fix: importer updates and formatting changes

Steinbeck-Lab · Apr 25, 2024 · d8bd65e · d8bd65e
1 parent 276deb7
commit d8bd65e
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Showing 27 changed files with 124 additions and 147 deletions.
diff --git a/app/Console/Commands/ImportEntries.php b/app/Console/Commands/ImportEntries.php
@@ -45,7 +45,7 @@ public function handle()
 
             $batchJobs = [];
             $i = 0;
-            Entry::select('id')->where('status', 'PASSED')->whereNull('molecule_id')->where('collection_id', $collection->id)->chunk(10000, function ($ids) use (&$batchJobs, &$i) {
+            Entry::select('id')->where('status', 'PASSED')->where('collection_id', $collection->id)->chunk(10000, function ($ids) use (&$batchJobs, &$i) {
                 array_push($batchJobs, new ImportEntriesBatch($ids->pluck('id')->toArray()));
                 $i = $i + 1;
             });

diff --git a/app/Events/ReportStatusChanged.php b/app/Events/ReportStatusChanged.php
@@ -2,14 +2,11 @@
 
 namespace App\Events;
 
-use Illuminate\Broadcasting\Channel;
+use App\Models\Report;
 use Illuminate\Broadcasting\InteractsWithSockets;
-use Illuminate\Broadcasting\PresenceChannel;
 use Illuminate\Broadcasting\PrivateChannel;
-use Illuminate\Contracts\Broadcasting\ShouldBroadcast;
 use Illuminate\Foundation\Events\Dispatchable;
 use Illuminate\Queue\SerializesModels;
-use App\Models\Report;
 
 class ReportStatusChanged
 {
@@ -18,10 +15,11 @@ class ReportStatusChanged
     /**
      * Create a new event instance.
      */
+    public $report;
+
+    public $new;
 
-     public $report;
-     public $new;
-     public $old;
+    public $old;
 
     public function __construct(Report $report, $new, $old)
     {

diff --git a/app/Events/ReportSubmitted.php b/app/Events/ReportSubmitted.php
@@ -2,14 +2,11 @@
 
 namespace App\Events;
 
-use Illuminate\Broadcasting\Channel;
+use App\Models\Report;
 use Illuminate\Broadcasting\InteractsWithSockets;
-use Illuminate\Broadcasting\PresenceChannel;
 use Illuminate\Broadcasting\PrivateChannel;
-use Illuminate\Contracts\Broadcasting\ShouldBroadcast;
 use Illuminate\Foundation\Events\Dispatchable;
 use Illuminate\Queue\SerializesModels;
-use App\Models\Report;
 
 class ReportSubmitted
 {

diff --git a/app/Filament/Dashboard/Imports/EntryImporter.php b/app/Filament/Dashboard/Imports/EntryImporter.php
@@ -7,6 +7,7 @@
 use Filament\Actions\Imports\ImportColumn;
 use Filament\Actions\Imports\Importer;
 use Filament\Actions\Imports\Models\Import;
+use Filament\Forms\Components\Checkbox;
 
 class EntryImporter extends Importer
 {
@@ -30,12 +31,24 @@ public static function getColumns(): array
         ];
     }
 
+    public static function getOptionsFormComponents(): array
+    {
+        return [
+            Checkbox::make('updateExisting')
+                ->label('Update existing records'),
+        ];
+    }
+
     public function resolveRecord(): ?Entry
     {
-        // return Entry::firstOrNew([
-        //     // Update existing records, matching them by `$this->data['column_name']`
-        //     'email' => $this->data['email'],
-        // ]);
+        if ($this->options['updateExisting'] ?? false) {
+            return Entry::firstOrNew([
+                'canonical_smiles' => $this->data['canonical_smiles'],
+                'reference_id' => $this->data['reference_id'],
+                'collection_id' => $this->options['collection_id'],
+            ]);
+        }
+
         $entry = new Entry();
         $entry->collection_id = $this->options['collection_id'];
 
@@ -46,11 +59,7 @@ public static function getCompletedNotificationBody(Import $import): string
     {
         ImportedCSVProcessed::dispatch($import);
 
