Merge pull request #330 from Steinbeck-Lab/development

Development
Steinbeck-Lab · Jan 15, 2025 · e4f8733 · e4f8733
2 parents 7e58a31 + 78e604c
commit e4f8733
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Showing 50 changed files with 3,346 additions and 1,499 deletions.
diff --git a/SocialiteProviders/src/NFDIAAI/NFDIAAIExtendSocialite.php b/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);
+    }
+}
diff --git a/SocialiteProviders/src/NFDIAAI/Provider.php b/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'],
+        ]);
+    }
+}
diff --git a/SocialiteProviders/src/NFDIAAI/composer.json b/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": "[email protected]"
+        }
+    ],
+    "require": {
+        "php": "^8.0",
+        "ext-json": "*",
+        "socialiteproviders/manager": "^4.4"
+    },
+    "autoload": {
+        "psr-4": {
+            "SocialiteProviders\\NFDIAAI\\": ""
+        }
+    }
+}
diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
@@ -32,49 +32,49 @@ public function handle()
         // Cache::flush();
 
         // Create the cache for all DashboardStats widgets
-        Cache::rememberForever('stats.collections', function () {
+        Cache::flexible('stats.collections', [172800, 259200], function () {
             return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for collections refreshed.');
 
-        Cache::rememberForever('stats.citations', function () {
+        Cache::flexible('stats.citations', [172800, 259200], function () {
             return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for citations refreshed.');
 
-        Cache::rememberForever('stats.organisms', function () {
+        Cache::flexible('stats.organisms', [172800, 259200], function () {
             return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for organisms refreshed.');
 
-        Cache::rememberForever('stats.geo_locations', function () {
+        Cache::flexible('stats.geo_locations', [172800, 259200], function () {
             return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for geo locations refreshed.');
 
-        Cache::rememberForever('stats.reports', function () {
+        Cache::flexible('stats.reports', [172800, 259200], function () {
             return DB::table('reports')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for reports refreshed.');
 
         // Create the cache for all DashboardStatsMid widgets
 
-        Cache::rememberForever('stats.molecules.non_stereo', function () {
+        Cache::flexible('stats.molecules.non_stereo', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=false')->get()[0]->count;
         });
         $this->info('Cache for molecules non-stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.stereo', function () {
+        Cache::flexible('stats.molecules.stereo', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=true')->get()[0]->count;
         });
         $this->info('Cache for molecules stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.parent', function () {
+        Cache::flexible('stats.molecules.parent', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=true')->get()[0]->count;
         });
         $this->info('Cache for molecules parent refreshed.');
 
-        Cache::rememberForever('stats.molecules', function () {
+        Cache::flexible('stats.molecules', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
         });
         $this->info('Cache for molecules refreshed.');

diff --git a/app/Console/Commands/GenerateHeatMapData.php b/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');
+    }
+}
diff --git a/app/Filament/Dashboard/Resources/CitationResource.php b/app/Filament/Dashboard/Resources/CitationResource.php
@@ -12,6 +12,7 @@
 use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
 class CitationResource extends Resource
@@ -76,6 +77,8 @@ public static function getPages(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.citations');
+        return Cache::flexible('stats.citations', [172800, 259200], function () {
+            return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -24,6 +24,7 @@
 use Filament\Tables\Table;
 use Illuminate\Database\Eloquent\Model;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
@@ -161,6 +162,8 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.collections');
+        return Cache::flexible('stats.collections', [172800, 259200], function () {
+            return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Pages/CreateCollection.php b/app/Filament/Dashboard/Resources/CollectionResource/Pages/CreateCollection.php
@@ -3,9 +3,15 @@
 namespace App\Filament\Dashboard\Resources\CollectionResource\Pages;
 
 use App\Filament\Dashboard\Resources\CollectionResource;
+use App\Models\Collection;
 use Filament\Resources\Pages\CreateRecord;
 
 class CreateCollection extends CreateRecord
 {
     protected static string $resource = CollectionResource::class;
+
+    protected function mutateFormDataBeforeCreate(array $data): array
+    {
+        return Collection::mutateFormData($data);
+    }
 }
diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource.php b/app/Filament/Dashboard/Resources/GeoLocationResource.php
@@ -10,6 +10,7 @@
 use Filament\Tables;
 use Filament\Tables\Table;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
 class GeoLocationResource extends Resource
@@ -83,6 +84,8 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.geo_locations');
+        return Cache::flexible('stats.geo_locations', [172800, 259200], function () {
+            return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php
@@ -15,10 +15,10 @@ class GeoLocationStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Molecules', Cache::rememberForever('stats.geo_locations'.$this->record->id.'molecules.count', function () {
+            Stat::make('Total Molecules', Cache::flexible('stats.geo_locations'.$this->record->id.'molecules.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Organisms', Cache::rememberForever('stats.geo_locations'.$this->record->id.'organisms.count', function () {
+            Stat::make('Total Organisms', Cache::flexible('stats.geo_locations'.$this->record->id.'organisms.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$this->record->id)->Join('molecule_organism', 'geo_location_molecule.molecule_id', '=', 'molecule_organism.molecule_id')->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -14,7 +14,6 @@
 use App\Filament\Dashboard\Resources\MoleculeResource\Widgets\MoleculeStats;
 use App\Models\Molecule;
 use Archilex\AdvancedTables\Filters\AdvancedFilter;
-use DB;
 use Filament\Forms\Components\Select;
 use Filament\Forms\Components\Textarea;
 use Filament\Forms\Components\TextInput;
@@ -30,6 +29,7 @@
 use Illuminate\Database\Eloquent\Builder;
 use Illuminate\Database\Eloquent\Collection;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Redirect;
 use Illuminate\Support\HtmlString;
 use pxlrbt\FilamentExcel\Actions\Tables\ExportBulkAction;
@@ -249,7 +249,9 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.molecules');
+        return Cache::flexible('stats.molecules', [172800, 259200], function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
+        });
     }
 
     public static function changeMoleculeStatus($record, $reason)

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php b/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php
@@ -15,10 +15,10 @@ class MoleculeStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Organisms', Cache::remember('stats.molecules'.$this->record->id.'organisms.count', 172800, function () {
+            Stat::make('Total Organisms', Cache::flexible('stats.molecules'.$this->record->id.'organisms.count', [172800, 259200], function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Geo Locations', Cache::remember('stats.molecules'.$this->record->id.'geo_locations.count', 172800, function () {
+            Stat::make('Total Geo Locations', Cache::flexible('stats.molecules'.$this->record->id.'geo_locations.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/OrganismResource.php b/app/Filament/Dashboard/Resources/OrganismResource.php
@@ -19,6 +19,7 @@
 use GuzzleHttp\Client;
 use Illuminate\Contracts\View\View;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Log;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
@@ -130,7 +131,9 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.organisms');
+        return Cache::flexible('stats.organisms', [172800, 259200], function () {
+            return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 
     protected static function getGNFMatches($name, $organism)