From 81582b5a16cda9185be50b70c30864a81cab63a2 Mon Sep 17 00:00:00 2001
From: Binal Patel <binalp@labkey.com>
Date: Mon, 11 May 2026 08:57:44 -0700
Subject: [PATCH 1/4] Ticket 54548: Header on reports (#691)

---
 .../resources/views/clinicalHistoryExport.html   |   5 +++++
 nirc_ehr/resources/views/necropsy.html           |   4 ++++
 nirc_ehr/resources/views/necropsy.view.xml       |   2 +-
 .../nirc_ehr/images/ull-logo-main-subsite.png    | Bin 0 -> 7359 bytes
 4 files changed, 10 insertions(+), 1 deletion(-)
 create mode 100644 nirc_ehr/resources/web/nirc_ehr/images/ull-logo-main-subsite.png

diff --git a/nirc_ehr/resources/views/clinicalHistoryExport.html b/nirc_ehr/resources/views/clinicalHistoryExport.html
index 8e15e246..d5470b84 100644
--- a/nirc_ehr/resources/views/clinicalHistoryExport.html
+++ b/nirc_ehr/resources/views/clinicalHistoryExport.html
@@ -1,3 +1,8 @@
+<div style="text-align: center; margin-bottom: 20px; display: flex">
+    <img src="<%=contextPath%>/nirc_ehr/images/ull-logo-main-subsite.png" alt="ULL Logo" style="height: 60px; vertical-align: middle; margin-right: 15px;" />
+    <span style="font-size: 20px; font-weight: bold; vertical-align: middle;">The University of Louisiana at Lafayette New Iberia Research Center<br>Animal Record</span>
+</div>
+
 <script type="text/javascript" nonce="<%=scriptNonce%>">
 
     Ext4.onReady(function (){
diff --git a/nirc_ehr/resources/views/necropsy.html b/nirc_ehr/resources/views/necropsy.html
index 3252fb6b..04fb4e46 100644
--- a/nirc_ehr/resources/views/necropsy.html
+++ b/nirc_ehr/resources/views/necropsy.html
@@ -16,6 +16,10 @@
       border-top: 1px solid black;
     }
 </style>
+<div style="text-align: center; margin-bottom: 20px; display: flex">
+    <img src="<%=contextPath%>/nirc_ehr/images/ull-logo-main-subsite.png" alt="ULL Logo" style="height: 60px; vertical-align: middle; margin-right: 15px;" />
+    <span style="font-size: 20px; font-weight: bold; vertical-align: middle;">The University of Louisiana at Lafayette New Iberia Research Center<br>Necropsy</span>
+</div>
 <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>
diff --git a/nirc_ehr/resources/views/necropsy.view.xml b/nirc_ehr/resources/views/necropsy.view.xml
index 37cdfd93..e10c5787 100644
--- a/nirc_ehr/resources/views/necropsy.view.xml
+++ b/nirc_ehr/resources/views/necropsy.view.xml
@@ -1,3 +1,3 @@
-<view xmlns="http://labkey.org/data/xml/view" template="print" title="Necropsy Report">
+<view xmlns="http://labkey.org/data/xml/view" template="print" title="Necropsy Report" frame="none">
     <requiresLogin/>
 </view>
\ No newline at end of file
diff --git a/nirc_ehr/resources/web/nirc_ehr/images/ull-logo-main-subsite.png b/nirc_ehr/resources/web/nirc_ehr/images/ull-logo-main-subsite.png
new file mode 100644
index 0000000000000000000000000000000000000000..24c9f7cb9b9990671cb667debcaa564573767f4b
GIT binary patch
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From a98d2909995316108da50898c918b31322c5c9f3 Mon Sep 17 00:00:00 2001
From: Binal Patel <binalp@labkey.com>
Date: Mon, 11 May 2026 11:14:53 -0700
Subject: [PATCH 2/4] Ticket 54565: Save draft on death form sends email when
 it shouldn't (#689)

* Don't send notification on Save Draft.

