From ee7ea685dc3a0551370077d2c057af2978f1e3ed Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Mon, 28 Aug 2023 08:28:37 -0500
Subject: [PATCH 01/44] Fixes for participant summary page layout.

---
 templates/program/nph/participant/index.html.twig | 10 ++++++----
 web/assets/css/nph.css                            |  4 ++++
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/templates/program/nph/participant/index.html.twig b/templates/program/nph/participant/index.html.twig
index 630ce7a09..1ce609056 100644
--- a/templates/program/nph/participant/index.html.twig
+++ b/templates/program/nph/participant/index.html.twig
@@ -80,7 +80,7 @@
                     {% set modulePanelDisplay = 'hidden' %}
                 {% endif %}
                 <div class="ModuleGroup {{ modulePanelDisplay }}" id="ModuleGroup{{ moduleNumber }}">
-                    <div class="row">
+                    <div>
                         <h4 class="col-md-12 participant-module-header">NPH Module {{ moduleNumber }} Collections</h4>
                         {% include 'program/nph/participant/partials/hair-nail-optin-badge.html.twig' %}
                     </div>
@@ -96,19 +96,20 @@
                                 {% set textDivSize = 'col-md-12' %}
                                 {% set dlwDiet = false %}
                             {% endif %}
-                            <div class="row">
+                            <div>
                                 <div class="col-md-12 well-sm well visit-diet-details {% if participantDietStatus != constant('App\\Helper\\NphParticipant::DIET_STARTED') %} collapsed {% endif %}" data-toggle="collapse" data-target="#{{ moduleNumber }}Visit{{ VisitCode }}"
                                      role="button" style="font-weight: bold">
                                     Visit {{ visit['visitDisplayName'] }}
                                     {% include 'program/nph/participant/partials/display-diet.html.twig' %}
                                 </div>
                                 <div style="margin-bottom: 20px" id="{{ moduleNumber }}Visit{{ VisitCode }}" class="collapse {% if participantDietStatus == constant('App\\Helper\\NphParticipant::DIET_STARTED') %} in {% endif %}">
-                                    <div class="row">
+                                    <div>
                                      {% if participant.dob %}
                                         <br>
+                                         <div class="col-md-12">
                                         <div class="{{ textDivSize }}">
                                         {% if participantDietStatus == constant('App\\Helper\\NphParticipant::DIET_STARTED') %}
-                                            <a class="btn btn-primary" role="button"
+                                            <a class="btn btn-primary generate-orders-button" role="button"
                                                href="{{ path('nph_generate_oder', {participantId: participant.id, module: moduleNumber, visit: VisitCode}) }}">
                                                 <i class="glyphicon glyphicon-plus-sign"></i> Generate Orders and Print Labels
                                             </a>
@@ -149,6 +150,7 @@
                                         </span>
                                 </div>
                                     {% endif %}
+                                         </div>
                                 </div>
                                     {% set displayedOrderIDS = [] %}
                                     {% set displayedTimePointHeaders = [] %}
diff --git a/web/assets/css/nph.css b/web/assets/css/nph.css
index 5675c6aa8..38c2ba8ea 100644
--- a/web/assets/css/nph.css
+++ b/web/assets/css/nph.css
@@ -173,6 +173,10 @@ div.order-row {
 .navbar-inverse .navbar-toggler {
     background-color: #FFFFFF;
 }
+.generate-orders-button {
+    margin-bottom: 15px;
+    margin-top: 10px;
+}
 
 .visit-diet-details:after {
     font-family: "Font Awesome 5 Free";

From 6396c1d5af9c3fe2c69aa250dbe77b115a28a2de Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 31 Aug 2023 08:10:16 -0500
Subject: [PATCH 02/44] hide dlw unless diet assigned, ordertype displayname

---
 src/Entity/NphOrder.php                              | 12 ++++++++++++
 src/Form/DlwType.php                                 |  4 ----
 .../order-participant-details-barcode.html.twig      |  2 +-
 templates/program/nph/participant/index.html.twig    |  2 +-
 4 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/Entity/NphOrder.php b/src/Entity/NphOrder.php
index 258d21fe9..bed62e816 100644
--- a/src/Entity/NphOrder.php
+++ b/src/Entity/NphOrder.php
@@ -19,6 +19,10 @@ class NphOrder
     public const TYPE_NAIL = 'nail';
     public const TYPE_DLW = 'urineDlw';
     public const TYPE_MODULE_3_SALIVA = 'saliva3';
+    private const TYPE_DISPLAY_OVERRIDE = [
+        '24urine' => '24 Hour Urine',
+        'urineDlw' => 'Urine DLW',
+    ];
 
     #[ORM\Id]
     #[ORM\GeneratedValue]
@@ -376,4 +380,12 @@ public function getMetadataArray(): ?array
         }
         return $metadata;
     }
+
+    public function getOrderTypeDisplayName(): string {
+        if (isset($this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()])) {
+            return $this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()];
+        } else {
+            return ucfirst($this->getOrderType());
+        }
+    }
 }
diff --git a/src/Form/DlwType.php b/src/Form/DlwType.php
index 45c6f9fa1..5e5e7e85b 100644
--- a/src/Form/DlwType.php
+++ b/src/Form/DlwType.php
@@ -42,19 +42,15 @@ public function buildForm(FormBuilderInterface $builder, array $options): void
                     if ($value < 0 || $value === null) {
                         $context->buildViolation('Participant weight required.')
                             ->addViolation();
-                        return false;
                     }
                     if ($value > 907) {
                         $context->buildViolation('Please verify the measurement is correct. Value should be less than 907 kg.')
                             ->addViolation();
-                        return  false;
                     }
                     if ($this->getNumDecimalPlaces($value) > 1) {
                         $context->buildViolation('Please verify the measurement is correct. Value can be entered up to the tenths (0.1) place.')
                             ->addViolation();
-                        return false;
                     }
-                    return true;
                 }),
                 'scale' => 1,
             ])
diff --git a/templates/program/nph/order/partials/order-participant-details-barcode.html.twig b/templates/program/nph/order/partials/order-participant-details-barcode.html.twig
index 2fe62d3a5..3b11a1b73 100644
--- a/templates/program/nph/order/partials/order-participant-details-barcode.html.twig
+++ b/templates/program/nph/order/partials/order-participant-details-barcode.html.twig
@@ -5,7 +5,7 @@
     <div class="col-sm-3 text-center">
         <strong class="text-primary">
             Module {{ order.module }} | Visit {{ order.visitType }} | {{ timePoints[order.timepoint] }} | {{ order
-            .orderType|capitalize }}
+            .getOrderTypeDisplayName() }}
         </strong>
         <div><svg id="order-barcode"></svg></div>
     </div>
diff --git a/templates/program/nph/participant/index.html.twig b/templates/program/nph/participant/index.html.twig
index 1ce609056..217e954b3 100644
--- a/templates/program/nph/participant/index.html.twig
+++ b/templates/program/nph/participant/index.html.twig
@@ -133,7 +133,7 @@
                                                      <span class="right-float dlw-collect-text">Last Saved {{ dlwSummary[moduleNumber][VisitCode]|date('n/j/Y g:ia', app.user.timezone) }}</span>
                                                  </div>
                                              {% endif %}
-                                         {% elseif dlwDiet %}
+                                         {% elseif dlwDiet and participantDietStatus == constant('App\\Helper\\NphParticipant::DIET_STARTED') %}
                                              <div class="dlw-collect-bg col-md-5 well well-sm right-float">
                                                  <a class="btn dlw-collect-button" role="button"
                                                     href="{{ path('nph_dlw_collect', {participantId: participant.id, module: moduleNumber, visit: VisitCode}) }}">

From 684ca03010d24fd580cf957fc5e2ebb241c1ed34 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 31 Aug 2023 08:12:29 -0500
Subject: [PATCH 03/44] Validation Fixes

---
 src/Nph/Order/Samples/Module3.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index b960973c3..e5dd93b35 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -171,7 +171,7 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 4mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 4,
           "warningMinVolume": 100,
@@ -188,11 +188,11 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 2.5mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
-          "maxVolume": 4,
+          "maxVolume": 2.4,
           "warningMinVolume": 100,
-          "warningMaxVolume": 4000,
+          "warningMaxVolume": 2400,
           "addNew": false,
           "collectMetadata": true,
           "metadataFields": [

From 6dd404d8ef17126f0b78c481fba260774838233c Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 31 Aug 2023 09:27:55 -0500
Subject: [PATCH 04/44] Calculate total volume on page load, use input groups
 on glycerol volume.

---
 .../program/nph/order/sample-finalize.html.twig    | 14 +++++++++-----
 web/assets/js/views/NphSampleFinalize.js           |  4 ++++
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 5a40f3133..ee33a5623 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -16,17 +16,21 @@
                 </td>
                 <td colspan="{{ colspan }}">
                     <label style="position: absolute; display: block; font-weight: normal">Saliva Volume</label>
-                    {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'style': 'width: 30%; float: left; top: 20px; position: relative'}}) }}
-                    <span style="top: 25px; position: relative">{{ aliquot['units'] }}</span>
+                    <div class="input-group" style="width: 45%; float: left; top: 20px; position: relative">
+                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control',}}) }}
+                        <span class="input-group-addon">{{ aliquot['units'] }}</span>
+                    </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
                     <label style="position: relative; display: block; font-weight: normal; float: right">Glycerol Volume</label>
-                    {{ form_widget(form[aliquotCode~metadataField['identifier']], {'attr': {'style': 'width: 30%; float: right; position: relative; right: 20px; top: -5px'}}) }}
-                    <span style="top: 5px; position: relative; left: 130px">μl</span>
+                    <div class="input-group" style="width: 45%; float: right; position: relative; top: -5px">
+                    {{ form_widget(form[aliquotCode~metadataField['identifier']], {'attr': {'class': 'form-control'}}) }}
+                    <span class="input-group-addon">μl</span>
+                    </div>
                 </td>
                 <td colspan="{{ colspan }}">
                     <span style="top: 25px; position: relative">=</span>
                     <span style="position: relative">Total Volume</span>
-                    <span style="position: relative; left: 20px; top: 5px" id="totalVol">#</span>
+                    <span style="position: relative; top: 25px" id="totalVol">#</span>
                 </td>
                 <td class="aliquot volume nopadleft" style="position: relative">
                     <span style="position: absolute; bottom: 7px; left: 0;">{{ aliquot['units'] }}</span>
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index a83eff2ab..4ee396089 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -107,6 +107,10 @@ $(document).ready(function () {
     }
 
     disableEnableAliquotFields();
+    calculateGlycerolVolume(
+        $("#nph_sample_finalize_SALIVAA2Volume_0"),
+        $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume")
+    );
     $(".aliquot-volume").trigger("keyup");
 
     $(".sample-modify-checkbox").on("change", disableEnableAliquotFields);

From 365831b1a99135d10d3d9564a1e2ab10bb743dd4 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 31 Aug 2023 09:29:37 -0500
Subject: [PATCH 05/44] Run php-cs-fixer

---
 src/Entity/NphOrder.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Entity/NphOrder.php b/src/Entity/NphOrder.php
index bed62e816..165850da9 100644
--- a/src/Entity/NphOrder.php
+++ b/src/Entity/NphOrder.php
@@ -381,11 +381,11 @@ public function getMetadataArray(): ?array
         return $metadata;
     }
 
-    public function getOrderTypeDisplayName(): string {
+    public function getOrderTypeDisplayName(): string
+    {
         if (isset($this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()])) {
             return $this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()];
-        } else {
-            return ucfirst($this->getOrderType());
         }
+        return ucfirst($this->getOrderType());
     }
 }

From 6515a9022c5b3a542097bb95bd50e94296c1169a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 5 Sep 2023 10:58:09 -0500
Subject: [PATCH 06/44] Added total volume constraint.

---
 src/Form/Nph/NphSampleFinalizeType.php | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 85b945d64..f23d7e59c 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -132,6 +132,20 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                 ]);
                 if (isset($aliquot['collectMetadata']) && $aliquot['collectMetadata']) {
                     foreach ($aliquot['metadataFields'] as $metadataField) {
+                        if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
+                            $metadataConstraints = [
+                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot, $metadataField) {
+                                    $formData = $context->getRoot()->getData();
+                                    $totalVolume = $formData["{$aliquotCode}Volume"][0] + ($formData[$aliquotCode . $metadataField['identifier']] / 1000);
+                                    if ($totalVolume > $aliquot['maxVolume']) {
+                                        $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a maximum of {$aliquot['maxVolume']} {$aliquot['units']}.")->addViolation();
+                                    }
+                                    if ($totalVolume < $aliquot['minVolume']) {
+                                        $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a minimum of {$aliquot['minVolume']} {$aliquot['units']}.")->addViolation();
+                                    }
+                                })
+                            ];
+                        }
                         $builder->add("{$aliquotCode}{$metadataField['identifier']}", $metadataField['entryType'], [
                             'label' => $metadataField['label'],
                             'required' => false,
@@ -140,10 +154,12 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                 'class' => $metadataField['class'] ?? '',
                             ],
                             'data' => $formData[$aliquotCode . $metadataField['identifier']][0] ?? null,
+                            'constraints' => $metadataConstraints ?? []
                         ]);
                     }
                 }
 
+
                 $volumeConstraints = [
                     new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot) {
                         $formData = $context->getRoot()->getData();

From 4c68cf56051ca9150db6dbf31b08e6897862d149 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 5 Sep 2023 11:02:34 -0500
Subject: [PATCH 07/44] Added form error.

---
 templates/program/nph/order/sample-finalize.html.twig | 1 +
 1 file changed, 1 insertion(+)

diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index ee33a5623..2f4206008 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -42,6 +42,7 @@
             <tr>
                 <td colspan="3" class="has-error">
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
+                    {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume']) }}
                 </td>
             </tr>
         {% endfor %}

From bdf4f159e9ff085079e7ee6ce82d1270e46701c1 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 12:59:09 -0500
Subject: [PATCH 08/44] Fix for checkboxes, save dlw finalization user.

