diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index b69ac9b6..ed395b5d 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -21,5 +21,5 @@ jobs: with: release-type: php package-name: release-please-action - token: ${{ secrets.GITHUB_TOKEN }} - prerelease: true \ No newline at end of file + token: ${{ secrets.RELEASE_PLEASE_TOKEN }} + prerelease: true diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Pages/EditCollection.php b/app/Filament/Dashboard/Resources/CollectionResource/Pages/EditCollection.php index 44c14375..4bae6a86 100644 --- a/app/Filament/Dashboard/Resources/CollectionResource/Pages/EditCollection.php +++ b/app/Filament/Dashboard/Resources/CollectionResource/Pages/EditCollection.php @@ -11,6 +11,15 @@ class EditCollection extends EditRecord { protected static string $resource = CollectionResource::class; + protected function mutateFormDataBeforeCreate(array $data): array + { + if (! $data['image']) { + $data['image'] = $this->record->image; + } + + return $data; + } + protected function getHeaderWidgets(): array { return [ diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php index 9af255f5..fda56f34 100644 --- a/app/Filament/Dashboard/Resources/MoleculeResource.php +++ b/app/Filament/Dashboard/Resources/MoleculeResource.php @@ -24,7 +24,6 @@ use Filament\Tables\Columns\ImageColumn; use Filament\Tables\Table; use Illuminate\Database\Eloquent\Collection; -use Illuminate\Support\Facades\Auth; use Illuminate\Support\Facades\Cache; use Illuminate\Support\Facades\Redirect; use Illuminate\Support\HtmlString; @@ -128,15 +127,7 @@ public static function table(Table $table): Table $record->active = ! $record->active; - $reasons = json_decode($record->comment, true); - array_push($reasons, [ - 'changed_status_to' => $record['active'], - 'changed_by' => Auth::user()->id, - 'changed_at' => now(), - 'reason' => $data['reason'], - 'bulk_action' => false, - ]); - $record->comment = json_encode($reasons); + $record->active ?: $record->comment = $data['reason']; $record->save(); }) @@ -158,15 +149,7 @@ public static function table(Table $table): Table foreach ($records as $record) { $record->active = ! $record->active; - $reasons = json_decode($record->comment, true); - array_push($reasons, [ - 'changed_status_to' => $record['active'], - 'changed_by' => Auth::user()->id, - 'changed_at' => now(), - 'reason' => $data['reason'], - 'bulk_action' => true, - ]); - $record->comment = json_encode($reasons); + $record->comment = $data['reason']; $record->save(); } diff --git a/app/Filament/Dashboard/Resources/ReportResource.php b/app/Filament/Dashboard/Resources/ReportResource.php index 9c154fec..a26e7ad1 100644 --- a/app/Filament/Dashboard/Resources/ReportResource.php +++ b/app/Filament/Dashboard/Resources/ReportResource.php @@ -2,11 +2,15 @@ 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 Archilex\AdvancedTables\Filters\AdvancedFilter; +use Filament\Forms\Components\Actions; +use Filament\Forms\Components\Actions\Action; +use Filament\Forms\Components\Grid; use Filament\Forms\Components\KeyValue; use Filament\Forms\Components\Select; use Filament\Forms\Components\SpatieTagsInput; @@ -16,10 +20,12 @@ use Filament\Forms\Form; use Filament\Forms\Get; use Filament\Resources\Resource; +use Filament\Support\Enums\VerticalAlignment; use Filament\Tables; use Filament\Tables\Columns\TextColumn; use Filament\Tables\Table; use Illuminate\Database\Eloquent\Builder; +use Illuminate\Support\HtmlString; use Illuminate\Support\Str; use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager; @@ -37,15 +43,65 @@ public static function form(Form $form): Form { return $form ->schema([ - ToggleButtons::make('is_change') - ->label('') - ->live() - ->default(false) - ->options([ - true => 'Request Changes to Data', - false => 'Report Synthetic Compound(s)', + Grid::make() + ->schema([ + ToggleButtons::make('is_change') + ->label('') + ->live() + ->default(false) + ->options([ + false => 'Report Synthetic Compound(s)', + true => 'Request Changes to Data', + ]) + ->inline() + ->columnSpan(2), + Actions::make([ + Action::make('approve') + ->hidden(function (Get $get, string $operation) { + return ! auth()->user()->roles()->exists() || $get('status') == 'rejected' || $get('status') == 'approved' || $operation == 'create'; + }) + ->form([ + Textarea::make('reason'), + ]) + ->action(function (array $data, Report $record, Molecule $molecule, $set): void { + + $record['status'] = 'approved'; + $record['reason'] = $data['reason']; + $record->save(); + + $set('status', 'rejected'); + + if ($record['mol_id_csv'] && ! $record['is_change']) { + $molecule_ids = explode(',', $record['mol_id_csv']); + $molecule = Molecule::whereIn('id', $molecule_ids)->get(); + foreach ($molecule as $mol) { + $mol->active = false; + $mol->save(); + } + } + }), + Action::make('reject') + ->color('danger') + ->hidden(function (Get $get, string $operation) { + return ! auth()->user()->roles()->exists() || $get('status') == 'rejected' || $get('status') == 'approved' || $operation == 'create'; + }) + ->form([ + Textarea::make('reason'), + ]) + ->action(function (array $data, Report $record, $set): void { + + $record['status'] = 'rejected'; + $record['reason'] = $data['reason']; + $record->save(); + + $set('status', 'rejected'); + }), + ]) + ->verticalAlignment(VerticalAlignment::End) + ->columnStart(4), ]) - ->inline(), + ->columns(3), + Select::make('report_type') ->label('Choose') ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Select what you want to report. Ex: Molecule, Citation, Collection, Organism.') @@ -70,15 +126,25 @@ public static function form(Form $form): Form return $get('is_change'); }), KeyValue::make('suggested_changes') + ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Enter the property (in the left column) and suggested change (in the right column)') ->addActionLabel('Add property') ->keyLabel('Property') ->valueLabel('Suggested change') ->hidden(function (Get $get) { return ! $get('is_change'); }), - TextInput::make('url') - ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Provide a link to the webpage that supports your claims.') - ->label('URL'), + TextInput::make('doi') + ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Provide the DOI link to the resource you are reporting so as to help curators verify.') + ->label('DOI') + ->url() + ->suffixAction( + fn (?string $state): Action => Action::make('visit') + ->icon('heroicon-s-link') + ->url( + $state, + shouldOpenInNewTab: true, + ), + ), Select::make('collections') ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Select the Collections you want to report. This will help our Curators in reviewing your report.') ->relationship('collections', 'title') @@ -90,7 +156,7 @@ public static function form(Form $form): Form } }) ->hidden(function (Get $get, string $operation) { - if ($operation == 'edit' || $operation == 'view') { + if ($operation != 'create') { if ($get('collections') == []) { return true; } @@ -117,7 +183,7 @@ public static function form(Form $form): Form } }) ->hidden(function (Get $get, string $operation) { - if ($operation == 'edit' || $operation == 'view') { + if ($operation != 'create') { if ($get('citations') == []) { return true; } @@ -142,7 +208,7 @@ public static function form(Form $form): Form } }) ->hidden(function (Get $get, string $operation) { - if ($operation == 'edit' || $operation == 'view') { + if ($operation != 'create') { if ($get('organisms') == []) { return true; } @@ -165,10 +231,8 @@ public static function form(Form $form): Form } }) ->hidden(function (Get $get, string $operation) { - if ($operation == 'edit' || $operation == 'view') { - if (is_null($get('mol_id_csv'))) { - return true; - } + if ($operation != 'create') { + return true; } elseif (! request()->has('compound_id') && $get('report_type') != 'molecule') { return true; } @@ -178,22 +242,10 @@ public static function form(Form $form): Form return true; } }), - SpatieTagsInput::make('tags') - ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Provide comma separated search terms that would help in finding your report when searched.') - ->splitKeys(['Tab', ',']) - ->type('reports'), - Select::make('status') - ->options([ - 'pending' => 'Pending', - 'approved' => 'Approved', - 'rejected' => 'Rejected', - ]) - ->hidden(function () { - return ! auth()->user()->hasRole('curator'); - }) - ->afterStateUpdated(function (?Report $record, ?string $state, ?string $old) { - ReportStatusChanged::dispatch($record, $state, $old); - }), + // SpatieTagsInput::make('tags') + // ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Provide comma separated search terms that would help in finding your report when searched.') + // ->splitKeys(['Tab', ',']) + // ->type('reports'), Textarea::make('comment') ->hintIcon('heroicon-m-question-mark-circle', tooltip: 'Provide your comments/observations on anything noteworthy in the Curation process.') ->hidden(function () { @@ -209,26 +261,63 @@ public static function table(Table $table): Table TextColumn::make('title') ->wrap() ->description(fn (Report $record): string => Str::of($record->evidence)->words(10)), - TextColumn::make('url') - ->url(fn (Report $record) => $record->url) - ->openUrlInNewTab(), - TextColumn::make('status') - ->badge() - ->color(function (Report $record) { - return match ($record->status) { - 'pending' => 