Behavior Obs Refinements

nirc_ehr/resources/queries/study/clinical_observations.js

@@ -31,6 +31,14 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
             EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Other' for 'Daily Enrichment', please enter Remark", "WARN");
         }
 
+        if (row.category === "Alopecia Score" && !row.observation) {
+            EHR.Server.Utils.addError(scriptErrors, 'observation', "Score required for 'Alopecia Score'.", "WARN");
+        }
+
+        if (row.category === "Alopecia Score" && !row.remark) {
+            EHR.Server.Utils.addError(scriptErrors, 'remark', "Remark required for 'Alopecia Score'.", "WARN");
+        }
+
         var yesRemarkRequired = (row.category === "Self Biting Observed" || row.category === "New Injury Observed" || row.category === "Other Stereotopy" || row.category === "Environmental Change" || row.category === "Special Enrichment");
         if (yesRemarkRequired && row.observation === "Yes" && !row.remark) {
             EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Yes' for " + row.category + ", please explain in the Remark", "WARN");
@@ -55,9 +63,10 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
                     var orderData = triggerHelper.handleScheduledObservations(row, qc.RowId, orderTasks[0]);
 
                     if (orderData) {
-                        row.caseid = orderData.caseId;
+                        row.caseId = orderData.caseId;
                         row.orderid = orderData.orderId;
                         row.area = orderData.area;
+                        row.type = orderData.type;
                     }
                 }
             }

nirc_ehr/resources/queries/study/observationOrdersByDate.sql

@@ -0,0 +1,52 @@
+SELECT
+s.*,
+co.qcstate.label AS obsStatus
+FROM
+    (SELECT
+    s1.*,
+    timestampadd('SQL_TSI_MINUTE', ((s1.hours * 60) + s1.minutes), s1.origDate) AS date,
+    ((s1.hours * 60) + s1.minutes) AS timeOffset
+
+    FROM (
+        SELECT
+        t1.lsid,
+        t1.dataset,
+        t1.id AS animalid,
+        coalesce(ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) AS time,
+        (coalesce(ft.hourofday, (hour(t1.date) * 100)) / 100) AS hours,
+
+        CASE WHEN ft.hourofday IS NOT NULL
+        THEN (((ft.hourofday / 100.0) - floor(ft.hourofday / 100)) * 100)
+        ELSE minute(t1.date)
+        END AS minutes,
+
+        dr.date AS origDate,
+
+        t1.frequency.meaning AS frequency,
+        t1.date AS startDate,
+        timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly AS timestamp), dr.dateOnly) + 1 AS daysElapsed,
+        t1.enddate,
+        t1.category,
+        t1.area,
+        t1.performedby,
+        t1.remark,
+        t1.caseid.objectid AS caseid,
+        t1.taskid,
+        t1.type,
+        t1.objectid,
+
+        t1.qcstate
+        FROM nirc_ehr.dateRange dr
+        JOIN
+
+        -- order by category to replace string with Daily Obs
+        (SELECT * FROM study.observation_order ORDER BY category) t1
+        ON (dr.dateOnly >= t1.dateOnly AND (dr.dateOnly <= t1.enddate OR t1.enddate IS NULL) AND
+          --technically the first day of the treatment is day 1, not day 0
+        ((mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly AS timestamp), dr.dateOnly) AS integer), t1.frequency.intervalindays) = 0 AND t1.frequency.intervalindays IS NOT NULL AND t1.frequency.dayofweek IS NULL)))
+        LEFT JOIN ehr_lookups.treatment_frequency_times ft ON ft.frequency = t1.frequency.meaning
+        WHERE t1.date IS NOT NULL
+
+    ) s1
+) s
+LEFT JOIN study.clinical_observations co ON co.scheduledDate IS NOT NULL AND s.date = co.scheduledDate AND co.orderId = s.objectid

