Merge in snapshot branch

WNPRC_EHR/resources/queries/study/WaterScheduleWithWeight.sql

@@ -20,6 +20,7 @@ SELECT
     frequencyMeaning AS frequencyMeaningCoalesced,
     timeofday AS timeofday,
     displaytimeofday AS displaytimeofday,
+    actionRequired AS actionRequired,
     qcstate AS qcstate,
 
     --(SELECT max(wg.qcstate) as label FROM study.waterGiven wg WHERE WCO.objectid = wg.treatmentid AND WCO.dateOrdered = wg.dateordered ) AS waterStatus,

WNPRC_EHR/resources/queries/study/WaterScheduleWithWeight/.qview.xml

@@ -20,6 +20,7 @@
         <column name="rawDate"/>
         <column name="mlsPerKg"/>
         <column name="conditionAtTime"/>
+        <column name="actionRequired"/>
         <column name="qcstate" />
         <column name="taskid" />
     </columns>

WNPRC_EHR/resources/queries/study/deaths.js

@@ -16,8 +16,35 @@ function onComplete(event, errors, helper) {
     var ids = helper.getRows().map(function (row) {
         return row.row.id;
     });
+    var animalDateMap= [];
+    let clientRows = helper.getRows();
+
+    console.log("number of rows "+ clientRows.length);
+    if (clientRows){
+
+        for (var i= 0; i < clientRows.length; i++){
+            console.log("animalId "+clientRows[i].row.id);
+
+            animalDateMap.push({
+                animalId: clientRows[i].row.id,
+                endDate : clientRows[i].row.date
+            });
+
+        }
+
+    }
+    /*console.log("array line 37 " + Object.values(animalDateMap).length);
+
+    for (var i = 0; i < animalDateMap.length; i++){
+        console.log("array value " + animalDateMap[i]);
+    }*/
+
+    WNPRC.Utils.getJavaHelper().removeWaterAmounts(animalDateMap);
 
     //Sends notification.
     var hostName = 'https://' + LABKEY.serverName;
     WNPRC.Utils.getJavaHelper().sendDeathNotification(ids, hostName);
+
+
+
 }

WNPRC_EHR/resources/queries/study/waterGiven.js

@@ -85,36 +85,19 @@ function onInit(event, helper){
 }
 
 function onUpsert(helper, scriptErrors, row, oldRow) {
-    /*if (row.volume == null){
-        EHR.Server.Utils.addError(scriptErrors, 'volume', 'This field is required', 'WARN');
-        console.log ("value of QCState "+ row.QCState)
-    }*/
-
     if (row.QCStateLabel == 'Scheduled'){
         EHR.Server.Validation.verifyDate(row, scriptErrors, helper);
     }
 
         if (row.Id && row.date)
         {
-            // volume is handled differently for requestsvs actual draws
             var errorQC = 'ERROR';
-            //if (EHR.Server.Security.getQCStateByLabel(row.QCStateLabel)['isRequest'] && !row.taskid)
-            //    errorQC = 'ERROR';
-            //else
-            //    errorQC = 'INFO';
 
             var map = helper.getProperty('waterInTransaction');
             var waters = [];
             if (map && map[row.Id])
             {
                 waters = map[row.Id];
-                /*for (var i=0;i<map.length; i++ ){
-                    console.log ('value of map '+ map[i]);
-                    waters.push (map[i]);
-                    console.log ("map in JS "+map[i].objectid + " " + map[i].volume);
-                }*/
-                //console.log("stablishing map "+ map);
-               // waters.push(map);
             }
             if (row.location=='laboratory'){
                 if (!row.restraint){
@@ -135,7 +118,7 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
 
 
             //TODO: Troubleshoot this function to determine if the animal has not gotten enough water for the last three days.
-            /*if (row.volume)
+           /* if (row.volume)
                 {
                     var msg = WNPRC.Utils.getJavaHelper().waterLastThreeDays(row.Id, row.date, waters);
                     if (msg != null){
@@ -164,8 +147,6 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
                 }
 
