Necropsy reporting enhancements

nirc_ehr/resources/queries/study/demographicsLastProject.query.xml

@@ -0,0 +1,13 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsLastProject" tableDbType="NOT_IN_DB">
+                <columns>
+                    <column columnName="project">
+                        <columnTitle>Last Project</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nirc_ehr/resources/queries/study/demographicsLastProject.sql

@@ -0,0 +1,10 @@
+
+SELECT
+    d2.id,
+    d2.project,
+    h.enddate as enddate
+
+FROM study.assignment d2
+         JOIN (SELECT id, max(date) as maxDate, max(enddate) as enddate FROM study.assignment h GROUP BY id) h
+              ON (h.id = d2.id and d2.date = h.maxdate)
+WHERE d2.qcstate.publicdata = true

nirc_ehr/resources/queries/study/demographicsLastProtocol.query.xml

@@ -0,0 +1,13 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsLastProtocol" tableDbType="NOT_IN_DB">
+                <columns>
+                    <column columnName="protocol">
+                        <columnTitle>Last Protocol</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nirc_ehr/resources/queries/study/demographicsLastProtocol.sql

@@ -0,0 +1,10 @@
+
+SELECT
+    d2.id,
+    d2.protocol,
+    h.enddate as enddate
+
+FROM study.protocolAssignment d2
+         JOIN (SELECT id, max(date) as maxDate, max(enddate) as enddate FROM study.protocolAssignment h GROUP BY id) h
+              ON (h.id = d2.id and d2.date = h.maxdate)
+WHERE d2.qcstate.publicdata = true

nirc_ehr/resources/queries/study/tissueDisposition.query.xml

@@ -5,14 +5,16 @@
                 <columns>
                     <column columnName="necropsyTissue">
                         <columnTitle>Tissue</columnTitle>
+                        <displayWidth>80</displayWidth>
                         <fk>
                             <fkDbSchema>ehr_lookups</fkDbSchema>
                             <fkTable>necropsy_tissue</fkTable>
                             <fkColumnName>value</fkColumnName>
                         </fk>
                     </column>
                     <column columnName="necropsyDispositionCode">
-                        <columnTitle>Tissue Disposition Codes</columnTitle>
+                        <columnTitle>Tissue Disposition Code</columnTitle>
+                        <displayWidth>180</displayWidth>
                         <fk>
                             <fkDbSchema>ehr_lookups</fkDbSchema>
                             <fkTable>necropsy_disposition_codes</fkTable>

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

@@ -7,5 +7,6 @@
         <column name="date"/>
         <column name="necropsyTissue"/>
         <column name="necropsyDispositionCode"/>
+        <column name="remark"/>
     </columns>
 </customView>

nirc_ehr/resources/views/necropsy.html

@@ -0,0 +1,94 @@
+
+<style>
+    .page-break {
+        page-break-before: always; /* Older CSS spec */
+        break-before: page;        /* Newer spec */
+    }
+
+    @media print {
+      .hide-on-print {
+        display: none !important;
+      }
+    }
+
+    /* Top border on panel header when printing */
+    .panel-heading {
+      border-top: 1px solid black;
+    }
+</style>
+<div class="hide-on-print">
+    <label for="animalId" style="margin-right: 10px;">Animal Id</label><input id="animalId" type="text" />
+    <button id="animalIdSubmit" name="animalIdSubmit">Submit</button>
+    <br>
+    <div id="animalIdError"></div>
+</div>
+<br>
+
+<div id="animalDeath"></div>
+<div id="animalNecropsy"></div>
+<div class="page-break"></div>
+<div id="grossPathology"></div>
+<div id="tissueDisposition"></div>
+
+<script type="text/javascript" nonce="<%=scriptNonce%>">
+    document.getElementById('animalIdSubmit')['onclick'] = function(){ submitNecropsyForm(); return false; }
+
+    const submitNecropsyForm = function() {
+        const animalId = document.getElementById('animalId').value;
+
+        if (!animalId) {
+            document.getElementById('animalIdError').innerHTML = 'Please enter an Animal Id';
+        }
+
+        const animalIdError = document.getElementById('animalIdError');
+        const animalDeath = document.getElementById('animalDeath');
+        const animalNecropsy = document.getElementById('animalNecropsy');
+        const grossPathology = document.getElementById('grossPathology');
+        const tissueDisposition = document.getElementById('tissueDisposition');
+
+        animalIdError.innerHTML = '';
+        animalDeath.innerHTML = '';
+        animalNecropsy.innerHTML = '';
+        grossPathology.innerHTML = '';
+        tissueDisposition.innerHTML = '';
+
+        const filterArray = [LABKEY.Filter.create('Id', animalId, LABKEY.Filter.Types.EQUAL)]
+
+        Ext4.create('LDK.panel.DetailsPanel', {
+            store: {
+                schemaName: 'study',
+                queryName: 'deaths',
+                filterArray: filterArray,
+                columns: 'Id,Id/demographics/species,date,reason,remark,performedby,Id/lastProtocol/protocol,Id/lastProject/project',
+            },
+            title: 'Death',
+            renderTo: 'animalDeath',
+            showBackBtn: false
+        });
+
+        Ext4.create('LDK.panel.DetailsPanel', {
+            store: {
+                schemaName: 'study',
+                queryName: 'necropsy',
+                filterArray: filterArray,
+            },
+            title: 'Necropsy',
+            renderTo: 'animalNecropsy',
+            showBackBtn: false
+        });
+
+        LDK.Utils.getReadOnlyQWP({
+            title: 'Gross Pathology',
+            schemaName: 'study',
+            queryName: 'grossPathology',
+            filterArray: filterArray,
+        }).render('grossPathology');
+
+        LDK.Utils.getReadOnlyQWP({
+            title: 'Tissue Disposition',
+            schemaName: 'study',
+            queryName: 'tissueDisposition',
+            filterArray: filterArray,
+        }).render('tissueDisposition');
+    }
+</script>

