Merge 26.7 to develop

Author: labkey-teamcity

nirc_ehr/resources/queries/study/cases.js

@@ -22,7 +22,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                 error = true;
             }
 
-            if(!triggerHelper.canCloseCase(row.category)) {
+            if(!triggerHelper.canCloseCase()) {
                 EHR.Server.Utils.addError(errors, 'enddate', 'Veterinarian permission required to close a case.', 'ERROR');
                 error = true;
             }

nirc_ehr/resources/queries/study/deaths.js

@@ -84,6 +84,13 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
         //only allow death record to be created if the animal is in the demographics table
         if (idMap[row.Id]) {
 
+            // Do not allow a death record to be completed while other data for this animal is still in 'Review Required' state.
+            // Records belonging to this death's own task are excluded, since they move to Completed in the same save.
+            var reviewRequiredDatasets = null;
+            if (row.QCStateLabel && row.QCStateLabel.toUpperCase() === 'COMPLETED') {
+                reviewRequiredDatasets = triggerHelper.getReviewRequiredDatasets(row.Id, row.taskid || null);
+            }
+
             // check if a death record already exists for this animal
             if (idMap[row.Id].calculated_status.toUpperCase() === 'DEAD' && deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'COMPLETED') {
                 EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death record already exists for this animal.', 'ERROR');
@@ -112,6 +119,9 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
                     deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'IN PROGRESS') {
                 EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death/Necropsy data entry is in progress for this animal', 'ERROR');
             }
+            else if (reviewRequiredDatasets) {
+                EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death record cannot be completed. There is still data in Review Required state for this animal in the following dataset(s): ' + reviewRequiredDatasets, 'ERROR');
+            }
             else if (!helper.isValidateOnly() && row.Id && row.date && row.QCStateLabel.toUpperCase() === 'COMPLETED') {
 
                 if (validIds.indexOf(row.id) !== -1) {

nirc_ehr/resources/queries/study/departure.js

@@ -15,6 +15,21 @@ function onInit(event, helper){
 
 }
 
+function onUpsert(helper, scriptErrors, row, oldRow) {
+
+    if (!helper.isETL()) {
+
+        // Do not allow a departure record to be completed while other data for this animal is still in 'Review Required' state.
+        // Records belonging to this departure's own task are excluded, since they move to Completed in the same save.
+        if (row.QCStateLabel && row.QCStateLabel.toUpperCase() === 'COMPLETED') {
+            var reviewRequiredDatasets = triggerHelper.getReviewRequiredDatasets(row.Id, row.taskid || null);
+            if (reviewRequiredDatasets) {
+                EHR.Server.Utils.addError(scriptErrors, 'Id', 'Departure record cannot be completed. There is still data in Review Required state for this animal in the following dataset(s): ' + reviewRequiredDatasets, 'ERROR');
+            }
+        }
+    }
+}
+
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_INSERT, 'study', 'departure', function(helper, scriptErrors, row, oldRow) {
 
     if (row.id) {

nirc_ehr/resources/queries/study/studyDataReviewRequired.sql

@@ -0,0 +1,9 @@
+SELECT sd.Id,
+       sd.Date,
+       sd.DataSet.Label AS datasetLabel,
+       sd.taskid,
+       sd.lsid
+
+FROM study.StudyData sd
+INNER JOIN core.QCState qc ON sd.QCState = qc.RowId
+WHERE qc.Label = 'Review Required'

nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRModule.java

@@ -27,9 +27,7 @@
 import org.labkey.api.ehr.demographics.SourceDemographicsProvider;
 import org.labkey.api.ehr.history.DefaultAlopeciaDataSource;
 import org.labkey.api.ehr.history.DefaultAnimalRecordFlagDataSource;
-import org.labkey.api.ehr.history.DefaultClinicalRemarksDataSource;
 import org.labkey.api.ehr.history.DefaultNotesDataSource;
-import org.labkey.api.ehr.history.DefaultVitalsDataSource;
 import org.labkey.api.ehr.security.EHRDataAdminPermission;
 import org.labkey.api.ldk.ExtendedSimpleModule;
 import org.labkey.api.ldk.buttons.ShowEditUIButton;
@@ -131,7 +129,6 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         ehrService.registerDemographicsProvider(new ProtocolAssignmentDemographicsProvider(this));
         ehrService.registerDemographicsProvider(new HousingDemographicsProvider(this));
         ehrService.registerDemographicsProvider(new CagematesDemographicsProvider(this));
-        ehrService.registerDemographicsProvider(new CagematesDemographicsProvider(this));
         ehrService.registerDemographicsProvider(new ActiveCasesDemographicsProvider(this));
         ehrService.registerDemographicsProvider(new ActiveTreatmentsDemographicsProvider(this));
         ehrService.registerDemographicsProvider(new SourceDemographicsProvider(this));
@@ -145,9 +142,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         EHRService.get().registerHistoryDataSource(new DeathDataSource(this));
         EHRService.get().registerHistoryDataSource(new DefaultAlopeciaDataSource(this));
         EHRService.get().registerHistoryDataSource(new DefaultAnimalRecordFlagDataSource(this));
-        EHRService.get().registerHistoryDataSource(new DefaultClinicalRemarksDataSource(this));
         EHRService.get().registerHistoryDataSource(new DefaultNotesDataSource(this));
-        EHRService.get().registerHistoryDataSource(new DefaultVitalsDataSource(this));
         EHRService.get().registerHistoryDataSource(new DepartureDataSource(this));
         EHRService.get().registerHistoryDataSource(new DrugAdminDataSource(this));
         EHRService.get().registerHistoryDataSource(new FlagsDataSource(this));

nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java

@@ -20,6 +20,7 @@
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
@@ -74,6 +75,7 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
+import java.util.TreeSet;
 
 public class NIRC_EHRTriggerHelper
 {
@@ -324,6 +326,23 @@ public boolean deathExists(String id)
         return false;
     }
 
+    /**
+     * Returns a comma-separated list of dataset labels that still have records in the 'Review Required'
+     * QC state for the given animal, or null if there are none. Records belonging to {@code taskId} are
+     * excluded, since they transition to Completed in the same save as the death record itself.
+     */
+    @Nullable
+    public String getReviewRequiredDatasets(String animalId, @Nullable String taskId)
+    {
+        TableInfo ti = getTableInfo("study", "studyDataReviewRequired");
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("Id"), animalId);
+        if (taskId != null)
+            filter.addCondition(FieldKey.fromString("taskid"), taskId, CompareType.NEQ_OR_NULL);
+
+        Set<String> datasets = new TreeSet<>(new TableSelector(ti, Collections.singleton("datasetLabel"), filter, null).getArrayList(String.class));
+        return datasets.isEmpty() ? null : String.join(", ", datasets);
+    }
+
     public void upsertWeightRecord(Map<String, Object> row) throws QueryUpdateServiceException, DuplicateKeyException, SQLException, BatchValidationException, InvalidKeyException
     {
         BatchValidationException errors = new BatchValidationException();
@@ -693,7 +712,7 @@ public long totalRecords(String schemaName, String queryName, String columnName,
         return ts.getRowCount();
     }
 
-    public boolean canCloseCase(String category)
+    public boolean canCloseCase()
     {
         if (_container.hasPermission(_user, EHRVeterinarianPermission.class))
             return true;

nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java

@@ -1225,6 +1225,61 @@ public void testDeathNecropsyForm() throws IOException, CommandException
 