---
 migrations/Version20230906173509.php          | 35 +++++++++++++++++++
 src/Controller/NphOrderController.php         |  1 +
 src/Entity/NphDlw.php                         | 16 +++++++++
 src/Service/Nph/NphOrderService.php           |  6 ++--
 templates/program/nph/order/collect.html.twig |  2 +-
 .../program/nph/order/dlw-collect.html.twig   |  9 +++++
 web/assets/js/views/NphSampleFinalize.js      |  2 +-
 7 files changed, 66 insertions(+), 5 deletions(-)
 create mode 100644 migrations/Version20230906173509.php

diff --git a/migrations/Version20230906173509.php b/migrations/Version20230906173509.php
new file mode 100644
index 000000000..7a30a0d18
--- /dev/null
+++ b/migrations/Version20230906173509.php
@@ -0,0 +1,35 @@
+<?php
+
+declare(strict_types=1);
+
+namespace DoctrineMigrations;
+
+use Doctrine\DBAL\Schema\Schema;
+use Doctrine\Migrations\AbstractMigration;
+
+/**
+ * Auto-generated Migration: Please modify to your needs!
+ */
+final class Version20230906173509 extends AbstractMigration
+{
+    public function getDescription(): string
+    {
+        return 'Adds user for NPH DLW Dosages for finalization records';
+    }
+
+    public function up(Schema $schema): void
+    {
+        $this->abortIf($this->connection->getDatabasePlatform()->getName() !== 'mysql', 'Migration can only be executed safely on \'mysql\'.');
+        $this->addSql('ALTER TABLE nph_dlw ADD user_id INT NOT NULL');
+        $this->addSql('ALTER TABLE nph_dlw ADD CONSTRAINT FK_3F1C65B7A76ED395 FOREIGN KEY (user_id) REFERENCES users (id)');
+        $this->addSql('CREATE INDEX IDX_3F1C65B7A76ED395 ON nph_dlw (user_id)');
+    }
+
+    public function down(Schema $schema): void
+    {
+        $this->abortIf($this->connection->getDatabasePlatform()->getName() !== 'mysql', 'Migration can only be executed safely on \'mysql\'.');
+        $this->addSql('ALTER TABLE nph_dlw DROP FOREIGN KEY FK_3F1C65B7A76ED395');
+        $this->addSql('DROP INDEX IDX_3F1C65B7A76ED395 ON nph_dlw');
+        $this->addSql('ALTER TABLE nph_dlw DROP user_id');
+    }
+}
diff --git a/src/Controller/NphOrderController.php b/src/Controller/NphOrderController.php
index 5433612a0..205f51b23 100644
--- a/src/Controller/NphOrderController.php
+++ b/src/Controller/NphOrderController.php
@@ -558,6 +558,7 @@ public function dlwSampleCollect(
             'module' => $module,
             'visit' => $visit,
             'disabled' => $disabled,
+            'dlwInfo' => $dlwObject,
             'form' => $dlwForm->createView()
         ]);
     }
diff --git a/src/Entity/NphDlw.php b/src/Entity/NphDlw.php
index 66d13a048..d06fe5d1a 100644
--- a/src/Entity/NphDlw.php
+++ b/src/Entity/NphDlw.php
@@ -41,6 +41,10 @@ class NphDlw
     #[ORM\Column(nullable: true)]
     private ?int $ModifiedTimezoneId = null;
 
+    #[ORM\ManyToOne]
+    #[ORM\JoinColumn(nullable: false)]
+    private ?User $User = null;
+
     public function getId(): int
     {
         return $this->id;
@@ -153,4 +157,16 @@ public function setModifiedTimezoneId(?int $ModifiedTimezoneId): static
 
         return $this;
     }
+
+    public function getUser(): ?User
+    {
+        return $this->User;
+    }
+
+    public function setUser(?User $User): static
+    {
+        $this->User = $User;
+
+        return $this;
+    }
 }
diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index 908d47e8f..212b337dc 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -49,6 +49,8 @@ public function __construct(
         $this->siteService = $siteService;
         $this->loggerService = $loggerService;
         $this->rdrApiService = $rdrApiService;
+        $this->user = $this->em->getRepository(User::class)->find($this->userService->getUser()->getId());
+        $this->site = $this->siteService->getSiteId();
     }
 
     public function loadModules(string $module, string $visit, string $participantId, string $biobankId): void
@@ -60,9 +62,6 @@ public function loadModules(string $module, string $visit, string $participantId
         $this->visit = $visit;
         $this->participantId = $participantId;
         $this->biobankId = $biobankId;
-
-        $this->user = $this->em->getRepository(User::class)->find($this->userService->getUser()->getId());
-        $this->site = $this->siteService->getSiteId();
     }
 
     public function getVisitDiet(): string
@@ -808,6 +807,7 @@ public function saveDlwCollection(NphDlw $formData, $participantId, $module, $vi
         $formData->setVisit($visit);
         $formData->setModifiedTimezoneId($this->getTimezoneid());
         $formData->setModifiedTs(new DateTime());
+        $formData->setUser($this->user);
         $this->em->persist($formData);
         $this->em->flush();
         return $formData;
diff --git a/templates/program/nph/order/collect.html.twig b/templates/program/nph/order/collect.html.twig
index 3b03b9f84..f68a173ff 100644
--- a/templates/program/nph/order/collect.html.twig
+++ b/templates/program/nph/order/collect.html.twig
@@ -4,7 +4,7 @@
 {% block body %}
     {% include 'program/nph/order/partials/order-header.html.twig' %}
     <div class="alert bg-light well-sm margin-top-15">
-        <span class="font-bold">{{ timePoints[order.timepoint] }} {{ order.orderType|capitalize }}</span>
+        <span class="font-bold">{{ timePoints[order.timepoint] }} {{ order.orderTypeDisplayName }}</span>
         <div class="pull-right">
             <a href="{{ path('nph_order_label_print', {'participantId': order.participantId, 'module': order.module, 'visit': order.visitType, 'sampleGroup': order.nphSamples[0].sampleGroup}) }}">
                 View Order Summary/Reprint Labels
diff --git a/templates/program/nph/order/dlw-collect.html.twig b/templates/program/nph/order/dlw-collect.html.twig
index 82e6fcef6..74ee9dc4c 100644
--- a/templates/program/nph/order/dlw-collect.html.twig
+++ b/templates/program/nph/order/dlw-collect.html.twig
@@ -2,6 +2,15 @@
 {% block title %} DLW Collect - {% endblock %}
 {% block body %}
 <div class="page-header">
+    {% if disabled %}
+    <div class="alert alert-success well-sm">
+        <strong>
+            Finalized
+            by {{ dlwInfo.User.email|default('Unknown') }}
+            on {{ dlwInfo.modifiedTs|date('n/j/Y g:ia', app.user.timezone) }}
+        </strong>
+    </div>
+    {% endif %}
     <h2>
         DLW Dosage
         <small>
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 4ee396089..52a6388b9 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -54,7 +54,7 @@ $(document).ready(function () {
     });
 
     $(document).on("click", ".clear-aliquot-widget", function () {
-        $(this).closest("tr").find("input").val("");
+        $(this).closest("tr").find("input:not(:read-only)").val("");
     });
 
     $(".aliquot-volume").keyup(function () {

From 433ddaf20232affa35f3470cb2927fe39247f42a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 13:10:56 -0500
Subject: [PATCH 09/44] Update Tests.

---
 tests/Service/NphOrderServiceTest.php |  3 ++-
 tests/testSetup.php                   | 10 ++++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/tests/Service/NphOrderServiceTest.php b/tests/Service/NphOrderServiceTest.php
index 7e672a650..145bacbe9 100644
--- a/tests/Service/NphOrderServiceTest.php
+++ b/tests/Service/NphOrderServiceTest.php
@@ -749,11 +749,12 @@ public function testSaveDlwCollection($participantId, $module, $visit, $formData
         $savedDlw = $this->service->saveDlwCollection($dlw, $participantId, $module, $visit);
         $this->assertSame($dlw->getActualDose(), $savedDlw->getActualDose());
         $this->assertSame($dlw->getParticipantWeight(), $savedDlw->getParticipantWeight());
+        $this->assertSame($dlw->getUser(), $savedDlw->getUser());
     }
 
     public function testGenerateDlwSummary()
     {
-        $dlw = $this->testSetup->generateNphDlw();
+        $dlw = $this->testSetup->generateNphDlw(self::getContainer()->get(UserService::class)->getUserEntity());
         $dlwRepository = $this->em->getRepository(NphDlw::class)->findOneBy(['id' => $dlw->getId()]);
         $dlwSummary = $this->service->generateDlwSummary([$dlwRepository]);
         $this->arrayHasKey($dlw->getModule(), $dlwSummary);
diff --git a/tests/testSetup.php b/tests/testSetup.php
index 33ce8e6ae..efa26cc78 100644
--- a/tests/testSetup.php
+++ b/tests/testSetup.php
@@ -9,8 +9,8 @@
 use App\Helper\NphParticipant;
 use App\Helper\Participant;
 use App\Service\SiteService;
+use App\Service\UserService;
 use Doctrine\ORM\EntityManagerInterface;
-use Google\Type\Date;
 
 class testSetup
 {
@@ -80,8 +80,7 @@ public function generateParticipant(
         string $lastName = null,
         \DateTime $dateOfBirth = null,
         array $rdrData = []
-    ): Participant
-    {
+    ): Participant {
         if ($id === null) {
             $id = 'P0000000001';
         }
@@ -104,6 +103,7 @@ public function generateParticipant(
     }
 
     public function generateNphDlw(
+        User $user,
         string $participantId = null,
         string $module = null,
         string $visit = null,
@@ -112,7 +112,8 @@ public function generateNphDlw(
         float $participantWeight = null,
         string $doseBatchId = null,
         \DateTime $dateModified = null,
-        int $modifiedTimezoneId = null): NphDlw
+        int $modifiedTimezoneId = null,
+    ): NphDlw
     {
         if ($participantId === null) {
             $participantId = 'P0000000001';
@@ -151,6 +152,7 @@ public function generateNphDlw(
         $dlw->setDoseBatchId($doseBatchId);
         $dlw->setModifiedTs($dateModified);
         $dlw->setModifiedTimezoneId($modifiedTimezoneId);
+        $dlw->setUser($user);
         $this->em->persist($dlw);
         $this->em->flush();
         return $dlw;

From 1cc098478d4bd9c4b636e1c6f30b65b468a35bd2 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 13:13:54 -0500
Subject: [PATCH 10/44] Remove nullable user.

---
 src/Entity/NphDlw.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Entity/NphDlw.php b/src/Entity/NphDlw.php
index d06fe5d1a..54cae10d4 100644
--- a/src/Entity/NphDlw.php
+++ b/src/Entity/NphDlw.php
@@ -43,7 +43,7 @@ class NphDlw
 
     #[ORM\ManyToOne]
     #[ORM\JoinColumn(nullable: false)]
-    private ?User $User = null;
+    private User $User;
 
     public function getId(): int
     {

From ee526a31e713f7e76e475ce278664f7343296bb9 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 14:34:18 -0500
Subject: [PATCH 11/44] Fix for saliva aliquot display.

---
 migrations/Version20230906173509.php                  |  3 ---
 templates/program/nph/order/sample-finalize.html.twig | 10 ++++++----
 web/assets/js/views/NphSampleFinalize.js              |  2 +-
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/migrations/Version20230906173509.php b/migrations/Version20230906173509.php
index 7a30a0d18..07c4c6946 100644
--- a/migrations/Version20230906173509.php
+++ b/migrations/Version20230906173509.php
@@ -7,9 +7,6 @@
 use Doctrine\DBAL\Schema\Schema;
 use Doctrine\Migrations\AbstractMigration;
 
-/**
- * Auto-generated Migration: Please modify to your needs!
- */
 final class Version20230906173509 extends AbstractMigration
 {
     public function getDescription(): string
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 2f4206008..1029150f3 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -28,11 +28,13 @@
                     </div>
                 </td>
                 <td colspan="{{ colspan }}">
-                    <span style="top: 25px; position: relative">=</span>
-                    <span style="position: relative">Total Volume</span>
-                    <span style="position: relative; top: 25px" id="totalVol">#</span>
+                    <label style="position: relative; display: block; font-weight: normal">Total Volume</label>
+                    <div class="input-group">
+                        <input type="text" id="totalVol" class="form-control">
+                        <span class="input-group-addon">mL</span>
+                    </div>
+                    </div>
                 </td>
-                <td class="aliquot volume nopadleft" style="position: relative">
                     <span style="position: absolute; bottom: 7px; left: 0;">{{ aliquot['units'] }}</span>
                     {% if not sample.disabled and not sample.unlocked %}
                         <i class="fa fa-eraser text-danger clear-aliquot-widget sample-finalize-eraser" role="button"></i>
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 52a6388b9..ca9404184 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -103,7 +103,7 @@ $(document).ready(function () {
         let sampleVolume = $(sampleVolumeField).val() ? parseInt($(sampleVolumeField).val()) * 1000 : 0;
         let glycerolVolume = $(glycerolVolumeField).val() ? parseInt($(glycerolVolumeField).val()) : 0;
         let totalVolume = ((sampleVolume + glycerolVolume) / 1000).toFixed(2);
-        $("#totalVol").html(`${totalVolume} mL`);
+        $("#totalVol").val(`${totalVolume}`);
     }
 
     disableEnableAliquotFields();

From 2e9f3a5e7b3cfd55308c1752cbe3521a61aa9b33 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 15:39:40 -0500
Subject: [PATCH 12/44] Removed flash, fixed showing finalized by unknown.

---
 src/Controller/NphOrderController.php | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/Controller/NphOrderController.php b/src/Controller/NphOrderController.php
index 205f51b23..a7b0f3e1f 100644
--- a/src/Controller/NphOrderController.php
+++ b/src/Controller/NphOrderController.php
@@ -543,9 +543,7 @@ public function dlwSampleCollect(
         $dlwForm->handleRequest($request);
         if ($dlwForm->isSubmitted()) {
             if ($dlwForm->isValid()) {
-                $nphOrderService->saveDlwCollection($dlwForm->getData(), $participantId, $module, $visit);
-                $timestamp = new \DateTime('now', new \DateTimeZone($this->getSecurityUser()->getTimezone()));
-                $this->addFlash('success', 'Saved by ' . $this->getSecurityUser()->getEmail() . ' on ' . $timestamp->format('m-d-Y h:i a'));
+                $dlwObject = $nphOrderService->saveDlwCollection($dlwForm->getData(), $participantId, $module, $visit);
                 $disabled = true;
             } else {
                 $disabled = false;

From 431e971f62d6634211b52664fa141b8f7fe07c57 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 6 Sep 2023 15:53:44 -0500
Subject: [PATCH 13/44] Remove second units for glyercol.

