From c1eb268ef5b0529f73eccbf8b4623d86299e0ef9 Mon Sep 17 00:00:00 2001
From: Brian Corrie <bdcorrie@gmail.com>
Date: Wed, 27 Nov 2024 19:58:03 +0000
Subject: [PATCH 1/6] Fix some wording about ADC in footer

---
 resources/views/footer_detailed.blade.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resources/views/footer_detailed.blade.php b/resources/views/footer_detailed.blade.php
index 8bf16833..43f011ae 100644
--- a/resources/views/footer_detailed.blade.php
+++ b/resources/views/footer_detailed.blade.php
@@ -16,7 +16,7 @@
 			<p>
 				The iReceptor Gateway integrates large, distributed, AIRR-seq data repositories, following standards for sharing and interoperability developed by the
 				<a href="http://airr-community.org/">Adaptive Immune Receptor Repertoire (AIRR) Community</a>.
-				The main goal of iReceptor is to connect this distributed network of AIRR-seq repositories into an AIRR Data Commons, allowing for the query, analysis, and visualization of AIRR-seq data across multiple projects, labs, and institutions.
+				The main goal of iReceptor is to connect this distributed network of AIRR-seq repositories in the AIRR Data Commons, allowing for the query, analysis, and visualization of AIRR-seq data across multiple projects, labs, and institutions.
 			</p>
 			<p>Present functionalities include:</p>
 			<ul>

From 1ed044367cc43dfbb67884e4ed7c62979b5e5a8b Mon Sep 17 00:00:00 2001
From: Brian Corrie <bdcorrie@gmail.com>
Date: Wed, 27 Nov 2024 21:44:05 +0000
Subject: [PATCH 2/6] Add age_unit_id to the list of ontology fields.

---
 app/FieldName.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/FieldName.php b/app/FieldName.php
index 9784c9cb..7f6e2d81 100644
--- a/app/FieldName.php
+++ b/app/FieldName.php
@@ -265,6 +265,6 @@ public static function getAPIVersions()
 
     public static function getOntologyFields()
     {
-        return ['tissue_id', 'organism_id', 'study_type_id', 'disease_diagnosis_id', 'cell_subset_id', 'collection_time_point_relative_unit_id', 'template_amount_unit_id'];
+        return ['tissue_id', 'organism_id', 'study_type_id', 'age_unit_id', 'disease_diagnosis_id', 'cell_subset_id', 'collection_time_point_relative_unit_id', 'template_amount_unit_id'];
     }
 }

From e17735a3fd981a46959f654bfcf50eb8313bd1ad Mon Sep 17 00:00:00 2001
From: Brian Corrie <bdcorrie@gmail.com>
Date: Wed, 27 Nov 2024 21:44:41 +0000
Subject: [PATCH 3/6] Remove explicit use of age_unit = year

---
 app/RestService.php | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/app/RestService.php b/app/RestService.php
index bb609263..85e0edd5 100644
--- a/app/RestService.php
+++ b/app/RestService.php
@@ -269,11 +269,6 @@ public static function generate_json_query($filters, $query_parameters = [], $ap
         // clean filters
         $filters = self::clean_filters($filters);
 
-        // add "age_unit" filter if "age_min" or "age_max" is set
-        if (isset($filters['ir_subject_age_min']) || isset($filters['ir_subject_age_max'])) {
-            $filters['age_unit'] = 'year';
-        }
-
         // if API version is 1.0
         if ($api_version == '1.0') {
             $ontology_fields = FieldName::getOntologyFields();

From 95bffc15a51d8e481a7e2d4bfd8af6b3d64b2825 Mon Sep 17 00:00:00 2001
From: Brian Corrie <bdcorrie@gmail.com>
Date: Wed, 27 Nov 2024 21:57:44 +0000
Subject: [PATCH 4/6] Updates for searching using age_unit.

---
 app/Http/Controllers/SampleController.php |  9 ++++-
 app/Sample.php                            | 42 +++++++++++++++--------
 resources/views/sample.blade.php          |  6 ++++
 3 files changed, 41 insertions(+), 16 deletions(-)

diff --git a/app/Http/Controllers/SampleController.php b/app/Http/Controllers/SampleController.php
index 82df22b2..a4f3e94c 100644
--- a/app/Http/Controllers/SampleController.php
+++ b/app/Http/Controllers/SampleController.php
@@ -14,7 +14,7 @@
 
