Derive observation type from its category and fix cagemate matching

nbri_ehr/resources/queries/study/clinical_observations.js

@@ -45,6 +45,13 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
             EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Yes' for " + row.category + ", please explain in the Remark", "WARN");
         }
 
+        // Always derive the type from the observation type's category rather than trusting the incoming value.
+        // The Observations form leaves it blank because it offers every type; the other forms set it explicitly,
+        // but their type pickers are filtered to the categories that agree with the value they set, so deriving
+        // here gives them the same answer. Deriving unconditionally also re-derives when a re-opened draft or a
+        // saved template carries a type left over from a different category.
+        row.type = triggerHelper.getObservationTypeCategory(row.category) === 'Behavior' ? 'Behavior' : 'Clinical';
+
         // Handle scheduled observations
         if (!helper.isValidateOnly() && row.scheduledDate) {
             var qc;

nbri_ehr/resources/queries/study/demographicsCagemates.sql

@@ -25,10 +25,12 @@ JOIN study.housing h2
 -- cagemates. Room is not consulted, since it is derived from this same id and so can never distinguish two rows.
 ON (h.cage = h2.cage
         AND h2.Id.demographics.calculated_status = 'Alive'
-        AND h2.enddateTimeCoalesced >= now()
+        AND h2.isActive = true
         AND h2.qcstate.publicdata = true)
 
-WHERE h.enddateTimeCoalesced >= now()
+-- a null location never resolved, so the row gets no cagemates rather than grouping with every other unresolved row
+WHERE h.cage IS NOT NULL
+AND h.isActive = true
 AND h.qcstate.publicdata = true
 GROUP BY h.id, h.cage
 

nbri_ehr/resources/web/nbri_ehr/model/sources/ObsDefaults.js

@@ -6,6 +6,13 @@
 EHR.model.DataModelManager.registerMetadata('ObsDefaults', {
     byQuery: {
         'study.clinical_observations': {
+            // This form offers every observation type, so it can't know the observation's type up front.
+            // Clearing the default inherited from ClinicalDefaults lets the trigger script derive it
+            // from the selected type's category.
+            type: {
+                hidden: true,
+                defaultValue: null
+            },
             category: {
                 lookup: {
                     columns: 'value,description',

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBehaviorRoundsFormType.java

@@ -46,7 +46,7 @@ public NBRIBehaviorRoundsFormType(DataEntryFormContext ctx, Module owner)
                 new NBRIAnimalDetailsFormSection(),
                 new NBRICaseTemplateFormSection("Case Template", "Case Template", "nbri_ehr-casetemplatepanel", Arrays.asList(ClientDependency.supplierFromPath("nbri_ehr/panel/CaseTemplatePanel.js"))),
                 new NBRICasesFormPanelSection("Behavior Case", ctx, true),
-                new NBRIClinicalObservationsFormSection(true, "cases"),
+                new NBRIClinicalObservationsFormSection(null, true, "cases"),
                 new NBRITreatmentGivenFormSection(true, "cases")
         ));
 

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBehavioralCasesFormType.java

@@ -50,7 +50,7 @@ public NBRIBehavioralCasesFormType(DataEntryFormContext ctx, Module owner)
                 new NBRICaseTemplateFormSection("Case Template", "Case Template", "nbri_ehr-casetemplatepanel", Arrays.asList(ClientDependency.supplierFromPath("nbri_ehr/panel/CaseTemplatePanel.js"))),
                 new NBRICasesFormPanelSection("Behavior Case", ctx, true),
                 new NBRIClinicalRemarksFormPanelSection(true, "cases", "Behavior Assessment", ctx, true),
-                new NBRIClinicalObservationsFormSection(true, "cases"),
+                new NBRIClinicalObservationsFormSection(null, true, "cases"),
                 new NBRIObservationOrdersFormSection(null, true, "cases"),
                 new NBRITreatmentGivenFormSection(true, "cases"),
                 new NBRITreatmentOrderFormSection(true, "cases")

