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Subject: [PATCH 1/2] fix: update DataCite Meta data for unpublished projects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 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 2/2] 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);
         }