Merge pull request #113 from Steinbeck-Lab/citations-doi-functionality

Citations doi functionality
Steinbeck-Lab · Jun 27, 2024 · f982a42 · f982a42
2 parents 95e8b2c + af35ec6
commit f982a42
Show file tree

Hide file tree

Showing 12 changed files with 271 additions and 27 deletions.
diff --git a/app/Filament/Dashboard/Resources/CitationResource.php b/app/Filament/Dashboard/Resources/CitationResource.php
@@ -6,14 +6,18 @@
 use App\Filament\Dashboard\Resources\CitationResource\RelationManagers\CollectionRelationManager;
 use App\Filament\Dashboard\Resources\CitationResource\RelationManagers\MoleculeRelationManager;
 use App\Models\Citation;
+use Closure;
+use Filament\Forms\Components\Section;
 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\Support\Facades\Cache;
+use Illuminate\Support\HtmlString;
 
 class CitationResource extends Resource
 {
@@ -31,11 +35,86 @@ public static function form(Form $form): Form
     {
         return $form
             ->schema([
-                TextInput::make('doi'),
-                TextInput::make('title'),
-                TextInput::make('authors'),
-                TextArea::make('citation_text'),
-            ])->columns(1);
+                Section::make()
+                    ->schema([
+                        TextInput::make('failMessage')
+                            ->default('')
+                            ->hidden()
+                            ->disabled(),
+                        TextInput::make('doi')
+                            ->label('DOI')
+                            ->live(onBlur: true)
+                            ->afterStateUpdated(function ($set, $state) {
+                                if (doiRegxMatch($state)) {
+                                    $citationDetails = fetchDOICitation($state);
+                                    if ($citationDetails) {
+                                        $set('title', $citationDetails['title']);
+                                        $set('authors', $citationDetails['authors']);
+                                        $set('citation_text', $citationDetails['citation_text']);
+                                        $set('failMessage', 'Success');
+                                    } else {
+                                        $set('failMessage', 'No citation found. Please fill in the details manually');
+                                    }
+                                } else {
+                                    $set('failMessage', 'Invalid DOI');
+                                }
+                            })
+                            ->helperText(function ($get) {
+
+                                if ($get('failMessage') == 'Fetching') {
+                                    return new HtmlString('<svg class="animate-spin -ml-1 mr-3 h-5 w-5 text-dark inline" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
+                                    <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
+                                    <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
+                                    </svg> ');
+                                } elseif ($get('failMessage') != 'Success') {
+                                    return new HtmlString('<span style="color:red">'.$get('failMessage').'</span>');
+                                } else {
+                                    return null;
+                                }
+                            })
+                            ->required()
+                            ->unique()
+                            ->rules([
+                                fn (Get $get): Closure => function (string $attribute, $value, Closure $fail) use ($get) {
+                                    if ($get('failMessage') != 'No citation found. Please fill in the details manually') {
+                                        $fail($get('failMessage'));
+                                    }
+                                },
+                            ])
+                            ->validationMessages([
+                                'unique' => 'The DOI already exists.',
+                            ]),
+                    ]),
+
+                Section::make()
+                    ->schema([
+                        TextInput::make('title')
+                            ->disabled(function ($get, string $operation) {
+                                if ($operation = 'edit' || $get('failMessage') == 'No citation found. Please fill in the details manually') {
+                                    return false;
+                                } else {
+                                    return true;
+                                }
+                            }),
+                        TextInput::make('authors')
+                            ->disabled(function ($get, string $operation) {
+                                if ($operation = 'edit' || $get('failMessage') == 'No citation found. Please fill in the details manually') {
+                                    return false;
+                                } else {
+                                    return true;
+                                }
+                            }),
+                        TextArea::make('citation_text')
+                            ->label('Citation text / URL')
+                            ->disabled(function ($get, string $operation) {
+                                if ($operation = 'edit' || $get('failMessage') == 'No citation found. Please fill in the details manually') {
+                                    return false;
+                                } else {
+                                    return true;
+                                }
+                            }),
+                    ])->columns(1),
+            ]);
     }
 
     public static function table(Table $table): Table

diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/CreateGeoLocation.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Pages/CreateGeoLocation.php
@@ -3,18 +3,9 @@
 namespace App\Filament\Dashboard\Resources\GeoLocationResource\Pages;
 
 use App\Filament\Dashboard\Resources\GeoLocationResource;
-use App\Models\Molecule;
 use Filament\Resources\Pages\CreateRecord;
 