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBulkBehaviorFormType.java

@@ -45,8 +45,8 @@ public NBRIBulkBehaviorFormType(DataEntryFormContext ctx, Module owner)
                 new NBRIClinicalRemarksFormSection("Behavior Assessment", ctx.getContainer().hasPermission(ctx.getUser(), NBRIEHRVetTechPermission.class),
                         ctx.getContainer().hasPermission(ctx.getUser(), EHRVeterinarianPermission.class),
                         ctx.getContainer().hasPermission(ctx.getUser(), AdminPermission.class)),
-                new NBRIClinicalObservationsFormSection(false, null),
-                new NBRIObservationOrdersFormSection("NBRI_DAILY_CLINICAL_OBS_ORDERS", false, null),
+                new NBRIClinicalObservationsFormSection(null, false, null),
+                new NBRIObservationOrdersFormSection(null, false, null),
                 new NBRITreatmentGivenFormSection(),
                 new NBRITreatmentOrderFormSection()
         ));

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBulkClinicalFormType.java

@@ -51,7 +51,7 @@ public NBRIBulkClinicalFormType(DataEntryFormContext ctx, Module owner)
                         ctx.getContainer().hasPermission(ctx.getUser(), EHRVeterinarianPermission.class),
                         ctx.getContainer().hasPermission(ctx.getUser(), AdminPermission.class)),
                 new NBRIWeightFormSection(true, true),
-                new NBRIClinicalObservationsFormSection(false, null),
+                new NBRIClinicalObservationsFormSection("NBRI_DAILY_CLINICAL_OBS", false, null),
                 new NBRIObservationOrdersFormSection("NBRI_DAILY_CLINICAL_OBS_ORDERS", false, null),
                 new NBRIProcedureFormSection(),
                 new NBRIProcedureOrderFormSection(),

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRICasesFormType.java

@@ -58,7 +58,7 @@ public NBRICasesFormType(DataEntryFormContext ctx, Module owner)
                 new NBRICasesFormPanelSection("Clinical Case", ctx, false),
                 new NBRIClinicalRemarksFormPanelSection(true, "cases", "Clinical Remarks", ctx, false),
                 new NBRIWeightFormSection(true, false, true, "cases"),
-                new NBRIClinicalObservationsFormSection(true, "cases"),
+                new NBRIClinicalObservationsFormSection("NBRI_DAILY_CLINICAL_OBS", true, "cases"),
                 new NBRIObservationOrdersFormSection(null, true, "cases"),
                 new NBRIProcedureFormSection(true, "cases"),
                 new NBRIProcedureOrderFormSection(true, "cases"),

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIClinicalObservationsFormType.java

@@ -37,7 +37,7 @@ public NBRIClinicalObservationsFormType(DataEntryFormContext ctx, Module owner)
         super(ctx, owner, NAME, NAME, "Clinical", Arrays.asList(
                 new NBRITaskFormSection(),
                 new NBRIAnimalDetailsFormSection(),
-                new NBRIClinicalObservationsFormSection(false, false),
+                new NBRIClinicalObservationsFormSection("NBRI_DAILY_CLINICAL_OBS", false),
                 new NBRIWeightFormSection(true, true)
         ));
 

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIClinicalRoundsFormType.java

@@ -50,7 +50,7 @@ public NBRIClinicalRoundsFormType(DataEntryFormContext ctx, Module owner)
                 new NBRICaseTemplateFormSection("Case Template", "Case Template", "nbri_ehr-casetemplatepanel", Arrays.asList(ClientDependency.supplierFromPath("nbri_ehr/panel/CaseTemplatePanel.js"))),
                 new NBRICasesFormPanelSection("Clinical Case", ctx, false),
                 new NBRIWeightFormSection(true, false, true, "cases"),
-                new NBRIClinicalObservationsFormSection(true, "cases"),
+                new NBRIClinicalObservationsFormSection("NBRI_DAILY_CLINICAL_OBS", true, "cases"),
                 new NBRIProcedureFormSection(true, "cases"),
                 new NBRITreatmentGivenFormSection(true, "cases"),
                 new NBRIVitalsFormSection(true, "cases"),

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIClinicalObservationsFormSection.java

@@ -22,24 +22,23 @@
 public class NBRIClinicalObservationsFormSection extends BaseFormSection
 {
     public static final String LABEL = "Observations";
-    private boolean _autoPopulateDailyObs;
+    private final String _dailyObsOption;
 