---
 templates/program/nph/order/sample-finalize.html.twig | 1 -
 1 file changed, 1 deletion(-)

diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 1029150f3..6681edba9 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -35,7 +35,6 @@
                     </div>
                     </div>
                 </td>
-                    <span style="position: absolute; bottom: 7px; left: 0;">{{ aliquot['units'] }}</span>
                     {% if not sample.disabled and not sample.unlocked %}
                         <i class="fa fa-eraser text-danger clear-aliquot-widget sample-finalize-eraser" role="button"></i>
                     {% endif %}

From c01ea1c857b43565a8180e8ab265903121e84abc Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 8 Sep 2023 10:05:54 -0500
Subject: [PATCH 14/44] Color button, Form warning fix, Tube volumes.

---
 src/Nph/Order/Samples/Module3.json                   | 12 ++++++------
 templates/program/nph/order/dlw-collect.html.twig    |  2 +-
 .../program/nph/order/sample-finalize.html.twig      |  7 ++++++-
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index e5dd93b35..7874604f3 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -164,10 +164,10 @@
       "aliquots": {
         "SALIVAA1": {
           "identifier": "SA1-U",
-          "container": "4mL Matrix tube (no glycerol)",
-          "description": "4mL Matrix tube",
+          "container": "5mL Matrix tube (no glycerol)",
+          "description": "5mL Matrix tube",
           "expectedAliquots": 1,
-          "expectedVolume": 2.4,
+          "expectedVolume": 4,
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
@@ -181,10 +181,10 @@
         },
         "SALIVAA2": {
           "identifier": "SA2-U",
-          "container": "2.5mL Matrix tube (w/glycerol)",
-          "description": "2.5mL Matrix tube",
+          "container": "5mL Matrix tube (w/glycerol)",
+          "description": "5mL Matrix tube",
           "expectedAliquots": 1,
-          "expectedVolume": 2,
+          "expectedVolume": 2.5,
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
diff --git a/templates/program/nph/order/dlw-collect.html.twig b/templates/program/nph/order/dlw-collect.html.twig
index 74ee9dc4c..46dd24ca4 100644
--- a/templates/program/nph/order/dlw-collect.html.twig
+++ b/templates/program/nph/order/dlw-collect.html.twig
@@ -100,7 +100,7 @@
             {{ form_rest(form) }}
             <div class="form-group margin-top-15">
                 {% if disabled %}
-                    <button type="button" class="btn btn-primary" id="form_edit" formnovalidate>Edit</button>
+                    <button type="button" class="btn btn-warning" id="form_edit" formnovalidate>Edit</button>
                 {% else %}
                     <button type="submit" class="btn btn-primary" id="form_submit">Save</button>
                 {% endif %}
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 6681edba9..ac335e0b1 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -180,7 +180,12 @@
                     {% include 'program/nph/order/partials/sample-finalize-participant-details.html.twig' %}
                 {% endif %}
                 <div class="panel-body">
-                    {{ form_start(sampleFinalizeForm, { attr: { class: 'warn-unsaved disable-enter prevent-resubmit'} }) }}
+                    {% if isFormDisabled %}
+                        {% set formClasses = 'disable-enter prevent-resumbit' %}
+                    {% else  %}
+                        {% set formClasses = 'warn-unsaved disable-enter prevent-resubmit' %}
+                    {% endif %}
+                    {{ form_start(sampleFinalizeForm, { attr: { class: formClasses} }) }}
                     {{ form_errors(sampleFinalizeForm) }}
                     <div class="form-group {% if not sampleFinalizeForm[sampleCode ~'CollectedTs'].vars.valid %}
                             has-error{% endif %}">

From a9809da973055c830ce332a30df61615df60d0d2 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 7 Sep 2023 13:05:19 -0500
Subject: [PATCH 15/44] Module 3 fixes

---
 src/Entity/NphOrder.php            | 12 ++++++++----
 src/Form/DlwType.php               | 10 ++++++++++
 src/Nph/Order/Samples/Module3.json |  5 +++--
 3 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/Entity/NphOrder.php b/src/Entity/NphOrder.php
index 165850da9..99e9fa7f1 100644
--- a/src/Entity/NphOrder.php
+++ b/src/Entity/NphOrder.php
@@ -20,8 +20,12 @@ class NphOrder
     public const TYPE_DLW = 'urineDlw';
     public const TYPE_MODULE_3_SALIVA = 'saliva3';
     private const TYPE_DISPLAY_OVERRIDE = [
-        '24urine' => '24 Hour Urine',
-        'urineDlw' => 'Urine DLW',
+        3 => [
+            'urine' => 'Spot Urine',
+            '24urine' => '24 Hour Urine',
+            'urineDlw' => 'Urine DLW',
+            'saliva3' => 'Saliva',
+        ],
     ];
 
     #[ORM\Id]
@@ -383,8 +387,8 @@ public function getMetadataArray(): ?array
 
     public function getOrderTypeDisplayName(): string
     {
-        if (isset($this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()])) {
-            return $this::TYPE_DISPLAY_OVERRIDE[$this->getOrderType()];
+        if (isset($this::TYPE_DISPLAY_OVERRIDE[$this->getModule()][$this->getOrderType()])) {
+            return $this::TYPE_DISPLAY_OVERRIDE[$this->getModule()][$this->getOrderType()];
         }
         return ucfirst($this->getOrderType());
     }
diff --git a/src/Form/DlwType.php b/src/Form/DlwType.php
index 5e5e7e85b..625485c9b 100644
--- a/src/Form/DlwType.php
+++ b/src/Form/DlwType.php
@@ -10,6 +10,7 @@
 use Symfony\Component\Form\FormBuilderInterface;
 use Symfony\Component\OptionsResolver\OptionsResolver;
 use Symfony\Component\Validator\Constraints\Callback;
+use Symfony\Component\Validator\Constraints\GreaterThan;
 use Symfony\Component\Validator\Constraints\NotBlank;
 use Symfony\Component\Validator\Constraints\Range;
 
@@ -33,6 +34,11 @@ public function buildForm(FormBuilderInterface $builder, array $options): void
                 'label' => 'Actual Dose (g)*',
                 'required' => true,
                 'scale' => 1,
+                'empty_data' => 0,
+                'constraints' => new GreaterThan([
+                    'value' => 0,
+                    'message' => 'Dose must be greater than 0.'
+                ])
             ])
             ->add('participantWeight', NumberType::class, [
                 'required' => true,
@@ -43,6 +49,10 @@ public function buildForm(FormBuilderInterface $builder, array $options): void
                         $context->buildViolation('Participant weight required.')
                             ->addViolation();
                     }
+                    if ($value == 0) {
+                        $context->buildViolation('Please verify the measurement is correct. Value should be greater than 0 kg.')
+                            ->addViolation();
+                    }
                     if ($value > 907) {
                         $context->buildViolation('Please verify the measurement is correct. Value should be less than 907 kg.')
                             ->addViolation();
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 7874604f3..9807ead67 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -117,6 +117,7 @@
       "temperature": "Refrigerated",
       "specimen": "Urine",
       "type": "urine",
+      "typeDisplayName": "Spot Urine",
       "identifier": "UrineS",
       "aliquots": {
         "RU1U": {
@@ -171,7 +172,7 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 4mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 4,
           "warningMinVolume": 100,
@@ -188,7 +189,7 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 2.5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 2.4,
           "warningMinVolume": 100,

From f2e78b07aa977af5152039d690bd5f56b75f760c Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 8 Sep 2023 14:35:51 -0500
Subject: [PATCH 16/44] Fixed eraser alignment on sample finalize, added error
 class.

---
 templates/program/nph/order/dlw-collect.html.twig     | 10 +++++-----
 templates/program/nph/order/sample-finalize.html.twig |  6 +++---
 web/assets/css/nph.css                                |  6 ++++++
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/templates/program/nph/order/dlw-collect.html.twig b/templates/program/nph/order/dlw-collect.html.twig
index 46dd24ca4..a71203d70 100644
--- a/templates/program/nph/order/dlw-collect.html.twig
+++ b/templates/program/nph/order/dlw-collect.html.twig
@@ -62,7 +62,7 @@
             {{ form_start(form, { attr: { class: 'disable-enter prevent-resubmit'} }) }}
             {{ form_errors(form) }}
             <div class="row">
-                <div class="col-md-4">
+                <div class="col-md-4 {% if not form['doseBatchId'].vars.valid%}has-error{% endif %}">
                     {{ form_label(form['doseBatchId'])}}
                     <div class="input-group">
                         <span class="input-group-addon">NPHDLW</span>
@@ -70,7 +70,7 @@
                     </div>
                     {{ form_errors(form['doseBatchId'])}}
                 </div>
-                <div class="col-md-3">
+                <div class="col-md-3 {% if not form['participantWeight'].vars.valid%}has-error{% endif %}">
                     {{ form_label(form['participantWeight'])}}
                     {{ form_widget(form['participantWeight'], {attr: {readonly: disabled}})}}
                     {{ form_errors(form['participantWeight'])}}
@@ -79,19 +79,19 @@
                 <div class="col-md-1">
                     <p style="margin-top: 2em; font-weight: bold">X 1.5 = </p>
                 </div>
-                <div class="col-md-4">
+                <div class="col-md-4 {% if not form['calculatedDose'].vars.valid%}has-error{% endif %}">
                     {{ form_label(form['calculatedDose']) }}
                     {{ form_widget(form['calculatedDose'], {attr: {readonly: disabled}}) }}
                     {{ form_errors(form['calculatedDose']) }}
                 </div>
             </div>
             <div class="row margin-top-30">
-                <div class="col-md-4">
+                <div class="col-md-4 {% if not form['actualDose'].vars.valid%}has-error{% endif %}">
                     {{ form_label(form['actualDose']) }}
                     {{ form_widget(form['actualDose'], {attr: {readonly: disabled}}) }}
                     {{ form_errors(form['actualDose']) }}
                 </div>
-                <div class="col-md-4">
+                <div class="col-md-4 {% if not form['doseAdministered'].vars.valid%}has-error{% endif %}">
                     {{ form_label(form['doseAdministered']) }}
                     {{ form_widget(form['doseAdministered'], {attr: {readonly: disabled}}) }}
                     {{ form_errors(form['doseAdministered']) }}
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index ac335e0b1..c6cd48b90 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -29,14 +29,14 @@
                 </td>
                 <td colspan="{{ colspan }}">
                     <label style="position: relative; display: block; font-weight: normal">Total Volume</label>
-                    <div class="input-group">
+                    <div class="input-group" style="float: right; position: relative; top: -5px">
                         <input type="text" id="totalVol" class="form-control">
                         <span class="input-group-addon">mL</span>
                     </div>
-                    </div>
                 </td>
+                <td style="position: relative">
                     {% if not sample.disabled and not sample.unlocked %}
-                        <i class="fa fa-eraser text-danger clear-aliquot-widget sample-finalize-eraser" role="button"></i>
+                        <i class="fa fa-eraser text-danger clear-aliquot-widget sample-metadata-eraser" role="button"></i>
                     {% endif %}
                 </td>
             </tr>
diff --git a/web/assets/css/nph.css b/web/assets/css/nph.css
index 38c2ba8ea..60a12c6a0 100644
--- a/web/assets/css/nph.css
+++ b/web/assets/css/nph.css
@@ -128,6 +128,12 @@ div.order-row {
     left: 33px;
     font-size: 22px
 }
+.sample-metadata-eraser {
+    position: absolute;
+    bottom: 20px;
+    left: 33px;
+    font-size: 22px
+}
 .aliquot-volume-units {
     position: absolute;
     bottom: 7px;

From a1f58cee560f4d2e603d540d288fa7b340922b39 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 09:40:40 -0500
Subject: [PATCH 17/44] Added code to allow multiple saliva collections.

---
 src/Entity/NphSample.php                      |   4 +-
 src/Form/Nph/NphSampleFinalizeType.php        |  31 +++--
 src/Nph/Order/Samples/Module3.json            |   4 +-
 .../nph/order/sample-finalize.html.twig       |  30 +++--
 web/assets/css/nph.css                        |   1 -
 web/assets/js/views/NphSampleFinalize.js      | 124 ++++++++++++------
 6 files changed, 128 insertions(+), 66 deletions(-)