'info', - 'approved' => 'success', - 'rejected' => 'danger', - }; - }), - TextColumn::make('comment')->wrap(), + Tables\Columns\TextColumn::make('name')->searchable() + ->formatStateUsing( + fn (Report $record): HtmlString => new HtmlString("DOI: {$record->doi}") + ) + ->description(fn (Report $record): string => $record->comment ?? '') + ->wrap(), ]) ->defaultSort('created_at', 'desc') ->filters([ - // + AdvancedFilter::make() + ->includeColumns(), ]) ->actions([ - Tables\Actions\EditAction::make(), + Tables\Actions\ViewAction::make(), + Tables\Actions\EditAction::make() + ->visible(function ($record) { + return auth()->user()->roles()->exists() && $record['status'] == 'submitted'; + }), + Tables\Actions\Action::make('approve') + // ->button() + ->hidden(function (Report $record) { + return ! auth()->user()->roles()->exists() || $record['status'] == 'draft' || $record['status'] == 'rejected' || $record['status'] == 'approved'; + }) + ->form([ + Textarea::make('reason'), + ]) + ->action(function (array $data, Report $record, Molecule $molecule): void { + + $record['status'] = 'approved'; + $record['reason'] = $data['reason']; + $record->save(); + + if ($record['mol_id_csv'] && ! $record['is_change']) { + $molecule_ids = explode(',', $record['mol_id_csv']); + $molecule = Molecule::whereIn('id', $molecule_ids)->get(); + foreach ($molecule as $mol) { + $mol->active = false; + $mol->save(); + } + } + }), + Tables\Actions\Action::make('reject') + // ->button() + ->color('danger') + ->hidden(function (Report $record) { + return ! auth()->user()->roles()->exists() || $record['status'] == 'draft' || $record['status'] == 'rejected' || $record['status'] == 'approved'; + }) + ->form([ + Textarea::make('reason'), + + ]) + ->action(function (array $data, Report $record): void { + + $record['status'] = 'rejected'; + $record['reason'] = $data['reason']; + $record->save(); + }), ]) ->bulkActions([ Tables\Actions\BulkActionGroup::make([ diff --git a/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php b/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php index c696a551..937c3131 100644 --- a/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php +++ b/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php @@ -65,7 +65,7 @@ protected function beforeCreate(): void protected function mutateFormDataBeforeCreate(array $data): array { $data['user_id'] = auth()->id(); - $data['status'] = 'pending'; + $data['status'] = 'submitted'; return $data; } diff --git a/app/Filament/Dashboard/Resources/ReportResource/Pages/EditReport.php b/app/Filament/Dashboard/Resources/ReportResource/Pages/EditReport.php index 5bf27158..faec4f41 100644 --- a/app/Filament/Dashboard/Resources/ReportResource/Pages/EditReport.php +++ b/app/Filament/Dashboard/Resources/ReportResource/Pages/EditReport.php @@ -13,7 +13,7 @@ class EditReport extends EditRecord protected function getHeaderActions(): array { return [ - Actions\DeleteAction::make(), + // Actions\DeleteAction::make(), ]; } } diff --git a/app/Filament/Dashboard/Resources/ReportResource/Pages/ListReports.php b/app/Filament/Dashboard/Resources/ReportResource/Pages/ListReports.php index 105cb4f4..dc0f0dff 100644 --- a/app/Filament/Dashboard/Resources/ReportResource/Pages/ListReports.php +++ b/app/Filament/Dashboard/Resources/ReportResource/Pages/ListReports.php @@ -3,11 +3,16 @@ namespace App\Filament\Dashboard\Resources\ReportResource\Pages; use App\Filament\Dashboard\Resources\ReportResource; +use App\Models\Report; +use Archilex\AdvancedTables\AdvancedTables; +use Archilex\AdvancedTables\Components\PresetView; use Filament\Actions; use Filament\Resources\Pages\ListRecords; class ListReports extends ListRecords { + use AdvancedTables; + protected static string $resource = ReportResource::class; protected function getHeaderActions(): array @@ -16,4 +21,26 @@ protected function getHeaderActions(): array Actions\CreateAction::make(), ]; } + + public function getPresetViews(): array + { + return [ + 'submitted' => PresetView::make() + ->modifyQueryUsing(fn ($query) => $query->where('status', 'submitted')) + ->favorite() + ->badge(Report::query()->where('status', 'submitted')->count()) + ->preserveAll() + ->default(), + 'approved' => PresetView::make() + ->modifyQueryUsing(fn ($query) => $query->where('status', 'approved')) + ->favorite() + ->badge(Report::query()->where('status', 'approved')->count()) + ->preserveAll(), + 'rejected' => PresetView::make() + ->modifyQueryUsing(fn ($query) => $query->where('status', 'rejected')) + ->favorite() + ->badge(Report::query()->where('status', 'rejected')->count()) + ->preserveAll(), + ]; + } } diff --git a/app/Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php