Merge pull request #558 from NFDI4Chem/development

fix: enabled nmrium data versioning defaults to 3
NFDI4Chem · Nov 4, 2022 · a8c3656 · a8c3656
2 parents f3af0b8 + 04ba04f
commit a8c3656
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Showing 20 changed files with 219 additions and 31 deletions.
diff --git a/app/Actions/Fortify/UpdateUserProfileInformation.php b/app/Actions/Fortify/UpdateUserProfileInformation.php
@@ -20,6 +20,7 @@ public function update($user, array $input)
     {
         Validator::make($input, [
             'first_name' => ['required', 'string', 'max:255'],
+            'name' => ['nullable', 'string', 'max:255'],
             'last_name' => ['required', 'string', 'max:255'],
             'email' => ['required', 'email', 'max:255', Rule::unique('users')->ignore($user->id)],
             'username' => ['required', 'string', 'max:255', Rule::unique('users')->ignore($user->id)],
@@ -38,6 +39,7 @@ public function update($user, array $input)
                 'first_name' => $input['first_name'],
                 'last_name' => $input['last_name'],
                 'username' => $input['username'],
+                'name' => $input['username'] ? $input['username'] : $user->name,
                 'email' => $input['email'],
             ])->save();
         }
@@ -55,6 +57,7 @@ protected function updateVerifiedUser($user, array $input)
         $user->forceFill([
             'first_name' => $input['first_name'],
             'last_name' => $input['last_name'],
+            'name' => $input['name'] ? $input['name'] : $user->name,
             'username' => $input['username'],
             'email' => $input['email'],
             'email_verified_at' => null,

diff --git a/app/Actions/Project/UpdateProject.php b/app/Actions/Project/UpdateProject.php
@@ -126,7 +126,7 @@ public function update(Project $project, array $input)
 
             $draft = $project->draft;
 
-            if($draft){
+            if ($draft) {
                 $draft->name = $project->name;
                 $draft->slug = $project->slug;
                 $draft->description = $project->description;

diff --git a/app/Console/Commands/AssignIdentifiers.php b/app/Console/Commands/AssignIdentifiers.php
@@ -33,7 +33,7 @@ public function handle(DOIService $doiService)
     {
         return DB::transaction(function () use ($doiService) {
             $projects = Project::where([
-                ['is_public', true]
+                ['is_public', true],
             ])->get();
             foreach ($projects as $project) {
                 $projectIdentifier = $project->identifier ? $project->identifier : null;

diff --git a/app/Http/Controllers/DatasetController.php b/app/Http/Controllers/DatasetController.php
@@ -46,6 +46,7 @@ public function nmriumInfo(Request $request, Dataset $dataset)
             $nmriumInfo = $spectra;
             $molecules = $request->get('molecules');
             $molecularInfo = $molecules;
+            $version = $request->get('version');
 
             $nmrium = $dataset->nmrium;
             if ($nmrium) {
@@ -60,6 +61,10 @@ public function nmriumInfo(Request $request, Dataset $dataset)
                 $nmriumData['molecules'] = $molecularInfo;
             }
 
+            if ($version && ! empty($version)) {
+                $nmriumData['version'] = $version;
+            }
+
             if (! empty($nmriumData)) {
                 if ($nmrium) {
                     $nmrium->nmrium_info = $nmriumData;

diff --git a/app/Http/Middleware/HandleInertiaRequests.php b/app/Http/Middleware/HandleInertiaRequests.php
@@ -4,6 +4,7 @@
 
 use App\Models\Announcement;
 use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Schema;
 use Inertia\Middleware;
 
 class HandleInertiaRequests extends Middleware
@@ -61,7 +62,7 @@ public function share(Request $request)
             'twitter' => (env('TWITTER_CLIENT_ID') !== null && env('TWITTER_CLIENT_ID') !== ''),
             'github' => (env('GITHUB_CLIENT_ID') !== null && env('GITHUB_CLIENT_ID') !== ''),
             'orcid' => (env('ORCID_CLIENT_ID') !== null && env('ORCID_CLIENT_ID') !== ''),
-            'config.announcements' => Announcement::active(),
+            'config.announcements' => Schema::hasTable('announcements') ? Announcement::active() : null,
             'url' => env('APP_URL'),
             'nmriumURL' => env('NMRIUM_URL'),
             'team' => $user ? $user->currentTeam : null,

diff --git a/app/Providers/JetstreamServiceProvider.php b/app/Providers/JetstreamServiceProvider.php
@@ -49,7 +49,7 @@ public function boot()
      */
     protected function configurePermissions()
     {
-        Jetstream::defaultApiTokenPermissions(['read']);
+        Jetstream::defaultApiTokenPermissions(['project:read']);
 