 class SampleController extends Controller
 {
-    protected const DEFAULT_FIELDS = ['full_text_search', 'study_id', 'study_title', 'study_type_id', 'study_group_description', 'lab_name', 'subject_id', 'organism_id', 'sex', 'ethnicity', 'ir_subject_age_min', 'ir_subject_age_max', 'disease_diagnosis_id', 'sample_id', 'pcr_target_locus', 'cell_subset_id', 'tissue_id', 'template_class', 'cell_phenotype', 'sequencing_platform'];
+    protected const DEFAULT_FIELDS = ['full_text_search', 'study_id', 'study_title', 'study_type_id', 'study_group_description', 'lab_name', 'subject_id', 'organism_id', 'sex', 'ethnicity', 'ir_subject_age_min', 'ir_subject_age_max', 'age_unit_id', 'disease_diagnosis_id', 'sample_id', 'pcr_target_locus', 'cell_subset_id', 'tissue_id', 'template_class', 'cell_phenotype', 'sequencing_platform'];
     protected $extra_fields = [];
 
     public function __construct()
@@ -191,6 +191,12 @@ public function index(Request $request, $type = '')
             $dna_type_list[$v] = $v;
         }
 
+        // age_unit ontology info
+        $subject_age_unit_ontology_list = [];
+        foreach ($metadata['age_unit_id'] as $v) {
+            $subject_age_unit_ontology_list[$v['id']] = $v['label'] . ' (' . $v['id'] . ')';
+        }
+
         // disease_diagnosis ontology info
         $subject_disease_diagnosis_ontology_list = [];
         foreach ($metadata['disease_diagnosis_id'] as $v) {
@@ -206,6 +212,7 @@ public function index(Request $request, $type = '')
         $data['subject_gender_list'] = $subject_gender_list;
         $data['subject_ethnicity_list'] = $subject_ethnicity_list;
         $data['subject_organism_ontology_list'] = $subject_organism_ontology_list;
+        $data['subject_age_unit_ontology_list'] = $subject_age_unit_ontology_list;
         $data['subject_disease_diagnosis_ontology_list'] = $subject_disease_diagnosis_ontology_list;
         $data['pcr_target_locus_list'] = $pcr_target_locus_list;
         $data['cell_type_ontology_list'] = $cell_type_ontology_list;
diff --git a/app/Sample.php b/app/Sample.php
index 53b6bfd4..76349bb4 100644
--- a/app/Sample.php
+++ b/app/Sample.php
@@ -811,23 +811,35 @@ public static function sort_sample_list($sample_list, $sort_column, $sort_order)
                 }
             }
 
-            $val1 = $a->{$sort_column};
-            $val2 = $b->{$sort_column};
-
-            if (is_array($val1) || is_object($val1) || is_array($val2) || is_object($val2)) {
-                $val1 = json_encode($val1);
-                $val2 = json_encode($val2);
-                $comparison_result = strcasecmp($val1, $val2);
-            } elseif ($field_type == 'integer' || $field_type == 'number') {
-                if ($val1 == $val2) {
-                    $comparison_result = 0;
-                } elseif ($val1 < $val2) {
-                    $comparison_result = -1;
+            if (! isset($a->{$sort_column}) && (! isset($b->{$sort_column}))) {
+                // If they are both not set they are equal
+                $comparison_result = 0;
+            } else if (! isset($a->{$sort_column})) {
+                // If a is not set and b is, then a < b
+                $comparison_result = -1;
+            } else if (! isset($b->{$sort_column})) {
+                // If b is not set then a > b
+                $comparison_result = 1;
+            } else {
+                // If we get here, both are set.
+                $val1 = $a->{$sort_column};
+                $val2 = $b->{$sort_column};
+
+                if (is_array($val1) || is_object($val1) || is_array($val2) || is_object($val2)) {
+                    $val1 = json_encode($val1);
+                    $val2 = json_encode($val2);
+                    $comparison_result = strcasecmp($val1, $val2);
+                } elseif ($field_type == 'integer' || $field_type == 'number') {
+                    if ($val1 == $val2) {
+                        $comparison_result = 0;
+                    } elseif ($val1 < $val2) {
+                        $comparison_result = -1;
+                    } else {
+                        $comparison_result = 1;
+                    }
                 } else {
-                    $comparison_result = 1;
+                    $comparison_result = strcasecmp($val1, $val2);
                 }
-            } else {
-                $comparison_result = strcasecmp($val1, $val2);
             }
 
             if ($sort_order == 'desc') {
diff --git a/resources/views/sample.blade.php b/resources/views/sample.blade.php
index 6623c08d..08f2d2e8 100644
--- a/resources/views/sample.blade.php
+++ b/resources/views/sample.blade.php
@@ -127,6 +127,12 @@
 									</div>
 								</div>
 