* Update/add log messages.
---
 nirc_ehr/resources/queries/study/deaths.js    | 29 ++++++++++++-------
 .../nirc_ehr/query/NIRC_EHRTriggerHelper.java |  2 +-
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/nirc_ehr/resources/queries/study/deaths.js b/nirc_ehr/resources/queries/study/deaths.js
index 99ef0498..626223e7 100644
--- a/nirc_ehr/resources/queries/study/deaths.js
+++ b/nirc_ehr/resources/queries/study/deaths.js
@@ -152,17 +152,24 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
 });
 
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'Deaths', function(event, errors, helper){
-    var deaths = helper.getDeaths();
-
-    if (deaths) {
-        var ids = [];
-        for (var id in deaths){
-            ids.push(id);
-        }
-        if (!helper.isETL() && event === 'insert') {
-            triggerHelper.sendDeathNotification(ids[0]);
+    var rows = helper.getRows() || [];
+    for (var i = 0; i < rows.length; i++) {
+        var row = rows[i].row;
+        var oldRow = rows[i].oldRow;
+
+        // Notification will get sent when:
+        // 1) a brand-new row saved directly as 'Request: Pending' (i.e., when a user clicks 'Submit Death'), or
+        // 2) a draft death record moving from 'In Progress' to 'Request: Pending'.
+        if (!helper.isETL() &&
+                row && row.Id &&
+                row.QCStateLabel &&
+                row.QCStateLabel.toUpperCase() === 'REQUEST: PENDING' &&
+                (!oldRow || !oldRow.QCStateLabel || oldRow.QCStateLabel.toUpperCase() === 'IN PROGRESS')) {
+            console.log("Sending NIRC Death Notification")
+            triggerHelper.sendDeathNotification(row.Id);
+
+            console.log("Updating Procedure Orders to Completed for Animal: " + row.Id + "")
+            triggerHelper.updateProcedureOrdersToCompleted([row.Id]);
         }
-
-        triggerHelper.updateProcedureOrdersToCompleted(ids);
     }
 });
\ No newline at end of file
diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java b/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java
index 74bd1adf..22112ed5 100644
--- a/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java
+++ b/nirc_ehr/src/org/labkey/nirc_ehr/query/NIRC_EHRTriggerHelper.java
@@ -950,7 +950,7 @@ public void updateProcedureOrdersToCompleted(List<String> ids)
 
         if (results.length == 0)
         {
-            _log.info("No prc_order rows found with 'Request: Approved' status for the provided IDs");
+            _log.info("No Procedure Orders found with 'Request: Approved' status for the provided IDs");
             return;
         }
 

From efc4a016a15f8e3f25c15f2a4aeaaacfbb38a459 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Tue, 12 May 2026 13:56:56 -0700
Subject: [PATCH 3/4] Acquisition Report (#696)

* Input parameters for start date, end date and project.
* Queries for active projects, acquisitions given parameters, acquisitions summary by species
* Grids for acquisitions by species and all acquisitions
* Plot for acquisitions by species
---
 .../queries/study/AcquisitionReport.sql       |   9 +
 .../study/AcquisitionReportBySpecies.sql      |  13 ++
 .../study/CurrentProtocolProjectReport.sql    |  12 +
 .../study/activeProjectsFromHousing.sql       |   5 +
 .../resources/views/acquisitionReport.html    | 217 ++++++++++++++++++
 .../views/acquisitionReport.view.xml          |   6 +
 .../org/labkey/nirc_ehr/NIRC_EHRModule.java   |   1 +
 7 files changed, 263 insertions(+)
 create mode 100644 nirc_ehr/resources/queries/study/AcquisitionReport.sql
 create mode 100644 nirc_ehr/resources/queries/study/AcquisitionReportBySpecies.sql
 create mode 100644 nirc_ehr/resources/queries/study/CurrentProtocolProjectReport.sql
 create mode 100644 nirc_ehr/resources/queries/study/activeProjectsFromHousing.sql
 create mode 100644 nirc_ehr/resources/views/acquisitionReport.html
 create mode 100644 nirc_ehr/resources/views/acquisitionReport.view.xml