             }
-
-
         }
         console.log ('parentid '+ row.parentid + ' lsid: '+row.lsid);
         if (row.id && row.date && row.performedby && row.parentid && !row.lsid){
@@ -195,10 +176,6 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
 
             }
         }
-
-
-        //EHR.Server.Validation.checkRestraint(row, scriptErrors);
-
 }
 function addWaterGivenDescription(row, waters){
     let clientDescription = '';

WNPRC_EHR/resources/queries/study/waterGiven.query.xml

@@ -47,9 +47,6 @@
                             <fkTable>husbandry_fruit</fkTable>
                             <fkColumnName>value</fkColumnName>
                         </fk>
-                    </column>
-                    <column columnName="remarks">
-
                     </column>
                     <column columnName="waterSource">
                         <columnTitle>Water Source</columnTitle>
@@ -59,6 +56,9 @@
                             <fkColumnName>value</fkColumnName>
                             <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
+                    </column>
+                    <column columnName="remarks">
+
                     </column>
                     <column columnName="location">
                         <columnTitle>Water Location</columnTitle>

WNPRC_EHR/resources/queries/study/waterOrders.js

@@ -7,7 +7,8 @@ let allowUsersMap = {};
 function onInit(event, helper){
     helper.setScriptOptions({
         allowFutureDates: true,
-        allowDatesInDistantPast: true
+        allowDatesInDistantPast: true,
+        skipWaterRegulationCheck: false
     });
     LABKEY.Query.selectRows({
         requiredVersion: 9.1,
@@ -35,9 +36,40 @@ function onInit(event, helper){
     });
 }
 
+function onInsert(helper, scriptErrors, row){
+    if (row.frequency !== 4 && row.waterSource === 'lixit'){
+        EHR.Server.Utils.addError(scriptErrors,"frequency", "Frequency should be 'Daily - Any Time' when selecting Lixit/Ad Lib", "ERROR");
+    }
 
-function onUpsert(helper, scriptErrors, row, oldRow){
+    if (row.id && row.waterSource === 'regulated' && row.frequency && row.assignedTo && row.provideFruit && row.date){
+        let lixitOrderMap = WNPRC.Utils.getJavaHelper().checkWaterLixit(row.id, row.date);
+        let lixitStartDate;
+        let lixitOrderObjectid;
+        let latestWaterSource;
+
+        if (lixitOrderMap != null){
+                lixitStartDate = new Date(lixitOrderMap.date);
+                lixitOrderObjectid = lixitOrderMap.objectid;
+                latestWaterSource = lixitOrderMap.waterSource;
+
+                if(latestWaterSource === "lixit" ) {
+                    let lixitEndDate = new Date(row.date);
+                    console.log(lixitEndDate)
+                    lixitEndDate.setDate(lixitEndDate.getDate()-1);
+                    console.log("startdate " + lixitStartDate + " objectid " + lixitOrderObjectid + "enddate " + lixitEndDate + " watersource " +row.waterSource);
+                    let jsonArray = WNPRC.Utils.getJavaHelper().closeWaterOrder(row.id, lixitStartDate, lixitEndDate, row.project, lixitOrderObjectid, true);
+                    if (jsonArray != null) {
+                        for (var i = 0; i < jsonArray.length; i++) {
+                            var errorObject = jsonArray[i];
+                            EHR.Server.Utils.addError(scriptErrors, errorObject.field, errorObject.message, errorObject.severity);
+                        }
+                    }
+                }
+        }
+    }
+}
 
+function onUpsert(helper, scriptErrors, row, oldRow){
     if (row.Id){
         EHR.Server.Utils.findDemographics({
             participant: row.Id,
@@ -54,13 +86,9 @@ function onUpsert(helper, scriptErrors, row, oldRow){
         });
         var animalRestricted = {};
         animalRestricted = WNPRC.Utils.getJavaHelper().checkIfAnimalInCondition(row.Id, row.date);
-        //console.log (animalRestricted);
         if (!animalRestricted && !row.skipWaterRegulationCheck){
             EHR.Server.Utils.addError(scriptErrors,'Id', 'Animal not assigned to water restriction protocol or is already in ' + row.waterSource + ' condition.', 'ERROR');
         }
-
-
-
     }
 