diff --git a/src/Entity/NphSample.php b/src/Entity/NphSample.php
index 02d4bc0ff..d320d96a2 100644
--- a/src/Entity/NphSample.php
+++ b/src/Entity/NphSample.php
@@ -528,7 +528,9 @@ public function getRdrSampleObj(string $sampleIdentifier, string $description, a
     public function getRdrAliquotsSampleObj(array $aliquotsInfo): array
     {
         $aliquotObj = [];
+        $counter = [];
         foreach ($this->getNphAliquots() as $aliquot) {
+            $counter[$aliquot->getAliquotCode()] = isset($counter[$aliquot->getAliquotCode()]) ? $counter[$aliquot->getAliquotCode()] + 1 : 0;
             $collectedTs = $aliquot->getAliquotTs();
             $collectedTs->setTimezone(new \DateTimeZone('UTC'));
             $aliquotsData = [
@@ -546,7 +548,7 @@ public function getRdrAliquotsSampleObj(array $aliquotsInfo): array
                     ['units' => 'uL',
                     'volume' => $metadata[$aliquot->getAliquotCode() . 'glycerolAdditiveVolume']
                 ];
-                $aliquotsData['volume'] += ($metadata[$aliquot->getAliquotCode() . 'glycerolAdditiveVolume'] / 1000);
+                $aliquotsData['volume'] += ($metadata[$aliquot->getAliquotCode() . 'glycerolAdditiveVolume'][$counter[$aliquot->getAliquotCode()]] / 1000);
             }
             if ($aliquot->getStatus()) {
                 $aliquotsData['status'] = $aliquot->getStatus();
diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index f23d7e59c..589e460b1 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -135,26 +135,39 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
                                 new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot, $metadataField) {
+                                    $key = intval($context->getObject()->getName());
                                     $formData = $context->getRoot()->getData();
-                                    $totalVolume = $formData["{$aliquotCode}Volume"][0] + ($formData[$aliquotCode . $metadataField['identifier']] / 1000);
+                                    $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
+                                    $totalVolume = $formData["{$aliquotCode}Volume"][$key] + ($glycerolVolume / 1000);
                                     if ($totalVolume > $aliquot['maxVolume']) {
                                         $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a maximum of {$aliquot['maxVolume']} {$aliquot['units']}.")->addViolation();
                                     }
                                     if ($totalVolume < $aliquot['minVolume']) {
                                         $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a minimum of {$aliquot['minVolume']} {$aliquot['units']}.")->addViolation();
                                     }
+                                    if ($glycerolVolume <= 0) {
+                                        $context->buildViolation("{$metadataField['label']} volume must be greater than 0")->addViolation();
+                                    }
+                                    if ($glycerolVolume >= 0.1 && $glycerolVolume <= 0.4) {
+                                        $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
+                                    }
                                 })
                             ];
                         }
-                        $builder->add("{$aliquotCode}{$metadataField['identifier']}", $metadataField['entryType'], [
-                            'label' => $metadataField['label'],
-                            'required' => false,
-                            'attr' => [
-                                'placeholder' => $metadataField['placeholder'] ?? '',
-                                'class' => $metadataField['class'] ?? '',
+                        $builder->add("{$aliquotCode}{$metadataField['identifier']}", Type\CollectionType::class, [
+                            'entry_type' => Type\TextType::class,
+                            'entry_options' => [
+                                'label' => $metadataField['label'],
+                                'required' => false,
+                                'attr' => [
+                                    'placeholder' => $metadataField['placeholder'] ?? '',
+                                    'class' => $metadataField['class'] ?? '',
+                                ],
+                                'constraints' => $metadataConstraints ?? [],
                             ],
-                            'data' => $formData[$aliquotCode . $metadataField['identifier']][0] ?? null,
-                            'constraints' => $metadataConstraints ?? []
+                            'allow_add' => true,
+                            'allow_delete' => true,
+                            'data' => $formData[$aliquotCode . $metadataField['identifier']] ?? [],
                         ]);
                     }
                 }
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 9807ead67..63f3402f8 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -185,7 +185,7 @@
           "container": "5mL Matrix tube (w/glycerol)",
           "description": "5mL Matrix tube",
           "expectedAliquots": 1,
-          "expectedVolume": 2.5,
+          "expectedVolume": 2.4,
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
@@ -194,7 +194,7 @@
           "maxVolume": 2.4,
           "warningMinVolume": 100,
           "warningMaxVolume": 2400,
-          "addNew": false,
+          "addNew": true,
           "collectMetadata": true,
           "metadataFields": [
             {
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index c6cd48b90..94a26bb72 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -10,33 +10,32 @@
             {% set colspan = 1 %}
         {% endif %}
         {% for metadataField in aliquot['metadataFields'] %}
-            <tr>
+            <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}">
                 <td colspan="1">
                     <p style="font-weight: bold;">{{ metadataField['label'] }}</p><span>(1ml = 1000uL)</span>
                 </td>
                 <td colspan="{{ colspan }}">
                     <label style="position: absolute; display: block; font-weight: normal">Saliva Volume</label>
-                    <div class="input-group" style="width: 45%; float: left; top: 20px; position: relative">
-                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control',}}) }}
+                    <div class="input-group {% if not form[aliquotCode ~ 'Volume'][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: left; top: 20px; position: relative">
+                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume', 'data-warning-target': aliquotCode ~ '-warning-target'}}) }}
                         <span class="input-group-addon">{{ aliquot['units'] }}</span>
                     </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
                     <label style="position: relative; display: block; font-weight: normal; float: right">Glycerol Volume</label>
-                    <div class="input-group" style="width: 45%; float: right; position: relative; top: -5px">
+                    <div class="input-group {% if not form[aliquotCode~metadataField['identifier']].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
                     {{ form_widget(form[aliquotCode~metadataField['identifier']], {'attr': {'class': 'form-control'}}) }}
                     <span class="input-group-addon">μl</span>
                     </div>
                 </td>
-                <td colspan="{{ colspan }}">
+                <td colspan="{{ colspan }}" style="position: relative">
                     <label style="position: relative; display: block; font-weight: normal">Total Volume</label>
-                    <div class="input-group" style="float: right; position: relative; top: -5px">
-                        <input type="text" id="totalVol" class="form-control">
+                    <span style="top: 35px; left: -5px; position: absolute">=</span>
+                    <div class="input-group" style="float: left; position: relative; top: -5px; width: 65%">
+                        <input type="text" readonly="readonly" id="totalVol[{{ i }}]]" class="form-control">
                         <span class="input-group-addon">mL</span>
                     </div>
-                </td>
-                <td style="position: relative">
-                    {% if not sample.disabled and not sample.unlocked %}
-                        <i class="fa fa-eraser text-danger clear-aliquot-widget sample-metadata-eraser" role="button"></i>
+                    {% if sample.unlocked %}
+                    <i class="fa fa-eraser text-danger clear-aliquot-widget sample-metadata-eraser" style="font-size: 22px" role="button"></i>
                     {% endif %}
                 </td>
             </tr>
@@ -44,6 +43,9 @@
                 <td colspan="3" class="has-error">
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
                     {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume']) }}
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target" style="display: none">
+                    Please verify the volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).
+                    </span>
                 </td>
             </tr>
         {% endfor %}
@@ -51,7 +53,7 @@
 {% endmacro %}
 {% macro displayAliquotRow(aliquotCode, aliquot, sample, form, i, disabled, skipVolume = false) %}
     {% set aliquotId = form[aliquotCode][i].vars.data %}
-    <tr class="aliquots-row-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}">
+    <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}">
         <td {% if not form[aliquotCode][i].vars.valid %}
             class="has-error"{% endif %}>
             {{ form_widget(form[aliquotCode][i], {
@@ -66,7 +68,7 @@
         {% if not skipVolume %}
             {{ _self.displayVolumeTD(aliquotCode, aliquot, sample, form, i) }}
         {% elseif skipVolume and sample.unlocked %}
-            <td colspan="2"><i class="fa fa-eraser text-danger clear-aliquot-widget" style="font-size: 22px" role="button"></i></td>
+            <td colspan="2"></td>
         {% endif %}
         {% if form['cancel_' ~ aliquotCode ~ '_' ~ aliquotId] is defined %}
             <td class="row">
@@ -302,7 +304,7 @@
                                         <tr>
                                             <td>
                                                 <a type="button" class="add-aliquot-widget"
-                                                   data-list-selector="#aliquots_fields_list_{{ aliquotCode }}">+ Add Line</a>
+                                                   data-list-selector="#aliquots_fields_list_{{ aliquotCode }}" data-aliquot-code="{{ aliquotCode }}">+ Add Line</a>
                                             </td>
                                         </tr>
                                     {% endif %}
diff --git a/web/assets/css/nph.css b/web/assets/css/nph.css
index 60a12c6a0..562d1f2d7 100644
--- a/web/assets/css/nph.css
+++ b/web/assets/css/nph.css
@@ -129,7 +129,6 @@ div.order-row {
     font-size: 22px
 }
 .sample-metadata-eraser {
-    position: absolute;
     bottom: 20px;
     left: 33px;
     font-size: 22px
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index ca9404184..4e5894e70 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -10,43 +10,11 @@ $(document).ready(function () {
     });
 
     $(".add-aliquot-widget").click(function () {
-        let list = $($(this).attr("data-list-selector"));
-        let aliquotId = list.data("aliquot-id");
-        let aliquotUnits = list.data("aliquot-units");
-        let counter = list.data("widget-counter");
-
-        // Grab the prototype template and replace the "__name__" used in the id and name of the prototype
-        let newCodeWidget = list.data("code-prototype").replace(/__name__/g, counter);
-        let newTsWidget = list.data("ts-prototype").replace(/__name__/g, counter);
-        let newVolumeWidget = list.data("volume-prototype").replace(/__name__/g, counter);
-
-        // Increment and update widget counter
-        counter++;
-        list.data("widget-counter", counter);
-
-        let newElem = $(list.attr("data-widget-tags")).html(
-            "<td>" +
-                newCodeWidget +
-                "</td>" +
-                '<td style="position: relative">' +
-                newTsWidget +
-                "</td>" +
-                "<td>" +
-                newVolumeWidget +
-                "</td>" +
-                "<td style='position: relative'><span style='position: absolute; bottom: 7px; left: 0;'>" +
-                aliquotUnits +
-                '</span><i class="fa fa-eraser text-danger clear-aliquot-widget"\' +\n' +
-                '                \' style="position: absolute; bottom: 10px; left: 33px; font-size: 22px" role="button"></i></td>'
-        );
-
-        $(".aliquots-row-" + aliquotId)
-            .last()
-            .after(newElem);
-
-        $(".order-ts").pmiDateTimePicker({
-            maxDate: new Date().setHours(23, 59, 59, 999)
-        });
+        if ($(this).data("aliquot-code") === "SALIVAA2") {
+            addGlycerolAliquotRow(this);
+        } else {
+            addNormalAliquotRow(this);
+        }
     });
 
     $(document).on("click", ".delete-aliquot-widget", function () {
@@ -57,6 +25,8 @@ $(document).ready(function () {
         $(this).closest("tr").find("input:not(:read-only)").val("");
     });
 
+    $(document).on("click");
+
     $(".aliquot-volume").keyup(function () {
         let inputValue = $(this).val();
         let minValue = $(this).data("warning-min-volume");
@@ -65,8 +35,14 @@ $(document).ready(function () {
             calculateGlycerolVolume(this, $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume"));
         }
         if (inputValue && inputValue >= minValue && inputValue <= maxValue) {
+            if ($(this).data("warning-target")) {
+                $("#" + $(this).data("warning-target")).show();
+            }
             $(this).closest("tr").find(".aliquot-volume-warning").show();
         } else {
+            if ($(this).data("warning-target")) {
+                $("#" + $(this).data("warning-target")).hide();
+            }
             $(this).closest("tr").find(".aliquot-volume-warning").hide();
         }
     });
@@ -100,12 +76,82 @@ $(document).ready(function () {
     };
 
     function calculateGlycerolVolume(sampleVolumeField, glycerolVolumeField) {
-        let sampleVolume = $(sampleVolumeField).val() ? parseInt($(sampleVolumeField).val()) * 1000 : 0;
-        let glycerolVolume = $(glycerolVolumeField).val() ? parseInt($(glycerolVolumeField).val()) : 0;
+        let sampleVolume = $(sampleVolumeField).val() ? parseFloat($(sampleVolumeField).val()) * 1000 : 0;
+        let glycerolVolume = $(glycerolVolumeField).val() ? parseFloat($(glycerolVolumeField).val()) : 0;
         let totalVolume = ((sampleVolume + glycerolVolume) / 1000).toFixed(2);
         $("#totalVol").val(`${totalVolume}`);
     }
 
+    function addNormalAliquotRow(element) {
+        let list = $($(element).attr("data-list-selector"));
+        let aliquotId = list.data("aliquot-id");
+        let aliquotUnits = list.data("aliquot-units");
+        let counter = list.data("widget-counter");
+
+        // Grab the prototype template and replace the "__name__" used in the id and name of the prototype
+        let newCodeWidget = list.data("code-prototype").replace(/__name__/g, counter);
+        let newTsWidget = list.data("ts-prototype").replace(/__name__/g, counter);
+        let newVolumeWidget = list.data("volume-prototype").replace(/__name__/g, counter);
+
+        // Increment and update widget counter
+        counter++;
+        list.data("widget-counter", counter);
+
+        let newElem = $(list.attr("data-widget-tags")).html(
+            "<td>" +
+                newCodeWidget +
+                "</td>" +
+                '<td style="position: relative">' +
+                newTsWidget +
+                "</td>" +
+                "<td>" +
+                newVolumeWidget +
+                "</td>" +
+                "<td style='position: relative'><span style='position: absolute; bottom: 7px; left: 0;'>" +
+                aliquotUnits +
+                '</span><i class="fa fa-eraser text-danger clear-aliquot-widget"\' +\n' +
+                '                \' style="position: absolute; bottom: 10px; left: 33px; font-size: 22px" role="button"></i></td>'
+        );
+
+        $(".aliquots-row-" + aliquotId)
+            .last()
+            .after(newElem);
+
+        $(".order-ts").pmiDateTimePicker({
+            maxDate: new Date().setHours(23, 59, 59, 999)
+        });
+    }
+
+    function addGlycerolAliquotRow(element) {
+        let list = $($(element).attr("data-list-selector"));
+        let aliquotId = list.data("aliquot-id");
+        let aliquotUnits = list.data("aliquot-units");
+        let counter = list.data("widget-counter");
+        let aliquotCode = $(element).data("aliquot-code");
+        let rows = $(".duplicate-target-" + aliquotCode).clone();
+        rows.each(function () {
+            let barcodeName = `nph_sample_finalize[SALIVAA2][${counter}]`;
+            let tsName = `nph_sample_finalize[SALIVAA2AliquotTs][${counter}]`;
+            let volumeName = `nph_sample_finalize[SALIVAA2Volume][${counter}]`;
+            let glycerolVolumeName = `nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][${counter}]`;
+            $(this).removeClass("duplicate-target-" + aliquotCode);
+            $(this).find("[name='nph_sample_finalize[SALIVAA2][0]']").attr("name", barcodeName);
+            $(this).find("[name='nph_sample_finalize[SALIVAA2AliquotTs][0]']").attr("name", tsName);
+            $(this).find("[name='nph_sample_finalize[SALIVAA2Volume][0]']").attr("name", volumeName);
+            $(this)
+                .find("[name='nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][0]']")
+                .attr("name", glycerolVolumeName);
+            $(this).find("input").val("");
+            $(this).find("input:not(#totalVol)").attr("readonly", false);
+        });
+        counter++;
+        list.data("widget-counter", counter);
+        $(element).closest("tr").before(rows);
+        $(".order-ts").pmiDateTimePicker({
+            maxDate: new Date().setHours(23, 59, 59, 999)
+        });
+    }
+
     disableEnableAliquotFields();
     calculateGlycerolVolume(
         $("#nph_sample_finalize_SALIVAA2Volume_0"),

From 8e94e7388bb1bf7ac38c3d47873b0826947fd7b4 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 09:47:52 -0500
Subject: [PATCH 18/44] set metadatafields data.

