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Performedby ETL fixes #605

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Merged
labkey-martyp merged 3 commits into from
Oct 8, 2025
Merged

Performedby ETL fixes #605

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c8ba6bb
performedby fixes
labkey-martyp Oct 8, 2025
c6c518a
Add performedby to deaths
labkey-martyp Oct 8, 2025
5e438ed
Allow insert if no qcstatelabel
labkey-martyp Oct 8, 2025
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1 change: 1 addition & 0 deletions nirc_ehr/resources/etls/ProjectAndAssignment.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
bulkLoad="true" batchSize="5000" targetOption="truncate">
<columnTransforms>
<column source="assignmentDate" target="date"/>
<column source="performedby" target="performedby" transformClass="org.labkey.nirc_ehr.columnTransform.NIRCUserCreateTransform"/>
</columnTransforms>
</destination>
</transform>
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1 change: 1 addition & 0 deletions nirc_ehr/resources/etls/birth.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
</alternateKeys>
<columnTransforms>
<column source="birthDate" target="date"/>
<column source="performedby" target="performedby" transformClass="org.labkey.nirc_ehr.columnTransform.NIRCUserCreateTransform"/>
</columnTransforms>
</destination>
</transform>
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1 change: 1 addition & 0 deletions nirc_ehr/resources/etls/deaths.xml
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Expand Up @@ -13,6 +13,7 @@
</alternateKeys>
<columnTransforms>
<column source="deathDate" target="date"/>
<column source="performedby" target="performedby" transformClass="org.labkey.nirc_ehr.columnTransform.NIRCUserCreateTransform"/>
</columnTransforms>
</destination>
</transform>
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1 change: 1 addition & 0 deletions nirc_ehr/resources/etls/demographics.xml
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Expand Up @@ -13,6 +13,7 @@
</alternateKeys>
<columnTransforms>
<column source="BIRTH_DATE" target="date"/>
<column source="performedby" target="performedby" transformClass="org.labkey.nirc_ehr.columnTransform.NIRCUserCreateTransform"/>
</columnTransforms>
</destination>
</transform>
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6 changes: 6 additions & 0 deletions nirc_ehr/resources/queries/dbo/q_births.sql
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@@ -1,5 +1,9 @@
SELECT anm.ANIMAL_ID_NUMBER AS participantId,
anm.BIRTH_DATE AS birthDate,
(CASE
WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown'
ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME)
|| '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby,
-- audit timestamp for modifications or animal event received for created
COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified
FROM Animal anm
Expand All @@ -12,4 +16,6 @@ AND anm.ANIMAL_ID_NUMBER LIKE 'A%' -- Animal born in centers are pre-appended wi
AND alt.DESCRIPTION IS NOT NULL
GROUP BY anm.ANIMAL_ID_NUMBER,
anm.BIRTH_DATE,
ae.STAFF_ID.STAFF_FIRST_NAME,
ae.STAFF_ID.STAFF_LAST_NAME,
ae.CREATED_DATETIME
6 changes: 6 additions & 0 deletions nirc_ehr/resources/queries/dbo/q_deaths.sql
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Expand Up @@ -2,6 +2,10 @@
SELECT an.ANIMAL_ID_NUMBER AS participantId,
an.DEATH_DATE AS deathDate,
an.TERMINATION_REASON_ID as reason,
(CASE
WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown'
ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME)
|| '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby,
COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified
FROM Animal an
LEFT JOIN AUDIT_TRAIL adt ON an.ANIMAL_ID = substring(PRIMARY_KEY_VALUES, length('ANIMAL_ID = '))
Expand All @@ -12,4 +16,6 @@ AND an.TERMINATION_REASON_ID != 10 -- Invalid Id
GROUP BY an.ANIMAL_ID_NUMBER,
an.DEATH_DATE,
an.TERMINATION_REASON_ID,
ae.STAFF_ID.STAFF_FIRST_NAME,
ae.STAFF_ID.STAFF_LAST_NAME,
ae.CREATED_DATETIME
6 changes: 1 addition & 5 deletions nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRSharedDatasetTrigger.java
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Expand Up @@ -26,11 +26,7 @@ private void verifyPerformedBy(TableInfo table, @Nullable Map<String, Object> ne
{
if (newRow != null && newRow.containsKey("performedby") && newRow.get("performedby") == null)
{
if (!newRow.containsKey("QCStateLabel") || newRow.get("QCStateLabel") == null)
{
errors.addFieldError("performedby", "Record in " + table.getTitle() + " cannot be submitted without Performed By if QCStateLabel is not found. Contact your administrator.");
}
else if (newRow.containsKey("QCStateLabel") && newRow.get("QCStateLabel").equals("Completed"))
if (newRow.containsKey("QCStateLabel") && "Completed".equals(newRow.get("QCStateLabel")))
{
errors.addFieldError("performedby", "Performed By must be entered in all records before submitting final. Table: " + table.getTitle());
}
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