chore: ran pint and deleted comments

Steinbeck-Lab · May 6, 2024 · 0a2bb27 · 0a2bb27
1 parent 18e57cb
commit 0a2bb27
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Showing 15 changed files with 59 additions and 65 deletions.
diff --git a/app/Console/Commands/AssignIdentifiers.php b/app/Console/Commands/AssignIdentifiers.php
@@ -2,9 +2,9 @@
 
 namespace App\Console\Commands;
 
-use Illuminate\Console\Command;
 use App\Models\Molecule;
 use App\Models\Ticker;
+use Illuminate\Console\Command;
 
 class AssignIdentifiers extends Command
 {
@@ -28,27 +28,27 @@ class AssignIdentifiers extends Command
     public function handle()
     {
         Molecule::select('id')->chunk(10000, function ($mols) {
-            foreach($mols as $mol){
+            foreach ($mols as $mol) {
                 $id = $mol->id;
-                echo($id);
-                echo("\r\n");
+                echo $id;
+                echo "\r\n";
                 // fetch molecule
                 $molecule = Molecule::whereId($id)->first();
-                if($molecule->identifier == null){
-                    // if molecule has_stereo false 
-                    if(!$molecule->has_stereo){
+                if ($molecule->identifier == null) {
+                    // if molecule has_stereo false
+                    if (! $molecule->has_stereo) {
                         $cnID = $this->fetchIdentifier();
-                        echo($cnID);
-                        echo("\r\n");
+                        echo $cnID;
+                        echo "\r\n";
                         $molecule->identifier = $cnID;
-                        if($molecule->is_parent){
+                        if ($molecule->is_parent) {
                             $variants = $molecule->variants;
                             $i = $molecule->ticker + 1;
-                            foreach($variants as $variant){
-                                $variantID = $cnID . '.' . $i;
+                            foreach ($variants as $variant) {
+                                $variantID = $cnID.'.'.$i;
                                 $variant->identifier = $variantID;
-                                echo($variantID);
-                                echo("\r\n");
+                                echo $variantID;
+                                echo "\r\n";
                                 $variant->save();
                                 $i += 1;
                             }
@@ -61,12 +61,14 @@ public function handle()
         });
     }
 
-    public function fetchIdentifier(){
+    public function fetchIdentifier()
+    {
         $ticker = Ticker::first();
         $identifier = $ticker->index + 1;
         $ticker->index = $identifier;
         $ticker->save();
         $CNP = 'CNP2_'.$identifier;
+
         return $CNP;
     }
 }
diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -5,6 +5,7 @@
 use App\Filament\Dashboard\Resources\CollectionResource\Pages;
 use App\Filament\Dashboard\Resources\CollectionResource\RelationManagers\CitationsRelationManager;
 use App\Filament\Dashboard\Resources\CollectionResource\RelationManagers\EntriesRelationManager;
+use App\Filament\Dashboard\Resources\CollectionResource\Widgets\CollectionStats;
 use App\Livewire\ShowJobStatus;
 use App\Models\Collection;
 use Filament\Forms\Components\Livewire;
@@ -20,8 +21,6 @@
 use Filament\Tables\Table;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use App\Filament\Dashboard\Resources\CollectionResource\Widgets\CollectionStats;
-
 
 class CollectionResource extends Resource
 {

diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Pages/ViewCollection.php b/app/Filament/Dashboard/Resources/CollectionResource/Pages/ViewCollection.php
@@ -3,9 +3,8 @@
 namespace App\Filament\Dashboard\Resources\CollectionResource\Pages;
 
 use App\Filament\Dashboard\Resources\CollectionResource;
-use Filament\Actions;
-use Filament\Resources\Pages\ViewRecord;
 use App\Filament\Dashboard\Resources\CollectionResource\Widgets\CollectionStats;
+use Filament\Resources\Pages\ViewRecord;
 
 class ViewCollection extends ViewRecord
 {

diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php b/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php
@@ -2,24 +2,18 @@
 
 namespace App\Filament\Dashboard\Resources\CollectionResource\Widgets;
 
