From 2ec13cd611d3517b40d7e32da162e2cbfb23036a Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:45:43 +0200
Subject: [PATCH 1/6] fix: display public samples in the user's dashboard in
 the absence of projects. fixes #1122

---
 resources/js/Pages/Dashboard.vue     | 5 ++++-
 resources/js/Pages/Project/Index.vue | 5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/resources/js/Pages/Dashboard.vue b/resources/js/Pages/Dashboard.vue
index bda6a09a..39d67691 100644
--- a/resources/js/Pages/Dashboard.vue
+++ b/resources/js/Pages/Dashboard.vue
@@ -44,7 +44,10 @@
                 </div>
             </div>
         </template>
-        <div v-if="projects.length > 0" class="px-8 py-8 mx-auto max-w-4xl">
+        <div
+            v-if="projects.length > 0 || samples.length > 0"
+            class="px-8 py-8 mx-auto max-w-4xl"
+        >
             <div>
                 <div class="sm:hidden">
                     <label for="tabs" class="sr-only">Select a tab</label>
diff --git a/resources/js/Pages/Project/Index.vue b/resources/js/Pages/Project/Index.vue
index 38a26f71..95b75752 100644
--- a/resources/js/Pages/Project/Index.vue
+++ b/resources/js/Pages/Project/Index.vue
@@ -35,8 +35,9 @@
                     <div class="mt-3 max-w-2xl text-sm text-gray-700">
                         nmrXiv is organized around projects. Projects can
                         contain as many samples as you wish and each sample
-                        receives its very own URL. To learn more, check out our
-                        documentation.
+                        receives its very own URL. Use the "UPLOAD" button on
+                        the upper left side to start uploading projects or
+                        samples. To learn more, check out our documentation.
                     </div>
                     <!-- <button
                         type="button"

From d5d76dca0a4fa243026d0febc9e280553312bf4f Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Mon, 29 Jul 2024 13:50:28 +0200
Subject: [PATCH 2/6] feat: add submitter details to separate samples. fixes
 #1147

---
 resources/js/Pages/Public/Sample/Show.vue | 43 +++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/resources/js/Pages/Public/Sample/Show.vue b/resources/js/Pages/Public/Sample/Show.vue
index b2cd41c5..0575eb75 100644
--- a/resources/js/Pages/Public/Sample/Show.vue
+++ b/resources/js/Pages/Public/Sample/Show.vue
@@ -156,6 +156,49 @@
                     "
                     class="mt-4"
                 >
+                    <div class="gap-y-6 sm:grid-cols-6 sm:gap-x-6">
+                        <div class="pt-2 sm:col-span-6">
+                            <h2
+                                class="text-xl font-extrabold mb-3 text-blue-gray-900"
+                            >
+                                Submitter
+                            </h2>
+                        </div>
+                    </div>
+                    <div class="mt-1 grid grid-cols-1 gap-4 sm:grid-cols-2">
+                        <div
+                            class="relative rounded-lg border border-gray-300 bg-white p-5 shadow-sm flex items-center space-x-3 hover:border-gray-400 focus-within:ring-2 focus-within:ring-offset-2 focus-within:ring-pink-500"
+                        >
+                            <div class="flex-shrink-0">
+                                <img
+                                    class="h-10 w-10 rounded-full"
+                                    :src="study.data.owner.profile_photo_url"
+                                    alt=""
+                                />
+                            </div>
+                            <div class="flex-1 min-w-0">
+                                <a class="focus:outline-none">
+                                    <span
+                                        class="absolute inset-0"
+                                        aria-hidden="true"
+                                    ></span>
+                                    <p
+                                        class="text-sm font-medium text-gray-900"
+                                    >
+                                        {{
+                                            study.data.owner.first_name +
+                                            " " +
+                                            study.data.owner.last_name
+                                        }}
+                                    </p>
+                                    <p class="text-sm text-gray-500 truncate">
+                                        @ {{ study.data.owner.username }}
+                                    </p>
+                                </a>
+                            </div>
+                        </div>
+                    </div>
+
                     <div class="relative">
                         <div
                             class="absolute inset-0 flex items-center"

