Merge pull request #1018 from biigle/merge-sync

Merge biigle/sync

app/Console/Commands/SyncPrune.php

@@ -0,0 +1,33 @@
+<?php
+
+namespace Biigle\Console\Commands;
+
+use Biigle\Services\Import\ArchiveManager;
+use Illuminate\Console\Command;
+
+class SyncPrune extends Command
+{
+    /**
+     * The console command name.
+     *
+     * @var string
+     */
+    protected $name = 'sync:prune';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Delete uploaded import files that are older than one week and where the import was not finished.';
+
+    /**
+     * Execute the command.
+     *
+     * @return void
+     */
+    public function handle(ArchiveManager $manager)
+    {
+        $manager->prune();
+    }
+}

app/Console/Commands/SyncUuids.php

@@ -0,0 +1,123 @@
+<?php
+
+namespace Biigle\Console\Commands;
+
+use Biigle\User;
+use File;
+use Hash;
+use Illuminate\Console\Command;
+
+class SyncUuids extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'sync:uuids
+        {file? : If a file is provided, use it for syncing. If not, output the contents of such a file.}
+        {--dry-run : Do not change the database records}
+        {--force : Synchronise matching users without asking}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Synchronize user UUIDs across BIIGLE instances';
+
+    /**
+     * Execute the command.
+     *
+     * @return void
+     */
+    public function handle()
+    {
+        if ($this->argument('file')) {
+            $this->handleSync();
+        } else {
+            $this->generateOutput();
+        }
+    }
+
+    /**
+     * Read the input file and perform interactive synchronization of user UUIDs.
+     */
+    protected function handleSync()
+    {
+        $matches = 0;
+        $input = collect(json_decode(File::get($this->argument('file')), true));
+        $inputUuids = $input->pluck('uuid');
+
+        // All users with a UUID not among those of the input are candidates for syncing.
+        $users = User::select('id', 'email', 'firstname', 'lastname')
+            ->whereNotIn('uuid', $inputUuids)
+            ->get();
+
+        // Remove input users with a UUID already in the database as they should not be
+        // considered for syncing.
+        $input = $input->whereNotIn('uuid', User::whereIn('uuid', $inputUuids)->pluck('uuid'));
+
+        // Find matches and sync.
+        foreach ($users as $user) {
+            foreach ($input as $inputUser) {
+                $emailMatches = Hash::check($user->email, $inputUser['email']);
+                $nameMatches = Hash::check($user->firstname, $inputUser['firstname']) && Hash::check($user->lastname, $inputUser['lastname']);
+
+                if ($emailMatches || $nameMatches) {
+                    $matches += 1;
+                }
+
+                $sync = false;
+                if ($emailMatches && $nameMatches) {
+                    $this->info("Found matching email address and name for {$user->firstname} {$user->lastname} ({$user->email}).");
+                    $sync = $this->option('force') || $this->confirm("Synchronize UUID with file?");
+                } elseif ($emailMatches) {
+                    $this->info("Found matching email address but different name for {$user->firstname} {$user->lastname} ({$user->email}).");
+                    $sync = $this->option('force') || $this->confirm("Synchronize UUID with file?");
+                } elseif ($nameMatches) {
+                    $this->info("Found matching name but different email address for {$user->firstname} {$user->lastname} ({$user->email}).");
+                    $sync = $this->option('force') || $this->confirm("Synchronize UUID with file?");
+                }
+
+                if ($sync) {
+                    $user->uuid = $inputUser['uuid'];
+                    if (!$this->option('dry-run')) {
+                        $user->save();
+                    }
+                    $this->warn("UUID synchronized for {$user->firstname} {$user->lastname} ({$user->email}).");
+                    break;
+                }
+            }
+        }
+
+        if ($matches === 0) {
+            $this->info('No candidates found');
+        } else {
+            $this->info('Finished');
+        }
+    }
+
+    /**
+     * Generate the output that can be used as file to synchronize user UUIDs.
+     */
+    protected function generateOutput()
+    {
+        $users = User::select('uuid', 'firstname', 'lastname', 'email')->get();
+        $bar = $this->output->createProgressBar($users->count());
+        $users =
+            $users->map(function ($user) use ($bar) {
+                $bar->advance();
+
+                return [
+                    'uuid' => $user->uuid,
+                    'firstname' => Hash::make($user->firstname),
+                    'lastname' => Hash::make($user->lastname),
+                    'email' => Hash::make($user->email),
+                ];
+            })->toJson(JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE);
+        $bar->finish();
+
+        echo $users;
+    }
+}

app/Console/Kernel.php

@@ -54,6 +54,10 @@ protected function schedule(Schedule $schedule): void
             ->withoutOverlapping()
             ->onOneServer();
 