-        $body = 'Your entry import has completed and '.number_format($import->successful_rows).' '.str('row')->plural($import->successful_rows).' imported.';
-
-        if ($failedRowsCount = $import->getFailedRowsCount()) {
-            $body .= ' '.number_format($failedRowsCount).' '.str('row')->plural($failedRowsCount).' failed to import.';
-        }
+        $body = 'Your entry import has completed. '.number_format($import->total_rows).' '.str('row')->plural($import->total_rows).' imported.';
 
         return $body;
     }

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource.php b/app/Filament/Dashboard/Resources/GeoLocationResource.php
@@ -3,24 +3,19 @@
 namespace App\Filament\Dashboard\Resources;
 
 use App\Filament\Dashboard\Resources\GeoLocationResource\Pages;
-use App\Filament\Dashboard\Resources\GeoLocationResource\RelationManagers;
 use App\Models\GeoLocation;
-use Filament\Forms;
+use Filament\Forms\Components\TextInput;
 use Filament\Forms\Form;
 use Filament\Resources\Resource;
 use Filament\Tables;
 use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
-use Filament\Forms\Components\TextInput;
-use Filament\Forms\Components\Fieldset;
 
 class GeoLocationResource extends Resource
 {
     protected static ?string $navigationGroup = 'Data';
 
     protected static ?int $navigationSort = 5;
-    
+
     protected static ?string $model = GeoLocation::class;
 
     protected static ?string $navigationIcon = 'heroicon-o-rectangle-stack';

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/CreateGeoLocation.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/CreateGeoLocation.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\CreateRecord;
 use App\Models\Molecule;
+use Filament\Resources\Pages\CreateRecord;
 
 class CreateGeoLocation extends CreateRecord
 {

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -5,10 +5,10 @@
 use App\Filament\Dashboard\Resources\MoleculeResource\Pages;
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\CitationsRelationManager;
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\CollectionsRelationManager;
-use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\MoleculesRelationManager;
-use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\PropertiesRelationManager;
 use App\Filament\Dashboard\Resources\MoleculeResource\RelationManagers\GeoLocationRelationManager;
+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\Models\Molecule;
 use Filament\Forms\Components\TextArea;
 use Filament\Forms\Components\TextInput;

diff --git a/...ment/Dashboard/Resources/MoleculeResource/RelationManagers/GeoLocationRelationManager.php b/...ment/Dashboard/Resources/MoleculeResource/RelationManagers/GeoLocationRelationManager.php
@@ -6,10 +6,8 @@
 use Filament\Forms\Form;
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
-use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 use Filament\Tables\Actions\AttachAction;
+use Filament\Tables\Table;
 
 class GeoLocationRelationManager extends RelationManager
 {
@@ -41,7 +39,7 @@ public function table(Table $table): Table
                     ->preloadRecordSelect()
                     ->form(fn (AttachAction $action): array => [
                         $action->getRecordSelect(),
-                        Forms\Components\TextInput::make('locations')
+                        Forms\Components\TextInput::make('locations'),
                     ]),
             ])
             ->actions([

diff --git a/...lament/Dashboard/Resources/MoleculeResource/RelationManagers/OrganismsRelationManager.php b/...lament/Dashboard/Resources/MoleculeResource/RelationManagers/OrganismsRelationManager.php
@@ -6,13 +6,8 @@
 use Filament\Forms\Form;
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
-use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Support\Facades\DB;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 use Filament\Tables\Actions\AttachAction;
-use Filament\Tables\Actions\EditAction;
-use App\Models\Organism;
+use Filament\Tables\Table;
 
 class OrganismsRelationManager extends RelationManager
 {
@@ -44,7 +39,7 @@ public function table(Table $table): Table
                     ->preloadRecordSelect()
                     ->form(fn (AttachAction $action): array => [
                         $action->getRecordSelect(),
-                        Forms\Components\TextInput::make('organism_parts')
+                        Forms\Components\TextInput::make('organism_parts'),
                     ]),
             ])
             ->actions([

diff --git a/app/Filament/Dashboard/Resources/OrganismResource.php b/app/Filament/Dashboard/Resources/OrganismResource.php
@@ -3,15 +3,12 @@
 namespace App\Filament\Dashboard\Resources;
 
 use App\Filament\Dashboard\Resources\OrganismResource\Pages;
-use App\Filament\Dashboard\Resources\OrganismResource\RelationManagers;
 use App\Models\Organism;
 use Filament\Forms;
 use Filament\Forms\Form;
 use Filament\Resources\Resource;
 use Filament\Tables;
 use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 
 class OrganismResource extends Resource
 {

diff --git a/app/Filament/Dashboard/Resources/OrganismResource/Pages/CreateOrganism.php b/app/Filament/Dashboard/Resources/OrganismResource/Pages/CreateOrganism.php
@@ -3,7 +3,6 @@
 namespace App\Filament\Dashboard\Resources\OrganismResource\Pages;
 
 use App\Filament\Dashboard\Resources\OrganismResource;
-use Filament\Actions;
 use Filament\Resources\Pages\CreateRecord;
 
 class CreateOrganism extends CreateRecord

diff --git a/app/Filament/Dashboard/Resources/ReportResource.php b/app/Filament/Dashboard/Resources/ReportResource.php
@@ -2,26 +2,26 @@
 
 namespace App\Filament\Dashboard\Resources;
 
