Query optimizations and feedback

nirc_ehr/resources/queries/dbo/q_clinremarks.sql

@@ -8,6 +8,10 @@ SELECT anmEvt.ANIMAL_EVENT_ID
        anmEvt.EVENT_ID.EVENT_ID                                                  AS category,
        anmEvt.DIAGNOSIS                                                          AS vetreview,
        anmCmt.TEXT                                                               AS remark,
+       CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN
+            ('C:\Program Files\Labkey\labkey\files\NIRC\EHR\@files\attachments'
+                || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH)))
+       ELSE NULL END AS attachmentFile,
        CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP)        AS modified
 FROM ANIMAL_EVENT anmEvt
          LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID

nirc_ehr/resources/queries/nirc_ehr/necropsyTasks/.qview.xml

@@ -3,6 +3,17 @@
         <column name="viewNecropsy"/>
         <column name="enterNecropsyData"/>
         <column name="animalId"/>
+        <column name="animalId/curLocation/cage">
+            <properties>
+                <property name="columnTitle" value="Location"/>
+            </properties>
+        </column>
+        <column name="animalId/activeProjectAssignments/project"/>
+        <column name="animalId/activeProtocolAssignments/protocolDisplayName">
+            <properties>
+                <property name="columnTitle" value="Protocol"/>
+            </properties>
+        </column>
         <column name="assignedTo"/>
         <column name="created"/>
         <column name="createdBy"/>

nirc_ehr/resources/queries/study/cases.js

@@ -42,7 +42,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
             if (!qc) {
                 console.error('Unable to find QCState: ' + row.QCState + '/' + row.QCStateLabel);
             }
-            else if (qc.Label == 'Completed' && row.caseid && row.Id && row.performedby && row.taskid && qc) {
+            else if ((qc.Label == 'Completed' || qc.Label == 'Review Required') && row.caseid && row.Id && row.performedby && row.taskid && qc) {
                 var ordersInTransaction = helper.getProperty('ordersInTransaction');
                 var oit = [];
                 if (ordersInTransaction && ordersInTransaction.length) {

nirc_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml

@@ -23,6 +23,8 @@
         <column name="openRemark"/>
         <column name="plan"/>
         <column name="closeRemark"/>
+        <column name="openDiagnosis"/>
+        <column name="closeDiagnosis"/>
     </columns>
     <filters>
         <filter column="category" operator="eq" value="Clinical"/>

nirc_ehr/resources/queries/study/clinical_observationsSummary/Clinical.qview.xml

@@ -5,13 +5,14 @@
     <columns>
         <column name="Id"/>
         <column name="date"/>
+        <column name="category"/>
         <column name="area"/>
         <column name="observation"/>
         <column name="remark"/>
         <column name="performedBy"/>
         <column name="QCState"/>
     </columns>
     <filters>
-        <filter column="category" operator="eq" value="Clinical"/>
+        <filter column="type" operator="eq" value="Clinical"/>
     </filters>
 </customView>

nirc_ehr/resources/queries/study/deathNotification.sql

@@ -0,0 +1,8 @@
+
+SELECT
+    Id,
+    date,
+    taskid,
+    performedBy.DisplayName AS performedBy,
+    reason.title AS reason
+FROM study.deaths

nirc_ehr/resources/queries/study/demographicsCagemates.sql

@@ -18,8 +18,7 @@ FROM study.housing h
 
 JOIN study.housing h2
 ON (h2.Id.demographics.calculated_status = 'Alive'
---         AND h.room = h2.room
-        AND (h.cage = h2.cage OR (h.cage IS NULL and h2.cage IS NULL)))
+        AND (h.cage = h2.cage))
 
 WHERE h.enddateTimeCoalesced >= now()
 GROUP BY h.id, h.room, h.cage

nirc_ehr/resources/queries/study/demographicsCurLocation.sql

@@ -27,7 +27,9 @@ coalesce(d2.room, '') as room_order,
 d2.room_sortValue @hidden,
 
 coalesce(d2.cage, '') as cage_order,
-d2.cage_sortValue @hidden
+d2.cage_sortValue @hidden,
+
+d2.performedBy.displayName AS performedBy
 
