Development

SocialiteProviders/src/NFDIAAI/NFDIAAIExtendSocialite.php

@@ -0,0 +1,18 @@
+<?php
+
+namespace SocialiteProviders\NFDIAAI;
+
+use SocialiteProviders\Manager\SocialiteWasCalled;
+
+class NFDIAAIExtendSocialite
+{
+    /**
+     * Register the provider.
+     *
+     * @return void
+     */
+    public function handle(SocialiteWasCalled $socialiteWasCalled)
+    {
+        $socialiteWasCalled->extendSocialite('nfdi-aai', Provider::class);
+    }
+}

SocialiteProviders/src/NFDIAAI/Provider.php

@@ -0,0 +1,66 @@
+<?php
+
+namespace SocialiteProviders\NFDIAAI;
+
+use GuzzleHttp\RequestOptions;
+use InvalidArgumentException;
+use SocialiteProviders\Manager\OAuth2\AbstractProvider;
+use SocialiteProviders\Manager\OAuth2\User;
+
+class Provider extends AbstractProvider
+{
+    const IDENTIFIER = 'NFDI-AAI';
+
+    /**
+     * {@inheritdoc}
+     */
+    protected $scopes = ['basic'];
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getAuthUrl($state)
+    {
+        return $this->buildAuthUrlFromBase('https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/auth', $state);
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getTokenUrl()
+    {
+        return 'https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/token';
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getUserByToken($token)
+    {
+        $response = $this->getHttpClient()->get('https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/userinfo', [
+            RequestOptions::HEADERS => [
+                'Authorization' => 'Bearer '.$token,
+            ],
+        ]);
+
+        return json_decode((string) $response->getBody(), true);
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function mapUserToObject(array $user)
+    {
+        if (! isset($user['id']) || empty($user['id'])) {
+            throw new InvalidArgumentException('The user data is invalid: a unique "id" is required.');
+        }
+
+        return (new User)->setRaw($user)->map([
+            'id' => $user['id'],
+            'nickname' => $user['username'],
+            'name' => $user['name'],
+            'email' => $user['email'],
+            'avatar' => $user['avatar'],
+        ]);
+    }
+}

SocialiteProviders/src/NFDIAAI/composer.json

@@ -0,0 +1,21 @@
+{
+    "name": "socialiteproviders/nfdi-aai",
+    "description": "NFDIAAI OAuth2 Provider for Laravel Socialite",
+    "license": "MIT",
+    "authors": [
+        {
+            "name": "VCNainala",
+            "email": "chandu.nainala@uni-jena.de"
+        }
+    ],
+    "require": {
+        "php": "^8.0",
+        "ext-json": "*",
+        "socialiteproviders/manager": "^4.4"
+    },
+    "autoload": {
+        "psr-4": {
+            "SocialiteProviders\\NFDIAAI\\": ""
+        }
+    }
+}

app/Console/Commands/GenerateHeatMapData.php

@@ -0,0 +1,79 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Collection;
+use Illuminate\Console\Command;
+
+class GenerateHeatMapData extends Command
+{
+    protected $signature = 'coconut:generate-heat-map-data';
+
+    protected $description = 'This generates Heat Map data for collection overlaps.';
+
+    public function handle()
+    {
+        $heat_map_data = [];
+        $collections = Collection::all();
+
+        // Store molecule identifiers
+        foreach ($collections as $collection) {
+            $molecule_identifiers = $collection->molecules()->pluck('identifier')->toArray();
+            $molecule_identifiers = array_map(function ($item) {
+                return preg_replace('/^CNP/i', '', $item);
+            }, $molecule_identifiers);
+            $heat_map_data['ids'][$collection->id . '|' . $collection->title] = $molecule_identifiers;
+        }
+
+        // Calculate percentage overlaps -> ol_d = overlap data
+        $heat_map_data['ol_d'] = [];
+        $collection_keys = array_keys($heat_map_data['ids']);
+
+        foreach ($collection_keys as $collection1_key) {
+            $heat_map_data['ol_d'][$collection1_key] = [];
+            $set1 = array_unique($heat_map_data['ids'][$collection1_key]);
+            $set1_count = count($set1);
+
+            foreach ($collection_keys as $collection2_key) {
+                $set2 = array_unique($heat_map_data['ids'][$collection2_key]);
+                $set2_count = count($set2);
+
+                // Calculate intersection
+                $intersection = array_intersect($set1, $set2);
+                $intersection_count = count($intersection);
+
+                // Calculate percentage overlap
+                if ($set1_count > 0 && $set2_count > 0) {
+                    // Using Jaccard similarity: intersection size / union size
+                    $union_count = $set1_count + $set2_count - $intersection_count;
+                    $overlap_percentage = ($intersection_count / $union_count) * 100;
+                } else {
+                    $overlap_percentage = 0;
+                }
+
+                $heat_map_data['ol_d'][$collection1_key][$collection2_key] = round($overlap_percentage, 2);
+
+                // Add additional overlap statistics -> ol_s = overlap_stats
+                $heat_map_data['ol_s'][$collection1_key][$collection2_key] = [
+                    //  ol = overlap count
+                    'ol' => $intersection_count,
+                    'c1_count' => $set1_count,
+                    'c2_count' => $set2_count,
+                    'p' => round($overlap_percentage, 2),
+                ];
+            }
+        }
+        unset($heat_map_data['ids']);
+
+        $json = json_encode($heat_map_data, JSON_UNESCAPED_SLASHES);
+
+        // Save the JSON to a file
+        $filePath = public_path('reports/heat_map_metadata.json');
+        if (! file_exists(dirname($filePath))) {
+            mkdir(dirname($filePath), 0777, true);
+        }
+        file_put_contents($filePath, $json);
+
+        $this->info('JSON metadata saved to public/reports/heat_map_metadata.json');
+    }
+}