b/app/Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php index a978843d..e75751fb 100644 --- a/app/Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php +++ b/app/Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php @@ -2,12 +2,15 @@ namespace App\Filament\Dashboard\Resources\ReportResource\RelationManagers; +use App\Models\Molecule; use Filament\Forms; use Filament\Forms\Form; use Filament\Resources\RelationManagers\RelationManager; use Filament\Tables; +use Filament\Tables\Columns\ImageColumn; use Filament\Tables\Table; use Illuminate\Database\Eloquent\Model; +use Illuminate\Support\HtmlString; class MoleculesRelationManager extends RelationManager { @@ -27,8 +30,45 @@ public function table(Table $table): Table { return $table ->recordTitleAttribute('canonical_smiles') + ->recordTitleAttribute('identifier') ->columns([ - Tables\Columns\TextColumn::make('canonical_smiles'), + ImageColumn::make('structure')->square() + ->label('Structure') + ->state(function ($record) { + return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk'; + }) + ->width(200) + ->height(200) + ->ring(5) + ->defaultImageUrl(url('/images/placeholder.png')), + Tables\Columns\TextColumn::make('id')->searchable()->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('identifier')->searchable()->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('identifier') + ->label('Details') + ->formatStateUsing( + fn (Molecule $molecule): HtmlString => new HtmlString("ID: {$molecule->id}
Identifier: {$molecule->identifier}
Name: {$molecule->name}") + ) + ->description(fn (Molecule $molecule): string => $molecule->standard_inchi) + ->wrap(), + Tables\Columns\TextColumn::make('name') + ->searchable() + ->wrap() + ->lineClamp(6) + ->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('synonyms') + ->searchable() + ->wrap() + ->lineClamp(6) + ->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('properties.exact_molecular_weight') + ->label('Mol.Wt') + ->numeric() + ->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('properties.np_likeness') + ->label('NP Likeness') + ->numeric() + ->toggleable(isToggledHiddenByDefault: true), + Tables\Columns\TextColumn::make('status'), ]) ->filters([ // diff --git a/app/Livewire/MoleculeHistoryTimeline.php b/app/Livewire/MoleculeHistoryTimeline.php index 47db6dfc..6efaa7f5 100644 --- a/app/Livewire/MoleculeHistoryTimeline.php +++ b/app/Livewire/MoleculeHistoryTimeline.php @@ -18,19 +18,17 @@ public function getHistory() $audit_data[$index]['event'] = $audit->getMetadata()['audit_event']; $audit_data[$index]['created_at'] = date('Y/m/d', strtotime($audit->getMetadata()['audit_created_at'])); foreach ($audit->getModified() as $key => $value) { - $audit_data[$index]['affected_column'] = $key; - $audit_data[$index]['old_value'] = $value['old']; - $audit_data[$index]['new_value'] = $value['new']; + $audit_data[$index]['affected_columns'][$key]['old_value'] = $value['old']; + $audit_data[$index]['affected_columns'][$key]['new_value'] = $value['new']; } } $initial_audit = []; $initial_audit['user_name'] = null; - $initial_audit['event'] = 'created'; + $initial_audit['event'] = null; $initial_audit['created_at'] = $this->mol->created_at->format('Y/m/d'); - $initial_audit['affected_column'] = null; - $initial_audit['old_value'] = null; - $initial_audit['new_value'] = null; + $initial_audit['affected_columns']['created']['old_value'] = null; + $initial_audit['affected_columns']['created']['new_value'] = null; array_unshift($audit_data, $initial_audit); $this->audit_data = $audit_data; diff --git a/app/Models/Molecule.php b/app/Models/Molecule.php index b61b3f96..93e94130 100644 --- a/app/Models/Molecule.php +++ b/app/Models/Molecule.php @@ -60,7 +60,6 @@ class Molecule extends Model implements Auditable protected $casts = [ 'synonyms' => 'array', 'cas' => 'array', - 'comment' => 'array', ]; /** diff --git a/app/Models/Report.php b/app/Models/Report.php index 57e464cc..e4c4cfb9 100644 --- a/app/Models/Report.php +++ b/app/Models/Report.php @@ -2,16 +2,19 @@ namespace App\Models; +use App\States\Report\ReportState; use Illuminate\Database\Eloquent\Factories\HasFactory; use Illuminate\Database\Eloquent\Model; use Illuminate\Database\Eloquent\Relations\BelongsTo; use Illuminate\Database\Eloquent\Relations\MorphToMany; use OwenIt\Auditing\Contracts\Auditable; +use Spatie\ModelStates\HasStates; use Spatie\Tags\HasTags; class Report extends Model implements Auditable { use HasFactory; + use HasStates; use HasTags; use \OwenIt\Auditing\Auditable; @@ -35,6 +38,7 @@ class Report extends Model implements Auditable protected $casts = [ 'suggested_changes' => 'array', + // 