---
 src/Form/Nph/NphSampleFinalizeType.php                | 6 +++++-
 templates/program/nph/order/sample-finalize.html.twig | 6 +++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 589e460b1..a71b4452d 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -131,6 +131,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     'data' => $tsData,
                 ]);
                 if (isset($aliquot['collectMetadata']) && $aliquot['collectMetadata']) {
+                    $aliquotMetadataCount = 0;
                     foreach ($aliquot['metadataFields'] as $metadataField) {
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
@@ -153,6 +154,8 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     }
                                 })
                             ];
+                            $metadataValue[] = $formData["{$aliquotCode}GlycerolAdditiveVolume"][$aliquotMetadataCount] ?? null;
+                            $aliquotMetadataCount++;
                         }
                         $builder->add("{$aliquotCode}{$metadataField['identifier']}", Type\CollectionType::class, [
                             'entry_type' => Type\TextType::class,
@@ -163,11 +166,12 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     'placeholder' => $metadataField['placeholder'] ?? '',
                                     'class' => $metadataField['class'] ?? '',
                                 ],
+                                'data' => $formData[$aliquotCode . $metadataField['identifier']][0] ?? null,
                                 'constraints' => $metadataConstraints ?? [],
                             ],
                             'allow_add' => true,
                             'allow_delete' => true,
-                            'data' => $formData[$aliquotCode . $metadataField['identifier']] ?? [],
+                            'data' => $metadataValue,
                         ]);
                     }
                 }
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 94a26bb72..7d7a09240 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -22,8 +22,8 @@
                     </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
                     <label style="position: relative; display: block; font-weight: normal; float: right">Glycerol Volume</label>
-                    <div class="input-group {% if not form[aliquotCode~metadataField['identifier']].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
-                    {{ form_widget(form[aliquotCode~metadataField['identifier']], {'attr': {'class': 'form-control'}}) }}
+                    <div class="input-group {% if not form[aliquotCode~metadataField['identifier']][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
+                    {{ form_widget(form[aliquotCode~metadataField['identifier']][i], {'attr': {'class': 'form-control'}}) }}
                     <span class="input-group-addon">μl</span>
                     </div>
                 </td>
@@ -42,7 +42,7 @@
             <tr>
                 <td colspan="3" class="has-error">
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
-                    {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume']) }}
+                    {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume'][i]) }}
                     <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target" style="display: none">
                     Please verify the volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).
                     </span>

From 19d74fe51a0f4473266336b1a588921eae7f5168 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 09:50:51 -0500
Subject: [PATCH 19/44] Fix for field not set

---
 src/Form/Nph/NphSampleFinalizeType.php | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index a71b4452d..c2aaec29d 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -131,7 +131,6 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     'data' => $tsData,
                 ]);
                 if (isset($aliquot['collectMetadata']) && $aliquot['collectMetadata']) {
-                    $aliquotMetadataCount = 0;
                     foreach ($aliquot['metadataFields'] as $metadataField) {
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
@@ -154,8 +153,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     }
                                 })
                             ];
-                            $metadataValue[] = $formData["{$aliquotCode}GlycerolAdditiveVolume"][$aliquotMetadataCount] ?? null;
-                            $aliquotMetadataCount++;
+                            $metadataValue = $formData["{$aliquotCode}GlycerolAdditiveVolume"] ?? [null];
                         }
                         $builder->add("{$aliquotCode}{$metadataField['identifier']}", Type\CollectionType::class, [
                             'entry_type' => Type\TextType::class,

From 108c4f249f4ee55ef6b5e2877fcf90bee26e3664 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 10:02:54 -0500
Subject: [PATCH 20/44] Added default for metadataValue

---
 src/Form/Nph/NphSampleFinalizeType.php | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index c2aaec29d..7ce4d4454 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -154,6 +154,8 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                 })
                             ];
                             $metadataValue = $formData["{$aliquotCode}GlycerolAdditiveVolume"] ?? [null];
+                        } else {
+                            $metadataValue = [null];
                         }
                         $builder->add("{$aliquotCode}{$metadataField['identifier']}", Type\CollectionType::class, [
                             'entry_type' => Type\TextType::class,

From 1cd361250c12537c7384b1fe04a3beb2f12d7052 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 10:06:34 -0500
Subject: [PATCH 21/44] Remove extra data variable.

---
 src/Form/Nph/NphSampleFinalizeType.php | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 7ce4d4454..0890191f7 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -166,7 +166,6 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     'placeholder' => $metadataField['placeholder'] ?? '',
                                     'class' => $metadataField['class'] ?? '',
                                 ],
-                                'data' => $formData[$aliquotCode . $metadataField['identifier']][0] ?? null,
                                 'constraints' => $metadataConstraints ?? [],
                             ],
                             'allow_add' => true,

From ee937cb5035c4f5100e1d9f3a86d5daa7caad33a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 14 Sep 2023 10:08:51 -0500
Subject: [PATCH 22/44] Remove useless code.

---
 web/assets/js/views/NphSampleFinalize.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 4e5894e70..7d90d2f3f 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -25,8 +25,6 @@ $(document).ready(function () {
         $(this).closest("tr").find("input:not(:read-only)").val("");
     });
 
-    $(document).on("click");
-
     $(".aliquot-volume").keyup(function () {
         let inputValue = $(this).val();
         let minValue = $(this).data("warning-min-volume");

From 80d59ac6e324ab6d5fe2cd99807857000b0f3bc9 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 15 Sep 2023 09:11:05 -0500
Subject: [PATCH 23/44] Updated javascript, fix for saving aliquot.

---
 src/Form/Nph/NphSampleFinalizeType.php        | 12 ++++------
 src/Nph/Order/Samples/Module3.json            | 16 +++++++++----
 src/Service/Nph/NphOrderService.php           |  2 +-
 .../nph/order/sample-finalize.html.twig       | 20 +++++++++++-----
 web/assets/js/views/NphSampleFinalize.js      | 23 ++++++++++---------
 5 files changed, 43 insertions(+), 30 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 0890191f7..5cad908af 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -139,21 +139,19 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
                                     $totalVolume = $formData["{$aliquotCode}Volume"][$key] + ($glycerolVolume / 1000);
-                                    if ($totalVolume > $aliquot['maxVolume']) {
-                                        $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a maximum of {$aliquot['maxVolume']} {$aliquot['units']}.")->addViolation();
-                                    }
-                                    if ($totalVolume < $aliquot['minVolume']) {
-                                        $context->buildViolation("{$metadataField['label']} cannot be entered.  This aliquot should contain a minimum of {$aliquot['minVolume']} {$aliquot['units']}.")->addViolation();
+                                    if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {
+                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxVolume']} {$metadataField['units']} Only.")
+                                            ->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                     if ($glycerolVolume <= 0) {
-                                        $context->buildViolation("{$metadataField['label']} volume must be greater than 0")->addViolation();
+                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain {$aliquot['minVolume']} {$aliquot['units']} Only.")->addViolation();
                                     }
                                     if ($glycerolVolume >= 0.1 && $glycerolVolume <= 0.4) {
                                         $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                 })
                             ];
-                            $metadataValue = $formData["{$aliquotCode}GlycerolAdditiveVolume"] ?? [null];
+                            $metadataValue = $formData["{$aliquotCode}glycerolAdditiveVolume"] ?? [null];
                         } else {
                             $metadataValue = [null];
                         }
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 63f3402f8..89df7ccce 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -173,11 +173,11 @@
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
           "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 4mL matrix aliquot tube barcode ID.",
-          "minVolume": 0,
+          "minVolume": 0.1,
           "maxVolume": 4,
           "warningMinVolume": 100,
           "warningMaxVolume": 4000,
-          "addNew": false,
+          "addNew": true,
           "collectMetadata": false
         },
         "SALIVAA2": {
@@ -191,9 +191,9 @@
           "barcodePrefix": "MC",
           "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 2.5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
-          "maxVolume": 2.4,
-          "warningMinVolume": 100,
-          "warningMaxVolume": 2400,
+          "maxVolume": 2,
+          "warningMinVolume": 0.1,
+          "warningMaxVolume": 2,
           "addNew": true,
           "collectMetadata": true,
           "metadataFields": [
@@ -203,6 +203,12 @@
               "type": "number",
               "label": "Calculated Volume for Glycerol Additive Sample",
               "units": "μL",
+              "minVolume": 0,
+              "maxVolume": 2400,
+              "warningMinVolume": 0,
+              "warningMaxVolume": 400,
+              "warningMinTotalVolume": 0.1,
+              "warningMaxTotalVolume": 2.4,
               "entryType": "Symfony\\Component\\Form\\Extension\\Core\\Type\\TextType",
               "required": true
             }
diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index 307d2d016..999df3bee 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -1071,7 +1071,7 @@ private function saveNphAliquotFinalizedInfo(NphSample $sample, array $aliquots,
                             }
                         }
                         if (!empty($formData["${aliquotCode}glycerolAdditiveVolume"])) {
-                            $nphAliquot->setAliquotMetadata(array_merge($nphAliquot->getAliquotMetadata(), ["${aliquotCode}glycerolAdditiveVolume" => $formData["${aliquotCode}glycerolAdditiveVolume"]]));
+                            $nphAliquot->setAliquotMetadata(array_merge($nphAliquot->getAliquotMetadata(), ["${aliquotCode}glycerolAdditiveVolume" => $formData["${aliquotCode}glycerolAdditiveVolume"][$key]]));
                         }
                         $this->em->persist($nphAliquot);
                         $this->em->flush();
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 7d7a09240..3b5daf181 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -10,28 +10,30 @@
             {% set colspan = 1 %}
         {% endif %}
         {% for metadataField in aliquot['metadataFields'] %}
-            <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}">
+            <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}" data-sample-index="{{ i }}">
                 <td colspan="1">
                     <p style="font-weight: bold;">{{ metadataField['label'] }}</p><span>(1ml = 1000uL)</span>
                 </td>
                 <td colspan="{{ colspan }}">
                     <label style="position: absolute; display: block; font-weight: normal">Saliva Volume</label>
                     <div class="input-group {% if not form[aliquotCode ~ 'Volume'][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: left; top: 20px; position: relative">
-                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume', 'data-warning-target': aliquotCode ~ '-warning-target'}}) }}
+                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume glycerol-volume sample', 'data-warning-target': aliquotCode ~ '-warning-target'}}) }}
                         <span class="input-group-addon">{{ aliquot['units'] }}</span>
                     </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
                     <label style="position: relative; display: block; font-weight: normal; float: right">Glycerol Volume</label>
                     <div class="input-group {% if not form[aliquotCode~metadataField['identifier']][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
-                    {{ form_widget(form[aliquotCode~metadataField['identifier']][i], {'attr': {'class': 'form-control'}}) }}
+                    {{ form_widget(form[aliquotCode~metadataField['identifier']][i], {'attr': {'class': 'form-control glycerol-volume aliquot-volume additive',
+                        'data-warning-target': aliquotCode ~ '-warning-target-glycerol', 'data-warning-max-volume': metadataField['warningMaxVolume'], 'data-warning-min-volume': metadataField['warningMinVolume']}}) }}
                     <span class="input-group-addon">μl</span>
                     </div>
                 </td>
-                <td colspan="{{ colspan }}" style="position: relative">
+                <td colspan="2" style="position: relative">
                     <label style="position: relative; display: block; font-weight: normal">Total Volume</label>
                     <span style="top: 35px; left: -5px; position: absolute">=</span>
                     <div class="input-group" style="float: left; position: relative; top: -5px; width: 65%">
-                        <input type="text" readonly="readonly" id="totalVol[{{ i }}]]" class="form-control">
+                        <input type="text" readonly="readonly" id="totalVol{{ i }}" class="form-control totalVol aliquot-volume" data-warning-min-volume="{{ metadataField['warningMinTotalVolume'] }}"
+                        data-warning-max-volume="{{ metadataField['warningMaxTotalVolume'] }}" data-warning-target="{{ aliquotCode }}-warning-target-total">
                         <span class="input-group-addon">mL</span>
                     </div>
                     {% if sample.unlocked %}
@@ -44,7 +46,13 @@
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
                     {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume'][i]) }}
                     <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target" style="display: none">
-                    Please verify the volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).
+                    Please verify the Saliva Volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).<br>
+                    </span>
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol" style="display: none">
+                    Please verify the Glycerol Volume unit of measurement is correct.  (Expected volume is in {{ metadataField['units'] }}).<br>
+                    </span>
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol" style="display: none">
+                    Please verify the Total Volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).<br>
                     </span>
                 </td>
             </tr>
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 7d90d2f3f..3dd671925 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -9,7 +9,7 @@ $(document).ready(function () {
         $("form[name='nph_sample_finalize']").submit();
     });
 
-    $(".add-aliquot-widget").click(function () {
+    $(document).on("click", ".add-aliquot-widget", function () {
         if ($(this).data("aliquot-code") === "SALIVAA2") {
             addGlycerolAliquotRow(this);
         } else {
@@ -25,13 +25,10 @@ $(document).ready(function () {
         $(this).closest("tr").find("input:not(:read-only)").val("");
     });
 
-    $(".aliquot-volume").keyup(function () {
-        let inputValue = $(this).val();
+    $(document).on("keyup", ".aliquot-volume", function () {
+        let inputValue = parseFloat($(this).val());
         let minValue = $(this).data("warning-min-volume");
         let maxValue = $(this).data("warning-max-volume");
-        if (this.id === "nph_sample_finalize_SALIVAA2Volume_0") {
-            calculateGlycerolVolume(this, $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume"));
-        }
         if (inputValue && inputValue >= minValue && inputValue <= maxValue) {
             if ($(this).data("warning-target")) {
                 $("#" + $(this).data("warning-target")).show();
@@ -45,8 +42,12 @@ $(document).ready(function () {
         }
     });
 
-    $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume").keyup(function () {
-        calculateGlycerolVolume($("#nph_sample_finalize_SALIVAA2Volume_0"), this);
+    $(document).on("keyup", ".glycerol-volume", function () {
+        calculateGlycerolVolume(
+            $(this).closest("tr").find(".sample"),
+            $(this).closest("tr").find(".additive"),
+            $(this).closest("tr").data("sample-index")
+        );
     });
 
     $(document).on("keyup", ".aliquot-barcode", function () {
@@ -73,11 +74,11 @@ $(document).ready(function () {
         });
     };
 
-    function calculateGlycerolVolume(sampleVolumeField, glycerolVolumeField) {
+    function calculateGlycerolVolume(sampleVolumeField, glycerolVolumeField, index) {
         let sampleVolume = $(sampleVolumeField).val() ? parseFloat($(sampleVolumeField).val()) * 1000 : 0;
         let glycerolVolume = $(glycerolVolumeField).val() ? parseFloat($(glycerolVolumeField).val()) : 0;
         let totalVolume = ((sampleVolume + glycerolVolume) / 1000).toFixed(2);
-        $("#totalVol").val(`${totalVolume}`);
+        $(`#totalVol${index}`).val(`${totalVolume}`);
     }
 
     function addNormalAliquotRow(element) {
@@ -140,7 +141,7 @@ $(document).ready(function () {
                 .find("[name='nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][0]']")
                 .attr("name", glycerolVolumeName);
             $(this).find("input").val("");
-            $(this).find("input:not(#totalVol)").attr("readonly", false);
+            $(this).find("input:not(.totalVol)").attr("readonly", false);
         });
         counter++;
         list.data("widget-counter", counter);

From 79cfd328c9f91588e9df9fcc35d2b986e7c33757 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 15 Sep 2023 10:03:45 -0500
Subject: [PATCH 24/44] Fix display error messages.