+use App\Models\Collection;
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
-use App\Models\Collection;
 
 class CollectionStats extends BaseWidget
 {
     public ?Collection $record = null;
-    
+
     protected function getStats(): array
     {
         return [
-            // Stat::make('Entries', $this->record->entries->count())
-            //     ->description('Total count')
-            //     ->color('primary'),
-            // Stat::make('Total Entries', Cache::rememberForever('stats.collections', function () {
-            //     return Collection::count();
-            // })),
             Stat::make('Total Entries', Cache::rememberForever('stats.collections'.$this->record->id.'entries.count', function () {
                 return $this->record->entries->count();
             })),
@@ -33,18 +27,20 @@ protected function getStats(): array
                 // refactor the below with eloquent relations if possible
                 $molecules = $this->record->molecules;
                 $count = 0;
-                foreach($molecules as $molecule) {
+                foreach ($molecules as $molecule) {
                     $count += $molecule->organisms()->count();
                 }
+
                 return $count;
             })),
             Stat::make('Total Geo Locations', Cache::rememberForever('stats.collections'.$this->record->id.'geo_locations.count', function () {
                 // refactor the below with eloquent relations if possible
                 $molecules = $this->record->molecules;
                 $count = 0;
-                foreach($molecules as $molecule) {
+                foreach ($molecules as $molecule) {
                     $count += $molecule->geoLocations()->count();
                 }
+
                 return $count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource.php b/app/Filament/Dashboard/Resources/GeoLocationResource.php
@@ -3,13 +3,13 @@
 namespace App\Filament\Dashboard\Resources;
 
 use App\Filament\Dashboard\Resources\GeoLocationResource\Pages;
+use App\Filament\Dashboard\Resources\GeoLocationResource\Widgets\GeoLocationStats;
 use App\Models\GeoLocation;
 use Filament\Forms\Components\TextInput;
 use Filament\Forms\Form;
 use Filament\Resources\Resource;
 use Filament\Tables;
 use Filament\Tables\Table;
-use App\Filament\Dashboard\Resources\GeoLocationResource\Widgets\GeoLocationStats;
 
 class GeoLocationResource extends Resource
 {

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/ViewGeoLocation.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/ViewGeoLocation.php
@@ -3,9 +3,8 @@
 namespace App\Filament\Dashboard\Resources\GeoLocationResource\Pages;
 
 use App\Filament\Dashboard\Resources\GeoLocationResource;
-use Filament\Actions;
-use Filament\Resources\Pages\ViewRecord;
 use App\Filament\Dashboard\Resources\GeoLocationResource\Widgets\GeoLocationStats;
+use Filament\Resources\Pages\ViewRecord;
 
 class ViewGeoLocation extends ViewRecord
 {

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php
@@ -2,15 +2,15 @@
 
 namespace App\Filament\Dashboard\Resources\GeoLocationResource\Widgets;
 
+use App\Models\GeoLocation;
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
-use App\Models\GeoLocation;
 
 class GeoLocationStats extends BaseWidget
 {
     public ?GeoLocation $record = null;
- 
+
     protected function getStats(): array
     {
         return [
@@ -21,9 +21,10 @@ protected function getStats(): array
                 // refactor the below with eloquent relations if possible
                 $molecules = $this->record->molecules;
                 $count = 0;
-                foreach($molecules as $molecule) {
+                foreach ($molecules as $molecule) {
                     $count += $molecule->organisms()->count();
                 }
+
                 return $count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -9,6 +9,7 @@
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\MoleculesRelationManager;
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\OrganismsRelationManager;
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\PropertiesRelationManager;
+use App\Filament\Dashboard\Resources\MoleculeResource\Widgets\MoleculeStats;
 use App\Models\Molecule;
 use Filament\Forms\Components\TextArea;
 use Filament\Forms\Components\TextInput;
@@ -18,7 +19,6 @@
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Table;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use App\Filament\Dashboard\Resources\MoleculeResource\Widgets\MoleculeStats;
 
 class MoleculeResource extends Resource
 {

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource/Pages/ViewMolecule.php b/app/Filament/Dashboard/Resources/MoleculeResource/Pages/ViewMolecule.php
@@ -3,9 +3,8 @@
 namespace App\Filament\Dashboard\Resources\MoleculeResource\Pages;
 
 use App\Filament\Dashboard\Resources\MoleculeResource;
-use Filament\Actions;
-use Filament\Resources\Pages\ViewRecord;
 use App\Filament\Dashboard\Resources\MoleculeResource\Widgets\MoleculeStats;
+use Filament\Resources\Pages\ViewRecord;
 
 class ViewMolecule extends ViewRecord
 {

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php b/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php
@@ -2,15 +2,15 @@
 
 namespace App\Filament\Dashboard\Resources\MoleculeResource\Widgets;
 