+        $schedule->command('sync:prune')
+            ->daily()
+            ->onOneServer();
+
         // Insert scheduled tasks here.
     }
 

app/Http/Controllers/Api/Export/Controller.php

@@ -0,0 +1,79 @@
+<?php
+
+namespace Biigle\Http\Controllers\Api\Export;
+
+use Biigle\Http\Controllers\Api\Controller as BaseController;
+use Illuminate\Http\Request;
+
+abstract class Controller extends BaseController
+{
+    /**
+     * Creates a new instance.
+     */
+    public function __construct()
+    {
+        $this->middleware('can:sudo');
+    }
+
+    /**
+     * Handle a generic export request.
+     *
+     * @param Request $request
+     * @return \Symfony\Component\HttpFoundation\BinaryFileResponse
+     */
+    public function show(Request $request)
+    {
+        if (!$this->isAllowed()) {
+            abort(404);
+        }
+
+        $this->validate($request, ['except' => 'filled', 'only' => 'filled']);
+        $query = $this->getQuery();
+
+        if ($request->filled('except')) {
+            $query = $query->whereNotIn('id', explode(',', $request->input('except')));
+        } elseif ($request->filled('only')) {
+            $query = $query->whereIn('id', explode(',', $request->input('only')));
+        }
+
+        $export = $this->getExport($query->pluck('id')->toArray());
+
+        return response()
+            ->download($export->getArchive(), $this->getExportFilename(), [
+                'Content-Type' => 'application/zip',
+            ])
+            ->deleteFileAfterSend(true);
+    }
+
+    /**
+     * Get the query for the model to export.
+     *
+     * @return \Illuminate\Database\Query\Builder
+     */
+    abstract protected function getQuery();
+
+    /**
+     * Get the new export instance.
+     *
+     * @param array $ids
+     * @return \Biigle\Services\Export\Export
+     */
+    abstract protected function getExport(array $ids);
+
+    /**
+     * Get the filename of the export archive.
+     *
+     * @return string
+     */
+    abstract protected function getExportFilename();
+
+    /**
+     * Determine if this kind of export is allowed by the config.
+     *
+     * @return bool
+     */
+    protected function isAllowed()
+    {
+        return false;
+    }
+}

app/Http/Controllers/Api/Export/LabelTreeExportController.php

@@ -0,0 +1,52 @@
+<?php
+
+namespace Biigle\Http\Controllers\Api\Export;
+
+use Biigle\LabelTree;
+use Biigle\Services\Export\LabelTreeExport;
+
+class LabelTreeExportController extends Controller
+{
+    /**
+     * @api {get} export/label-trees Get a label tree export
+     * @apiGroup Sync
+     * @apiName ShowLabelTreeExport
+     *
+     * @apiParam (Optional arguments) {String} except Comma separated IDs of the label trees that should not be included in the export file.
+     * @apiParam (Optional arguments) {String} only Comma separated IDs of the label trees that should only be included in the export file.
+     * @apiDescription The response is a ZIP archive that can be used for the label tree import. By default all label trees are exported.
+     * @apiPermission admin
+     */
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getQuery()
+    {
+        return LabelTree::getQuery();
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getExport(array $ids)
+    {
+        return new LabelTreeExport($ids);
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getExportFilename()
+    {
+        return 'biigle_label_tree_export.zip';
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function isAllowed()
+    {
+        return in_array('labelTrees', config('sync.allowed_exports'));
+    }
+}

app/Http/Controllers/Api/Export/PublicLabelTreeExportController.php

@@ -0,0 +1,36 @@
+<?php
+
+namespace Biigle\Http\Controllers\Api\Export;
+
+use Biigle\Http\Controllers\Api\Controller as BaseController;
+use Biigle\Http\Requests\ShowPublicLabelTreeExport;
+use Biigle\Services\Export\PublicLabelTreeExport;
+
+class PublicLabelTreeExportController extends BaseController
+{
+    /**
+     * Handle a public label tree export request.
+     *
+     * @api {get} public-export/label-trees/:id Download a label tree
+     * @apiGroup Sync
+     * @apiName ShowPublicLabelTreeExport
+     * @apiDescription The response is a ZIP archive that contains a JSON file with label tree attributes and a CSV file with label attributes.
+     *
+     * @apiParam {Number} id The label tree ID
+     *
+     * @apiPermission labelTreeMemberIfPrivate
+     *
+     * @param ShowPublicLabelTreeExport $request
+     * @return \Symfony\Component\HttpFoundation\BinaryFileResponse
+     */
+    public function show(ShowPublicLabelTreeExport $request)
+    {
+        $export = new PublicLabelTreeExport([$request->tree->id]);
+
+        return response()
+            ->download($export->getArchive(), 'biigle_label_tree_export.zip', [
+                'Content-Type' => 'application/zip',
+            ])
+            ->deleteFileAfterSend(true);
+    }
+}

app/Http/Controllers/Api/Export/UserExportController.php

@@ -0,0 +1,52 @@
+<?php
+
+namespace Biigle\Http\Controllers\Api\Export;
+
+use Biigle\Services\Export\UserExport;
+use Biigle\User;
+
+class UserExportController extends Controller
+{
+    /**
+     * @api {get} export/users Get a user export
+     * @apiGroup Sync
+     * @apiName ShowUserExport
+     *
+     * @apiParam (Optional arguments) {String} except Comma separated IDs of the users that should not be included in the export file.
+     * @apiParam (Optional arguments) {String} only Comma separated IDs of the users that should only be included in the export file.
+     * @apiDescription The response is a ZIP archive that can be used for the user import. By default all users are exported.
+     * @apiPermission admin
+     */
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getQuery()
+    {
+        return User::getQuery();
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getExport(array $ids)
+    {
+        return new UserExport($ids);
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function getExportFilename()
+    {
+        return 'biigle_user_export.zip';
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    protected function isAllowed()
+    {
+        return in_array('users', config('sync.allowed_exports'));
+    }
+}