WIP: feat(collections): add collection versioning

app/Actions/Coconut/SearchMolecule.php

@@ -285,13 +285,23 @@
     private function buildTagsStatement($offset)
     {
         if ($this->tagType == 'dataSource') {
-            $this->collection = Collection::where('title', $this->query)->first();
-            if ($this->collection) {
-                $query = $this->collection->molecules()
+            $matched = Collection::query()
+                ->where('title', $this->query)
+                ->where('is_latest', true)
+                ->first()
+                ?? Collection::where('title', $this->query)->first();
+            if ($matched) {
+                $latest = $matched->is_latest
+                    ? $matched
+                    : ($matched->lineageVersionsQuery()->where('is_latest', true)->first() ?? $matched);
+
+                $this->collection = $latest;
+
+                $query = $latest->molecules()
                     ->whereIn('molecules.id', function ($query) {
                         $query->select('molecule_id')
                             ->from('entries')
-                            ->where('collection_id', $this->collection->id)
+                            ->where('collection_id', $latest->id)
                             ->distinct();
                     });
 

app/Console/Commands/DashWidgetsRefresh.php

@@ -36,6 +36,7 @@ public function handle()
             return DB::table('collections')
                 ->selectRaw('count(*) as count')
                 ->where('status', 'PUBLISHED')
+                ->where('is_latest', true)
                 ->get()[0]->count;
         });
         $this->info('Cache for collections refreshed.');

app/Console/Commands/ImportCollectionVersion.php

@@ -0,0 +1,36 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Collection;
+use App\Services\CollectionVersioning\CollectionVersionImporter;
+use Illuminate\Console\Command;
+
+class ImportCollectionVersion extends Command
+{
+    protected $signature = 'coconut:import-collection-version {new_collection_id : The new version collection ID}';
+
+    protected $description = 'Run the full collection version migration pipeline';
+
+    public function handle(CollectionVersionImporter $importer): int
+    {
+        $collection = Collection::query()->find($this->argument('new_collection_id'));
+        if (! $collection) {
+            $this->error('Collection not found.');
+
+            return self::FAILURE;
+        }
+
+        try {
+            $result = $importer->import($collection);
+            $this->info('Collection version migration completed.');
+            $this->table(array_keys($result), [array_values($result)]);
+
+            return self::SUCCESS;
+        } catch (\Throwable $e) {
+            $this->error($e->getMessage());
+
+            return self::FAILURE;
+        }
+    }
+}

app/Console/Commands/ImportEntries.php

@@ -34,9 +34,12 @@ public function handle()
         $collection_id = $this->argument('collection_id');
 
         if (! is_null($collection_id)) {
-            $collections = Collection::where('id', $collection_id)->get();
+            $collections = Collection::query()->where('id', $collection_id)->eligibleForLegacyPipeline()->get();
         } else {
-            $collections = Collection::where('status', 'DRAFT')->get();
+            $collections = Collection::query()
+                ->where('status', 'DRAFT')
+                ->eligibleForLegacyPipeline()
+                ->get();
         }
 
         foreach ($collections as $collection) {

app/Console/Commands/PreviewCollectionVersion.php

@@ -0,0 +1,35 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Collection;
+use App\Services\CollectionVersioning\CollectionVersionImporter;
+use Illuminate\Console\Command;
+
+class PreviewCollectionVersion extends Command
+{
+    protected $signature = 'coconut:preview-collection-version {new_collection_id : The new version collection ID}';
+
+    protected $description = 'Preview SMILES diff counts for a collection version migration';
+
+    public function handle(CollectionVersionImporter $importer): int
+    {
+        $collection = Collection::query()->find($this->argument('new_collection_id'));
+        if (! $collection) {
+            $this->error('Collection not found.');
+
+            return self::FAILURE;
+        }
+
+        try {
+            $preview = $importer->preview($collection);
+            $this->table(array_keys($preview), [array_values($preview)]);
+
+            return self::SUCCESS;
+        } catch (\Throwable $e) {
+            $this->error($e->getMessage());
+
+            return self::FAILURE;
+        }
+    }
+}

app/Console/Commands/ProcessEntries.php

@@ -38,6 +38,9 @@ public function handle()
             $i = 0;
 