---
 templates/program/nph/order/sample-finalize.html.twig | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 3b5daf181..c4ae71064 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -17,14 +17,14 @@
                 <td colspan="{{ colspan }}">
                     <label style="position: absolute; display: block; font-weight: normal">Saliva Volume</label>
                     <div class="input-group {% if not form[aliquotCode ~ 'Volume'][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: left; top: 20px; position: relative">
-                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume glycerol-volume sample', 'data-warning-target': aliquotCode ~ '-warning-target'}}) }}
+                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume glycerol-volume sample', 'data-warning-target': aliquotCode ~ '-warning-target' ~ i}) }}
                         <span class="input-group-addon">{{ aliquot['units'] }}</span>
                     </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
                     <label style="position: relative; display: block; font-weight: normal; float: right">Glycerol Volume</label>
                     <div class="input-group {% if not form[aliquotCode~metadataField['identifier']][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
                     {{ form_widget(form[aliquotCode~metadataField['identifier']][i], {'attr': {'class': 'form-control glycerol-volume aliquot-volume additive',
-                        'data-warning-target': aliquotCode ~ '-warning-target-glycerol', 'data-warning-max-volume': metadataField['warningMaxVolume'], 'data-warning-min-volume': metadataField['warningMinVolume']}}) }}
+                        'data-warning-target': aliquotCode ~ '-warning-target-glycerol' ~ i, 'data-warning-max-volume': metadataField['warningMaxVolume'], 'data-warning-min-volume': metadataField['warningMinVolume']}}) }}
                     <span class="input-group-addon">μl</span>
                     </div>
                 </td>
@@ -33,7 +33,7 @@
                     <span style="top: 35px; left: -5px; position: absolute">=</span>
                     <div class="input-group" style="float: left; position: relative; top: -5px; width: 65%">
                         <input type="text" readonly="readonly" id="totalVol{{ i }}" class="form-control totalVol aliquot-volume" data-warning-min-volume="{{ metadataField['warningMinTotalVolume'] }}"
-                        data-warning-max-volume="{{ metadataField['warningMaxTotalVolume'] }}" data-warning-target="{{ aliquotCode }}-warning-target-total">
+                        data-warning-max-volume="{{ metadataField['warningMaxTotalVolume'] }}" data-warning-target="{{ aliquotCode }}-warning-target-total{{ i }}">
                         <span class="input-group-addon">mL</span>
                     </div>
                     {% if sample.unlocked %}

From f87ee2fd0a6a0f71b992ff050fab3668a7be6031 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 15 Sep 2023 10:06:48 -0500
Subject: [PATCH 25/44] More javascript

---
 templates/program/nph/order/sample-finalize.html.twig | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index c4ae71064..20580b708 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -17,7 +17,7 @@
                 <td colspan="{{ colspan }}">
                     <label style="position: absolute; display: block; font-weight: normal">Saliva Volume</label>
                     <div class="input-group {% if not form[aliquotCode ~ 'Volume'][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: left; top: 20px; position: relative">
-                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume glycerol-volume sample', 'data-warning-target': aliquotCode ~ '-warning-target' ~ i}) }}
+                        {{ form_widget(form[aliquotCode ~ 'Volume'][i], {'attr': {'class': 'form-control aliquot-volume glycerol-volume sample', 'data-warning-target': aliquotCode ~ '-warning-target' ~ i}}) }}
                         <span class="input-group-addon">{{ aliquot['units'] }}</span>
                     </div>
                     <span style="top: 25px; left: 10px; position: relative">+</span>
@@ -45,13 +45,13 @@
                 <td colspan="3" class="has-error">
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
                     {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume'][i]) }}
-                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target" style="display: none">
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target{{ i }}" style="display: none">
                     Please verify the Saliva Volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).<br>
                     </span>
-                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol" style="display: none">
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol{{ i }}" style="display: none">
                     Please verify the Glycerol Volume unit of measurement is correct.  (Expected volume is in {{ metadataField['units'] }}).<br>
                     </span>
-                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol" style="display: none">
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol{{ i }}" style="display: none">
                     Please verify the Total Volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).<br>
                     </span>
                 </td>

From 9e19136259e9c47040246fd9ff85c4c3e32ea796 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 19 Sep 2023 08:20:45 -0500
Subject: [PATCH 26/44] Finalization fixes, changes to warnings.

---
 src/Form/Nph/NphSampleFinalizeType.php          |  8 ++++++--
 src/Nph/Order/Samples/Module3.json              |  8 ++++----
 .../program/nph/order/sample-finalize.html.twig | 17 ++++++++++++++---
 web/assets/js/views/NphSampleFinalize.js        | 14 +++++++++++++-
 4 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 5cad908af..4acf8b99a 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -143,12 +143,16 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                         $context->buildViolation("Glycerol Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxVolume']} {$metadataField['units']} Only.")
                                             ->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
-                                    if ($glycerolVolume <= 0) {
-                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain {$aliquot['minVolume']} {$aliquot['units']} Only.")->addViolation();
+                                    if ($glycerolVolume == 0) {
+                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. Volume should be greater than 0")->addViolation();
                                     }
                                     if ($glycerolVolume >= 0.1 && $glycerolVolume <= 0.4) {
                                         $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
+                                    if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {
+                                        $context->buildViolation("Total Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxTotalVolume']} {$metadataField['units']} Only.")
+                                            ->atPath($aliquotCode . $metadataField['identifier'] . "totalVol")->addViolation();
+                                    }
                                 })
                             ];
                             $metadataValue = $formData["{$aliquotCode}glycerolAdditiveVolume"] ?? [null];
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 89df7ccce..c1f313a2e 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -175,8 +175,8 @@
           "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 4mL matrix aliquot tube barcode ID.",
           "minVolume": 0.1,
           "maxVolume": 4,
-          "warningMinVolume": 100,
-          "warningMaxVolume": 4000,
+          "warningMinVolume": 0.1,
+          "warningMaxVolume": 0.4,
           "addNew": true,
           "collectMetadata": false
         },
@@ -193,7 +193,7 @@
           "minVolume": 0,
           "maxVolume": 2,
           "warningMinVolume": 0.1,
-          "warningMaxVolume": 2,
+          "warningMaxVolume": 0.4,
           "addNew": true,
           "collectMetadata": true,
           "metadataFields": [
@@ -206,7 +206,7 @@
               "minVolume": 0,
               "maxVolume": 2400,
               "warningMinVolume": 0,
-              "warningMaxVolume": 400,
+              "warningMaxVolume": 0.4,
               "warningMinTotalVolume": 0.1,
               "warningMaxTotalVolume": 2.4,
               "entryType": "Symfony\\Component\\Form\\Extension\\Core\\Type\\TextType",
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 20580b708..7b5370f09 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -9,8 +9,13 @@
         {% else %}
             {% set colspan = 1 %}
         {% endif %}
+        {% if i == 0 %}
+            {% set firstIteration = true %}
+        {% else %}
+            {% set firstIteration = false %}
+        {% endif %}
         {% for metadataField in aliquot['metadataFields'] %}
-            <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}" data-sample-index="{{ i }}">
+            <tr class="aliquots-row-{{ aliquotCode }}{% if firstIteration %} duplicate-target-{{ aliquotCode }} {% endif %}" id="aliquots_{{ aliquotCode }}_{{ i }}" data-sample-index="{{ i }}">
                 <td colspan="1">
                     <p style="font-weight: bold;">{{ metadataField['label'] }}</p><span>(1ml = 1000uL)</span>
                 </td>
@@ -41,7 +46,7 @@
                     {% endif %}
                 </td>
             </tr>
-            <tr>
+            <tr class="{% if firstIteration %} duplicate-target-{{ aliquotCode }} {% endif %}">
                 <td colspan="3" class="has-error">
                     {{ form_errors(form[aliquotCode ~ 'Volume'][i]) }}
                     {{ form_errors(form[aliquotCode ~ 'glycerolAdditiveVolume'][i]) }}
@@ -56,12 +61,18 @@
                     </span>
                 </td>
             </tr>
+            {% set firstIteration = false %}
         {% endfor %}
     {% endif %}
 {% endmacro %}
 {% macro displayAliquotRow(aliquotCode, aliquot, sample, form, i, disabled, skipVolume = false) %}
+    {% if i == 0 %}
+        {% set firstIteration = true %}
+    {% else %}
+        {% set firstIteration = false %}
+    {% endif %}
     {% set aliquotId = form[aliquotCode][i].vars.data %}
-    <tr class="aliquots-row-{{ aliquotCode }} duplicate-target-{{ aliquotCode }}" id="aliquots_{{ aliquotCode }}_{{ i }}">
+    <tr class="aliquots-row-{{ aliquotCode }}{% if firstIteration %} duplicate-target-{{ aliquotCode }} {% endif %}" id="aliquots_{{ aliquotCode }}_{{ i }}">
         <td {% if not form[aliquotCode][i].vars.valid %}
             class="has-error"{% endif %}>
             {{ form_widget(form[aliquotCode][i], {
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 3dd671925..b344cb4a0 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -79,6 +79,16 @@ $(document).ready(function () {
         let glycerolVolume = $(glycerolVolumeField).val() ? parseFloat($(glycerolVolumeField).val()) : 0;
         let totalVolume = ((sampleVolume + glycerolVolume) / 1000).toFixed(2);
         $(`#totalVol${index}`).val(`${totalVolume}`);
+        $(`#totalVol${index}`).each(function () {
+            if (
+                $(this).data("warning-max-volume") &&
+                $(this).val() > $(this).data("warning-max-volume") &&
+                $(this).parent().parent().siblings().children().hasClass("has-error") &&
+                !$(this).parent().hasClass("has-error")
+            ) {
+                $(this).parent().addClass("has-error");
+            }
+        });
     }
 
     function addNormalAliquotRow(element) {
@@ -127,7 +137,7 @@ $(document).ready(function () {
         let aliquotUnits = list.data("aliquot-units");
         let counter = list.data("widget-counter");
         let aliquotCode = $(element).data("aliquot-code");
-        let rows = $(".duplicate-target-" + aliquotCode).clone();
+        let rows = $(".duplicate-target-" + aliquotId).clone();
         rows.each(function () {
             let barcodeName = `nph_sample_finalize[SALIVAA2][${counter}]`;
             let tsName = `nph_sample_finalize[SALIVAA2AliquotTs][${counter}]`;
@@ -141,6 +151,7 @@ $(document).ready(function () {
                 .find("[name='nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][0]']")
                 .attr("name", glycerolVolumeName);
             $(this).find("input").val("");
+            $(this).find(".text-warning").hide();
             $(this).find("input:not(.totalVol)").attr("readonly", false);
         });
         counter++;
@@ -156,6 +167,7 @@ $(document).ready(function () {
         $("#nph_sample_finalize_SALIVAA2Volume_0"),
         $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume")
     );
+
     $(".aliquot-volume").trigger("keyup");
 
     $(".sample-modify-checkbox").on("change", disableEnableAliquotFields);

From bcd319c91a316dab78866f8cc4072fdb0ae20aa7 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 19 Sep 2023 08:25:54 -0500
Subject: [PATCH 27/44] Run php-cs-fixer

---
 src/Form/Nph/NphSampleFinalizeType.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 4acf8b99a..8d4214136 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -144,14 +144,14 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                             ->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                     if ($glycerolVolume == 0) {
-                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. Volume should be greater than 0")->addViolation();
+                                        $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
                                     }
                                     if ($glycerolVolume >= 0.1 && $glycerolVolume <= 0.4) {
                                         $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                     if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {
                                         $context->buildViolation("Total Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxTotalVolume']} {$metadataField['units']} Only.")
-                                            ->atPath($aliquotCode . $metadataField['identifier'] . "totalVol")->addViolation();
+                                            ->atPath($aliquotCode . $metadataField['identifier'] . 'totalVol')->addViolation();
                                     }
                                 })
                             ];

From 35f317944d138bd933dea6deed0f3407b5184a89 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 19 Sep 2023 08:35:03 -0500
Subject: [PATCH 28/44] Remove unused use.

---
 src/Form/Nph/NphSampleFinalizeType.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 8d4214136..3ba944a8d 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -134,7 +134,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     foreach ($aliquot['metadataFields'] as $metadataField) {
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
-                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot, $metadataField) {
+                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $metadataField) {
                                     $key = intval($context->getObject()->getName());
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
@@ -146,7 +146,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     if ($glycerolVolume == 0) {
                                         $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
                                     }
-                                    if ($glycerolVolume >= 0.1 && $glycerolVolume <= 0.4) {
+                                    if ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
                                         $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                     if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {

From c520b86ff9b33d3cab3a34d7dfc1ea849a8a4176 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 19 Sep 2023 11:55:47 -0500
Subject: [PATCH 29/44] Fix for DLWDose Sending.