diff --git a/nirc_ehr/resources/queries/study/AcquisitionReport.sql b/nirc_ehr/resources/queries/study/AcquisitionReport.sql
new file mode 100644
index 00000000..52bbfd2b
--- /dev/null
+++ b/nirc_ehr/resources/queries/study/AcquisitionReport.sql
@@ -0,0 +1,9 @@
+SELECT d.Id,
+       d.gender,
+       d.species,
+       d.Birth,
+       d.Id.MostRecentArrival.Center_Arrival,
+       cpp.project
+FROM study.demographics d
+         LEFT JOIN CurrentProtocolProjectReport cpp ON cpp.Id = d.Id
+ORDER BY d.Id ASC
\ No newline at end of file
diff --git a/nirc_ehr/resources/queries/study/AcquisitionReportBySpecies.sql b/nirc_ehr/resources/queries/study/AcquisitionReportBySpecies.sql
new file mode 100644
index 00000000..5fbe7a7d
--- /dev/null
+++ b/nirc_ehr/resources/queries/study/AcquisitionReportBySpecies.sql
@@ -0,0 +1,13 @@
+PARAMETERS(StartDate TIMESTAMP, EndDate TIMESTAMP, Project VARCHAR)
+
+SELECT s.species, s.project, s.speciesName, COUNT(*) as Total FROM
+    (
+        SELECT
+            species,
+            species.scientific_name AS speciesName,
+            Center_Arrival,
+            project
+        FROM study.AcquisitionReport ar
+        WHERE CAST(COALESCE(StartDate, '1900-01-01') as date) <= ar.Center_Arrival AND CAST(COALESCE(EndDate, curdate()) as date) >= CAST(ar.Center_Arrival as date) AND Project = ar.project
+    ) s
+GROUP BY s.species, s.project, s.speciesName
\ No newline at end of file
diff --git a/nirc_ehr/resources/queries/study/CurrentProtocolProjectReport.sql b/nirc_ehr/resources/queries/study/CurrentProtocolProjectReport.sql
new file mode 100644
index 00000000..ff4c24ce
--- /dev/null
+++ b/nirc_ehr/resources/queries/study/CurrentProtocolProjectReport.sql
@@ -0,0 +1,12 @@
+
+SELECT DISTINCT Id, protocol.title as protocol, project FROM
+    (
+        SELECT DISTINCT d.Id,
+                        a.project.name as project, a.enddate AS projectenddate,
+                        pa.protocol, pa.enddate AS protocolenddate
+        FROM study.demographics d
+                 JOIN study.assignment a ON a.Id = d.Id
+                 JOIN study.protocolAssignment pa ON pa.Id = d.Id
+        WHERE a.enddate IS NULL
+    ) sub
+WHERE sub.protocolenddate IS NULL
\ No newline at end of file
diff --git a/nirc_ehr/resources/queries/study/activeProjectsFromHousing.sql b/nirc_ehr/resources/queries/study/activeProjectsFromHousing.sql
new file mode 100644
index 00000000..3387bce9
--- /dev/null
+++ b/nirc_ehr/resources/queries/study/activeProjectsFromHousing.sql
@@ -0,0 +1,5 @@
+SELECT
+    Id.activeProjectAssignments.project,
+    COUNT(*) as Total
+FROM housing
+GROUP BY Id.activeProjectAssignments.project
\ No newline at end of file
diff --git a/nirc_ehr/resources/views/acquisitionReport.html b/nirc_ehr/resources/views/acquisitionReport.html
new file mode 100644
index 00000000..8834f92b
--- /dev/null
+++ b/nirc_ehr/resources/views/acquisitionReport.html
@@ -0,0 +1,217 @@
+<style>
+    #nirc_ehr-acquisition-report {
+        font-family: Arial, sans-serif;
+        max-width: 400px;
+        padding: 20px;
+        background-color: #f9f9f9;
+        border: 1px solid #ddd;
+        border-radius: 4px;
+    }
+
+    #nirc_ehr-acquisition-report .form-group {
+        margin-bottom: 15px;
+    }
+
+    #nirc_ehr-acquisition-report label {
+        display: block;
+        margin-bottom: 5px;
+        font-weight: bold;
+        color: #333;
+    }
+
+    #nirc_ehr-acquisition-report select,
+    #nirc_ehr-acquisition-report input[type="date"] {
+        width: 100%;
+        padding: 8px 10px;
+        border: 1px solid #ccc;
+        border-radius: 4px;
+        font-size: 14px;
+        box-sizing: border-box;
+    }
+
+    #nirc_ehr-acquisition-report select:focus,
+    #nirc_ehr-acquisition-report input[type="date"]:focus {
+        outline: none;
+        border-color: #5897fb;
+        box-shadow: 0 0 3px rgba(88, 151, 251, 0.5);
+    }
+
+    #acquisitionReportBySpeciesPlot,
+    #acquisitionReportBySpeciesResults,
+    #acquisitionReportResults {
+        margin-top: 20px;
+    }
+</style>
+
+<form id="nirc_ehr-acquisition-report">
+    <div class="form-group">
+        <label for="activeProjectsDropdown">Active Projects:</label>
+        <select id="activeProjectsDropdown" disabled>
+            <option value="">Loading...</option>
+        </select>
+    </div>
+
+    <div class="form-group">
+        <label for="startDate">Start Date:</label>
+        <input type="date" id="startDate" name="startDate">
+    </div>
+
+    <div class="form-group">
+        <label for="endDate">End Date:</label>
+        <input type="date" id="endDate" name="endDate">
+    </div>
+
+    <button type="submit">Submit</button>
+</form>
+
+<div id="acquisitionReportBySpeciesPlot"></div>
+<div id="acquisitionReportBySpeciesResults"></div>
+<div id="acquisitionReportResults"></div>
+
+<script type="text/javascript" nonce="<%=scriptNonce%>">
+
+    const dropdown = document.getElementById('activeProjectsDropdown');
+
+    document.getElementById("nirc_ehr-acquisition-report").addEventListener("submit", handleSubmit);
+
+    function handleSubmit(event) {
+        event.preventDefault(); // Prevents form submission
+
+        const project = document.getElementById("activeProjectsDropdown").value;
+        const startDate = document.getElementById("startDate").value;
+        const endDate = document.getElementById("endDate").value;
+
+        // Clear previous results
+        document.getElementById("acquisitionReportBySpeciesPlot").innerHTML = "";
+        document.getElementById("acquisitionReportBySpeciesResults").innerHTML = "";
+        document.getElementById("acquisitionReportResults").innerHTML = "";
+
+        // Validate required fields
+        const missingFields = [];
+        if (!project) missingFields.push("Project");
+        if (!startDate) missingFields.push("Start Date");
