[bot] Merge 26.3 to develop

nirc_ehr/resources/data/calculated_status_codes.tsv

@@ -0,0 +1,7 @@
+code
+Alive
+Alive - In Progress
+Dead
+ERROR
+No Record
+Shipped

nirc_ehr/resources/data/editable_lookups.tsv

@@ -23,6 +23,7 @@ ehr_lookups	blood_draw_tube_type	Clinical	Blood Draw Tube Type	Used in blood dra
 ehr_lookups	blood_sample_type	Clinical	Blood Sample Types	Used in blood draw datasets.
 ehr_lookups	blood_tube_volumes	Clinical	Blood Tube Volumes	Used in blood draw datasets.
 ehr_lookups	cage_type	Colony Management	Cage Type	Used in cage details.
+ehr_lookups	calculated_status_codes	Colony Management	Calculated Status	Animal status values.
 ehr_lookups	capillary_refill_time	Clinical	Capillary Refill Times	Used clinical observations.
 ehr_lookups	card_format	Colony Management	Card Format	
 ehr_lookups	census_activity_status	Colony Management	Census Activity Status	

nirc_ehr/resources/data/lookup_sets.tsv

@@ -18,9 +18,9 @@ behavior_mgmt_codes	Behavior Management Codes	value
 behavior_types	Behavior Types	value
 blood_draw_reason	Blood Draw Reason	value
 blood_sample_type	Blood Sample Types	value
-card_format	Card Format	value	title
 cage_type	Cage Type	value	title
 capillary_refill_time	Capillary Refill Time	value
+card_format	Card Format	value	title
 census_activity_status	Census Activity Status	value	title
 clinremarks_category	Clinremarks Category	value	title
 congenital_abnormalities	Congenital Abnormalities	value	title

nirc_ehr/resources/data/lookupsManifest.tsv

@@ -23,6 +23,7 @@ blood_draw_tube_type
 blood_sample_type
 blood_tube_volumes
 cage_type
+calculated_status_codes
 capillary_refill_time
 card_format
 census_activity_status

nirc_ehr/resources/data/lookupsManifestTest.tsv

@@ -22,6 +22,7 @@ blood_draw_tube_type
 blood_sample_type
 blood_tube_volumes
 cage_type
+calculated_status_codes
 capillary_refill_time
 card_format
 census_activity_status

nirc_ehr/resources/queries/study/aliases.sql

@@ -2,12 +2,13 @@
 
 SELECT Id,
        Id as alias
-FROM study.Animal
+FROM study.Animal where Dataset.Demographics.calculated_status != 'Alive - In Progress'
 UNION
 SELECT Id,
     Name as alias
 FROM nirc_ehr.IdHistory
 UNION
 SELECT Id,
     Alias as alias
-FROM study.alias
+FROM study.alias where Id.demographics.calculated_status != 'Alive - In Progress'
+'

nirc_ehr/resources/queries/study/arrival.js

@@ -96,6 +96,8 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
             }
         }
 
+        row.calculated_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive';
+
         if(!oldRow) {
             //if not already present, insert into demographics
             helper.getJavaHelper().createDemographicsRecord(row.Id, row, extraDemographicsFieldMappings);

nirc_ehr/resources/queries/study/birth.js

@@ -78,10 +78,12 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                 'qcstate': helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId()
             }
 
+            var calc_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive';
+
             var obj = {
                 Id: row.Id,
                 date: row.date,
-                calculated_status: 'Alive',
+                calculated_status: calc_status,
                 dam: row['Id/demographics/dam'] || null,
                 sire: row['Id/demographics/sire'] || null,
                 species: row['Id/demographics/species'] || null,

nirc_ehr/resources/queries/study/housing.js

@@ -5,6 +5,89 @@ var prevDate;
 let triggerHelper = new org.labkey.nirc_ehr.query.NIRC_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
 let animalIds = [];
 