'status' => ReportState::class, ]; /** diff --git a/app/States/Report/ApprovedState.php b/app/States/Report/ApprovedState.php new file mode 100644 index 00000000..d4dfd9aa --- /dev/null +++ b/app/States/Report/ApprovedState.php @@ -0,0 +1,13 @@ +default(DraftState::class) + ->allowTransition(DraftState::class, SubmittedState::class); + } else { + return parent::config() + ->default(DraftState::class) + ->allowTransition(DraftState::class, SubmittedState::class) + ->allowTransition(SubmittedState::class, ProcessingState::class) + ->allowTransition([SubmittedState::class, ProcessingState::class], RejectedState::class, ToRejected::class) + ->allowTransition([SubmittedState::class, ProcessingState::class], ApprovedState::class, ToApproved::class); + } + + } +} diff --git a/app/States/Report/SubmittedState.php b/app/States/Report/SubmittedState.php new file mode 100644 index 00000000..f025b6ff --- /dev/null +++ b/app/States/Report/SubmittedState.php @@ -0,0 +1,20 @@ +report->state = new ApprovedState($this->report); + $this->report->comments = $this->reason; + + $this->report->save(); + + return $this->report; + } + + public function form(): array + { + return [ + Textarea::make('comments') + ->required() + ->minLength(1) + ->maxLength(1000) + ->rows(5) + ->helperText(__('This reason will be sent to the report creator.')), + ]; + } +} diff --git a/app/States/Report/ToRejected.php b/app/States/Report/ToRejected.php new file mode 100644 index 00000000..b71f01df --- /dev/null +++ b/app/States/Report/ToRejected.php @@ -0,0 +1,41 @@ +report->state = new RejectedState($this->report); + $this->report->comments = $this->reason; + + $this->report->save(); + + return $this->report; + } + + public function form(): array + { + return [ + Textarea::make('comments') + ->required() + ->minLength(1) + ->maxLength(1000) + ->rows(5) + ->helperText(__('This reason will be sent to the report creator.')), + ]; + } +} diff --git a/composer.json b/composer.json index 566649f9..5d6faf9b 100644 --- a/composer.json +++ b/composer.json @@ -28,6 +28,7 @@ "league/flysystem-aws-s3-v3": "^3.0", "livewire/livewire": "^3.0", "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", @@ -36,6 +37,7 @@ "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", "spatie/schema-org": "^3.23", "stechstudio/filament-impersonate": "*", @@ -103,6 +105,10 @@ { "type": "composer", "url": "https://filament-filter-sets.composer.sh" + }, + { + "type": "composer", + "url": "https://model-states-for-filament.composer.sh" } ] } diff --git a/composer.lock b/composer.lock index 24d566dd..6b3a6712 100644 --- a/composer.lock +++ b/composer.lock @@ -4,20 +4,20 @@ "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies", "This file is @generated automatically" ], - "content-hash": "9aeed4c020fef8e2baf0a41088bef26f", + "content-hash": "00e53096c3100ad2d23005e4f69defc3", "packages": [ { "name": "anourvalar/eloquent-serialize", - "version": "1.2.23", + "version": "1.2.24", "source": { "type": "git", "url": "https://github.com/AnourValar/eloquent-serialize.git", - "reference": "fd7bc1dc2c98fe705647ab4b81d13ea3d599ea1f" + "reference": "77e3fc7da44fa96b6148a1613dd76fe954a5f279" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/AnourValar/eloquent-serialize/zipball/fd7bc1dc2c98fe705647ab4b81d13ea3d599ea1f", - "reference": "fd7bc1dc2c98fe705647ab4b81d13ea3d599ea1f", + "url": 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@@ }, { "name": "phpunit/phpunit", - "version": "10.5.30", + "version": "10.5.33", "source": { "type": "git", "url": "https://github.com/sebastianbergmann/phpunit.git", - "reference": "b15524febac0153876b4ba9aab3326c2ee94c897" + "reference": "4def7a9cda75af9c2bc179ed53a8e41313e7f7cf" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/sebastianbergmann/phpunit/zipball/b15524febac0153876b4ba9aab3326c2ee94c897", - "reference": "b15524febac0153876b4ba9aab3326c2ee94c897", + "url": "https://api.github.com/repos/sebastianbergmann/phpunit/zipball/4def7a9cda75af9c2bc179ed53a8e41313e7f7cf", + "reference": "4def7a9cda75af9c2bc179ed53a8e41313e7f7cf", "shasum": "" }, "require": { @@ -14215,7 +14444,7 @@ "phar-io/manifest": "^2.0.4", "phar-io/version": "^3.2.1", "php": ">=8.1", - "phpunit/php-code-coverage": "^10.1.15", + "phpunit/php-code-coverage": "^10.1.16", "phpunit/php-file-iterator": "^4.1.0", "phpunit/php-invoker": "^4.0.0", "phpunit/php-text-template": "^3.0.1", @@ -14273,7 +14502,7 @@ "support": { "issues": "https://github.com/sebastianbergmann/phpunit/issues", "security": "https://github.com/sebastianbergmann/phpunit/security/policy", - "source": "https://github.com/sebastianbergmann/phpunit/tree/10.5.30" + "source": "https://github.com/sebastianbergmann/phpunit/tree/10.5.33" }, "funding": [ { @@ -14289,7 +14518,7 @@ "type": "tidelift" } ], - "time": "2024-08-13T06:09:37+00:00" + "time": "2024-09-09T06:06:56+00:00" }, { "name": "sebastian/cli-parser", diff --git a/config/model-states.php b/config/model-states.php new file mode 100644 index 00000000..57ef8cb2 --- /dev/null +++ b/config/model-states.php @@ -0,0 +1,10 @@ + Spatie\ModelStates\DefaultTransition::class, + +]; diff --git a/database/migrations/2024_09_09_150749_add_columns_on_reports_table.php b/database/migrations/2024_09_09_150749_add_columns_on_reports_table.php new file mode 100644 index 00000000..5a05fbf6 --- /dev/null +++ b/database/migrations/2024_09_09_150749_add_columns_on_reports_table.php @@ -0,0 +1,30 @@ +longText('query')->nullable(); + $table->renameColumn('url', 'doi'); + $table->string('doi')->nullable()->change(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::table('reports', function (Blueprint $table) { + $table->dropColumn(['doi', 'query']); + }); + } +}; diff --git a/database/migrations/2024_09_09_150750_change_columns_on_molecules_table.php b/database/migrations/2024_09_09_150750_change_columns_on_molecules_table.php new file mode 100644 index 00000000..a2ce3881 --- /dev/null +++ b/database/migrations/2024_09_09_150750_change_columns_on_molecules_table.php @@ -0,0 +1,28 @@ +longText('comment')->nullable()->change(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::table('molecules', function (Blueprint $table) { + $table->json('comment')->nullable()->change(); + }); + } +}; diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml new file mode 100755 index 00000000..8b960853 --- /dev/null +++ b/docker-compose.prod.yml @@ -0,0 +1,104 @@ +services: + app: + build: + context: . + dockerfile: ./resources/dc-ops/production/Dockerfile + args: + WWWGROUP: '${WWWGROUP}' + image: coconut-8.3/app + container_name: coconut_app + networks: + - coconut + depends_on: + - pgsql + - redis + # - typesense + volumes: + - www-data:/var/www + pgsql: + image: "informaticsmatters/rdkit-cartridge-debian:latest" + ports: + - '${FORWARD_DB_PORT:-5432}:5432' + environment: + PGPASSWORD: '${DB_PASSWORD:-secret}' + POSTGRES_DB: '${DB_DATABASE}' + POSTGRES_USER: '${DB_USERNAME}' + POSTGRES_PASSWORD: '${DB_PASSWORD:-secret}' + volumes: + - 'coconut-pgsql:/var/lib/postgresql/data' + - './docker/pgsql/create-testing-database.sql:/docker-entrypoint-initdb.d/10-create-testing-database.sql' + networks: + - coconut + healthcheck: + test: + - CMD + - pg_isready + - '-q' + - '-d' + - '${DB_DATABASE}' + - '-U' + - '${DB_USERNAME}' + retries: 3 + timeout: 5s + redis: + image: 'redis:alpine' + ports: + - '${FORWARD_REDIS_PORT:-6379}:6379' + volumes: + - 'coconut-redis:/data' + networks: + - coconut + healthcheck: + test: + - CMD + - redis-cli + - ping + retries: 3 + timeout: 5s + nginx: + build: + context: . + dockerfile: ./resources/dc-ops/nginx/Dockerfile + container_name: coconut_nginx + restart: unless-stopped + ports: + - 80:80 + networks: + - coconut + depends_on: + - app + volumes: + - www-data:/var/www + # typesense: + # image: 'typesense/typesense:0.25.2' + # ports: + # - '${FORWARD_TYPESENSE_PORT:-8108}:8108' + # environment: + # TYPESENSE_DATA_DIR: '${TYPESENSE_DATA_DIR:-/typesense-data}' + # TYPESENSE_API_KEY: '${TYPESENSE_API_KEY:-xyz}' + # TYPESENSE_ENABLE_CORS: '${TYPESENSE_ENABLE_CORS:-true}' + # volumes: + # - 'coconut-typesense:/typesense-data' + # networks: + # - coconut + # healthcheck: + # test: + # - CMD + # - wget + # - '--no-verbose' + # - '--spider' + # - 'http://localhost:8108/health' + # retries: 5 + # timeout: 7s +networks: + coconut: + driver: bridge +volumes: + coconut-pgsql: + driver: local + coconut-redis: + driver: local + www-data: + driver: local + # coconut-typesense: + # driver: local diff --git a/resources/dc-ops/nginx/Dockerfile b/resources/dc-ops/nginx/Dockerfile new file mode 100755 index 00000000..1eb7ac41 --- /dev/null +++ b/resources/dc-ops/nginx/Dockerfile @@ -0,0 +1,12 @@ +FROM nginx:alpine + +# Remove default configuration file +RUN rm /etc/nginx/conf.d/default.conf + +# Copy custom configuration file from the current directory +COPY ./resources/dc-ops/nginx/default.conf /etc/nginx/conf.d + +# Expose port 80 +EXPOSE 80 + +CMD ["nginx", "-g", "daemon off;"] \ No newline at end of file diff --git a/resources/dc-ops/nginx/default.conf b/resources/dc-ops/nginx/default.conf new file mode 100755 index 00000000..4c6cbf44 --- /dev/null +++ b/resources/dc-ops/nginx/default.conf @@ -0,0 +1,20 @@ +server { + listen 80; + index index.php index.html; + error_log /var/log/nginx/error.log; + access_log /var/log/nginx/access.log; + root /var/www/public; + location ~ \.php$ { + try_files $uri =404; + fastcgi_split_path_info ^(.