 FROM study.housing d2
 

nirc_ehr/resources/queries/study/notificationAnimalProject.sql

@@ -0,0 +1,8 @@
+-- Add more here to make a single query for animal details in notifications
+SELECT
+    Id,
+    date,
+    project.name AS project,
+    enddate
+FROM study.assignment
+WHERE enddate IS NULL

nirc_ehr/resources/queries/study/observationSchedule.sql

@@ -80,7 +80,7 @@ FROM
 
         LEFT JOIN ehr_lookups.treatment_frequency_times ft ON ft.frequency = t1.frequency.meaning
 
-        WHERE t1.date is not null AND t1.qcstate.publicdata = true
+        WHERE t1.date is not null
 
         ) s1
 

nirc_ehr/resources/queries/study/treatmentSchedule.sql

@@ -1,102 +1,68 @@
-/*
- * Copyright (c) 2010-2014 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
- */
 
 SELECT
 d.id,
 d.calculated_status,
 s.*,
-s.objectid as treatmentid,
-drug.qcstate.label as treatmentStatus,
-s.objectid || '-pkSeparator-' || s.date as primaryKey -- -pkSeparator- is used to separate the two parts of the primary key in RecordTreatmentButton.js
-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.objectid,
-  t1.dataset,
-  t1.id as animalid,
-
-  coalesce(tt.time, ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) as time,
-  (coalesce(tt.time, ft.hourofday, (hour(t1.date) * 100)) / 100) as hours,
-  CASE
-    WHEN (tt.time IS NOT NULL OR ft.hourofday IS NOT NULL) THEN (((coalesce(tt.time, ft.hourofday) / 100.0) - floor(coalesce(tt.time, ft.hourofday) / 100)) * 100)
-    ELSE minute(t1.date)
-  END as minutes,
-  dr.date as origDate,
-  CASE
-    WHEN (tt.time IS NULL) THEN 'Default'
-    ELSE 'Custom'
-  END as timeType,
-
-  CASE
-    WHEN snomed.code IS NOT NULL THEN 'Diet'
-    ELSE IFDEFINED(t1.category)
-  END as category,
-  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.code,
-  t1.treatmentRecord,
-  t1.volume,
-  t1.vol_units,
-  t1.concentration,
-  t1.conc_units,
-  t1.amount,
-  t1.amount_units,
-  t1.amountWithUnits,
-  t1.amountAndVolume,
-  t1.dosage,
-  t1.dosage_units,
-  t1.route,
-  IFDEFINED(t1.reason) AS reason,
-  t1.performedby,
-  t1.remark,
-  t1.caseid,
-  t1.orderedby,
-
-  t1.qcstate
-
-FROM nirc_ehr.dateRange dr
-
-JOIN study."Treatment Orders" 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.treatment_times tt ON (tt.treatmentid = t1.objectid)
-LEFT JOIN ehr_lookups.treatment_frequency_times ft ON (ft.frequency = t1.frequency.meaning AND tt.rowid IS NULL)
-
-LEFT JOIN (
+s.objectid AS treatmentid,
+drug.qcstate.label AS treatmentStatus,
+s.objectid || '-pkSeparator-' || s.date AS primaryKey -- -pkSeparator- is used to separate the two parts of the primary key in RecordTreatmentButton.js
+FROM study.demographics d
+JOIN(
     SELECT
-      sc.code
-    from ehr_lookups.snomed_subset_codes sc
-    WHERE sc.primaryCategory = 'Diet'
-    GROUP BY sc.code
-) snomed ON snomed.code = t1.code
-
---NOTE: if we run this report on a future interval, we want to include those treatments
-WHERE t1.date is not null
-
-) s1
-
-) s ON (s.animalid = d.id) LEFT JOIN
-study.drug drug ON s.objectid = drug.treatmentid AND s.date = IFDEFINED(drug.scheduledDate)
-
-WHERE (d.lastDayatCenter Is Null or d.lastDayAtCenter > s.enddate OR s.enddate IS NULL)
-
-
---account for date/time in schedule
-and s.date >= s.startDate and (s.enddate IS NULL OR s.date <= s.enddate)
+    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.objectid,
+        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.category,
+        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.code,
+        t1.treatmentRecord,
+        t1.volume,
+        t1.vol_units,
+        t1.concentration,
+        t1.conc_units,
+        t1.amount,
+        t1.amount_units,
+        t1.amountWithUnits,
+        t1.amountAndVolume,
+        t1.dosage,
+        t1.dosage_units,
+        t1.route,
+        IFDEFINED(t1.reason) AS reason,
+        t1.performedby,
+        t1.remark,
+        t1.caseid,
+        t1.orderedby,
+        t1.qcstate
+        FROM nirc_ehr.dateRange dr
+        JOIN study."Treatment Orders" t1 ON (dr.dateOnly >= t1.dateOnly 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
+        --NOTE: if we run this report on a future interval, we want to include those treatments
+        WHERE t1.date IS NOT NULL
+
+    ) s1
+
+) s ON (s.animalid = d.id) 
+LEFT JOIN study.drug drug ON s.objectid = drug.treatmentid AND s.date = IFDEFINED(drug.scheduledDate)
+
+WHERE (d.lastDayatCenter IS NULL OR d.lastDayAtCenter > s.enddate OR s.enddate IS NULL)
+    AND s.date >= s.startDate AND (s.enddate IS NULL OR s.date <= s.enddate)