             $collection = Collection::whereId($collectionId['collection_id'])->first();
+            if (! $collection || $collection->isVersionMigrationActive()) {
+                continue;
+            }
             $collection->jobs_status = 'PROCESSING';
             $collection->job_info = 'Processing entries using ChEMBL Pipeline.';
             $collection->save();

app/Filament/Dashboard/Resources/CollectionResource.php

@@ -166,6 +166,18 @@ public static function infolist(Schema $schema): Schema
                         TextEntry::make('identifier')
                             ->label('Identifier')
                             ->placeholder('No identifier'),
+                        TextEntry::make('version')
+                            ->label('Version'),
+                        TextEntry::make('is_latest')
+                            ->label('Latest')
+                            ->formatStateUsing(fn ($state) => $state ? 'Yes' : 'No'),
+                        TextEntry::make('doi')
+                            ->label('Version DOI')
+                            ->placeholder('Not minted'),
+                        TextEntry::make('doi_base')
+                            ->label('Base DOI (latest)')
+                            ->state(fn (Collection $record) => $record->lineageRoot()->doi_base)
+                            ->placeholder('Not minted'),
                     ])
                     ->columns(2),
                 Section::make('Display Image')
@@ -217,6 +229,7 @@ public static function table(Table $table): Table
                         'EMBARGO' => 'warning',
                         'PUBLISHED' => 'success',
                         'REJECTED' => 'danger',
+                        'SUPERSEDED' => 'gray',
                         default => 'gray',
                     }),
             ])

app/Filament/Dashboard/Resources/CollectionResource/Pages/ViewCollection.php

@@ -4,6 +4,11 @@
 
 use App\Filament\Dashboard\Resources\CollectionResource;
 use App\Filament\Dashboard\Resources\CollectionResource\Widgets\CollectionStats;
+use App\Models\Collection;
+use App\Services\CollectionVersioning\CollectionVersionCreator;
+use App\Services\CollectionVersioning\CollectionVersionImporter;
+use Filament\Actions\Action;
+use Filament\Notifications\Notification;
 use Filament\Resources\Pages\ViewRecord;
 
 class ViewCollection extends ViewRecord
@@ -16,4 +21,80 @@ protected function getHeaderWidgets(): array
             CollectionStats::class,
         ];
     }
+
+    protected function getHeaderActions(): array
+    {
+        return [
+            Action::make('createNewVersion')
+                ->label('Create new version')
+                ->icon('heroicon-o-document-duplicate')
+                ->visible(fn (Collection $record) => $record->is_latest
+                    && $record->status === 'PUBLISHED'
+                    && ! $record->isVersionMigrationActive())
+                ->requiresConfirmation()
+                ->modalHeading('Create new collection version')
+                ->modalDescription('This clones metadata into a new DRAFT version with the same CNPC identifier. Import CSV entries, then use Preview and Process new version.')
+                ->action(function (Collection $record, CollectionVersionCreator $creator) {
+                    $new = $creator->createFrom($record);
+                    Notification::make()
+                        ->title('New version created')
+                        ->body("Version {$new->version} is ready for CSV import.")
+                        ->success()
+                        ->send();
+
+                    $this->redirect(CollectionResource::getUrl('view', ['record' => $new]));
+                }),
+            Action::make('previewVersionMigration')
+                ->label('Preview migration')
+                ->icon('heroicon-o-eye')
+                ->visible(fn (Collection $record) => $record->version_migration_status === Collection::VERSION_MIGRATION_PENDING)
+                ->action(function (Collection $record, CollectionVersionImporter $importer) {
+                    try {
+                        $preview = $importer->preview($record);
+                        Notification::make()
+                            ->title('Migration preview')
+                            ->body(sprintf(
+                                'Dropped: %d | Retained: %d | New: %d | Revoke candidates: %d',
+                                $preview['old_only_count'],
+                                $preview['retained_count'],
+                                $preview['new_only_count'],
+                                $preview['revoke_candidate_count'],
+                            ))
+                            ->info()
+                            ->send();
+                    } catch (\Throwable $e) {
+                        Notification::make()->title('Preview failed')->body($e->getMessage())->danger()->send();
+                    }
+                }),
+            Action::make('processNewVersion')
+                ->label('Process new version')
+                ->icon('heroicon-o-play')
+                ->color('success')
+                ->visible(fn (Collection $record) => in_array($record->version_migration_status, [
+                    Collection::VERSION_MIGRATION_PENDING,
+                    Collection::VERSION_MIGRATION_PROCESSING,
+                ], true))
+                ->requiresConfirmation()
+                ->modalHeading('Process collection version migration')
+                ->modalDescription('This validates entries, diffs by standardized SMILES, migrates live data, revokes dropped exclusive molecules, and archives the previous version.')
+                ->action(function (Collection $record, CollectionVersionImporter $importer) {
+                    try {
+                        $result = $importer->import($record);
+                        Notification::make()
+                            ->title('Version migration completed')
+                            ->body(sprintf(
+                                'Revoked: %d | Retained: %d | New: %d',
+                                $result['revoked'],
+                                $result['retained'],
+                                $result['new_only'],
+                            ))
+                            ->success()
+                            ->send();
+                        $this->redirect(CollectionResource::getUrl('view', ['record' => $record->fresh()]));
+                    } catch (\Throwable $e) {
+                        Notification::make()->title('Migration failed')->body($e->getMessage())->danger()->send();
+                    }
+                }),
+        ];
+    }
 }

