Query customizer for HL7 Pivot tables #881

spamhurts · 2026-01-27T22:29:48Z

Rationale

Added calculated at-time columns for assignments and accounts to HL7 Pivot tables. Started creating qviews for routine lab results.

Copilot

Pull request overview

This pull request adds calculated at-time columns (assignments and accounts) and age columns to HL7 Pivot tables through both Java customizer code and query XML configuration changes. It also introduces a composite key field for each pivot table and creates a new query view (qview) for routine chemistry results.

Changes:

Added Java customizer logic to append assignment and age calculated columns to HL7 pivot tables
Added composite key fields (id + date concatenation) to all HL7 pivot table SQL queries
Configured key field metadata and added DefaultEHRCustomizer to all HL7 pivot table query.xml files
Created a new RoutineChemistry.qview.xml file with specific column selections for biochemistry results
Applied ltrim/rtrim to TestName in HL7BiochemistryPivot for whitespace handling

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 19 comments.

Show a summary per file

File	Description
SNPRC_EHRCustomizer.java	Added logic to detect HL7 pivot tables and append assignment and age calculated columns
HL7BiochemistryPivot.sql	Added key field and trimmed TestName in the IN clause
HL7BiochemistryPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7CulturePivot.sql	Added key field composed of id and date
HL7CulturePivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7HematologyPivot.sql	Added key field composed of id and date
HL7HematologyPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7HistologyPivot.sql	Added key field composed of id and date
HL7HistologyPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7MiscPivot.sql	Added key field composed of id and date
HL7MiscPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7ParasitologyPivot.sql	Added key field composed of id and date
HL7ParasitologyPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7SurveillancePivot.sql	Added key field but with incorrect column references
HL7SurveillancePivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7UnknownPivot.sql	Added key field composed of id and date
HL7UnknownPivot.query.xml	Added DefaultEHRCustomizer and key field configuration
HL7UrinalysisPivot.sql	Added key field composed of id and date
HL7Urinalysis.query.xml	Added DefaultEHRCustomizer and key field configuration
RoutineChemistry.qview.xml	New query view defining specific columns for routine chemistry results

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Copilot · 2026-01-27T22:50:28Z

snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.query.xml

    <metadata>
        <tables xmlns="http://labkey.org/data/xml">
            <table tableName="HL7UnknownPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />


This table now has two customizers being applied: DefaultEHRCustomizer from the XML configuration and SNPRC_EHRCustomizer from the Java code (lines 207-212 of SNPRC_EHRCustomizer.java). Both customizers may attempt to add assignment and age columns, potentially causing conflicts or duplicate columns. Verify that these customizers work together correctly without creating duplicate calculated columns.

Suggested change

<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />

Copilot · 2026-01-27T22:50:28Z

snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.sql

@@ -1,5 +1,6 @@
 select Id,
    date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field references undefined columns. The query selects from snprc_ehr.HL7SurveillancePivotInner which doesn't have an alias obr, and the columns are already aliased as Id and date in that inner query. Change obr.ANIMAL_ID to Id and obr.OBSERVATION_DATE_TM to date to match the existing column names in the SELECT list.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

Id || '-' || CAST(date AS VARCHAR) as key,

Copilot · 2026-01-27T22:50:29Z

snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.sql

 SELECT
    obr.ANIMAL_ID as id,
    obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field is composed only of id and date concatenation, but the query groups by additional columns (MESSAGE_ID, PROCEDURE_NAME, PROCEDURE_ID, COMMENT) which means multiple rows can have the same key value. This will cause issues since the key field is marked as isKeyField in the query.xml file. Consider including additional distinguishing fields in the key formula to ensure uniqueness, or reconsider whether this composite key is appropriate for the data structure.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

obr.ANIMAL_ID

|| '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR)

|| '-' || COALESCE(CAST(obr.MESSAGE_ID AS VARCHAR), '')

|| '-' || COALESCE(CAST(obr.PROCEDURE_ID AS VARCHAR), '')

|| '-' || COALESCE(COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), '')

|| '-' || COALESCE(nte.COMMENT, '') as key,

Copilot · 2026-01-27T22:50:29Z

snprc_ehr/resources/queries/snprc_ehr/HL7UrinalysisPivot.sql

 SELECT
    obr.ANIMAL_ID as id,
    obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field is composed only of id and date concatenation, but the query groups by additional columns (MESSAGE_ID, PROCEDURE_NAME, PROCEDURE_ID, COMMENT) which means multiple rows can have the same key value. This will cause issues since the key field is marked as isKeyField in the query.xml file. Consider including additional distinguishing fields in the key formula to ensure uniqueness, or reconsider whether this composite key is appropriate for the data structure.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

obr.ANIMAL_ID

|| '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR)

|| '-' || CAST(obr.MESSAGE_ID AS VARCHAR)

|| '-' || CAST(obr.SET_ID AS VARCHAR)

|| '-' || COALESCE(COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), '')

|| '-' || CAST(obr.PROCEDURE_ID AS VARCHAR)

|| '-' || COALESCE(nte.COMMENT, '') as key,

Copilot · 2026-01-27T22:50:29Z

snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.query.xml

    <metadata>
        <tables xmlns="http://labkey.org/data/xml">
            <table tableName="HL7SurveillancePivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />


This table now has two customizers being applied: DefaultEHRCustomizer from the XML configuration and SNPRC_EHRCustomizer from the Java code (lines 207-212 of SNPRC_EHRCustomizer.java). Both customizers may attempt to add assignment and age columns, potentially causing conflicts or duplicate columns. Verify that these customizers work together correctly without creating duplicate calculated columns.