 class CreateGeoLocation extends CreateRecord
 {
     protected static string $resource = GeoLocationResource::class;
-
-    protected function beforeCreate(): void
-    {
-        // $molecule = Molecule::where('identifier', $this->data['molecule_id'])->get();
-        // $this->data['molecule_id'] = $molecule[0]->id;
-        // dd($this->data);
-        // $this->data->molecules()->attach($molecule);
-    }
 }
diff --git a/app/Filament/Dashboard/Resources/ReportResource.php b/app/Filament/Dashboard/Resources/ReportResource.php
@@ -35,7 +35,7 @@ public static function form(Form $form): Form
     {
         return $form
             ->schema([
-                Select::make('choice')
+                Select::make('report_type')
                     ->label('You want to report:')
                     ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Select what you want to report. Ex: Molecule, Citation, Collection, Organism.')
                     ->live()
@@ -71,7 +71,7 @@ public static function form(Form $form): Form
                             if ($get('collections') == []) {
                                 return true;
                             }
-                        } elseif (! request()->has('collection_uuid') && $get('choice') != 'collection') {
+                        } elseif (! request()->has('collection_uuid') && $get('report_type') != 'collection') {
                             return true;
                         }
                     })
@@ -93,7 +93,7 @@ public static function form(Form $form): Form
                             if ($get('citations') == []) {
                                 return true;
                             }
-                        } elseif (! request()->has('citation_id') && $get('choice') != 'citation') {
+                        } elseif (! request()->has('citation_id') && $get('report_type') != 'citation') {
                             return true;
                         }
                     })
@@ -113,7 +113,7 @@ public static function form(Form $form): Form
                             if ($get('organisms') == []) {
                                 return true;
                             }
-                        } elseif (! request()->has('organism_id') && $get('choice') != 'organism') {
+                        } elseif (! request()->has('organism_id') && $get('report_type') != 'organism') {
                             return true;
                         }
                     })
@@ -131,7 +131,7 @@ public static function form(Form $form): Form
                             if (is_null($get('mol_id_csv'))) {
                                 return true;
                             }
-                        } elseif (! request()->has('compound_id') && $get('choice') != 'molecule') {
+                        } elseif (! request()->has('compound_id') && $get('report_type') != 'molecule') {
                             return true;
                         }
                     })

diff --git a/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php b/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php
@@ -37,25 +37,25 @@ protected function afterFill(): void
 
     protected function beforeCreate(): void
     {
-        if ($this->data['choice'] == 'collection') {
+        if ($this->data['report_type'] == 'collection') {
             $this->data['citations'] = [];
-            $this->data['molecules'] = null;
+            $this->data['mol_id_csv'] = null;
             $this->data['organisms'] = [];
-        } elseif ($this->data['choice'] == 'citation') {
+        } elseif ($this->data['report_type'] == 'citation') {
             $this->data['collections'] = [];
-            $this->data['molecules'] = null;
+            $this->data['mol_id_csv'] = null;
             $this->data['organisms'] = [];
-        } elseif ($this->data['choice'] == 'molecule') {
+        } elseif ($this->data['report_type'] == 'molecule') {
             $this->data['collections'] = [];
             $this->data['citations'] = [];
             $this->data['organisms'] = [];
-        } elseif ($this->data['choice'] == 'organism') {
+        } elseif ($this->data['report_type'] == 'organism') {
             $this->data['collections'] = [];
             $this->data['citations'] = [];
-            $this->data['molecules'] = null;
+            $this->data['mol_id_csv'] = null;
         }
 
-        if (! ($this->data['collections'] || $this->data['citations'] || $this->data['molecules'] || $this->data['organisms'])) {
+        if (! ($this->data['collections'] || $this->data['citations'] || $this->data['mol_id_csv'] || $this->data['organisms'])) {
             Notification::make()
                 ->danger()
                 ->title('Select at least one Collection/Citation/Molecule/Organism')

diff --git a/...Filament/Dashboard/Resources/ReportResource/RelationManagers/CitationsRelationManager.php b/...Filament/Dashboard/Resources/ReportResource/RelationManagers/CitationsRelationManager.php
@@ -7,6 +7,7 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Model;
 
 class CitationsRelationManager extends RelationManager
 {
@@ -46,4 +47,13 @@ public function table(Table $table): Table
                 ]),
             ]);
     }
+
+    public static function canViewForRecord(Model $ownerRecord, string $pageClass): bool
+    {
+        if ($ownerRecord->report_type === 'citation') {
+            return true;
+        }
+
+        return false;
+    }
 }
diff --git a/...lament/Dashboard/Resources/ReportResource/RelationManagers/CollectionsRelationManager.php b/...lament/Dashboard/Resources/ReportResource/RelationManagers/CollectionsRelationManager.php
@@ -7,6 +7,7 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Model;
 
 class CollectionsRelationManager extends RelationManager
 {
@@ -46,4 +47,13 @@ public function table(Table $table): Table
                 ]),
             ]);
     }
+
+    public static function canViewForRecord(Model $ownerRecord, string $pageClass): bool
+    {
+        if ($ownerRecord->report_type === 'collection') {
+            return true;
+        }
+
+        return false;
+    }
 }
diff --git a/...Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php b/...Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php
@@ -7,6 +7,7 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Model;
 
 class MoleculesRelationManager extends RelationManager
 {
@@ -46,4 +47,13 @@ public function table(Table $table): Table
                 ]),
             ]);
     }
+
+    public static function canViewForRecord(Model $ownerRecord, string $pageClass): bool
+    {
+        if ($ownerRecord->report_type === 'molecule') {
+            return true;
+        }
+
+        return false;
+    }
 }
diff --git a/...Filament/Dashboard/Resources/ReportResource/RelationManagers/OrganismsRelationManager.php b/...Filament/Dashboard/Resources/ReportResource/RelationManagers/OrganismsRelationManager.php
@@ -7,6 +7,7 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Model;
 
 class OrganismsRelationManager extends RelationManager
 {
@@ -45,4 +46,13 @@ public function table(Table $table): Table
                 ]),
             ]);
     }
+
+    public static function canViewForRecord(Model $ownerRecord, string $pageClass): bool
+    {
+        if ($ownerRecord->report_type === 'organism') {
+            return true;
+        }
+
+        return false;
+    }
 }