app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php

@@ -151,6 +151,10 @@ public function table(Table $table): Table
                     ->label('Reference ID')
                     ->searchable(),
                 TextColumn::make('status'),
+                TextColumn::make('is_archived')
+                    ->label('Archived')
+                    ->badge()
+                    ->toggleable(isToggledHiddenByDefault: true),
             ])
             ->filters([
                 SelectFilter::make('status')
@@ -165,11 +169,16 @@ public function table(Table $table): Table
             ->headerActions([
                 ImportAction::make()
                     ->importer(EntryImporter::class)
+                    ->hidden(fn () => $this->ownerRecord->status === 'SUPERSEDED')
                     ->options([
                         'collection_id' => $this->ownerRecord->id,
                     ]),
                 Action::make('process')
                     ->hidden(function () {
+                        if ($this->ownerRecord->isVersionMigrationActive()) {
+                            return true;
+                        }
+
                         return $this->ownerRecord->entries()->where('status', 'SUBMITTED')->count() < 1;
                     })
                     ->action(function () {
@@ -190,9 +199,11 @@ public function table(Table $table): Table
                 ViewAction::make()
                     ->iconButton(),
                 EditAction::make()
-                    ->iconButton(),
+                    ->iconButton()
+                    ->hidden(fn () => $this->ownerRecord->status === 'SUPERSEDED'),
                 DeleteAction::make()
-                    ->iconButton(),
+                    ->iconButton()
+                    ->hidden(fn () => $this->ownerRecord->status === 'SUPERSEDED'),
             ])
             ->toolbarActions([
                 BulkActionGroup::make([

app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php

@@ -14,11 +14,17 @@
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Model;
 
 class MoleculesRelationManager extends RelationManager
 {
     protected static string $relationship = 'molecules';
 
+    public static function canViewForRecord(Model $ownerRecord, string $pageClass): bool
+    {
+        return $ownerRecord->status !== 'SUPERSEDED';
+    }
+
     public function form(Schema $schema): Schema
     {
         return $schema

app/Filament/Dashboard/Widgets/DashboardStats.php

@@ -24,7 +24,7 @@ protected function getStats(): array
         });
 
         $totalCollections = Cache::flexible('stats.collections', [172800, 259200], function () {
-            return DB::table('collections')->selectRaw('count(*)')->whereRaw("status = 'PUBLISHED'")->get()[0]->count;
+            return DB::table('collections')->selectRaw('count(*)')->whereRaw("status = 'PUBLISHED'")->where('is_latest', true)->get()[0]->count;
         });
 
         $uniqueOrganisms = Cache::flexible('stats.organisms', [172800, 259200], function () {

app/Helper.php

@@ -75,6 +75,7 @@ function getCollectionStatuses()
         'EMBARGO' => 'Embargo',
         'PUBLISHED' => 'Published',
         'REJECTED' => 'Rejected',
+        'SUPERSEDED' => 'Superseded',
     ];
 }
 

app/Http/Controllers/CollectionController.php

@@ -18,19 +18,33 @@ public function __invoke(Request $request, $id)
         }
 
         $collection = Cache::flexible('collections.'.$id, [172800, 259200], function () use ($id) {
-            return Collection::where('identifier', $id)->first();
+            return Collection::query()
+                ->where('identifier', $id)
+                ->orderByDesc('is_latest')
+                ->orderByDesc('version')
+                ->first();
         });
 
         if (! $collection) {
             abort(404);
         }
 
+        $latest = $collection->is_latest
+            ? $collection
+            : ($collection->lineageVersionsQuery()->where('is_latest', true)->first() ?? $collection);
+
         $query = [
             'type' => 'tags',
-            'q' => str_replace(' ', '+', $collection->title),
+            'q' => str_replace(' ', '+', $latest->title),
             'tagType' => 'dataSource',
         ];
 
+        if ($request->has('version')) {
+            $query['version'] = (int) $request->query('version');
+        } elseif (! $collection->is_latest) {
+            $query['version'] = $collection->version;
+        }
+
         $baseUrl = config('app.url');
 
         return redirect()->to($baseUrl.'/search?'.http_build_query($query));

app/Livewire/CollectionList.php

@@ -41,6 +41,7 @@ public function render()
         // $search = strtolower($this->query ?? '');
         $query = Collection::query()
             ->where('status', 'PUBLISHED')
+            ->where('is_latest', true)
             ->where(function ($query) use ($search) {
                 $query->whereRaw('LOWER(title) ILIKE ?', ['%'.$search.'%'])
                     ->orWhereRaw('LOWER(description) ILIKE ?', ['%'.$search.'%']);