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Merged
spamhurts merged 4 commits into from
Jan 29, 2026
Merged

Query customizer for HL7 Pivot tables #881

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1b61f66
Added assignments at time calculated columns to HL7 Pivot query results
spamhurts Jan 20, 2026
98ddb95
Added Routine Chemistry query view
spamhurts Jan 27, 2026
320a2ef
Added escape comment to qview
spamhurts Jan 27, 2026
4a0a66e
fixed issue with surveillance query alias
spamhurts Jan 29, 2026
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7BiochemistryPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Biochemistry Results Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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3 changes: 2 additions & 1 deletion snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.sql
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SELECT
obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
Expand All @@ -20,6 +21,6 @@ GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, COALESCE (lp.Se

IN
(
select DISTINCT TestName as TEST_NAME from snprc_ehr.labwork_panels t
select DISTINCT ltrim(Rtrim(TestName)) as TEST_NAME from snprc_ehr.labwork_panels t
where t.includeInPanel = true AND t.ServiceId.Dataset='Biochemistry'
)
43 changes: 43 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot/RoutineChemistry.qview.xml
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<!-- $S is the escape code for / -->
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
<columns>
<column name="Id"/>
<column name="Date"/>
<column name="CREATININE::RESULT"/>
<column name="CREATININE::ABNORMAL_FLAGS"/>
<column name="GLUCOSE::RESULT"/>
<column name="GLUCOSE::ABNORMAL_FLAGS"/>
<column name="BUN$SCREAT RATIO::RESULT"/>
<column name="BUN$SCREAT RATIO::ABNORMAL_FLAGS"/>
<column name="TOTAL PROTEIN::RESULT"/>
<column name="TOTAL PROTEIN::ABNORMAL_FLAGS"/>
<column name="ALBUMIN::RESULT"/>
<column name="ALBUMIN::ABNORMAL_FLAGS"/>
<column name="GLOBULIN (CALC)::RESULT"/>
<column name="GLOBULIN (CALC)::ABNORMAL_FLAGS"/>
<column name="A$SG RATIO (CALC)::RESULT"/>
<column name="A$SG RATIO (CALC)::ABNORMAL_FLAGS"/>
<column name="ALT $S SGPT::RESULT"/>
<column name="ALT $S SGPT::ABNORMAL_FLAGS"/>
<column name="AST $S SGOT::RESULT"/>
<column name="AST $S SGOT::ABNORMAL_FLAGS"/>
<column name="ALK PHOSPHATASE::RESULT"/>
<column name="ALK PHOSPHATASE::ABNORMAL_FLAGS"/>
<column name="SODIUM::RESULT"/>
<column name="SODIUM::ABNORMAL_FLAGS"/>
<column name="POTASSIUM::RESULT"/>
<column name="POTASSIUM::ABNORMAL_FLAGS"/>
<column name="CHLORIDE::RESULT"/>
<column name="CHLORIDE::ABNORMAL_FLAGS"/>
<column name="CARBON DIOXIDE::RESULT"/>
<column name="CARBON DIOXIDE::ABNORMAL_FLAGS"/>
<column name="ANION GAP (CALC)::RESULT"/>
<column name="ANION GAP (CALC)::ABNORMAL_FLAGS"/>
<column name="COMMENT"/>
</columns>
<sorts>
<sort column="Id"/>
<sort column="Date" descending="true"/>
</sorts>
</customView>

7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7CulturePivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Culture and Sensitivity Results Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql
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SELECT
obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7HematologyPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Hematology Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.sql
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SELECT
obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7HistologyPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Histology Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.sql
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SELECT obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7MiscPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Misc Tests Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql
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SELECT obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.query.xml
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<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7ParasitologyPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Parasitology Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.sql
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SELECT obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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5 changes: 5 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.query.xml
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Expand Up @@ -2,11 +2,16 @@
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7SurveillancePivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Surveillance Pivot</tableTitle>
<columns>
<column columnName="PROCEDURE_NAME">
<isHidden>true</isHidden>
</column>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
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21 changes: 11 additions & 10 deletions snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.sql
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select Id,
date,
PROCEDURE_NAME,
PROCEDURE_ID,
COMMENT,
TestName,
MAX(ABNORMAL_FLAGS) as ABNORMAL_FLAGS,
COALESCE(MAX(RESULT), GROUP_CONCAT(QUALITATIVE_RESULT)) as RESULT
from snprc_ehr.HL7SurveillancePivotInner
select spi.Id,
spi.date,
spi.Id || '-' || CAST(spi.date AS VARCHAR) as key,
spi.PROCEDURE_NAME,
spi.PROCEDURE_ID,
spi.COMMENT,
spi.TestName,
MAX(spi.ABNORMAL_FLAGS) as ABNORMAL_FLAGS,
COALESCE(MAX(spi.RESULT), GROUP_CONCAT(spi.QUALITATIVE_RESULT)) as RESULT
from snprc_ehr.HL7SurveillancePivotInner as spi

GROUP BY id, date, PROCEDURE_NAME, PROCEDURE_NAME, PROCEDURE_ID, COMMENT, TestName
GROUP BY spi.id, spi.date, spi.PROCEDURE_NAME, spi.PROCEDURE_NAME, spi.PROCEDURE_ID, spi.COMMENT, spi.TestName
PIVOT RESULT, ABNORMAL_FLAGS BY TestName

IN
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.query.xml
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Expand Up @@ -2,7 +2,14 @@
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7UnknownPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Unknown Panel Category Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.sql
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SELECT
obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
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7 changes: 7 additions & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7Urinalysis.query.xml
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Expand Up @@ -2,7 +2,14 @@
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="HL7UrinalysisPivot" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Urinalysis Pivot</tableTitle>
<columns>
<column columnName="Key">
<isKeyField>true</isKeyField>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
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1 change: 1 addition & 0 deletions snprc_ehr/resources/queries/snprc_ehr/HL7UrinalysisPivot.sql
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SELECT
obr.ANIMAL_ID as id,
obr.OBSERVATION_DATE_TM as date,
obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
obr.MESSAGE_ID,
COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
obr.PROCEDURE_ID,
Expand Down
10 changes: 10 additions & 0 deletions snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java
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Expand Up @@ -123,6 +123,7 @@ public void doSharedCustomization(AbstractTableInfo ti)
{
ti.getMutableColumn("project").setLabel("Charge Id");
}

}

public UserSchema getEHRUserSchema(AbstractTableInfo ds, String name)
Expand Down Expand Up @@ -202,6 +203,14 @@ public void doTableSpecificCustomizations(AbstractTableInfo ti)
{
customizeTasks(ti);
}

// add assignments and age to hl7 pivot tables
if (ti.getName().toLowerCase().contains("hl7") && ti.getName().toLowerCase().contains("pivot")) {
UserSchema snprc_ehrSchema = getEHRUserSchema(ti, SNPRC_EHRSchema.NAME);
appendAssignmentAtTimeColumn(snprc_ehrSchema, ti, DATE_COLUMN);
appendAgeAtTimeColumn(snprc_ehrSchema, ti, DATE_COLUMN);
}

}

/**
Expand All @@ -225,6 +234,7 @@ private void addCalculatedColumns(AbstractTableInfo table)
appendAssignmentAtTimeColumn(ehrSchema, table, DATE_COLUMN);
appendAgeAtTimeColumn(ehrSchema, table, DATE_COLUMN);
}

}

/**
Expand Down