Suggested change

<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />

Copilot · 2026-01-27T22:50:32Z

snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql

 SELECT
    obr.ANIMAL_ID as id,
    obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field is composed only of id and date concatenation, but the query groups by additional columns (MESSAGE_ID, PROCEDURE_NAME, PROCEDURE_ID, COMMENT) which means multiple rows can have the same key value. This will cause issues since the key field is marked as isKeyField in the query.xml file. Consider including additional distinguishing fields in the key formula to ensure uniqueness, or reconsider whether this composite key is appropriate for the data structure.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR)

|| '-' || COALESCE(CAST(obr.MESSAGE_ID AS VARCHAR), '')

|| '-' || COALESCE(CAST(obr.PROCEDURE_ID AS VARCHAR), '')

|| '-' || COALESCE(CAST(obr.SET_ID AS VARCHAR), '')

|| '-' || COALESCE(nte.COMMENT, '') as key,

Copilot · 2026-01-27T22:50:33Z

snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.sql

@@ -1,5 +1,6 @@
 SELECT obr.ANIMAL_ID as id,
       obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field is composed only of id and date concatenation, but the query groups by additional columns (MESSAGE_ID, PROCEDURE_NAME, PROCEDURE_ID, COMMENT) which means multiple rows can have the same key value. This will cause issues since the key field is marked as isKeyField in the query.xml file. Consider including additional distinguishing fields in the key formula to ensure uniqueness, or reconsider whether this composite key is appropriate for the data structure.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

obr.ANIMAL_ID

|| '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR)

|| '-' || COALESCE(obr.MESSAGE_ID, '')

|| '-' || COALESCE(CAST(obr.SET_ID AS VARCHAR), '')

|| '-' || COALESCE(CAST(obr.PROCEDURE_ID AS VARCHAR), '')

|| '-' || COALESCE(CAST(nte.COMMENT AS VARCHAR), '')

as key,

Copilot · 2026-01-27T22:50:33Z

snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql

@@ -1,5 +1,6 @@
 SELECT obr.ANIMAL_ID as id,
       obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,


The key field is composed only of id and date concatenation, but the query groups by additional columns (MESSAGE_ID, PROCEDURE_NAME, PROCEDURE_ID, COMMENT) which means multiple rows can have the same key value. This will cause issues since the key field is marked as isKeyField in the query.xml file. Consider including additional distinguishing fields in the key formula to ensure uniqueness, or reconsider whether this composite key is appropriate for the data structure.

Suggested change

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,

obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) || '-' ||

CAST(obr.MESSAGE_ID AS VARCHAR) || '-' || CAST(obr.PROCEDURE_ID AS VARCHAR) || '-' ||

COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) || '-' || COALESCE(nte.COMMENT, '') as key,

Copilot · 2026-01-27T22:50:33Z

snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.query.xml

    <metadata>
        <tables xmlns="http://labkey.org/data/xml">
            <table tableName="HL7BiochemistryPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />


This table now has two customizers being applied: DefaultEHRCustomizer from the XML configuration and SNPRC_EHRCustomizer from the Java code (lines 207-212 of SNPRC_EHRCustomizer.java). Both customizers may attempt to add assignment and age columns, potentially causing conflicts or duplicate columns. Verify that these customizers work together correctly without creating duplicate calculated columns.

Suggested change

<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />

Copilot · 2026-01-27T22:50:34Z

snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.query.xml

    <metadata>
        <tables xmlns="http://labkey.org/data/xml">
            <table tableName="HL7MiscPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />


This table now has two customizers being applied: DefaultEHRCustomizer from the XML configuration and SNPRC_EHRCustomizer from the Java code (lines 207-212 of SNPRC_EHRCustomizer.java). Both customizers may attempt to add assignment and age columns, potentially causing conflicts or duplicate columns. Verify that these customizers work together correctly without creating duplicate calculated columns.

Suggested change

<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />

spamhurts added 3 commits January 20, 2026 16:12

Added assignments at time calculated columns to HL7 Pivot query results

1b61f66

Added Routine Chemistry query view

98ddb95

Added escape comment to qview

320a2ef

spamhurts requested review from RameshRapa, Copilot and jallentxbiomed January 27, 2026 22:44

Copilot started reviewing on behalf of spamhurts January 27, 2026 22:44 View session

Copilot AI reviewed Jan 27, 2026

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Query customizer for HL7 Pivot tables #881

Query customizer for HL7 Pivot tables #881

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	obr.ANIMAL_ID \|\| '-' \|\| CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
	Id \|\| '-' \|\| CAST(date AS VARCHAR) as key,

-    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
+    obr.ANIMAL_ID
+        || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR)
+        || '-' || COALESCE(CAST(obr.MESSAGE_ID AS VARCHAR), '')
+        || '-' || COALESCE(CAST(obr.PROCEDURE_ID AS VARCHAR), '')
+        || '-' || COALESCE(COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), '')
+        || '-' || COALESCE(nte.COMMENT, '') as key,

-    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) || '-' ||
+    CAST(obr.MESSAGE_ID AS VARCHAR) || '-' || CAST(obr.PROCEDURE_ID AS VARCHAR) || '-' ||
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) || '-' || COALESCE(nte.COMMENT, '') as key,

Query customizer for HL7 Pivot tables #881

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spamhurts commented Jan 27, 2026

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