+\.php)(/.+)$; + fastcgi_pass app:9000; + fastcgi_index index.php; + include fastcgi_params; + fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name; + fastcgi_param PATH_INFO $fastcgi_path_info; + } + location / { + try_files $uri $uri/ /index.php?$query_string; + gzip_static on; + } +} \ No newline at end of file diff --git a/resources/dc-ops/production/Dockerfile b/resources/dc-ops/production/Dockerfile new file mode 100755 index 00000000..6670f457 --- /dev/null +++ b/resources/dc-ops/production/Dockerfile @@ -0,0 +1,117 @@ +FROM php:8.3-fpm + +# Copy composer.lock and composer.json +COPY composer.lock composer.json /var/www/ + +# Set working directory +WORKDIR /var/www + +ARG POSTGRES_VERSION=15 + +# Install dependencies +RUN apt-get update && apt-get install -y \ + build-essential \ + libpng-dev \ + libjpeg62-turbo-dev \ + libfreetype6-dev \ + locales \ + zip \ + jpegoptim optipng pngquant gifsicle \ + vim \ + unzip \ + git \ + curl \ + libonig-dev \ + libzip-dev \ + libicu-dev \ + libgd-dev \ + libpq-dev + +RUN apt-get update \ + && mkdir -p /etc/apt/keyrings \ + && apt-get install -y gnupg gosu curl ca-certificates zip unzip git supervisor sqlite3 libcap2-bin libpng-dev dnsutils librsvg2-bin fswatch \ + && curl -sS 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x14aa40ec0831756756d7f66c4f4ea0aae5267a6c' | gpg --dearmor | tee /etc/apt/keyrings/ppa_ondrej_php.gpg > /dev/null \ + && echo "deb [signed-by=/etc/apt/keyrings/ppa_ondrej_php.gpg] https://ppa.launchpadcontent.net/ondrej/php/ubuntu jammy main" > /etc/apt/sources.list.d/ppa_ondrej_php.list \ + && apt-get update \ + && apt-get install -y php8.3-cli php8.3-dev \ + php8.3-pgsql php8.3-sqlite3 php8.3-gd \ + php8.3-curl \ + php8.3-imap php8.3-mysql php8.3-mbstring \ + php8.3-xml php8.3-zip php8.3-bcmath php8.3-soap \ + php8.3-intl php8.3-readline \ + php8.3-ldap \ + php8.3-msgpack php8.3-igbinary php8.3-redis php8.3-swoole \ + php8.3-memcached php8.3-pcov php8.3-imagick php8.3-xdebug \ + && curl -sLS https://getcomposer.org/installer | php -- --install-dir=/usr/bin/ --filename=composer \ + && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \ + && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_VERSION.x nodistro main" > /etc/apt/sources.list.d/nodesource.list \ + && apt-get update \ + && apt-get install -y nodejs \ + && npm install -g npm \ + && npm install -g pnpm \ + && npm install -g bun \ + && curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | gpg --dearmor | tee /etc/apt/keyrings/yarn.gpg >/dev/null \ + && echo "deb [signed-by=/etc/apt/keyrings/yarn.gpg] https://dl.yarnpkg.com/debian/ stable main" > /etc/apt/sources.list.d/yarn.list \ + && curl -sS https://www.postgresql.org/media/keys/ACCC4CF8.asc | gpg --dearmor | tee /etc/apt/keyrings/pgdg.gpg >/dev/null \ + && echo "deb [signed-by=/etc/apt/keyrings/pgdg.gpg] http://apt.postgresql.org/pub/repos/apt jammy-pgdg main" > /etc/apt/sources.list.d/pgdg.list \ + && apt-get update \ + && apt-get install -y yarn \ + && apt-get install -y mysql-client \ + && apt-get install -y postgresql-client-$POSTGRES_VERSION \ + && apt-get -y autoremove \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +# Install imagick +RUN apt-get update && apt-get install -y --no-install-recommends \ + libmagickwand-dev && \ + git clone https://github.com/Imagick/imagick.git --depth 1 /tmp/imagick && \ + cd /tmp/imagick && \ + phpize && \ + ./configure && \ + make && \ + make install && \ + docker-php-ext-enable imagick && \ + apt-get purge -y --auto-remove git && \ + rm -rf /var/lib/apt/lists/* /tmp/imagick + +# Clear cache +RUN apt-get clean && rm -rf /var/lib/apt/lists/* + +# Install extensions +RUN docker-php-ext-configure pgsql --with-pgsql=/usr/include/postgresql/ +RUN docker-php-ext-install pdo pdo_mysql pdo_pgsql pgsql mbstring zip exif pcntl +RUN docker-php-ext-configure gd --with-external-gd +RUN docker-php-ext-install gd +RUN docker-php-ext-configure intl +RUN docker-php-ext-install intl +RUN docker-php-ext-install bcmath + + +RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \ + && apt-get install -y nodejs + +# Install composer +RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local/bin --filename=composer + +# Add user for laravel application +RUN groupadd -g 1000 www +RUN useradd -u 1000 -ms /bin/bash -g www www + +# Copy existing application directory contents +COPY . /var/www + +RUN composer install --optimize-autoloader --no-scripts --prefer-dist +RUN npm ci +RUN npm run build + +# Copy existing application directory permissions +COPY --chown=www:www . /var/www + +# Change current user to www +USER www + +# Expose port 9000 and start php-fpm server +EXPOSE 9000 + +CMD ["php-fpm"] \ No newline at end of file diff --git a/resources/dc-ops/production/php.ini b/resources/dc-ops/production/php.ini new file mode 100755 index 00000000..0d8ce9e2 --- /dev/null +++ b/resources/dc-ops/production/php.ini @@ -0,0 +1,5 @@ +[PHP] +post_max_size = 100M +upload_max_filesize = 100M +variables_order = EGPCS +pcov.directory = . diff --git a/resources/dc-ops/production/start-container b/resources/dc-ops/production/start-container new file mode 100755 index 00000000..40c55dfe --- /dev/null +++ b/resources/dc-ops/production/start-container @@ -0,0 +1,26 @@ +#!