app/Livewire/CollectionOverlap.php

@@ -0,0 +1,37 @@
+<?php
+
+namespace App\Livewire;
+
+use Livewire\Component;
+
+class CollectionOverlap extends Component
+{
+    public $collections = [];
+
+    public function mount()
+    {
+        $jsonPath = public_path('reports/heat_map_metadata.json');
+
+        if (! file_exists($jsonPath)) {
+            throw new \Exception('Density chart data file not found');
+        }
+
+        $jsonContent = file_get_contents($jsonPath);
+        $decodedData = json_decode($jsonContent, true);
+
+        if (json_last_error() !== JSON_ERROR_NONE) {
+            throw new \Exception('Error decoding JSON data: '.json_last_error_msg());
+        }
+
+        // Store in the public property
+        $this->collections = $decodedData['ol_d'];
+
+    }
+
+    public function render()
+    {
+        return view('livewire.collection-overlap', [
+            'collectionsData' => json_encode($this->collections),
+        ]);
+    }
+}

app/Livewire/EntryDetailsDisplay.php

@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Livewire;
+
+use Livewire\Component;
+
+class EntryDetailsDisplay extends Component
+{
+    public $mol = null;
+
+    public $collection = null;
+
+    public $reference = null;
+
+    public $entry_details = [];
+
+    public function getEntryDetails()
+    {
+        $this->entry_details = $this->mol->entries()->where('collection_id', $this->collection->id)->where('reference_id', $this->reference)->get();
+    }
+
+    public function render()
+    {
+        return view('livewire.entry-details-display', [
+            'entry_details' => $this->entry_details,
+        ]);
+    }
+}

app/Providers/EventServiceProvider.php

@@ -31,6 +31,9 @@ class EventServiceProvider extends ServiceProvider
     public function boot(): void
     {
         //
+        Event::listen(function (\SocialiteProviders\Manager\SocialiteWasCalled $event) {
+            $event->extendSocialite('regapp', \SocialiteProviders\NFDIAAI\Provider::class);
+        });
     }
 