+use App\Models\Molecule;
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
-use App\Models\Molecule;
 
 class MoleculeStats extends BaseWidget
 {
     public ?Molecule $record = null;
- 
+
     protected function getStats(): array
     {
         return [

diff --git a/app/Filament/Dashboard/Resources/OrganismResource.php b/app/Filament/Dashboard/Resources/OrganismResource.php
@@ -3,13 +3,13 @@
 namespace App\Filament\Dashboard\Resources;
 
 use App\Filament\Dashboard\Resources\OrganismResource\Pages;
+use App\Filament\Dashboard\Resources\OrganismResource\Widgets\OrganismStats;
 use App\Models\Organism;
 use Filament\Forms;
 use Filament\Forms\Form;
 use Filament\Resources\Resource;
 use Filament\Tables;
 use Filament\Tables\Table;
-use App\Filament\Dashboard\Resources\OrganismResource\Widgets\OrganismStats;
 
 class OrganismResource extends Resource
 {

diff --git a/app/Filament/Dashboard/Resources/OrganismResource/Pages/ViewOrganism.php b/app/Filament/Dashboard/Resources/OrganismResource/Pages/ViewOrganism.php
@@ -3,9 +3,8 @@
 namespace App\Filament\Dashboard\Resources\OrganismResource\Pages;
 
 use App\Filament\Dashboard\Resources\OrganismResource;
-use Filament\Actions;
-use Filament\Resources\Pages\ViewRecord;
 use App\Filament\Dashboard\Resources\OrganismResource\Widgets\OrganismStats;
+use Filament\Resources\Pages\ViewRecord;
 
 class ViewOrganism extends ViewRecord
 {

diff --git a/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php b/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php
@@ -2,15 +2,15 @@
 
 namespace App\Filament\Dashboard\Resources\OrganismResource\Widgets;
 
+use App\Models\Organism;
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
-use App\Models\Organism;
 use Illuminate\Support\Facades\Cache;
 
 class OrganismStats extends BaseWidget
 {
     public ?Organism $record = null;
- 
+
     protected function getStats(): array
     {
         return [
@@ -21,9 +21,10 @@ protected function getStats(): array
                 // refactor the below with eloquent relations if possible
                 $molecules = $this->record->molecules;
                 $count = 0;
-                foreach($molecules as $molecule) {
+                foreach ($molecules as $molecule) {
                     $count += $molecule->geoLocations()->count();
                 }
+
                 return $count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Widgets/DashboardStats.php b/app/Filament/Dashboard/Widgets/DashboardStats.php
@@ -2,14 +2,13 @@
 
 namespace App\Filament\Dashboard\Widgets;
 
-use Filament\Widgets\StatsOverviewWidget as BaseWidget;
-use Filament\Widgets\StatsOverviewWidget\Stat;
-use App\Models\Collection;
 use App\Models\Citation;
-use App\Models\Molecule;
-use App\Models\Organism;
+use App\Models\Collection;
 use App\Models\GeoLocation;
+use App\Models\Organism;
 use App\Models\Report;
+use Filament\Widgets\StatsOverviewWidget as BaseWidget;
+use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
 
 class DashboardStats extends BaseWidget
@@ -20,6 +19,7 @@ public function getColumns(): int
     {
         return 4;
     }
+
     protected function getStats(): array
     {
         return [
@@ -29,7 +29,7 @@ protected function getStats(): array
             Stat::make('Total Citations', Cache::rememberForever('stats.citations', function () {
                 return Citation::count();
             })),
-            
+
             Stat::make('Total Organisms', Cache::rememberForever('stats.organisms', function () {
                 return Organism::count();
             })),

diff --git a/app/Filament/Dashboard/Widgets/DashboardStatsMid.php b/app/Filament/Dashboard/Widgets/DashboardStatsMid.php
@@ -2,17 +2,16 @@
 
 namespace App\Filament\Dashboard\Widgets;
 
+use App\Models\Molecule;
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
-use App\Models\Molecule;
-
 
 class DashboardStatsMid extends BaseWidget
 {
     protected static ?int $sort = 1;
 
-    protected int | string | array $columnSpan = 'full';
+    protected int|string|array $columnSpan = 'full';
 
     protected function getStats(): array
     {
@@ -23,23 +22,23 @@ protected function getStats(): array
             Stat::make('Total Non-Stereo Molecules', Cache::rememberForever('stats.molecules.non_stereo', function () {
                 return Molecule::where([
                     ['has_stereo', false],
-                    ['is_parent', false]
+                    ['is_parent', false],
                 ])->count();
             })),
             Stat::make('Total Stereo Molecules', Cache::rememberForever('stats.molecules.stereo', function () {
                 return Molecule::where([
-                    ['has_stereo', true]
+                    ['has_stereo', true],
                 ])->count();
             }))
-            ->description(
-                 'Total parent molecules: '.Cache::rememberForever('stats.molecules.parent', function () {
-                    return Molecule::where([
-                        ['has_stereo', false],
-                        ['is_parent', true]
+                ->description(
+                    'Total parent molecules: '.Cache::rememberForever('stats.molecules.parent', function () {
+                        return Molecule::where([
+                            ['has_stereo', false],
+                            ['is_parent', true],
                         ])->count();
-                })
-            )
-            ->color('primary'),
+                    })
+                )
+                ->color('primary'),
         ];
     }
 }