+							    <div class="form-group">
+									{{ Form::label('age_unit_id', __('short.age_unit_id')) }}
+									@include('help', ['id' => 'age_unit_id'])
+									{{ Form::select('age_unit_id[]', $subject_age_unit_ontology_list, '', array('class' => 'form-control multiselect-ui', 'multiple' => 'multiple')) }}
+								</div>
+
 							    <div class="form-group">
 									{{ Form::label('disease_diagnosis', __('short.disease_diagnosis')) }}
 									@include('help', ['id' => 'disease_diagnosis'])

From b47962e6c0113961d40c11fef625609452859dd9 Mon Sep 17 00:00:00 2001
From: StyleCI Bot <bot@styleci.io>
Date: Wed, 27 Nov 2024 21:59:28 +0000
Subject: [PATCH 5/6] Apply fixes from StyleCI

---
 app/Sample.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/Sample.php b/app/Sample.php
index 76349bb4..96a58bd6 100644
--- a/app/Sample.php
+++ b/app/Sample.php
@@ -814,10 +814,10 @@ public static function sort_sample_list($sample_list, $sort_column, $sort_order)
             if (! isset($a->{$sort_column}) && (! isset($b->{$sort_column}))) {
                 // If they are both not set they are equal
                 $comparison_result = 0;
-            } else if (! isset($a->{$sort_column})) {
+            } elseif (! isset($a->{$sort_column})) {
                 // If a is not set and b is, then a < b
                 $comparison_result = -1;
-            } else if (! isset($b->{$sort_column})) {
+            } elseif (! isset($b->{$sort_column})) {
                 // If b is not set then a > b
                 $comparison_result = 1;
             } else {

From 366babfa3a70d0470b666dabcb4cd76b0378374f Mon Sep 17 00:00:00 2001
From: Brian Corrie <bdcorrie@gmail.com>
Date: Thu, 28 Nov 2024 00:53:28 +0000
Subject: [PATCH 6/6] Minor text changes, add new funding.

---
 resources/views/footer_detailed.blade.php | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/resources/views/footer_detailed.blade.php b/resources/views/footer_detailed.blade.php
index 43f011ae..f3a0ebfe 100644
--- a/resources/views/footer_detailed.blade.php
+++ b/resources/views/footer_detailed.blade.php
@@ -16,7 +16,7 @@
 			<p>
 				The iReceptor Gateway integrates large, distributed, AIRR-seq data repositories, following standards for sharing and interoperability developed by the
 				<a href="http://airr-community.org/">Adaptive Immune Receptor Repertoire (AIRR) Community</a>.
-				The main goal of iReceptor is to connect this distributed network of AIRR-seq repositories in the AIRR Data Commons, allowing for the query, analysis, and visualization of AIRR-seq data across multiple projects, labs, and institutions.
+				The main goal of iReceptor is to connect the distributed network of AIRR-seq repositories in the AIRR Data Commons, allowing for the query, analysis, and visualization of AIRR-seq data across multiple projects, labs, and institutions.
 			</p>
 			<p>Present functionalities include:</p>
 			<ul>
@@ -28,6 +28,7 @@
 				<li><strong>Download Sequences, Clones, Cells</strong> and their related Repertoire metadata in AIRR compliant file formats, easily importable to other AIRR-seq analysis tools</li>
 			    <li><strong>Analyze Sequences, Clones, Cells</strong> and their related Repertoire metadata using <strong>community built analysis tools</strong>.</li>
 			</ul>
+            <p>iReceptor is a collaborator in the <a href="https://airr-knowledge.org/">AIRR Knowledge Commons</a>, funded by a U24 (U24AI177622) from the <a href="http://www.niaid.nih.gov/">National Institute of Allergy and Infectious Diseases</a>, a component of the US <a href="https://www.nih.gov/">National Institutes of Health.</a></p>
 			<p>iReceptor was a leading member of the CIHR/EU Horizon 2020 funded <a href="http://www.ireceptor-plus.com/">iReceptor Plus Consortium</a>.</p>
 
 			<p>For more information, see the <a href="http://www.ireceptor.org/">iReceptor public website</a> or refer to the paper <a href="http://doi.org/10.1111/imr.12666">iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories</a>.  If you are interested in hosting a data repository or if you want to provide feedback on this developing community resource, email <a href="mailto:support@ireceptor.org">support@ireceptor.org</a>.</p>