---
 src/Service/Nph/NphOrderService.php | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index 999df3bee..82aeaa3f3 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -661,14 +661,14 @@ public function getRdrObject(NphOrder $order, NphSample $sample, string $type =
         $samplesMetadata = $this->getSamplesMetadata($order);
         $obj->sample = $sample->getRdrSampleObj($sampleIdentifier, $sampleDescription, $samplesMetadata);
         $aliquotsInfo = $this->getAliquots($sample->getSampleCode());
-        if ($order->getModule() === '3' && $order->getVisitType() === $order::TYPE_DLW) {
-            $dlwInfo = $this->em->getRepository(NphDlw::class)->findOneBy(['module' => $order->getModule(), 'visitType' => $order->getVisitType(), 'NphParticipant' => $order->getParticipantId()]);
-            $obj['dlwdose'] = [
-              'batchid' => $dlwInfo->getBatchId(),
+        if ($order->getModule() === '3' && $order->getOrderType() === $order::TYPE_DLW) {
+            $dlwInfo = $this->em->getRepository(NphDlw::class)->findOneBy(['module' => $order->getModule(), 'visit' => $order->getVisitType(), 'NphParticipant' => $order->getParticipantId()]);
+            $obj->dlwDose = [
+              'batchid' => $dlwInfo->getDoseBatchId(),
               'participantweight' => $dlwInfo->getParticipantWeight(),
               'dose' => $dlwInfo->getActualDose(),
               'calculateddose' => ($dlwInfo->getParticipantWeight() * 1.5),
-                'dosetime' => $dlwInfo->getDoseAdministered()->format('Y-m-d\TH:i:s\Z')
+                'doseAdministered' => $dlwInfo->getDoseAdministered()->format('Y-m-d\TH:i:s\Z')
             ];
         }
         if ($aliquotsInfo) {

From 12ba6c9b713a98f6d627eb73f24d13e5b1a1dcd4 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 19 Sep 2023 22:22:52 -0500
Subject: [PATCH 30/44] Change validations to javascript to handle field not in
 type.

---
 src/Form/Nph/NphSampleFinalizeType.php        | 14 +++-----------
 src/Nph/Order/Samples/Module3.json            |  6 +++---
 .../nph/order/sample-finalize.html.twig       |  2 +-
 web/assets/js/views/NphSampleFinalize.js      | 19 +++++++++++++++++++
 4 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 3ba944a8d..e837e164d 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -138,20 +138,12 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     $key = intval($context->getObject()->getName());
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
-                                    $totalVolume = $formData["{$aliquotCode}Volume"][$key] + ($glycerolVolume / 1000);
-                                    if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {
-                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxVolume']} {$metadataField['units']} Only.")
-                                            ->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
-                                    }
                                     if ($glycerolVolume == 0) {
                                         $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
-                                    }
-                                    if ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
+                                    } elseif ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
                                         $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
-                                    }
-                                    if ($totalVolume > $metadataField['warningMaxTotalVolume'] || $totalVolume < $metadataField['warningMinTotalVolume']) {
-                                        $context->buildViolation("Total Volume Please verify the volume is correct this aliquot should contain {$metadataField['warningMaxTotalVolume']} {$metadataField['units']} Only.")
-                                            ->atPath($aliquotCode . $metadataField['identifier'] . 'totalVol')->addViolation();
+                                    } elseif ($glycerolVolume > $metadataField['maxVolume']) {
+                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                     }
                                 })
                             ];
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index c1f313a2e..2e71c43e4 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -204,11 +204,11 @@
               "label": "Calculated Volume for Glycerol Additive Sample",
               "units": "μL",
               "minVolume": 0,
-              "maxVolume": 2400,
+              "maxVolume": 400,
               "warningMinVolume": 0,
               "warningMaxVolume": 0.4,
-              "warningMinTotalVolume": 0.1,
-              "warningMaxTotalVolume": 2.4,
+              "warningMinTotalVolume": 100,
+              "warningMaxTotalVolume": 2400,
               "entryType": "Symfony\\Component\\Form\\Extension\\Core\\Type\\TextType",
               "required": true
             }
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 7b5370f09..925ab222e 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -56,7 +56,7 @@
                     <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol{{ i }}" style="display: none">
                     Please verify the Glycerol Volume unit of measurement is correct.  (Expected volume is in {{ metadataField['units'] }}).<br>
                     </span>
-                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-glycerol{{ i }}" style="display: none">
+                    <span class="text-warning aliquot-volume-warning" id="{{ aliquotCode }}-warning-target-total{{ i }}" style="display: none">
                     Please verify the Total Volume unit of measurement is correct.  (Expected volume is in {{ aliquot['units'] }}).<br>
                     </span>
                 </td>
diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index b344cb4a0..e02209e7b 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -87,6 +87,16 @@ $(document).ready(function () {
                 !$(this).parent().hasClass("has-error")
             ) {
                 $(this).parent().addClass("has-error");
+                $(this)
+                    .parent()
+                    .parent()
+                    .parent()
+                    .next()
+                    .find("li")
+                    .append(
+                        `<li><span class="glyphicon glyphicon-exclamation-sign"></span> Please verify the total volume is correct.  This aliquot should contain a maximum of 2.4 mL.</li>`
+                    );
+                $(this).trigger("keyup");
             }
         });
     }
@@ -143,6 +153,9 @@ $(document).ready(function () {
             let tsName = `nph_sample_finalize[SALIVAA2AliquotTs][${counter}]`;
             let volumeName = `nph_sample_finalize[SALIVAA2Volume][${counter}]`;
             let glycerolVolumeName = `nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][${counter}]`;
+            let targetName = `SALIVAA2-warning-target${counter}`;
+            let glycerolTarget = `SALIVAA2-warning-target-glycerol${counter}`;
+            let totalTarget = `SALIVAA2-warning-target-total${counter}`;
             $(this).removeClass("duplicate-target-" + aliquotCode);
             $(this).find("[name='nph_sample_finalize[SALIVAA2][0]']").attr("name", barcodeName);
             $(this).find("[name='nph_sample_finalize[SALIVAA2AliquotTs][0]']").attr("name", tsName);
@@ -150,8 +163,14 @@ $(document).ready(function () {
             $(this)
                 .find("[name='nph_sample_finalize[SALIVAA2glycerolAdditiveVolume][0]']")
                 .attr("name", glycerolVolumeName);
+            $(this).find("#SALIVAA2-warning-target0").attr("id", targetName);
+            $(this).find("#SALIVAA2-warning-target-glycerol0").attr("id", glycerolTarget);
+            $(this).find("#SALIVAA2-warning-target-total0").attr("id", totalTarget);
+            $(this).find("");
             $(this).find("input").val("");
             $(this).find(".text-warning").hide();
+            $(this).find(".help-block").remove();
+            $(this).find(".has-error").removeClass("has-error");
             $(this).find("input:not(.totalVol)").attr("readonly", false);
         });
         counter++;

From c1a2c2e1cbd052c0057193ed1732733d715ec195 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 20 Sep 2023 09:31:11 -0500
Subject: [PATCH 31/44] Fix eraser, only check volumes on set aliquots.

---
 src/Form/Nph/NphSampleFinalizeType.php           | 16 +++++++++-------
 .../program/nph/order/sample-finalize.html.twig  |  2 +-
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index e837e164d..f96bb5da6 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -134,16 +134,18 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     foreach ($aliquot['metadataFields'] as $metadataField) {
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
-                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $metadataField) {
+                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot, $metadataField) {
                                     $key = intval($context->getObject()->getName());
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
-                                    if ($glycerolVolume == 0) {
-                                        $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
-                                    } elseif ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
-                                        $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
-                                    } elseif ($glycerolVolume > $metadataField['maxVolume']) {
-                                        $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
+                                    if (isset($formData[$aliquotCode][$key])) {
+                                        if ($glycerolVolume == 0) {
+                                            $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
+                                        } elseif ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
+                                            $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
+                                        } elseif ($glycerolVolume > $metadataField['maxVolume']) {
+                                            $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
+                                        }
                                     }
                                 })
                             ];
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 925ab222e..6f61073db 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -41,7 +41,7 @@
                         data-warning-max-volume="{{ metadataField['warningMaxTotalVolume'] }}" data-warning-target="{{ aliquotCode }}-warning-target-total{{ i }}">
                         <span class="input-group-addon">mL</span>
                     </div>
-                    {% if sample.unlocked %}
+                    {% if not sample.disabled %}
                     <i class="fa fa-eraser text-danger clear-aliquot-widget sample-metadata-eraser" style="font-size: 22px" role="button"></i>
                     {% endif %}
                 </td>

From b40126a7d33fbbe08b34eba473910af1713c572d Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 20 Sep 2023 09:48:46 -0500
Subject: [PATCH 32/44] Remove unused use statement.

---
 src/Form/Nph/NphSampleFinalizeType.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index f96bb5da6..2d70341d1 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -134,7 +134,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     foreach ($aliquot['metadataFields'] as $metadataField) {
                         if ($metadataField['identifier'] === 'glycerolAdditiveVolume') {
                             $metadataConstraints = [
-                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $aliquot, $metadataField) {
+                                new Constraints\Callback(function ($value, $context) use ($aliquotCode, $metadataField) {
                                     $key = intval($context->getObject()->getName());
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];

From 2cb8a56c607d66c4bd525fd4ac0c7a744a3917d6 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 20 Sep 2023 12:06:08 -0500
Subject: [PATCH 33/44] Fix javascript validations.

---
 src/Form/Nph/NphSampleFinalizeType.php | 2 --
 src/Nph/Order/Samples/Module3.json     | 7 ++++---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 2d70341d1..56c56d645 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -141,8 +141,6 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     if (isset($formData[$aliquotCode][$key])) {
                                         if ($glycerolVolume == 0) {
                                             $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
-                                        } elseif ($glycerolVolume > $metadataField['warningMinVolume'] && $glycerolVolume <= $metadataField['warningMaxVolume']) {
-                                            $context->buildViolation('Glycerol Volume Please verify the unit of measurement is correct. (For reference 1mL = 1000uL)')->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                         } elseif ($glycerolVolume > $metadataField['maxVolume']) {
                                             $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                         }
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 2e71c43e4..c6634728e 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -192,8 +192,8 @@
           "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 2.5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 2,
-          "warningMinVolume": 0.1,
-          "warningMaxVolume": 0.4,
+          "warningMinVolume": 100,
+          "warningMaxVolume": 2000,
           "addNew": true,
           "collectMetadata": true,
           "metadataFields": [
@@ -205,10 +205,11 @@
               "units": "μL",
               "minVolume": 0,
               "maxVolume": 400,
-              "warningMinVolume": 0,
+              "warningMinVolume": 0.1,
               "warningMaxVolume": 0.4,
               "warningMinTotalVolume": 100,
               "warningMaxTotalVolume": 2400,
+              "maxTotalVolume": 2.4,
               "entryType": "Symfony\\Component\\Form\\Extension\\Core\\Type\\TextType",
               "required": true
             }

From 34663b546e9bfffb7253e83ec4d0a7b139415094 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 20 Sep 2023 12:06:28 -0500
Subject: [PATCH 34/44] Fixed javascript. Don't use rounded value for check.

---
 web/assets/js/views/NphSampleFinalize.js | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index e02209e7b..0f331a753 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -75,14 +75,16 @@ $(document).ready(function () {
     };
 
     function calculateGlycerolVolume(sampleVolumeField, glycerolVolumeField, index) {
+        let totalVolumeField = $(`#totalVol${index}`);
         let sampleVolume = $(sampleVolumeField).val() ? parseFloat($(sampleVolumeField).val()) * 1000 : 0;
         let glycerolVolume = $(glycerolVolumeField).val() ? parseFloat($(glycerolVolumeField).val()) : 0;
-        let totalVolume = ((sampleVolume + glycerolVolume) / 1000).toFixed(2);
-        $(`#totalVol${index}`).val(`${totalVolume}`);
+        let totalVolume = sampleVolume + glycerolVolume;
+        let totalVolumeRounded = (totalVolume / 1000).toFixed(2);
+        totalVolumeField.val(`${totalVolumeRounded}`);
         $(`#totalVol${index}`).each(function () {
             if (
                 $(this).data("warning-max-volume") &&
-                $(this).val() > $(this).data("warning-max-volume") &&
+                totalVolume > $(this).data("warning-max-volume") &&
                 $(this).parent().parent().siblings().children().hasClass("has-error") &&
                 !$(this).parent().hasClass("has-error")
             ) {
@@ -182,10 +184,6 @@ $(document).ready(function () {
     }
 
     disableEnableAliquotFields();
-    calculateGlycerolVolume(
-        $("#nph_sample_finalize_SALIVAA2Volume_0"),
-        $("#nph_sample_finalize_SALIVAA2glycerolAdditiveVolume")
-    );
 
     $(".aliquot-volume").trigger("keyup");
 

From 61fda7d622840ca7228a5b88c16d503426251347 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Wed, 20 Sep 2023 12:40:21 -0500
Subject: [PATCH 35/44] Don't worry about total volume validations.

---
 web/assets/js/views/NphSampleFinalize.js | 26 +++++-------------------
 1 file changed, 5 insertions(+), 21 deletions(-)

diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 0f331a753..48541b8df 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -80,27 +80,11 @@ $(document).ready(function () {
         let glycerolVolume = $(glycerolVolumeField).val() ? parseFloat($(glycerolVolumeField).val()) : 0;
         let totalVolume = sampleVolume + glycerolVolume;
         let totalVolumeRounded = (totalVolume / 1000).toFixed(2);
-        totalVolumeField.val(`${totalVolumeRounded}`);
-        $(`#totalVol${index}`).each(function () {
-            if (
-                $(this).data("warning-max-volume") &&
-                totalVolume > $(this).data("warning-max-volume") &&
-                $(this).parent().parent().siblings().children().hasClass("has-error") &&
-                !$(this).parent().hasClass("has-error")
-            ) {
-                $(this).parent().addClass("has-error");
-                $(this)
-                    .parent()
-                    .parent()
-                    .parent()
-                    .next()
-                    .find("li")
-                    .append(
-                        `<li><span class="glyphicon glyphicon-exclamation-sign"></span> Please verify the total volume is correct.  This aliquot should contain a maximum of 2.4 mL.</li>`
-                    );
-                $(this).trigger("keyup");
-            }
-        });
+        if (totalVolume > totalVolumeField.data("warning-max-volume")) {
+            totalVolumeField.val("");
+        } else {
+            totalVolumeField.val(`${totalVolumeRounded}`);
+        }
     }
 
     function addNormalAliquotRow(element) {

From 7b48749afcb79b312e2c8cbf369b7048d2598e27 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 21 Sep 2023 12:02:56 -0500
Subject: [PATCH 36/44] Updated barcode error messages.