From 2b60501f2e5650657f79bdd40c3eb22b4132b87e Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Tue, 30 Jul 2024 10:44:25 +0200
Subject: [PATCH 3/6] fix: update DataCite Meta data for unpublished projects
 fixes #1143

---
 app/Console/Commands/UpdateProjectsDOI.php | 77 ++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 app/Console/Commands/UpdateProjectsDOI.php

diff --git a/app/Console/Commands/UpdateProjectsDOI.php b/app/Console/Commands/UpdateProjectsDOI.php
new file mode 100644
index 00000000..8025e6ed
--- /dev/null
+++ b/app/Console/Commands/UpdateProjectsDOI.php
@@ -0,0 +1,77 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Project;
+use App\Services\DOI\DOIService;
+use Carbon\Carbon;
+use Illuminate\Console\Command;
+
+class UpdateProjectsDOI extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'nmrxiv:update-projects-dois {operator?} {update-date?}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Update DataCite DOI metadata of all the projects updated before or after a given date.';
+
+    /**
+     * The DOI service instance.
+     *
+     * @var \App\Services\DOI\DOIService
+     */
+    protected $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        parent::__construct();
+
+        // Assign the DOI service instance
+        $this->doiService = $doiService;
+    }
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        // $operator takes values from
+        // {'>' : after a certain update date,
+        //  '<' : before a certain update date,
+        //  '=' : at a certain update date}
+        $operator = $this->argument('operator');
+        $date = $this->argument('update-date');
+        $date = $date ? Carbon::parse($date) : null;
+
+        // Fetch the projects based on the date
+        $projects = $date ? Project::where('updated_at', $operator, $date)->get() : Project::all();
+        foreach ($projects as $project) {
+            echo $project->identifier."\r\n";
+            foreach ($project->studies as $study) {
+                echo $study->identifier."\r\n";
+                foreach ($study->datasets as $dataset) {
+                    echo $dataset->identifier."\r\n";
+                    $dataset->updateDOIMetadata($this->doiService);
+                    $dataset->addRelatedIdentifiers($this->doiService);
+                }
+                $study->updateDOIMetadata($this->doiService);
+                $study->addRelatedIdentifiers($this->doiService);
+            }
+            $project->updateDOIMetadata($this->doiService);
+            $project->addRelatedIdentifiers($this->doiService);
+        }
+    }
+}

From 72681488f0f9dfd81b3f8258cef66fa9ad393d23 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:49:43 +0200
Subject: [PATCH 4/6] fix: add related identifiers to the doi metadata of
 separate samples. fixes #1151

---
 app/Jobs/ProcessSubmission.php |  2 +-
 app/Models/HasDOI.php          | 29 +++++++++++++++++------------
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/app/Jobs/ProcessSubmission.php b/app/Jobs/ProcessSubmission.php
index 7bb31ff5..b939d3b6 100644
--- a/app/Jobs/ProcessSubmission.php
+++ b/app/Jobs/ProcessSubmission.php
@@ -174,7 +174,7 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
                         $studyPublisher->publish($study);
                     }
                 }
-
+                $updater->update($_studies);
                 //Notification::send($this->prepareSendList($project), new StudyPublishNotification($_studies));
                 event(new StudyPublish($_studies, $this->prepareSendList($project)));
 
diff --git a/app/Models/HasDOI.php b/app/Models/HasDOI.php
index 44afbf74..626206ff 100644
--- a/app/Models/HasDOI.php
+++ b/app/Models/HasDOI.php
@@ -273,12 +273,14 @@ public function addRelatedIdentifiers($doiService)
             $this->save();
 