 
@@ -84,27 +112,31 @@ function onUpsert(helper, scriptErrors, row, oldRow){
     if (rowDate.getTime() > endDate.getTime()){
         EHR.Server.Utils.addError(scriptErrors,'endDate', 'EndDate cannot be before StartDate', 'ERROR');
     }
-
-    if (!row.frequency && row.waterSource == 'regulated'){
+    if (!row.frequency && row.waterSource === 'regulated'){
         EHR.Server.Utils.addError(scriptErrors, 'frequency', 'Frequency is required when entering regulated water orders.', 'ERROR');
     }
-    if (!row.volume && row.waterSource == 'regulated'){
+    if (!row.volume && row.waterSource === 'regulated'){
         //console.log ("water vol "+ row.volume);
         EHR.Server.Utils.addError(scriptErrors, 'volume', 'Volume is required when entering regulated water orders.', 'ERROR');
     }
-
-    if (!row.assignedTo && row.waterSource == 'regulated'){
+    if (!row.assignedTo && row.waterSource === 'regulated'){
         EHR.Server.Utils.addError(scriptErrors, 'assignedTo', 'Assigned To is required when entering regulated water orders.', 'ERROR');
     }
-
+    if (!row.provideFruit && row.waterSource === 'regulated'){
+        EHR.Server.Utils.addError(scriptErrors, 'provideFruit', 'Provide Fruit is required when entering regulated water orders.', 'INFO');
+    }
     if (!row.waterSource){
         EHR.Server.Utils.addError(scriptErrors, 'waterSource', 'Water Source is required when entering new orders.', 'ERROR');
     }
+    if (row.volume !== undefined && row.volume!== null && row.waterSource === 'lixit'){
+        EHR.Server.Utils.addError(scriptErrors,"volume", "Volume should be blank when selecting Lixit/Ad Lib for Water Source", "ERROR");
+    }
+    if (row.frequency !== 4 && row.waterSource === 'lixit'){
+        EHR.Server.Utils.addError(scriptErrors,"frequency", "Frequency should be 'Daily - Any Time' when selecting Lixit/Ad Lib", "ERROR");
+    }
+
 
-    //console.log ("value of ObjectId "+oldRow.objectid + " Value of new objectId "+ row.objectid);
-   //console.log ('skipWaterRegulation '+ row.skipWaterRegulationCheck);
-   // if (oldRow && row.date && row.Id && row.frequency && (oldRow.objectid != row.objectid)) {
-    if (row.project && row.objectid && row.Id && row.date && row.frequency && row.assignedTo && row.waterSource != 'lixit' && !row.skipWaterRegulationCheck) {
+    if (row.project && row.objectid && row.Id && row.date && row.frequency && row.assignedTo && row.waterSource !== 'lixit' && !row.skipWaterRegulationCheck && !row.closingRecord ) {
         let jsonArray = WNPRC.Utils.getJavaHelper().checkWaterRegulation(row.id, row.date, row.enddate ? row.enddate : null, row.frequency, row.waterSource, row.objectid, row.project, this.extraContext);
         if (jsonArray != null) {
             for (var i = 0; i < jsonArray.length; i++) {
@@ -115,35 +147,19 @@ function onUpsert(helper, scriptErrors, row, oldRow){
         row.date = rowDate;
     }
 