nirc_ehr/resources/queries/study/treatmentSchedule/.qview.xml

@@ -7,7 +7,6 @@
         <column name="Id/curLocation/cage"/>
 
         <column name="date"/>
-        <column name="timeOfDay"/>
         <column name="daysElapsed"/>
 
         <column name="frequency"/>

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

@@ -379,6 +379,11 @@
                 <datatype>varchar</datatype>
                 <propertyURI>urn:ehr.labkey.org/#CaseId</propertyURI>
             </column>
+            <column columnName="attachmentFile">
+                <columnTitle>Attachment File</columnTitle>
+                <datatype>varchar</datatype>
+                <rangeURI>http://cpas.fhcrc.org/exp/xml#fileLink</rangeURI>
+            </column>
         </columns>
     </table>
     <table tableName="demographics" tableDbType="TABLE">
@@ -643,6 +648,11 @@
                 <propertyURI>urn:ehr.labkey.org/#CaseId</propertyURI>
             </column>
         </columns>
+        <indices>
+            <index type="non-unique">
+                <column>cage</column>
+            </index>
+        </indices>
     </table>
     <table tableName="inbreeding" tableDbType="TABLE">
         <columns>

nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java

@@ -1,11 +1,14 @@
 package org.labkey.nirc_ehr;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.module.ModuleProperty;
@@ -16,6 +19,7 @@
 import org.labkey.api.study.StudyService;
 import org.labkey.api.util.JobRunner;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.writer.PrintWriters;
 
 import java.io.File;
@@ -33,6 +37,7 @@
 public class NIRCOrchardFileGenerator
 {
     public static final String NIRCOrchardFileLocation = "NIRCOrchardFileLocation";
+    private static final Logger _log = LogHelper.getLogger(NIRCOrchardFileGenerator.class, "Orchard update on trigger.");
 
     public void generateOrchardFile(Container c, User u, String taskid)
     {
@@ -80,6 +85,13 @@ public FileWriteTask(Container c, User u, String taskid, String orchardFileLocat
         @Override
         public void run()
         {
+            if (orchardFileLocation == null)
+            {
+                // Don't run if we don't have a location to write the file
+                _log.warn("Orchard file location is null, cannot generate Orchard file for taskid: " + taskid);
+                return;
+            }
+
             JobRunner.getDefault().execute(() ->
             {
                 TableInfo ti = getTableInfo(c, u, "study", "orchardData");

nirc_ehr/src/org/labkey/nirc_ehr/demographics/HousingDemographicsProvider.java

@@ -42,6 +42,7 @@ protected Collection<FieldKey> getFieldKeys()
         keys.add(FieldKey.fromString("reason"));
         keys.add(FieldKey.fromString("remark"));
         keys.add(FieldKey.fromString("location"));
+        keys.add(FieldKey.fromString("performedBy"));
 
         return keys;
     }