     }
 
+    @Test
+    public void testDeathAndDepartureBlockedByReviewRequiredData() throws Exception
+    {
+        String animalId = "REVREQ1";
+        String taskId = UUID.randomUUID().toString();
+
+        goToEHRFolder();
+
+        log("Creating a live animal with a weight record in Review Required state");
+        getApiHelper().deleteAllRecords("study", "deaths", new Filter("Id", animalId));
+        getApiHelper().deleteAllRecords("study", "departure", new Filter("Id", animalId));
+        getApiHelper().deleteAllRecords("study", "weight", new Filter("Id", animalId));
+        getApiHelper().deleteAllRecords("study", "demographics", new Filter("Id", animalId));
+
+        String[] demographicsFields = {"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"};
+        Object[][] demographicsData = {{animalId, "Rhesus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}};
+        getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), getApiHelper().prepareInsertCommand("study", "demographics", "lsid", demographicsFields, demographicsData), getExtraContext());
+
+        // The weight record carries the same taskid used by the death/departure rows below so the exclusion
+        // scenarios can prove that records belonging to the completing record's own task are excluded from
+        // the review-required check. Both scenarios are validate-only, so nothing persists between them.
+        String[] weightInsertFields = {"Id", "date", "weight", "taskid", FIELD_QCSTATELABEL, "performedby"};
+        Object[][] weightInsertData = {{animalId, new Date(), 8.5, taskId, EHRQCState.REVIEW_REQUIRED.label, 1004}};
+        getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), getApiHelper().prepareInsertCommand("study", "weight", "lsid", weightInsertFields, weightInsertData), getExtraContext());
+
+        String[] deathFields = {"Id", "date", "reason", "deathWeight", "taskid", FIELD_QCSTATELABEL, FIELD_OBJECTID, FIELD_LSID, "_recordid", "performedby"};
+        verifyCompletionBlockedByReviewRequired("deaths", "Death", deathFields,
+                new Object[]{animalId, new Date(), "4", 8.5, null, EHRQCState.COMPLETED.label, null, null, "recordID", 1004},
+                new Object[]{animalId, new Date(), "4", 8.5, taskId, EHRQCState.COMPLETED.label, null, null, "recordID", 1004});
+
+        String[] departureFields = {"Id", "date", "destination", "taskid", FIELD_QCSTATELABEL, FIELD_OBJECTID, FIELD_LSID, "_recordid", "performedby"};
+        verifyCompletionBlockedByReviewRequired("departure", "Departure", departureFields,
+                new Object[]{animalId, new Date(), "Oregon NPRC", null, EHRQCState.COMPLETED.label, null, null, "recordID", 1004},
+                new Object[]{animalId, new Date(), "Oregon NPRC", taskId, EHRQCState.COMPLETED.label, null, null, "recordID", 1004});
+    }
+
+    // Asserts that completing a record (death, departure) is blocked while other data for the animal is in
+    // Review Required state, and that a record whose taskid matches the review-required data is NOT blocked
+    // (its records move to Completed in the same save). rowWithoutTaskId/rowWithTaskId differ only in taskid.
+    private void verifyCompletionBlockedByReviewRequired(String queryName, String recordNoun, String[] fields, Object[] rowWithoutTaskId, Object[] rowWithTaskId)
+    {
+        // testValidationMessage defaults extraContext.targetQC to 'In Progress', and the global targetQC always
+        // overrides row-level QCStateLabel (see ehr/security.js normalizeQCState), so it must be forced to
+        // 'Completed' for the trigger to see a completing record.
+        Map<String, Object> completedTargetQC = Map.of("targetQC", EHRQCState.COMPLETED.label);
+
+        log("Completing a " + queryName + " record while other data is in Review Required state should be blocked");
+        Map<String, List<String>> expected = new HashMap<>();
+        expected.put("Id", Collections.singletonList("ERROR: " + recordNoun + " record cannot be completed. There is still data in Review Required state for this animal in the following dataset(s): Weight"));
+        getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", queryName, fields, new Object[][]{rowWithoutTaskId}, expected, completedTargetQC);
+
+        log("Review Required records on the " + queryName + " record's own task should not block completion");
+        getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", queryName, fields, new Object[][]{rowWithTaskId}, new HashMap<>(), completedTargetQC);
+    }
+
     @Test
     public void testClinicalCasesWorkflow()
     {