         } elseif ($this instanceof Study) {
-            $relatedIdentifier = [
-                'relatedIdentifier' => $this->project->doi,
-                'relatedIdentifierType' => 'DOI',
-                'relationType' => 'IsPartOf',
-            ];
-            array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            if ($this->project) {
+                $relatedIdentifier = [
+                    'relatedIdentifier' => $this->project->doi,
+                    'relatedIdentifierType' => 'DOI',
+                    'relationType' => 'IsPartOf',
+                ];
+                array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            }
             foreach ($this->datasets as &$dataset) {
                 $relatedIdentifier = [
                     'relatedIdentifier' => $dataset->doi,
@@ -291,12 +293,15 @@ public function addRelatedIdentifiers($doiService)
             $this->datacite_schema = $doiResponse;
             $this->save();
         } elseif ($this instanceof Dataset) {
-            $relatedIdentifier = [
-                'relatedIdentifier' => $this->project->doi,
-                'relatedIdentifierType' => 'DOI',
-                'relationType' => 'IsPartOf',
-            ];
-            array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            if ($this->project) {
+                $relatedIdentifier = [
+                    'relatedIdentifier' => $this->project->doi,
+                    'relatedIdentifierType' => 'DOI',
+                    'relationType' => 'IsPartOf',
+                ];
+                array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            }
+
             $relatedIdentifier = [
                 'relatedIdentifier' => $this->study->doi,
                 'relatedIdentifierType' => 'DOI',

From 8b81b73bd32998e9b818718a4b5aa5d764d672a1 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Tue, 30 Jul 2024 14:10:04 +0200
Subject: [PATCH 5/6] enable update DataCite Meta data additionally for
 unpublished samples

---
 .../{UpdateProjectsDOI.php => UpdateDOI.php}  | 31 +++++++++++--------
 1 file changed, 18 insertions(+), 13 deletions(-)
 rename app/Console/Commands/{UpdateProjectsDOI.php => UpdateDOI.php} (67%)

diff --git a/app/Console/Commands/UpdateProjectsDOI.php b/app/Console/Commands/UpdateDOI.php
similarity index 67%
rename from app/Console/Commands/UpdateProjectsDOI.php
rename to app/Console/Commands/UpdateDOI.php
index 8025e6ed..807aedc8 100644
--- a/app/Console/Commands/UpdateProjectsDOI.php
+++ b/app/Console/Commands/UpdateDOI.php
@@ -3,11 +3,12 @@
 namespace App\Console\Commands;
 
 use App\Models\Project;
+use App\Models\Study;
 use App\Services\DOI\DOIService;
 use Carbon\Carbon;
 use Illuminate\Console\Command;
 
-class UpdateProjectsDOI extends Command
+class UpdateDOI extends Command
 {
     /**
      * The name and signature of the console command.
@@ -21,7 +22,7 @@ class UpdateProjectsDOI extends Command
      *
      * @var string
      */
-    protected $description = 'Update DataCite DOI metadata of all the projects updated before or after a given date.';
+    protected $description = 'Update DataCite DOI metadata of all the projects, studies, and datasets updated before or after a given date.';
 
     /**
      * The DOI service instance.
@@ -56,20 +57,24 @@ public function handle()
         $date = $this->argument('update-date');
         $date = $date ? Carbon::parse($date) : null;
 
-        // Fetch the projects based on the date
+        // Fetch the projects and samples (studies) based on the date
         $projects = $date ? Project::where('updated_at', $operator, $date)->get() : Project::all();
+        $studies = $date ? Study::where('updated_at', $operator, $date)->get() : Study::all();
+
+        // Cover all studies within or without projects
+        foreach ($studies as $study) {
+            echo $study->identifier."\r\n";
+            foreach ($study->datasets as $dataset) {
+                echo $dataset->identifier."\r\n";
+                $dataset->updateDOIMetadata($this->doiService);
+                $dataset->addRelatedIdentifiers($this->doiService);
+            }
+            $study->updateDOIMetadata($this->doiService);
+            $study->addRelatedIdentifiers($this->doiService);
+        }
+
         foreach ($projects as $project) {
             echo $project->identifier."\r\n";
-            foreach ($project->studies as $study) {
-                echo $study->identifier."\r\n";
-                foreach ($study->datasets as $dataset) {
-                    echo $dataset->identifier."\r\n";
-                    $dataset->updateDOIMetadata($this->doiService);
-                    $dataset->addRelatedIdentifiers($this->doiService);
-                }
-                $study->updateDOIMetadata($this->doiService);
-                $study->addRelatedIdentifiers($this->doiService);
-            }
             $project->updateDOIMetadata($this->doiService);
             $project->addRelatedIdentifiers($this->doiService);
         }