-    public NBRIClinicalObservationsFormSection(boolean autoPopulateDailyObs, boolean initCollapsed)
+    public NBRIClinicalObservationsFormSection(String dailyObsOption, boolean initCollapsed)
     {
         super("study", "clinical_observations", LABEL, "ehr-clinicalobservationgridpanel", true, initCollapsed, true);
 
-        _autoPopulateDailyObs = autoPopulateDailyObs;
+        _dailyObsOption = dailyObsOption;
         addClientDependency(ClientDependency.supplierFromPath("ehr/plugin/ClinicalObservationsCellEditing.js"));
         addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/data/ClinicalObservationClientStore.js"));
         addClientDependency(ClientDependency.supplierFromPath("ehr/grid/ClinicalObservationGridPanel.js"));
-        addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/buttons/clinicalObsGridButton.js"));
         addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/buttons/addClinicalObsButton.js"));
         setClientStoreClass("NBRI_EHR.data.ClinicalObservationsClientStore");
     }
 
-    public NBRIClinicalObservationsFormSection(boolean isChild, String parentQueryName)
+    public NBRIClinicalObservationsFormSection(String dailyObsOption, boolean isChild, String parentQueryName)
     {
-        this(false, true);
+        this(dailyObsOption, true);
 
         if (isChild && null != parentQueryName)
         {
@@ -57,12 +56,9 @@ public List<String> getTbarButtons()
     {
         List<String> defaults = super.getTbarButtons();
 
-        if (_autoPopulateDailyObs)
+        if (_dailyObsOption != null)
         {
-            defaults.add("NBRI_AUTO_POPULATE_DAILY_OBS");
-        }
-        else {
-            defaults.add("NBRI_DAILY_CLINICAL_OBS");
+            defaults.add(_dailyObsOption);
         }
 
         return defaults;

nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIObservationOrdersFormSection.java

@@ -32,7 +32,6 @@ public NBRIObservationOrdersFormSection(String dailyObsOption, boolean initColla
         _dailyObsOption = dailyObsOption;
         addClientDependency(ClientDependency.supplierFromPath("ehr/plugin/ClinicalObservationsCellEditing.js"));
         addClientDependency(ClientDependency.supplierFromPath("ehr/grid/ClinicalObservationGridPanel.js"));
-        addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/buttons/clinicalObsGridButton.js"));
         addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/buttons/addClinicalObsButton.js"));
 
         setClientStoreClass("NBRI_EHR.data.ObsOrdersClientStore");

nbri_ehr/src/org/labkey/nbri_ehr/query/NBRI_EHRTriggerHelper.java

@@ -80,6 +80,7 @@ public class NBRI_EHRTriggerHelper
     private User _user;
     private static final Logger _log = LogManager.getLogger(NBRI_EHRTriggerHelper.class);
     private final Map<String,Object> _cachedDrugFormulary = new HashMap<>();
+    private final Map<String,String> _cachedObservationTypeCategories = new HashMap<>();
 
     // Maps an originating observation order's taskid to the task its scheduled observations are grouped under,
     // for the duration of a single save batch (the same helper instance is reused across rows in the batch).
@@ -924,6 +925,26 @@ public void ensureDailyClinicalObservationOrders(String id, String caseid, final
         }
     }
 
+    /**
+     * Returns the category of an observation type from ehr.observation_types, or null when the type has no
+     * category or is not found. Cached for the life of the save batch.
+     */
+    public String getObservationTypeCategory(String observationType)
+    {
+        if (observationType == null)
+            return null;
+
+        if (!_cachedObservationTypeCategories.containsKey(observationType))
+        {
+            TableInfo ti = getTableInfo("ehr", "observation_types");
+            SimpleFilter filter = new SimpleFilter(FieldKey.fromString("value"), observationType);
+            List<String> categories = new TableSelector(ti, Collections.singleton("category"), filter, null).getArrayList(String.class);
+            _cachedObservationTypeCategories.put(observationType, categories.isEmpty() ? null : categories.get(0));
+        }
+
+        return _cachedObservationTypeCategories.get(observationType);
+    }
+
     // This helper function propagates clinical observations through clinical cases
     public Map<String, Object> handleScheduledObservations(Map<String, Object> row, String qcstate, String orderTasks) throws SQLException, BatchValidationException, QueryUpdateServiceException, DuplicateKeyException
     {