     /**

composer.json

@@ -9,54 +9,56 @@
     "license": "MIT",
     "require": {
         "php": "^8.3",
-        "archilex/filament-filter-sets": "^3.7",
-        "bezhansalleh/filament-exceptions": "^2.1.1",
+        "archilex/filament-filter-sets": "^3.7.35",
+        "bezhansalleh/filament-exceptions": "^2.1.2",
         "bezhansalleh/filament-panel-switch": "*",
-        "bezhansalleh/filament-shield": "^3.2",
-        "dompdf/dompdf": "^3.0",
-        "filament/filament": "^3.2.127",
-        "filament/forms": "^3.2",
-        "filament/spatie-laravel-media-library-plugin": "^3.2",
-        "filament/spatie-laravel-tags-plugin": "^3.2",
-        "guzzlehttp/guzzle": "^7.2",
+        "bezhansalleh/filament-shield": "^3.3.4",
+        "dompdf/dompdf": "^3.0.1",
+        "filament/filament": "^3.2.131",
+        "filament/forms": "^3.2.131",
+        "filament/spatie-laravel-media-library-plugin": "^3.2.131",
+        "filament/spatie-laravel-tags-plugin": "^3.2.131",
+        "guzzlehttp/guzzle": "^7.9.2",
         "kenepa/banner": "^0.0.9",
-        "laravel/framework": "^11.34.2",
+        "laravel/framework": "^11.36.1",
         "laravel/horizon": "*",
-        "laravel/jetstream": "^5.0",
+        "laravel/jetstream": "^5.3.4",
         "laravel/octane": "^2.6",
         "laravel/prompts": "^0.1.25",
-        "laravel/sanctum": "^4.0",
-        "laravel/socialite": "^5.14",
-        "laravel/telescope": "^5.2",
-        "laravel/tinker": "^2.9",
-        "league/flysystem-aws-s3-v3": "^3.0",
-        "livewire/livewire": "^3.0",
+        "laravel/sanctum": "^4.0.7",
+        "laravel/socialite": "^5.16.1",
+        "laravel/telescope": "^5.2.6",
+        "laravel/tinker": "^2.10",
+        "league/flysystem-aws-s3-v3": "^3.29",
+        "livewire/livewire": "^3.5.12",
         "lomkit/laravel-rest-api": "*",
-        "maartenpaauw/model-states-for-filament": "^2.3",
-        "mpdf/mpdf": "^8.2",
-        "owen-it/laravel-auditing": "^13.6",
-        "predis/predis": "^2.2",
-        "pxlrbt/filament-excel": "^2.3.3",
-        "pxlrbt/filament-spotlight": "^1.2",
-        "shuvroroy/filament-spatie-laravel-backup": "^2.1",
-        "spatie/laravel-backup": "^8.6",
-        "spatie/laravel-cookie-consent": "^3.3",
-        "spatie/laravel-model-states": "^2.7",
-        "spatie/laravel-permission": "^6.3",
+        "maartenpaauw/model-states-for-filament": "^2.4",
+        "mpdf/mpdf": "^8.2.5",
+        "owen-it/laravel-auditing": "^13.6.8",
+        "predis/predis": "^2.3",
+        "pxlrbt/filament-excel": "^2.3.4",
+        "pxlrbt/filament-spotlight": "^1.3",
+        "shuvroroy/filament-spatie-laravel-backup": "^2.2.3",
+        "socialiteproviders/generators": "^4.7",
+        "socialiteproviders/manager": "^4.7",
+        "spatie/laravel-backup": "^8.8.2",
+        "spatie/laravel-cookie-consent": "^3.3.2",
+        "spatie/laravel-model-states": "^2.9",
+        "spatie/laravel-permission": "^6.10.1",
         "spatie/schema-org": "^3.23",
         "stechstudio/filament-impersonate": "*",
-        "stephenjude/filament-debugger": "^3.0",
-        "tapp/filament-auditing": "^3.0",
-        "tecnickcom/tc-lib-pdf": "^8.0"
+        "stephenjude/filament-debugger": "^3.1.2",
+        "tapp/filament-auditing": "^3.0.8",
+        "tecnickcom/tc-lib-pdf": "^8.0.82"
     },
     "require-dev": {
-        "fakerphp/faker": "^1.23",
-        "laravel/pint": "^1.15",
-        "laravel/sail": "^1.29",
-        "mockery/mockery": "^1.6",
-        "nunomaduro/collision": "^8.1",
-        "phpunit/phpunit": "^10.5",
-        "spatie/laravel-ignition": "^2.4"
+        "fakerphp/faker": "^1.24.1",
+        "laravel/pint": "^1.18.3",
+        "laravel/sail": "^1.39.1",
+        "mockery/mockery": "^1.6.12",
+        "nunomaduro/collision": "^8.5",
+        "phpunit/phpunit": "^10.5.39",
+        "spatie/laravel-ignition": "^2.9"
     },
     "autoload": {
         "files": [
@@ -65,7 +67,8 @@
         "psr-4": {
             "App\\": "app/",
             "Database\\Factories\\": "database/factories/",
-            "Database\\Seeders\\": "database/seeders/"
+            "Database\\Seeders\\": "database/seeders/",
+            "SocialiteProviders\\NFDIAAI\\": "SocialiteProviders/src/NFDIAAI/"
         }
     },
     "autoload-dev": {