From e9cb9dd93793526f6f19b4e2a41b5ddb483c8d3d Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Tue, 30 Jul 2024 17:32:03 +0200
Subject: [PATCH 6/6] fix: add links to the homepage metrics fixes #1131

---
 resources/js/Pages/Welcome.vue | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/resources/js/Pages/Welcome.vue b/resources/js/Pages/Welcome.vue
index fc545a93..57fead37 100644
--- a/resources/js/Pages/Welcome.vue
+++ b/resources/js/Pages/Welcome.vue
@@ -284,8 +284,9 @@
                                         >
                                             <path
                                                 d="M7 3.41a1 1 0 0 0-.668-.943L2.275 1.039a.987.987 0 0 0-.877.166c-.25.192-.398.493-.398.812V12.2c0 .454.296.853.725.977l3.948 1.365A1 1 0 0 0 7 13.596V3.41ZM9 13.596a1 1 0 0 0 1.327.946l3.948-1.365c.429-.124.725-.523.725-.977V2.017c0-.32-.147-.62-.398-.812a.987.987 0 0 0-.877-.166L9.668 2.467A1 1 0 0 0 9 3.41v10.186Z"
-                                            ></path></svg
-                                        ><span class="self-baseline text-dark"
+                                            ></path>
+                                        </svg>
+                                        <span class="self-baseline text-dark"
                                             >Documentation</span
                                         ></a
                                     ><a
@@ -302,8 +303,9 @@
                                         >
                                             <path
                                                 d="M8 .198a8 8 0 0 0-8 8 7.999 7.999 0 0 0 5.47 7.59c.4.076.547-.172.547-.384 0-.19-.007-.694-.01-1.36-2.226.482-2.695-1.074-2.695-1.074-.364-.923-.89-1.17-.89-1.17-.725-.496.056-.486.056-.486.803.056 1.225.824 1.225.824.714 1.224 1.873.87 2.33.666.072-.518.278-.87.507-1.07-1.777-.2-3.644-.888-3.644-3.954 0-.873.31-1.586.823-2.146-.09-.202-.36-1.016.07-2.118 0 0 .67-.214 2.2.82a7.67 7.67 0 0 1 2-.27 7.67 7.67 0 0 1 2 .27c1.52-1.034 2.19-.82 2.19-.82.43 1.102.16 1.916.08 2.118.51.56.82 1.273.82 2.146 0 3.074-1.87 3.75-3.65 3.947.28.24.54.73.54 1.48 0 1.07-.01 1.93-.01 2.19 0 .21.14.46.55.38A7.972 7.972 0 0 0 16 8.199a8 8 0 0 0-8-8Z"
-                                            ></path></svg
-                                        ><span class="self-baseline text-dark"
+                                            ></path>
+                                        </svg>
+                                        <span class="self-baseline text-dark"
                                             >GitHub</span
                                         ></a
                                     ><a
@@ -405,19 +407,28 @@
                             class="mt-4 grid grid-cols-1 gap-y-12 gap-x-6 sm:grid-cols-3"
                         >
                             <p class="text-center">
-                                <span class="block text-2xl font-bold"
-                                    >{{ projects }} Projects</span
+                                <a
+                                    href="/projects"
+                                    class="block text-2xl font-bold"
                                 >
+                                    {{ projects }} Projects
+                                </a>
                             </p>
                             <p class="text-center">
-                                <span class="block text-2xl font-bold"
-                                    >{{ compounds }} Compounds</span
+                                <a
+                                    href="/compounds"
+                                    class="block text-2xl font-bold"
                                 >
+                                    {{ compounds }} Compounds
+                                </a>
                             </p>
                             <p class="text-center">
-                                <span class="block text-2xl font-bold"
-                                    >{{ spectra }} Spectra</span
+                                <a
+                                    href="/spectra"
+                                    class="block text-2xl font-bold"
                                 >
+                                    {{ spectra }} Spectra
+                                </a>
                             </p>
                             <!-- <p>
                                 <span class="block text-2xl font-bold"