on the current date");
ds.addColumn(col);
}

if (ds.getColumn("packageCategory") == null)
{
var col = getWrappedCol(us, ds, "packageCategory", "demographicsPackageCategories", "Id", "Id");
var col = getWrappedCol(us, ds, "packageCategory", "demographicsPackageCategories", ID_COL, ID_COL);
col.setLabel("Package Category");
col.setDescription("Shows the package category for procedures");
ds.addColumn(col);
}

if (ds.getColumn("activeAssignments") == null)
{
var col = getWrappedCol(us, ds, "activeAssignments", "demographicsActiveAssignment", "Id", "Id");
var col = getWrappedCol(us, ds, "activeAssignments", "demographicsActiveAssignment", ID_COL, ID_COL);
col.setLabel("IACUC Assignments - Active");
col.setDescription("Shows all protocols to which the animal is actively assigned on the current date");
ds.addColumn(col);
}

if (ds.getColumn("activeGroups") == null)
{
var col = getWrappedCol(us, ds, "activeGroups", "demographicsAnimalGroups", "Id", "Id");
var col = getWrappedCol(us, ds, "activeGroups", "demographicsAnimalGroups", ID_COL, ID_COL);
col.setLabel("Animal Groups - Active");
col.setDescription("Shows all groups to which the animal is actively assigned on the current date");
ds.addColumn(col);
}

if (ds.getColumn("MostRecentTBDate") == null)
{
var col = getWrappedCol(us, ds, "MostRecentTBDate", "demographicsMostRecentTBDate", "Id", "Id");
var col = getWrappedCol(us, ds, "MostRecentTBDate", "demographicsMostRecentTBDate", ID_COL, ID_COL);
col.setLabel("Most Recent TB");
col.setDescription("Queries the most recent TB date for the animal.");
ds.addColumn(col);
}
if (ds.getColumn("LastBCS") == null)
{
var col = getWrappedCol(us, ds, "LastBCS", "demographicsLastBCS", "Id", "Id");
var col = getWrappedCol(us, ds, "LastBCS", "demographicsLastBCS", ID_COL, ID_COL);
col.setLabel("Most Recent BCS");
col.setDescription("Queries the most recent BCS value for the animal.");
ds.addColumn(col);
Expand All @@ -546,7 +556,7 @@ private void customizeAnimalTable(AbstractTableInfo ds)
// Change label and description 8/31/2017 tjh
if (ds.getColumn("MostRecentArrival") != null)
{
var col = getWrappedCol(us, ds, "MostRecentArrival", "demographicsArrival", "Id", "Id");
var col = getWrappedCol(us, ds, "MostRecentArrival", "demographicsArrival", ID_COL, ID_COL);
ds.removeColumn(col);
col.setLabel("Acquisition");
col.setDescription("Calculates the earliest and most recent acquisition per animal.");
Expand All @@ -556,7 +566,7 @@ private void customizeAnimalTable(AbstractTableInfo ds)
// Change label and description 8/31/2017 tjh
if (ds.getColumn("MostRecentDeparture") != null)
{
var col = getWrappedCol(us, ds, "MostRecentDeparture", "demographicsMostRecentDeparture", "Id", "Id");
var col = getWrappedCol(us, ds, "MostRecentDeparture", "demographicsMostRecentDeparture", ID_COL, ID_COL);
ds.removeColumn(col);
col.setLabel("Disposition");
col.setDescription("Calculates the earliest and most recent departure per animal, if applicable, and most recent acquisition.");
Expand All @@ -568,7 +578,7 @@ private void customizeAnimalTable(AbstractTableInfo ds)
{
if (ds.getColumn("GenDemoCustomizer") == null)
{
var col = getWrappedCol(us, ds, "GenDemoCustomizer", "GenDemoCustomizer", "Id", "Id");
var col = getWrappedCol(us, ds, "GenDemoCustomizer", "GenDemoCustomizer", ID_COL, ID_COL);
col.setLabel("Genetic Assays");
col.setDescription("Show if genetic assays exist for ID");
ds.addColumn(col);
Expand Down