+function onInit(event, helper){
+    helper.setScriptOptions({
+        skipHousingCheck: true
+    });
+
+    helper.decodeExtraContextProperty('housingInTransaction');
+
+    helper.registerRowProcessor(function(helper, row){
+        if (!row)
+            return;
+
+        if (!row.Id || !row.room){
+            return;
+        }
+
+        var housingInTransaction = helper.getProperty('housingInTransaction');
+        housingInTransaction = housingInTransaction || {};
+        housingInTransaction[row.Id] = housingInTransaction[row.Id] || [];
+
+        // this is a failsafe in case the client did not provide housing JSON.  it ensures
+        // the current row is part of housingInTransaction
+        var shouldAdd = true;
+        if (row.objectid){
+            LABKEY.ExtAdapter.each(housingInTransaction[row.Id], function(r){
+                if (r.objectid == row.objectid){
+                    shouldAdd = false;
+                    return false;
+                }
+            }, this);
+        }
+
+        if (shouldAdd){
+            housingInTransaction[row.Id].push({
+                objectid: row.objectid,
+                date: row.date,
+                enddate: row.enddate,
+                qcstate: row.QCState,
+                room: row.room,
+                cage: row.cage,
+                divider: row.divider
+            });
+        }
+
+        helper.setProperty('housingInTransaction', housingInTransaction);
+    });
+}
+
+function onUpsert(helper, scriptErrors, row, oldRow){
+    //verify we dont have 2 opened records for the same ID
+    if (!helper.isETL() && !row.enddate && row.Id){
+        var map = helper.getProperty('housingInTransaction');
+        if (map && map[row.Id]){
+            var housingRecords = map[row.Id];
+            for (var i=0;i<housingRecords.length;i++){
+                if (row.objectid == housingRecords[i].objectid){
+                    console.log ('same housing record');
+                    continue;
+                }
+
+                if (!housingRecords[i].enddate){
+                    EHR.Server.Utils.addError(scriptErrors, 'enddate', 'Cannot enter multiple open-ended housing records for the same animal', 'WARN');
+                }
+            }
+        }
+    }
+
+    if (!helper.isETL() && row && row.Id && row.date && !row.enddate){
+        var objectid = row.objectid || null;
+        //if this record is active and public, deactivate any old housing records
+        var map = helper.getProperty('housingInTransaction');
+        var housingRecords = [];
+        if (map && map[row.Id]){
+            housingRecords = map[row.Id];
+        }
+
+        //NOTE: downstream java code should handle type conversion of housingInTransaction
+        var msg = helper.getJavaHelper().validateFutureOpenEndedHousing(row.Id, row.date, objectid, housingRecords);
+        if (msg){
+            EHR.Server.Utils.addError(scriptErrors, 'Id', msg, 'WARN');
+        }
+    }
+}
+
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'housing', function (helper, scriptErrors, row, oldRow) {
 
         if (helper.isETL()) {

nirc_ehr/resources/queries/study/observationSchedule.sql

@@ -2,11 +2,11 @@ SELECT
     g.id,
     g.scheduledDate,
     COUNT(g.caseid) cases,
-    GROUP_CONCAT(g.observations, ';') AS observations,
-    SUM(obsCount) AS obsCount,
-    GROUP_CONCAT(g.obsOrderIds, ';') AS orderIds,
-    GROUP_CONCAT(g.status, ';') AS status,
-    GROUP_CONCAT(g.taskids, ';') AS taskids,
+    o.observations,
+    SUM(g.obsCount) AS obsCount,
+    o.orderIds,
+    o.status,
+    o.taskids,
     MAX(g.type) AS type,
     MAX(g.caseid) AS caseid
 FROM
@@ -16,21 +16,29 @@ FROM
         sch.date AS scheduledDate,
         sch.caseid,
         sch.type,
-        GROUP_CONCAT(sch.objectid, ';') AS obsOrderIds,
-        GROUP_CONCAT(sch.category, ';') AS observations,
-        GROUP_CONCAT(obsStatus, ';') AS status,
-        GROUP_CONCAT(DISTINCT(sch.taskid), ';') AS taskids,
-        COUNT(sch.category) AS obsCount,
-        COUNT(sch.obsStatus) AS statusCount
-    FROM (
-        SELECT * FROM observationOrdersByDate
-    ) sch
+        COUNT(sch.category) AS obsCount
+    FROM observationOrdersByDate sch
     GROUP BY
         sch.animalId,
         sch.date,
         sch.caseid,
         sch.type
 ) g
+LEFT JOIN (
+    SELECT
+        obs.animalId AS id,
+        obs.date AS scheduledDate,
+        GROUP_CONCAT(DISTINCT obs.category, ';') AS observations,
+        GROUP_CONCAT(obs.objectid, ';') AS orderIds,
+        GROUP_CONCAT(obs.obsStatus, ';') AS status,
+        GROUP_CONCAT(DISTINCT(obs.taskid), ';') AS taskids
+    FROM observationOrdersByDate obs
+    GROUP BY obs.animalId, obs.date
+) o ON g.id = o.id AND g.scheduledDate = o.scheduledDate
 GROUP BY
     g.id,
-    g.scheduledDate
+    g.scheduledDate,
+    o.observations,
+    o.orderIds,
+    o.status,
+    o.taskids