-    //if (oldRow && oldRow.waterSource == 'regulated' && row.waterSource == 'lixit'){
-    //TODO: by pass water regulation to change water order to lixit and also chnage the water regulated animals data
-    if ( row.waterSource == 'lixit' && !row.skipWaterRegulationCheck && !oldRow){
-
-        let jsonArray = WNPRC.Utils.getJavaHelper().changeWaterScheduled(row.id,row.date,row.waterSource, row.project, row.objectid,this.extraContext);
-        let jsonExtraContext = this.extraContext.extraContextArray;
-
-        if (jsonArray != null){
-            for (var i=0; i < jsonArray.length; i++){
-                let errorObject = JSON.parse(jsonArray[i]);
-                EHR.Server.Utils.addError(scriptErrors,errorObject.field, errorObject.message, errorObject.severity);
-
-            }
-            if (jsonExtraContext != null){
-                for (var i = 0; i < jsonExtraContext.length; i++){
-                    let extraContextObject = jsonExtraContext[i];
-                    let date =  extraContextObject.date;
-                    let dateOnly = new Date(date.getTime());
-                    dateOnly = dateOnly.getFullYear()+ "-" +dateOnly.getMonth()+ "-" + dateOnly.getDate();
-                    let infoMessage = "Water Order for "+ row.Id + " started on " + dateOnly + " with frequency of " + extraContextObject.frequency + " and volume of " + extraContextObject.volume + "ml will close.";
-                    EHR.Server.Utils.addError(scriptErrors,"waterSource",infoMessage,"INFO")
-
-                }
-
+    if (row.Id && row.date && row.enddate && row.project && row.objectid &&  row.closingRecord){
+        let jsonArray = WNPRC.Utils.getJavaHelper().closeWaterOrder(row.id, row.date, row.enddate, row.project, row.objectid, row.closingRecord);
+        if (jsonArray != null) {
+            for (var i = 0; i < jsonArray.length; i++) {
+                var errorObject = jsonArray[i];
+                EHR.Server.Utils.addError(scriptErrors, errorObject.field, errorObject.message, errorObject.severity);
             }
-
         }
     }
 
+    if ( row.waterSource === 'lixit'  && row.volume === undefined && row.project  && row.assignedTo && !row.skipWaterRegulationCheck){
+        changeWaterScheduled(row, scriptErrors);
+    }
 }
 
 function onUpdate(helper, scriptErrors, row, oldRow){
@@ -211,17 +227,40 @@ function onUpdate(helper, scriptErrors, row, oldRow){
                 }
             }            
         }
+    }
 
-
-        if (row.id !== oldRow.id || row.date !== oldRow.date || row.volume !== oldRow.volume)
-        {
-            //EHR.Server.Utils.addError(scriptErrors,'date');
-
-        }
-
+    if ( row.waterSource === 'lixit'  && row.project  && row.volume === undefined && row.assignedTo && !row.skipWaterRegulationCheck){
+        changeWaterScheduled(row, scriptErrors);
     }
 }
 
 function addErrorMessage(key,scriptErrors){
     EHR.Server.Utils.addError(scriptErrors, key, 'User does not have permission to modify this field.', 'ERROR');
 }
+
+function changeWaterScheduled(row, scriptErrors){
+
+    let jsonArray = WNPRC.Utils.getJavaHelper().changeWaterScheduled(row.id,row.date,row.waterSource, row.project, row.objectid,this.extraContext);
+    let jsonExtraContext = this.extraContext.extraContextArray;
+
+    if (jsonArray != null){
+        for (var i=0; i < jsonArray.length; i++){
+            let errorObject = jsonArray[i];
+            EHR.Server.Utils.addError(scriptErrors,errorObject.field, errorObject.message, errorObject.severity);
+        }
+        if (jsonExtraContext != null){
+            for (var j = 0; j < jsonExtraContext.length; j++){
+                let extraContextObject = jsonExtraContext[j];
+                let date =  extraContextObject.date;
+                let dateOnly = new Date(date.getTime());
+                let monthString = dateOnly.getMonth();
+                monthString++;
+
+                dateOnly = dateOnly.getFullYear()+ "-" + monthString + "-" + dateOnly.getDate();
+                let infoMessage = "Water Order for "+ row.Id + " started on " + dateOnly + " with frequency of " + extraContextObject.frequency + " and volume of " + extraContextObject.volume + "ml will close.";
+                EHR.Server.Utils.addError(scriptErrors,"waterSource",infoMessage,"INFO");
+            }
+        }
+    }
+
+}