nirc_ehr/resources/queries/study/observationSchedule.sql

@@ -2,93 +2,31 @@ 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,
-    MAX(g.type) as type,
-    MAX(g.caseid) as caseid
+    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,
+    MAX(g.type) AS type,
+    MAX(g.caseid) AS caseid
 FROM
 (
     SELECT
-        sch.id,
-        sch.date as scheduledDate,
+        sch.animalId as id,
+        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
-            d.id,
-            s.*,
-            co.qcstate.label as obsStatus
-        FROM study.demographics d JOIN
-        (SELECT
-            s1.*,
-            timestampadd('SQL_TSI_MINUTE', ((s1.hours * 60) + s1.minutes), s1.origDate) as date,
-            ((s1.hours * 60) + s1.minutes) as timeOffset
-
-        FROM (
-
-        SELECT
-            t1.lsid,
-            t1.dataset,
-            t1.id as animalid,
-
-            coalesce(ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) as time,
-            (coalesce(ft.hourofday, (hour(t1.date) * 100)) / 100) as hours,
-
-            CASE WHEN ft.hourofday IS NOT NULL
-            THEN (((ft.hourofday / 100.0) - floor(ft.hourofday / 100)) * 100)
-            ELSE minute(t1.date)
-            END as minutes,
-
-            dr.date as origDate,
-
-            t1.frequency.meaning as frequency,
-            t1.date as startDate,
-            timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly as timestamp), dr.dateOnly) + 1 as daysElapsed,
-            t1.enddate,
-            t1.category,
-            t1.area,
-            t1.performedby,
-            t1.remark,
-            t1.caseid,
-            t1.taskid,
-            t1.type,
-            t1.objectid,
-
-            t1.qcstate
-
-        FROM nirc_ehr.dateRange dr
-
-        JOIN
-
-        -- order by category to replace string with Daily Obs
-        (SELECT * FROM
-            study.observation_order
-        ORDER BY category) t1
-            ON (dr.dateOnly >= t1.dateOnly and dr.dateOnly <= t1.enddateCoalesced AND
-              --technically the first day of the treatment is day 1, not day 0
-            ((mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly as timestamp), dr.dateOnly) as integer), t1.frequency.intervalindays) = 0 And t1.frequency.intervalindays is not null And t1.frequency.dayofweek is null)))
-
-        LEFT JOIN ehr_lookups.treatment_frequency_times ft ON ft.frequency = t1.frequency.meaning
-
-        WHERE t1.date is not null
-
-        ) s1
-
-        ) s ON (s.animalid = d.id)
-        LEFT JOIN study.clinical_observations co ON co.scheduledDate IS NOT NULL AND s.date = co.scheduledDate AND co.orderId = s.objectid
+        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
     GROUP BY
-        sch.id,
+        sch.animalId,
         sch.date,
         sch.caseid,
         sch.type

nirc_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml

@@ -24,7 +24,6 @@
         <dataset name="housing" id="1018" category="Colony Management" type="Standard"/>
         <dataset name="inbreeding" id="1021" category="Colony Management" type="Standard"/>
         <dataset name="necropsy" id="1019" category="Pathology" type="Standard"/>
-        <dataset name="obs" id="1025" category="Clinical" type="Standard"/>
         <dataset name="nhpTraining" id="1040" category="Behavior" type="Standard"/>
         <dataset name="observation_order" id="1049" category="Clinical" type="Standard"/>
         <dataset name="notes" id="1027" category="Colony Management" type="Standard"/>

nirc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml

@@ -291,7 +291,7 @@
         </columns>
     </table>
     <table tableName="clinical_observations" tableDbType="TABLE">
-        <tableTitle>Clinical Observations</tableTitle>
+        <tableTitle>Clinical/Behavior Observations</tableTitle>
         <columns>
             <column columnName="Id">
                 <datatype>varchar</datatype>
@@ -678,29 +678,6 @@
         </columns>
         <tableTitle>Inbreeding Coefficients</tableTitle>
     </table>
-    <table tableName="obs" tableDbType="TABLE">
-        <tableTitle>Observations</tableTitle>
-        <columns>
-            <column columnName="Id">
-                <datatype>varchar</datatype>
-                <propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
-                <importAliases>
-                    <importAlias>ptid</importAlias>
-                </importAliases>
-            </column>
-            <column columnName="date">
-                <datatype>timestamp</datatype>
-                <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
-                <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
-            </column>
-            <column columnName="category">
-                <datatype>varchar</datatype>
-            </column>
-            <column columnName="diagnosis">
-                <datatype>varchar</datatype>
-            </column>
-        </columns>
-    </table>
     <table tableName="necropsy" tableDbType="TABLE">
         <tableTitle>Necropsy</tableTitle>
         <columns>

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

@@ -152,12 +152,12 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         EHRService.get().registerHistoryDataSource(new NIRCCaseCloseDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCCaseOpenDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCClinicalObservationsDataSource(this));
+        EHRService.get().registerHistoryDataSource(new NIRCBehaviorObservationsDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCClinicalRemarksDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCEndTreatmentOrderDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCHousingDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCObservationOrdersDataSource(this));
         EHRService.get().registerHistoryDataSource(new NIRCVitalsDataSource(this));
-        EHRService.get().registerHistoryDataSource(new ObservationsDataSource(this));
         EHRService.get().registerHistoryDataSource(new PairingsDataSource(this));
         EHRService.get().registerHistoryDataSource(new PhysicalExamDataSource(this));
         EHRService.get().registerHistoryDataSource(new PregnancyDataSource(this));

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

@@ -0,0 +1,12 @@
+package org.labkey.nirc_ehr.history;
+
+import org.labkey.api.module.Module;
+
+public class NIRCBehaviorObservationsDataSource extends NIRCObservationsDataSource
+{
+    public NIRCBehaviorObservationsDataSource(Module module)
+    {
+        super("study", "behaviorObservations", "Behavior Observations", "Behavior Observations", module);
+    }
+}
+