+use App\Events\ReportStatusChanged;
 use App\Filament\Dashboard\Resources\ReportResource\Pages;
 use App\Filament\Dashboard\Resources\ReportResource\RelationManagers;
+use App\Models\Citation;
+use App\Models\Molecule;
 use App\Models\Report;
 use Filament\Forms\Components\Select;
+use Filament\Forms\Components\SpatieTagsInput;
 use Filament\Forms\Components\TextArea;
 use Filament\Forms\Components\TextInput;
 use Filament\Forms\Form;
+use Filament\Forms\Get;
 use Filament\Resources\Resource;
 use Filament\Tables;
 use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Support\Str;
-use App\Events\ReportStatusChanged;
-use App\Models\Molecule;
-use App\Models\Citation;
 use Illuminate\Http\Request;
-use Filament\Forms\Get;
+use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use Filament\Forms\Components\SpatieTagsInput;
 
 class ReportResource extends Resource
 {
@@ -32,7 +32,7 @@ class ReportResource extends Resource
     protected static ?int $navigationSort = 1;
 
     protected static ?string $navigationIcon = 'heroicon-o-rectangle-stack';
-    
+
     public static function form(Form $form): Form
     {
         return $form
@@ -46,9 +46,9 @@ public static function form(Form $form): Form
                         'collection' => 'Collection',
                     ])
                     ->hidden(function (string $operation) {
-                        if($operation == 'create' && (!request()->has('collection_uuid') && !request()->has('citation_id') && !request()->has('compound_id'))) {
+                        if ($operation == 'create' && (! request()->has('collection_uuid') && ! request()->has('citation_id') && ! request()->has('compound_id'))) {
                             return false;
-                        }else {
+                        } else {
                             return true;
                         }
                     }),
@@ -60,18 +60,17 @@ public static function form(Form $form): Form
                     ->relationship('collections', 'title')
                     ->multiple()
                     ->preload()
-                    ->hidden(function (Get $get, String $operation) {
-                        if($operation == 'edit' || $operation == 'view') {
-                            if($get('collections') == []) {
-                                return true;   
+                    ->hidden(function (Get $get, string $operation) {
+                        if ($operation == 'edit' || $operation == 'view') {
+                            if ($get('collections') == []) {
+                                return true;
                             }
-                        }
-                        elseif(!request()->has('collection_uuid') && $get('choice') != 'collection') {
+                        } elseif (! request()->has('collection_uuid') && $get('choice') != 'collection') {
                             return true;
                         }
                     })
-                    ->disabled(function (String $operation) {
-                        if($operation == 'edit') {
+                    ->disabled(function (string $operation) {
+                        if ($operation == 'edit') {
                             return true;
                         }
                     })
@@ -83,18 +82,17 @@ public static function form(Form $form): Form
                     })
                     ->multiple()
                     // ->preload()
-                    ->hidden(function (Get $get, String $operation) {
-                        if($operation == 'edit' || $operation == 'view') {
-                            if($get('citations') == []) {
-                                return true;   
+                    ->hidden(function (Get $get, string $operation) {
+                        if ($operation == 'edit' || $operation == 'view') {
+                            if ($get('citations') == []) {
+                                return true;
                             }
-                        }
-                        elseif(!request()->has('citation_id') && $get('choice') != 'citation') {
+                        } elseif (! request()->has('citation_id') && $get('choice') != 'citation') {
                             return true;
                         }
                     })
-                    ->disabled(function (String $operation) {
-                        if($operation == 'edit') {
+                    ->disabled(function (string $operation) {
+                        if ($operation == 'edit') {
                             return true;
                         }
                     })
@@ -117,18 +115,17 @@ public static function form(Form $form): Form
                 TextInput::make('mol_id_csv')
                     ->label('Molecules')
                     ->placeholder('Enter the Identifiers separated by commas')
-                    ->hidden(function (Get $get, String $operation) {
-                        if($operation == 'edit' || $operation == 'view') {
-                            if(is_null($get('mol_id_csv'))) {
-                                return true;   
+                    ->hidden(function (Get $get, string $operation) {
+                        if ($operation == 'edit' || $operation == 'view') {
+                            if (is_null($get('mol_id_csv'))) {
+                                return true;
                             }
-                        }
-                        elseif(!request()->has('compound_id') && $get('choice') != 'molecule') {
+                        } elseif (! request()->has('compound_id') && $get('choice') != 'molecule') {
                             return true;
                         }
                     })
-                    ->disabled(function (String $operation) {
-                        if($operation == 'edit') {
+                    ->disabled(function (string $operation) {
+                        if ($operation == 'edit') {
                             return true;
                         }
                     }),