Merge 25.10 to develop

labkey-teamcity · labkey-teamcity · commit 5c7a2f94b76c · 2025-10-15T11:17:23.000Z
diff --git a/nirc_ehr/resources/data/editable_lookups.tsv b/nirc_ehr/resources/data/editable_lookups.tsv
@@ -46,6 +46,7 @@ drug_defaults	Clinical	Formulary	Default values in drug and treatment datasets.
 ear_types	Clinical	Ear Types	Clinical observation fixed values.
 esig_events	Colony Management	Esig Events
 euthanasia_type	Colony Management	Euthanasia Type
+exam_findings	Clinical	Exam Findings	Physical exam values.
 exemption_category	Colony Management	Exemption Category
 expense_class	Colony Management	Expense Class
 fecal_score	Clinical	Fecal Score	Clinical observation fixed values.
@@ -120,6 +121,7 @@ stool_score	Clinical	Stool Score
 stool_types	Clinical	Stool Types
 tb_obs_score	Clinical	TB Observation Scores	Clinical observation fixed values.
 temperament	Behavior	Temperament	Behavior observation fixed values.
+testicular_volume    	Clinical	Testicular Volume   	Testicular volume values.
 termination_reason_codes	Clinical	Termination Reason Codes	Clinical observation fixed values.
 trauma_size	Clinical	Trauma Size	Clinical observation fixed values.
 treatment_frequency	Clinical	Treatment Frequency	Used in treatment and drug datasets.
@@ -134,4 +136,5 @@ wound_score	Clinical	Wound Score	Clinical observation fixed values.
 wound_severity	Clinical	Wound Severity	Clinical observation fixed values.
 wound_status_behavior	Behavior	Wound Status	Behavioral observation fixed values.
 wound_status_clinical	Clinical	Wound Status	Clinical observation fixed values.
-yes_no_order	Clinical	Yes/No Values in Order	Used for yes/no values in various datasets. Includes sort order.
+yes_no_order	Clinical	Yes/No Values in Order	Used for yes/no values in various datasets. Includes sort order.
+yes_no_only	Clinical	Yes/No Forced Selection	Must choose yes or no.
diff --git a/nirc_ehr/resources/data/exam_findings.tsv b/nirc_ehr/resources/data/exam_findings.tsv
@@ -0,0 +1,3 @@
+value
+No significant findings
+See remarks
diff --git a/nirc_ehr/resources/data/lookup_sets.tsv b/nirc_ehr/resources/data/lookup_sets.tsv
@@ -39,6 +39,7 @@ ear_types	Ear Types	value	title
 editable_lookups	List of UI editable lookup values	value
 esig_events	ESig Events	value	title
 euthanasia_type	Euthanasia Type	value	title
+exam_findings	Exam Findings	value
 exemption_category	Exemption Category	value	title
 expense_class	Expense Class	value	description
 fecal_score	Fecal Score	value	description
@@ -103,6 +104,7 @@ stool_score	Stool Score	value
 stool_types	Stool Types	value
 tb_obs_score	TB Obs Score	value
 temperament	Temperament	value	title
+testicular_volume	Testicular Volume	value	title
 trauma_size	Trauma Size	value
 turgor_score	Turgor Score	value
 termination_reason_codes	Termination Reason Codes Codes	value	title
@@ -114,4 +116,5 @@ wound_score	Wound Score	value
 wound_severity	Wound Severity	value
 wound_status_behavior	Wound Status Behavior	value
 wound_status_clinical	Wound Status Clinical	value
-yes_no_order	Yes/No Values in Order	value
+yes_no_order	Yes/No Values in Order	value
+yes_no_only	Yes/No Forced Selection	value
diff --git a/nirc_ehr/resources/data/lookupsManifest.tsv b/nirc_ehr/resources/data/lookupsManifest.tsv
@@ -44,6 +44,7 @@ ear_types
 editable_lookups
 esig_events
 euthanasia_type
+exam_findings
 exemption_category
 expense_class
 fecal_score
@@ -112,6 +113,7 @@ stool_score
 stool_types
 tb_obs_score
 temperament
+testicular_volume
 trauma_size
 treatment_frequency
 treatment_frequency_times
@@ -125,4 +127,5 @@ wound_score
 wound_severity
 wound_status_behavior
 wound_status_clinical
-yes_no_order
+yes_no_only
+yes_no_order
diff --git a/nirc_ehr/resources/data/lookupsManifestTest.tsv b/nirc_ehr/resources/data/lookupsManifestTest.tsv
@@ -43,6 +43,7 @@ ear_types
 editable_lookups
 esig_events
 euthanasia_type
+exam_findings
 exemption_category
 expense_class
 fecal_score
@@ -114,6 +115,7 @@ stool_score
 stool_types
 tb_obs_score
 temperament
+testicular_volume
 trauma_size
 treatment_frequency
 treatment_frequency_times
@@ -127,4 +129,5 @@ wound_score
 wound_severity
 wound_status_behavior
 wound_status_clinical
+yes_no_only
 yes_no_order
diff --git a/nirc_ehr/resources/data/observation_types.tsv b/nirc_ehr/resources/data/observation_types.tsv
@@ -43,8 +43,13 @@ SIB Score	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryN
 Special Enrichment	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
 Stool		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"stool_types","displayField":"value","sortFields":"sort_order","valueField":"value"}	ehr_lookups	stool_types	value
 Temperament	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"temperament","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	temperament	value
+Testicular volume-Left		"{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""testicular_volume"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}"	ehr_lookups	testicular_volume	value
+Testicular volume-Right		"{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""testicular_volume"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}"	ehr_lookups	testicular_volume	value
 Vaginal/Uterine Prolapse		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"vaginal_uterine_prolapse","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	vaginal_uterine_prolapse	value