WNPRC_EHR/resources/queries/study/waterSchedule.sql

@@ -10,9 +10,9 @@ d.calculated_status AS calculated_status,
 s.*,
 s.objectid as treatmentid,
 --(SELECT max(d.qcstate) as label FROM study.drug d WHERE s.objectid = d.treatmentid AND s.date = d.timeordered) as treatmentStatus,
-COALESCE((SELECT max(wg.qcstate) as label FROM study.waterGiven wg WHERE wg.treatmentid LIKE '%' || s.objectid || '%'  AND s.date = wg.dateordered AND wg.volume IS NOT NULL ),10) as waterStatus,
+COALESCE((SELECT max(wg.qcstate) as label FROM study.waterGiven wg WHERE wg.treatmentid LIKE '%' || s.objectid || '%'  AND s.date = wg.dateordered AND (wg.volume IS NOT NULL OR wg.waterSource = 'lixit') ),10) as waterStatus,
 --COALESCE((SELECT max(wg.qcstate) as label FROM study.waterGiven wg WHERE s.objectid IN (wg.treatmentid)  AND s.date = wg.dateordered AND wg.volume IS NOT NULL ),10) as waterStatus,
-COALESCE((SELECT max(wg.treatmentid) as treatmentIds FROM study.waterGiven wg WHERE s.date = wg.dateordered AND wg.volume IS NOT NULL ),'objectId') as watertreatment
+COALESCE((SELECT max(wg.treatmentid) as treatmentIds FROM study.waterGiven wg WHERE s.date = wg.dateordered AND (wg.volume IS NOT NULL OR wg.waterSource = 'lixit') ),'objectId') as watertreatment
 
 
 FROM study.demographics d

WNPRC_EHR/resources/queries/study/waterScheduleCoalesced/Treatments AM.qview.xml

@@ -21,6 +21,7 @@
     <filters>
         <filter column="dateOrdered" operator="dategte" value="-30d"/>
         <filter column="timeofday" operator="eq" value="AM"/>
+        <filter column="waterSource/title" operator="eq" value="Regulated"/>
         <filter column="Id/dataset/demographics/calculated_status" operator="eq" value="Alive"/>
     </filters>
 </customView>

WNPRC_EHR/resources/queries/study/waterScheduleCoalesced/Treatments PM.qview.xml

@@ -21,6 +21,7 @@
     <filters>
         <filter column="dateOrdered" operator="dategte" value="-30d"/>
         <filter column="timeofday" operator="eq" value="PM"/>
+        <filter column="waterSource/title" operator="eq" value="Regulated"/>
         <filter column="Id/dataset/demographics/calculated_status" operator="eq" value="Alive"/>
     </filters>
 </customView>

WNPRC_EHR/resources/queries/study/waterScheduleCoalesced/Treatments.qview.xml

@@ -25,7 +25,8 @@
     </sorts>
     <filters>
         <filter column="dateOrdered" operator="dategte" value="-30d"/>
-        <filter column="Id/dataset/demographics/calculated_status" operator="eq" value="Alive"/>
-        <filter column="qcstate" operator="neqornull" value="Completed"/>
+        <filter column="calculated_status" operator="eq" value="Alive"/>
+        <filter column="waterSource/title" operator="eq" value="Regulated"/>
+        <filter column="qcstate/label" operator="neqornull" value="Completed"/>
     </filters>
 </customView>

WNPRC_EHR/resources/views/ehrBegin.html

@@ -78,7 +78,7 @@
             items: [
                 {name: 'Animal Utilization By Category', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=colonyAssignmentSummary'},
                 {name: 'Blood Draw Summary', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=ScheduledBlood'},
-                {name: 'Colony Population By Age', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-.view?schemaName=study&query.queryName=colonyPopulationByAge'},
+                {name: 'Colony Population By Age', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=colonyPopulationByAge'},
                 {name: 'MHC Genotype Summary', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/query-executeQuery.view?schemaName=study&query.queryName=alleleFrequencies'},
                 {name: 'Population Summary', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/ehr-populationOverview.view'},
                 {name: 'Colony Census', url: '<%=contextPath%>' + ctx['EHRStudyContainer'] + '/wnprc_ehr-colonyCensus.view'},