/usr/bin/env bash + +if [ "$SUPERVISOR_PHP_USER" != "root" ] && [ "$SUPERVISOR_PHP_USER" != "sail" ]; then + echo "You should set SUPERVISOR_PHP_USER to either 'sail' or 'root'." + exit 1 +fi + +if [ ! -z "$WWWUSER" ]; then + usermod -u $WWWUSER sail +fi + +if [ ! -d /.composer ]; then + mkdir /.composer +fi + +chmod -R ugo+rw /.composer + +if [ $# -gt 0 ]; then + if [ "$SUPERVISOR_PHP_USER" = "root" ]; then + exec "$@" + else + exec gosu $WWWUSER "$@" + fi +else + exec /usr/bin/supervisord -c /etc/supervisor/conf.d/supervisord.conf +fi diff --git a/resources/dc-ops/production/supervisord.conf b/resources/dc-ops/production/supervisord.conf new file mode 100755 index 00000000..5ad4a8a5 --- /dev/null +++ b/resources/dc-ops/production/supervisord.conf @@ -0,0 +1,9 @@ +[supervisord] +nodaemon=true + +# [program:php-fpm] +# command=/usr/sbin/php-fpm8.3 -F +# autostart=true +# autorestart=true +# stderr_logfile=/var/log/supervisor/php-fpm.err.log +# stdout_logfile=/var/log/supervisor/php-fpm.out.log diff --git a/resources/views/livewire/download.blade.php b/resources/views/livewire/download.blade.php index 2bebccf4..7c007c14 100644 --- a/resources/views/livewire/download.blade.php +++ b/resources/views/livewire/download.blade.php @@ -1,7 +1,7 @@
-
+

+ class="mx-auto w-full px-6 md:px-0 max-w-2xl border-t border-gray-900/10 pt-12 sm:pt-16 lg:mx-0 lg:max-w-none lg:border-t-0 lg:pt-0">
+ September 2024 - release notes

COCONUT data is released under @@ -77,7 +77,7 @@ class="text-sm font-semibold leading-6 text-indigo-600 hover:text-indigo-500">Do

-
+

Need older versions?

Download previous releases (Zenodo) @@ -324,9 +324,9 @@ class="mt-3 text-lg font-semibold leading-6 text-gray-900 group-hover:text-gray-
- - Coming soon + CompoundDiscovererCOCONUT_ 2.csv (Sept 2024)
diff --git a/resources/views/livewire/molecule-details.blade.php b/resources/views/livewire/molecule-details.blade.php index fdb7e943..9d24297f 100644 --- a/resources/views/livewire/molecule-details.blade.php +++ b/resources/views/livewire/molecule-details.blade.php @@ -385,25 +385,33 @@ classification
diff --git a/resources/views/livewire/molecule-history-timeline.blade.php b/resources/views/livewire/molecule-history-timeline.blade.php index 3f4f9260..4931df16 100644 --- a/resources/views/livewire/molecule-history-timeline.blade.php +++ b/resources/views/livewire/molecule-history-timeline.blade.php @@ -1,4 +1,4 @@ -
+

-

{{$audit['event']}} {{$audit['affected_column']}}

{{$audit['user_name']}}

+

+

{{$audit['user_name']}} {{$audit['event']}}

+ @foreach ($audit['affected_columns'] as $column_name => $column_values) + +
+
+ {{$column_name}} +
+ + + + + @switch($column_name) + @case('comment') + {{$column_values['new_value']}} + @break + @case('active') + @if ($column_values['new_value']) + Activated + @else + Deactivated + @endif + @break + @case('created') + Initial creation of the compound on COCONUT + @break + @default + Old Value: {{$column_values['old_value']}}
+ New Value: {{$column_values['new_value']}} + @endswitch + +
+
+
+ + + @endforeach +

diff --git a/resources/views/vendor/filament-auditing/tables/columns/key-value.blade.php b/resources/views/vendor/filament-auditing/tables/columns/key-value.blade.php index c0b15ec6..0389b3e2 100644 --- a/resources/views/vendor/filament-auditing/tables/columns/key-value.blade.php +++ b/resources/views/vendor/filament-auditing/tables/columns/key-value.blade.php @@ -1,16 +1,26 @@ +@php + $data = isset($state) ? $state : $getState() +@endphp +
- @foreach($getState() ?? [] as $key => $value) - - {{ $key }} - - @unless(is_array($value)) - {{ $value }} - @else - - @foreach ($value as $nestedValue) - {{$nestedValue['id']}} - @endforeach - - @endunless - @endforeach -
+
    + @foreach($data ?? [] as $key => $value) +
  • + + {{ Str::title($key) }}: + + + @unless(is_array($value)) + {{ $value }} + @else + + @foreach ($value as $nestedValue) + {{$nestedValue['id']}} + @endforeach + + @endunless + +
    • + @endforeach +
+
\ No newline at end of file