 Verified Id?		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	yes_no_order	value
 Wound Severity	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_severity","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	wound_severity	value
 Wound Status	Behavior	{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status_behavior","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	wound_status_behavior	value
-Clinical Wound Status		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status_clinical","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	wound_status_clinical	value
+Clinical Wound Status		{"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status_clinical","displayField":"value","valueField":"value","sortFields":"sort_order"}	ehr_lookups	wound_status_clinical	value
+Annual Physical Exam		"{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}"	ehr_lookups	exam_findings	value
+Introductory Physical Exam		"{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}"	ehr_lookups	exam_findings	value
+Preshipment Physical Exam		"{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}"	ehr_lookups	exam_findings	value
diff --git a/nirc_ehr/resources/data/testicular_volume.tsv b/nirc_ehr/resources/data/testicular_volume.tsv
@@ -0,0 +1,13 @@
+value	sort_order
+1 mL	1
+2 mL	2
+3 mL	3
+4 mL	4
+5 mL	5
+6 mL	6
+8 mL	7
+10 mL	8
+12 mL	9
+15 mL	10
+20 mL	11
+25 mL	12
diff --git a/nirc_ehr/resources/data/yes_no_only.tsv b/nirc_ehr/resources/data/yes_no_only.tsv
@@ -0,0 +1,3 @@
+value	sort_order
+Yes	1
+No	2
diff --git a/nirc_ehr/resources/etls/ProjectAndAssignment.xml b/nirc_ehr/resources/etls/ProjectAndAssignment.xml
@@ -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>
diff --git a/nirc_ehr/resources/etls/birth.xml b/nirc_ehr/resources/etls/birth.xml
@@ -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>
diff --git a/nirc_ehr/resources/etls/deaths.xml b/nirc_ehr/resources/etls/deaths.xml
@@ -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>
diff --git a/nirc_ehr/resources/etls/demographics.xml b/nirc_ehr/resources/etls/demographics.xml
@@ -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>
diff --git a/nirc_ehr/resources/queries/dbo/q_births.sql b/nirc_ehr/resources/queries/dbo/q_births.sql
@@ -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
@@ -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
diff --git a/nirc_ehr/resources/queries/dbo/q_deaths.sql b/nirc_ehr/resources/queries/dbo/q_deaths.sql
@@ -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 = '))
@@ -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
diff --git a/nirc_ehr/resources/reports/additionalReports.tsv b/nirc_ehr/resources/reports/additionalReports.tsv
@@ -18,7 +18,7 @@ observationSchedule	Daily Reports	js	Today's Observation Schedule	true		study	ob
 activeClinicalObservationOrders	Clinical	query	Active Clinical Observation Orders	true		study	observation_order	Active Clinical Orders		date	false	false		qcstate/publicdata	This report contains a list of today's treatments to be administered
 activeBehaviorObservationOrders	Behavior	query	Active Behavior Observation Orders	true		study	observation_order	Active Behavior Orders		date	false	false		qcstate/publicdata	This report contains a list of today's treatments to be administered
 observationOrders	Clinical	query	Observation Orders	true		study	observation_order			date	false	false		qcstate/publicdata	This report contains a list of today's treatments to be administered
-alopecia	Clinical	query	Alopecia Scores	TRUE		study	clinical_observations	Alopecia Scores		date	FALSE	FALSE		qcstate/publicdata	This report contains the alopecia scores for the animal
+alopecia	Behavior	query	Alopecia Scores	TRUE		study	clinical_observations	Alopecia Scores		date	FALSE	FALSE		qcstate/publicdata	This report contains the alopecia scores for the animal
 behaviorCases	Behavior	query	Active Behavior Cases	true		study	activeBehaviorCases			date	false	false		qcstate/publicdata	This displays active behavioral cases
 allBehaviorCases	Behavior	query	Behavior Cases	true		study	behaviorCases			date	false	false		qcstate/publicdata	This displays all behavioral cases
 bloodSchedule															
@@ -46,3 +46,4 @@ pairings
 behaviorRemarks	Behavior	query	Behavior Remarks	true		study	BehaviorClinRemarks			date	false	false		qcstate/publicdata	This report contains the behavior remarks entered about each animal
 clinObsBehavior	Behavior	query	Observations	true		study	behaviorObservations			date	false	false		qcstate/publicdata	This report contains one record for each encounter with each animal, including surergies, exams, procedures, etc.
 clinremarks	Clinical	query	Clinical Remarks	true		study	ClinicalClinRemarks			date	false	false		qcstate/publicdata	This report contains the clinical remarks entered about each animal
+physicalExam	Clinical	query	Exam History	True		study	physicalExam			date	false	false		qcstate/publicdata	This report displays physical exam data for the selected animal
diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRSharedDatasetTrigger.java b/nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRSharedDatasetTrigger.java
@@ -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());
             }

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+value`
	`2`	`+No significant findings`
	`3`	`+See remarks`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+value sort_order`
	`2`	`+Yes 1`
	`3`	`+No 2`