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCCasesFormType.java

@@ -1,5 +1,6 @@
 package org.labkey.nirc_ehr.dataentry.form;
 
+import org.json.JSONObject;
 import org.labkey.api.ehr.dataentry.AbstractFormSection;
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.ehr.dataentry.FormSection;
@@ -117,4 +118,18 @@ protected List<String> getMoreActionButtonConfigs()
         configs.remove("DISCARD");
         return configs;
     }
+
+    @Override
+    public JSONObject toJSON()
+    {
+        JSONObject ret = super.toJSON();
+
+        //this form involves extra work on save, so relax warning thresholds to reduce error logging
+        ret.put("perRowWarningThreshold", 0.5);
+        ret.put("totalTransactionWarningThrehsold", 60);
+        ret.put("perRowValidationWarningThrehsold", 6);
+        ret.put("totalValidationTransactionWarningThrehsold", 60);
+
+        return ret;
+    }
 }

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCClinicalObservationsFormType.java

@@ -1,5 +1,6 @@
 package org.labkey.nirc_ehr.dataentry.form;
 
+import org.json.JSONObject;
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.ehr.dataentry.FormSection;
 import org.labkey.api.module.Module;
@@ -48,4 +49,18 @@ protected List<String> getButtonConfigs()
 
         return ret;
     }
+
+    @Override
+    public JSONObject toJSON()
+    {
+        JSONObject ret = super.toJSON();
+
+        //this form involves extra work on save, so relax warning thresholds to reduce error logging
+        ret.put("perRowWarningThreshold", 0.5);
+        ret.put("totalTransactionWarningThrehsold", 60);
+        ret.put("perRowValidationWarningThrehsold", 6);
+        ret.put("totalValidationTransactionWarningThrehsold", 60);
+
+        return ret;
+    }
 }

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCDeathNecropsyFormType.java

@@ -1,5 +1,6 @@
 package org.labkey.nirc_ehr.dataentry.form;
 
+import org.json.JSONObject;
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.ehr.dataentry.FormSection;
 import org.labkey.api.ehr.security.EHRVeterinarianPermission;
@@ -71,4 +72,18 @@ protected List<String> getMoreActionButtonConfigs()
         configs.remove("DISCARD");
         return configs;
     }
+
+    @Override
+    public JSONObject toJSON()
+    {
+        JSONObject ret = super.toJSON();
+
+        //this form involves extra work on save, so relax warning thresholds to reduce error logging
+        ret.put("perRowWarningThreshold", 0.5);
+        ret.put("totalTransactionWarningThrehsold", 60);
+        ret.put("perRowValidationWarningThrehsold", 6);
+        ret.put("totalValidationTransactionWarningThrehsold", 60);
+
+        return ret;
+    }
 }

nirc_ehr/src/org/labkey/nirc_ehr/history/NIRCObservationsDataSource.java

@@ -19,6 +19,7 @@
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Collection;
+import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
@@ -56,6 +57,7 @@ protected List<HistoryRow> processRows(Container c, TableSelector ts, final bool
                 rowMap.put("taskRowId", results.getInt(FieldKey.fromString("taskId/rowid")));
                 rowMap.put("formType", results.getString(FieldKey.fromString("taskId/formtype")));
                 rowMap.put("objectId", results.getString(FieldKey.fromString("objectId")));
+                rowMap.put("category", results.getString(FieldKey.fromString("category")));
                 rowMap.put("html", html);
 
                 Date roundedDate = DateUtils.truncate((Date)rowMap.get("date"), Calendar.MINUTE);
@@ -73,6 +75,7 @@ protected List<HistoryRow> processRows(Container c, TableSelector ts, final bool
         for (String key : idMap.keySet())
         {
             List<Map<String, Object>> toAdd = idMap.get(key);
+            toAdd.sort(Comparator.comparing(m -> String.valueOf(m.getOrDefault("category", "")), String.CASE_INSENSITIVE_ORDER));
 
             Date date = null;
             String subjectId = null;