---
 src/Nph/Order/Samples/Module3.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index c6634728e..7ee610437 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -172,7 +172,7 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 4mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
           "minVolume": 0.1,
           "maxVolume": 4,
           "warningMinVolume": 0.1,
@@ -189,7 +189,7 @@
           "units": "mL",
           "barcodeLength" : 10,
           "barcodePrefix": "MC",
-          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 2.5mL matrix aliquot tube barcode ID.",
+          "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 2,
           "warningMinVolume": 100,

From 65326cec5560ec6b3a2c11b31958f0cf96d41514 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 21 Sep 2023 12:48:00 -0500
Subject: [PATCH 37/44] Allow volume error messages to have a prefix added.

---
 src/Form/Nph/NphSampleFinalizeType.php | 13 ++++++++++---
 src/Nph/Order/Samples/Module3.json     |  1 +
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index 56c56d645..fbd5d6c25 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -140,9 +140,9 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
                                     if (isset($formData[$aliquotCode][$key])) {
                                         if ($glycerolVolume == 0) {
-                                            $context->buildViolation('Glycerol Volume Please verify the volume is correct. Volume should be greater than 0')->addViolation();
+                                            $context->buildViolation('Glycerol Volume: Please verify the volume is correct. Volume should be greater than 0')->addViolation();
                                         } elseif ($glycerolVolume > $metadataField['maxVolume']) {
-                                            $context->buildViolation("Glycerol Volume Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
+                                            $context->buildViolation("Glycerol Volume: Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                         }
                                     }
                                 })
@@ -184,13 +184,20 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                     })
                 ];
                 if (isset($aliquot['minVolume'])) {
+                    $errorMessage = 'Volume must be greater than 0';
+                    if (isset($aliquot['errorMessageVolumePrefix'])) {
+                        $errorMessage = "{$aliquot['errorMessageVolumePrefix']} {$errorMessage}";
+                    }
                     $volumeConstraints[] = new Constraints\GreaterThan([
                         'value' => $aliquot['minVolume'],
-                        'message' => 'Volume must be greater than 0'
+                        'message' => $errorMessage
                     ]);
                 }
                 if (isset($aliquot['maxVolume'])) {
                     $errorMessage = "Please verify the volume is correct.  This aliquot should contain a maximum of {$aliquot['maxVolume']} {$aliquot['units']}.";
+                    if (isset($aliquot['errorMessageVolumePrefix'])) {
+                        $errorMessage = "{$aliquot['errorMessageVolumePrefix']} {$errorMessage}";
+                    }
                     $volumeConstraints[] = new Constraints\LessThanOrEqual([
                         'value' => $aliquot['maxVolume'],
                         'message' => $errorMessage
diff --git a/src/Nph/Order/Samples/Module3.json b/src/Nph/Order/Samples/Module3.json
index 7ee610437..9e72a0c58 100644
--- a/src/Nph/Order/Samples/Module3.json
+++ b/src/Nph/Order/Samples/Module3.json
@@ -192,6 +192,7 @@
           "barcodeErrorMessage": "Aliquot barcode ID invalid. Please enter a valid 5mL matrix aliquot tube barcode ID.",
           "minVolume": 0,
           "maxVolume": 2,
+          "errorMessageVolumePrefix": "Saliva Volume:",
           "warningMinVolume": 100,
           "warningMaxVolume": 2000,
           "addNew": true,

From 59091a0c008fbe105cbc37dc740457bd3b3b6575 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Thu, 21 Sep 2023 13:48:44 -0500
Subject: [PATCH 38/44] Remove restore/remove checkboxes on add lines.

---
 web/assets/js/views/NphSampleFinalize.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 48541b8df..4981116c1 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -134,6 +134,7 @@ $(document).ready(function () {
         let counter = list.data("widget-counter");
         let aliquotCode = $(element).data("aliquot-code");
         let rows = $(".duplicate-target-" + aliquotId).clone();
+        $(rows).find('input[type="checkbox"]').remove();
         rows.each(function () {
             let barcodeName = `nph_sample_finalize[SALIVAA2][${counter}]`;
             let tsName = `nph_sample_finalize[SALIVAA2AliquotTs][${counter}]`;

From da326d2cdd63036f374a4f117b75c5005a5ad459 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 22 Sep 2023 08:51:34 -0500
Subject: [PATCH 39/44] Change error message

---
 src/Form/Nph/NphSampleFinalizeType.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index fbd5d6c25..bea031a14 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -140,7 +140,7 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
                                     if (isset($formData[$aliquotCode][$key])) {
                                         if ($glycerolVolume == 0) {
-                                            $context->buildViolation('Glycerol Volume: Please verify the volume is correct. Volume should be greater than 0')->addViolation();
+                                            $context->buildViolation('Glycerol Volume: Volume must be greater than 0')->addViolation();
                                         } elseif ($glycerolVolume > $metadataField['maxVolume']) {
                                             $context->buildViolation("Glycerol Volume: Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
                                         }

From 8915fc6f8e793155c8ca1fa1b5cca497ad4d9fcd Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Fri, 22 Sep 2023 12:31:54 -0500
Subject: [PATCH 40/44] Changed volume is required error message to contain
 prefix, changed units

---
 src/Form/Nph/NphSampleFinalizeType.php             | 14 ++++++++++++--
 .../program/nph/order/sample-finalize.html.twig    |  2 +-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/Form/Nph/NphSampleFinalizeType.php b/src/Form/Nph/NphSampleFinalizeType.php
index bea031a14..d42c06dca 100644
--- a/src/Form/Nph/NphSampleFinalizeType.php
+++ b/src/Form/Nph/NphSampleFinalizeType.php
@@ -139,7 +139,9 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                                     $formData = $context->getRoot()->getData();
                                     $glycerolVolume = $formData[$aliquotCode . $metadataField['identifier']][$key];
                                     if (isset($formData[$aliquotCode][$key])) {
-                                        if ($glycerolVolume == 0) {
+                                        if ($glycerolVolume === null) {
+                                            $context->buildViolation('Glycerol Volume: Volume is required')->addViolation();
+                                        } elseif ($glycerolVolume === 0) {
                                             $context->buildViolation('Glycerol Volume: Volume must be greater than 0')->addViolation();
                                         } elseif ($glycerolVolume > $metadataField['maxVolume']) {
                                             $context->buildViolation("Glycerol Volume: Please verify the volume is correct. This aliquot should contain a maximum of {$metadataField['maxVolume']} {$metadataField['units']}.")->atPath($aliquotCode . $metadataField['identifier'])->addViolation();
@@ -176,9 +178,17 @@ public function buildForm(FormBuilderInterface $builder, array $options)
                         $key = intval($context->getObject()->getName());
                         if ($aliquot['expectedVolume'] && ($formData[$aliquotCode][$key] || $formData["{$aliquotCode}AliquotTs"][$key])
                             && $value === null) {
-                            $context->buildViolation('Volume is required')->addViolation();
+                            $errorMessage = 'Volume is required';
+                            if (isset($aliquot['errorMessageVolumePrefix'])) {
+                                $errorMessage = "{$aliquot['errorMessageVolumePrefix']} {$errorMessage}";
+                            }
+                            $context->buildViolation($errorMessage)->addViolation();
                         }
                         if ($aliquot['expectedVolume'] === null && !empty($value)) {
+                            $errorMessage = 'Volume should not be entered';
+                            if (isset($aliquot['errorMessageVolumePrefix'])) {
+                                $errorMessage = "{$aliquot['errorMessageVolumePrefix']} {$errorMessage}";
+                            }
                             $context->buildViolation('Volume should not be entered')->addViolation();
                         }
                     })
diff --git a/templates/program/nph/order/sample-finalize.html.twig b/templates/program/nph/order/sample-finalize.html.twig
index 6f61073db..2a07c4c1f 100644
--- a/templates/program/nph/order/sample-finalize.html.twig
+++ b/templates/program/nph/order/sample-finalize.html.twig
@@ -30,7 +30,7 @@
                     <div class="input-group {% if not form[aliquotCode~metadataField['identifier']][i].vars.valid%}has-error{% endif %}" style="width: 45%; float: right; position: relative; top: -5px">
                     {{ form_widget(form[aliquotCode~metadataField['identifier']][i], {'attr': {'class': 'form-control glycerol-volume aliquot-volume additive',
                         'data-warning-target': aliquotCode ~ '-warning-target-glycerol' ~ i, 'data-warning-max-volume': metadataField['warningMaxVolume'], 'data-warning-min-volume': metadataField['warningMinVolume']}}) }}
-                    <span class="input-group-addon">μl</span>
+                    <span class="input-group-addon">{{ metadataField['units'] }}</span>
                     </div>
                 </td>
                 <td colspan="2" style="position: relative">

From 5a930966a9a0805bd51843cf531cedbc6e494cd9 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Mon, 25 Sep 2023 14:20:39 -0500
Subject: [PATCH 41/44] Only send DLW Info if DLW Info exists.

---
 src/Service/Nph/NphOrderService.php | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index 82aeaa3f3..cf9be4132 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -18,6 +18,7 @@
 use DateTime;
 use Doctrine\ORM\EntityManagerInterface;
 use Doctrine\ORM\PersistentCollection;
+use function PHPUnit\Framework\isNull;
 
 class NphOrderService
 {
@@ -663,13 +664,15 @@ public function getRdrObject(NphOrder $order, NphSample $sample, string $type =
         $aliquotsInfo = $this->getAliquots($sample->getSampleCode());
         if ($order->getModule() === '3' && $order->getOrderType() === $order::TYPE_DLW) {
             $dlwInfo = $this->em->getRepository(NphDlw::class)->findOneBy(['module' => $order->getModule(), 'visit' => $order->getVisitType(), 'NphParticipant' => $order->getParticipantId()]);
-            $obj->dlwDose = [
-              'batchid' => $dlwInfo->getDoseBatchId(),
-              'participantweight' => $dlwInfo->getParticipantWeight(),
-              'dose' => $dlwInfo->getActualDose(),
-              'calculateddose' => ($dlwInfo->getParticipantWeight() * 1.5),
-                'doseAdministered' => $dlwInfo->getDoseAdministered()->format('Y-m-d\TH:i:s\Z')
-            ];
+            if (!is_null($dlwInfo) && !empty($dlwInfo)) {
+                $obj->dlwDose = [
+                    'batchid' => $dlwInfo->getDoseBatchId(),
+                    'participantweight' => $dlwInfo->getParticipantWeight(),
+                    'dose' => $dlwInfo->getActualDose(),
+                    'calculateddose' => ($dlwInfo->getParticipantWeight() * 1.5),
+                    'doseAdministered' => $dlwInfo->getDoseAdministered()->format('Y-m-d\TH:i:s\Z')
+                ];
+            }
         }
         if ($aliquotsInfo) {
             $obj->aliquots = $sample->getRdrAliquotsSampleObj($aliquotsInfo);

From 1d6456ff86f9c5eb4633043645e3fb67858074d2 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Mon, 25 Sep 2023 14:22:03 -0500
Subject: [PATCH 42/44] Remove unused import.

---
 src/Service/Nph/NphOrderService.php | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index cf9be4132..0814a0eb4 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -18,7 +18,6 @@
 use DateTime;
 use Doctrine\ORM\EntityManagerInterface;
 use Doctrine\ORM\PersistentCollection;
-use function PHPUnit\Framework\isNull;
 
 class NphOrderService
 {

From f6e7e76836cd60b519b0435f2e949c34d307434c Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Mon, 25 Sep 2023 14:31:00 -0500
Subject: [PATCH 43/44] Use truthy type conversion.

---
 src/Service/Nph/NphOrderService.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Service/Nph/NphOrderService.php b/src/Service/Nph/NphOrderService.php
index 0814a0eb4..fd4c35e54 100644
--- a/src/Service/Nph/NphOrderService.php
+++ b/src/Service/Nph/NphOrderService.php
@@ -663,7 +663,7 @@ public function getRdrObject(NphOrder $order, NphSample $sample, string $type =
         $aliquotsInfo = $this->getAliquots($sample->getSampleCode());
         if ($order->getModule() === '3' && $order->getOrderType() === $order::TYPE_DLW) {
             $dlwInfo = $this->em->getRepository(NphDlw::class)->findOneBy(['module' => $order->getModule(), 'visit' => $order->getVisitType(), 'NphParticipant' => $order->getParticipantId()]);
-            if (!is_null($dlwInfo) && !empty($dlwInfo)) {
+            if ($dlwInfo) {
                 $obj->dlwDose = [
                     'batchid' => $dlwInfo->getDoseBatchId(),
                     'participantweight' => $dlwInfo->getParticipantWeight(),

From 6d94eca43d89c038ffa23e33d872da7c0ca40c44 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.c.johnson@vumc.org>
Date: Tue, 26 Sep 2023 11:40:38 -0500
Subject: [PATCH 44/44] If salivaa2 aliquot clear previous row inputs.

---
 web/assets/js/views/NphSampleFinalize.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/web/assets/js/views/NphSampleFinalize.js b/web/assets/js/views/NphSampleFinalize.js
index 4981116c1..1b3f31924 100644
--- a/web/assets/js/views/NphSampleFinalize.js
+++ b/web/assets/js/views/NphSampleFinalize.js
@@ -22,6 +22,9 @@ $(document).ready(function () {
     });
 
     $(document).on("click", ".clear-aliquot-widget", function () {
+        if ($(this).closest("tr").attr("class") && $(this).closest("tr").attr("class").includes("SALIVAA2")) {
+            $(this).closest("tr").prev().find("input:not(:read-only)").val("");
+        }
         $(this).closest("tr").find("input:not(:read-only)").val("");
     });