+        if (!endDate) missingFields.push("End Date");
+
+        if (missingFields.length > 0) {
+            document.getElementById("acquisitionReportResults").innerHTML =
+                '<div style="color: red; padding: 10px;">Please enter the following required fields: ' + missingFields.join(", ") + '</div>';
+            return;
+        }
+
+        // Build filters array
+        const filters = [];
+
+        if (startDate) {
+            filters.push(LABKEY.Filter.create('Center_Arrival', startDate, LABKEY.Filter.Types.DATE_GREATER_THAN_OR_EQUAL));
+        }
+
+        if (endDate) {
+            filters.push(LABKEY.Filter.create('Center_Arrival', endDate, LABKEY.Filter.Types.DATE_LESS_THAN_OR_EQUAL));
+        }
+
+        if (project) {
+            filters.push(LABKEY.Filter.create('project', project, LABKEY.Filter.Types.EQUAL));
+        }
+
+        // Create BarPlot for AcquisitionReportBySpecies
+        LABKEY.Query.selectRows({
+            schemaName: 'study',
+            queryName: 'AcquisitionReportBySpecies',
+            parameters: {
+                StartDate: startDate,
+                EndDate: endDate,
+                Project: project
+            },
+            success: function(results) {
+                if (results.rows.length) {
+                    const plot = new LABKEY.vis.BarPlot({
+                        renderTo: 'acquisitionReportBySpeciesPlot',
+                        rendererType: 'd3',
+                        width: 800,
+                        height: 300,
+                        labels: {
+                            main: { value: 'Acquisitions by Species' },
+                            yLeft: { value: 'Total' }
+                        },
+                        aes: {
+                            x: 'speciesName',
+                            y: 'Total'
+                        },
+                        scales: {
+                            x: { scaleType: 'discrete' },
+                            yLeft: { scaleType: 'continuous' }
+                        },
+                        options: {
+                            color: '#5897fb',
+                            showValues: true
+                        },
+                        data: results.rows
+                    });
+                    plot.render();
+                } else {
+                    document.getElementById("acquisitionReportBySpeciesPlot").innerHTML = "No data available for the selected parameters.";
+                }
+            },
+            failure: function(error) {
+                console.error('Failed to load bar plot data:', error);
+            }
+        });
+
+        // Create QueryWebPart for AcquisitionReportBySpecies with parameters
+        new LABKEY.QueryWebPart({
+            renderTo: 'acquisitionReportBySpeciesResults',
+            schemaName: 'study',
+            queryName: 'AcquisitionReportBySpecies',
+            title: 'Acquisition Report By Species',
+            columns: 'species,project,Total',
+            parameters: {
+                StartDate: startDate,
+                EndDate: endDate,
+                Project: project
+            }
+        });
+
+        // Create QueryWebPart for AcquisitionReport
+        new LABKEY.QueryWebPart({
+            renderTo: 'acquisitionReportResults',
+            schemaName: 'study',
+            queryName: 'AcquisitionReport',
+            title: 'All Acquisitions',
+            filterArray: filters
+        });
+    }
+
+    // Use selectRows API to get active projects from study.activeProjects
+    LABKEY.Query.selectRows({
+        schemaName: 'study',
+        queryName: 'activeProjectsFromHousing',
+        success: function(data) {
+            dropdown.innerHTML = '';
+            const defaultOption = document.createElement('option');
+            defaultOption.value = '';
+            defaultOption.text = 'Select a project...';
+            dropdown.appendChild(defaultOption);
+
+            if (data && data.rows) {
+                data.rows.forEach(function(row) {
+                    let value = row.project || row.projectId || row.id;
+                    let text = row.name || row.displayName || row.project;
+
+                    // Do not add null or undefined values to the options
+                    if (value != null && text != null) {
+                        let option = document.createElement('option');
+                        option.value = value;
+                        option.text = text;
+                        dropdown.appendChild(option);
+                    }
+                });
+            }
+            dropdown.disabled = false;
+        },
+        failure: function(error) {
+            console.error('Failed to load active projects:', error);
+            dropdown.innerHTML = '<option value="">Failed to load projects</option>';
+        }
+    });
+
+</script>
diff --git a/nirc_ehr/resources/views/acquisitionReport.view.xml b/nirc_ehr/resources/views/acquisitionReport.view.xml
new file mode 100644
index 00000000..bbbab5f4
--- /dev/null
+++ b/nirc_ehr/resources/views/acquisitionReport.view.xml
@@ -0,0 +1,6 @@
+<view xmlns="http://labkey.org/data/xml/view" title="Acquisition Report">
+    <dependencies>
+        <dependency path="ehr.context" />
+        <dependency path="vis/vis"/>
+    </dependencies>
+</view>
\ No newline at end of file
diff --git a/nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRModule.java b/nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRModule.java
index 2ecd4dfa..8339e493 100644
--- a/nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRModule.java
+++ b/nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRModule.java
@@ -193,6 +193,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         NotificationService.get().registerNotification(new NIRCPregnancyOutcomeNotification(this));
 
         EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Printable Necropsy Report", this, DetailsURL.fromString("/nirc_ehr-necropsy.view"), "Pathology");
+        EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Acquisition Report", this, DetailsURL.fromString("/nirc_ehr-acquisitionReport.view"), "Population Overview");
 
 
         // Ensure N: is mounted if it's configured, as it's being mapped in via a symlink/shortcut, so we can't

From a00c53171ce109c30beec958980bafc30946e0f6 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Mon, 18 May 2026 09:33:37 -0700
Subject: [PATCH 4/4] Override editUIButtonHandler to set showImport to false
 (#699)

---
 nirc_ehr/resources/web/nirc_ehr/nircOverrides.js | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/nirc_ehr/resources/web/nirc_ehr/nircOverrides.js b/nirc_ehr/resources/web/nirc_ehr/nircOverrides.js
index 67e2f5a4..39f89d19 100644
--- a/nirc_ehr/resources/web/nirc_ehr/nircOverrides.js
+++ b/nirc_ehr/resources/web/nirc_ehr/nircOverrides.js
@@ -1 +1,11 @@
-EHR.Utils.rowEditorPlugin = 'NIRC_EHR.plugin.RowEditor';
\ No newline at end of file
+EHR.Utils.rowEditorPlugin = 'NIRC_EHR.plugin.RowEditor';
+
+EHR.Utils.editUIButtonHandler = function(schemaName, queryName, dataRegionName, paramMap, copyFilters){
+    var params = {
+        schemaName: schemaName,
+        'query.queryName': queryName,
+        showImport: false
+    };
+
+    this.editUIButtonCore(schemaName, queryName, dataRegionName, paramMap, undefined, params);
+};
\ No newline at end of file