nirc_ehr/resources/views/necropsy.view.xml

@@ -0,0 +1,3 @@
+<view xmlns="http://labkey.org/data/xml/view" template="print" title="Necropsy Report">
+    <requiresLogin/>
+</view>

nirc_ehr/resources/web/nirc_ehr/model/sources/BehaviorDefaults.js

@@ -51,7 +51,7 @@ EHR.model.DataModelManager.registerMetadata('BehaviorDefaults', {
                     store: {
                         type: 'labkey-store',
                         schemaName: 'core',
-                        sql: 'SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.users',
+                        sql: "SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.PrincipalsWithoutAdmin WHERE active = TRUE AND Type = 'u'",
                         autoLoad: true
                     }
                 }

nirc_ehr/resources/web/nirc_ehr/model/sources/ClinicalCase.js

@@ -134,7 +134,7 @@ EHR.model.DataModelManager.registerMetadata('ClinicalCase', {
                     store: {
                         type: 'labkey-store',
                         schemaName: 'core',
-                        sql: 'SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.users',
+                        sql: "SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.PrincipalsWithoutAdmin WHERE active = TRUE AND Type = 'u'",
                         autoLoad: true
                     }
                 }

nirc_ehr/resources/web/nirc_ehr/model/sources/NIRCDefault.js

@@ -24,7 +24,7 @@ EHR.model.DataModelManager.registerMetadata('Default', {
                     // from the display when a value is selected from the dropdown even though the 'userid' value gets saved as a text (this behavior was only seen
                     // in the form panel but not in the grid panel).
                     // casting it as a varchar when loading the store fixes this issue.
-                    sql: 'SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.users',
+                    sql: "SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.PrincipalsWithoutAdmin WHERE active = TRUE AND Type = 'u'",
                     autoLoad: true
                 }
             }

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

@@ -37,6 +37,7 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.query.DefaultSchema;
+import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.security.roles.RoleManager;
@@ -188,6 +189,9 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         NotificationService.get().registerNotification(new NIRCProcedureOverdueNotification());
         NotificationService.get().registerNotification(new NIRCPregnancyOutcomeNotification());
 
+        EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Printable Necropsy Report", this, DetailsURL.fromString("/nirc_ehr-necropsy.view"), "Pathology");
+
+
         // Ensure N: is mounted if it's configured, as it's being mapped in via a symlink/shortcut, so we can't
         // recognize paths using it based solely on their drive letter and mount just-in-time
         if (NetworkDrive.getNetworkDrive("N:\\") != null)

nirc_ehr/src/org/labkey/nirc_ehr/table/NIRC_EHRCustomizer.java

@@ -974,6 +974,20 @@ private void customizeAnimalTable(AbstractTableInfo ds)
             col.setLabel("Alias");
             ds.addColumn(col);
         }
+        if (ds.getColumn("lastProtocol") == null)
+        {
+            var col = getWrappedCol(us, ds, "lastProtocol", "demographicsLastProtocol", "Id", "Id");
+            col.setLabel("Assignment - Final Protocol");
+            col.setDescription("This calculates the final protocol assignment for the animal.  This is distinct from active protocol assignment because it will return a protocol assignment for dead animals");
+            ds.addColumn(col);
+        }
+        if (ds.getColumn("lastProject") == null)
+        {
+            var col = getWrappedCol(us, ds, "lastProject", "demographicsLastProject", "Id", "Id");
+            col.setLabel("Assignment - Final Project");
+            col.setDescription("This calculates the final project assignment for the animal.  This is distinct from active project assignment because it will return a project assignment for dead animals");
+            ds.addColumn(col);
+        }
     }
 
     private void customizeProtocolTable(AbstractTableInfo ti)