         Jetstream::role('owner', 'Owner', [
             'project:create',

diff --git a/composer.json b/composer.json
@@ -39,6 +39,7 @@
         "tightenco/ziggy": "^1.0"
     },
     "require-dev": {
+        "brianium/paratest": "^6.6",
         "fakerphp/faker": "^1.9.1",
         "laravel/pint": "^1.0",
         "laravel/sail": "^1.15",

diff --git a/composer.lock b/composer.lock
diff --git a/database/factories/UserFactory.php b/database/factories/UserFactory.php
@@ -26,8 +26,11 @@ public function definition()
     {
         return [
             'name' => $this->faker->name(),
+            'first_name' => $this->faker->firstName(),
+            'last_name' => $this->faker->lastName(),
             'email' => $this->faker->unique()->safeEmail(),
             'email_verified_at' => now(),
+            'username' => $this->faker->userName(),
             'password' => '$2y$10$92IXUNpkjO0rOQ5byMi.Ye4oKoEa3Ro9llC/.og/at2.uheWG/igi', // password
             'remember_token' => Str::random(10),
         ];

diff --git a/phpunit.xml b/phpunit.xml
@@ -21,8 +21,8 @@
         <server name="APP_ENV" value="testing"/>
         <server name="BCRYPT_ROUNDS" value="4"/>
         <server name="CACHE_DRIVER" value="array"/>
-        <server name="DB_CONNECTION" value="sqlite"/> 
-        <server name="DB_DATABASE" value=":memory:"/>
+        <env name="DB_CONNECTION" value="pgsql"/>
+        <env name="DB_DATABASE" value="testing"/>
         <server name="MAIL_MAILER" value="array"/>
         <server name="QUEUE_CONNECTION" value="sync"/>
         <server name="SESSION_DRIVER" value="array"/>

diff --git a/resources/js/Shared/SpectraEditor.vue b/resources/js/Shared/SpectraEditor.vue
@@ -363,6 +363,7 @@ export default {
             currentMolecules: [],
             reset: false,
             info: null,
+            version: null,
         };
     },
     computed: {
@@ -395,6 +396,7 @@ export default {
                         this.saveStudyPreview(e.data.data.data);
                     }
                 }
+                this.version = e.data.data.version;
                 if (e.data.type == "nmr-wrapper:data-change") {
                     let actionType = e.data.data.actionType;
                     // console.log(actionType);
@@ -479,6 +481,10 @@ export default {
                             if (spectra && spectra.length <= 0) {
                                 this.loadFromURL(url);
                             } else {
+                                let nmriumVersion = 3;
+                                if (nmrium_info && nmrium_info["version"]) {
+                                    nmriumVersion = nmrium_info["version"]
+                                }
                                 let mols = [];
                                 if (this.isString(nmrium_info.molecules)) {
                                     mols = JSON.parse(nmrium_info.molecules);
@@ -496,6 +502,7 @@ export default {
                                     data: {
                                         spectra: spectra,
                                         molecules: mols,
+                                        version: nmriumVersion
                                     },
                                     type: "nmrium",
                                 };
@@ -547,6 +554,7 @@ export default {
                         {
                             spectra: this.selectedSpectraData,
                             molecules: this.currentMolecules,
+                            version: this.version ? this.version : 3
                         }
                     )
                     .catch((err) => {

diff --git a/resources/js/Shared/SpectraViewer.vue b/resources/js/Shared/SpectraViewer.vue
@@ -351,6 +351,10 @@ export default {
                                 nmrium_info = JSON.parse(
                                     response.data.nmrium_info
                                 );
+                                let nmriumVersion = 3;
+                                if (nmrium_info && nmrium_info["version"]) {
+                                    nmriumVersion = nmrium_info["version"]
+                                }
                                 if (nmrium_info && nmrium_info["spectra"]) {
                                     if (this.isString(nmrium_info["spectra"])) {
                                         spectra = JSON.parse(
@@ -378,11 +382,11 @@ export default {
                                                 "\n" + mol.molfile + "\n";
                                         });
                                     }
-
                                     let data = {
                                         data: {
                                             spectra: spectra,
                                             molecules: mols,
+                                            version: nmriumVersion
                                         },
                                         type: "nmrium",
                                     };

diff --git a/routes/web.php b/routes/web.php
@@ -220,8 +220,10 @@
             Route::put('users/edit/{user}/password', [UsersController::class, 'updatePassword'])
             ->name('console.users.update-password');
 
-            Route::put('users/edit/{user}/role', [UsersController::class, 'updateRole'])
-            ->name('console.users.update-role');
+            Route::group(['middleware' => ['permission:manage roles']], function () {
+                Route::put('users/edit/{user}/role', [UsersController::class, 'updateRole'])
+                ->name('console.users.update-role');
+            });
 
             Route::delete('users/edit/{user}/photo', [UsersController::class, 'destroyPhoto'])
             ->name('console.users.destroy-photo');

diff --git a/tests/Feature/ApiTokenPermissionsTest.php b/tests/Feature/ApiTokenPermissionsTest.php
@@ -27,19 +27,18 @@ public function test_api_token_permissions_can_be_updated()
         $token = $user->tokens()->create([
             'name' => 'Test Token',
             'token' => Str::random(40),
-            'abilities' => ['create', 'read'],
+            'abilities' => ['project:create', 'project:read'],
         ]);
 
         $response = $this->put('/user/api-tokens/'.$token->id, [
             'name' => $token->name,
             'permissions' => [
-                'delete',
-                'missing-permission',
+                'project:delete',
             ],
         ]);
 
-        $this->assertTrue($user->fresh()->tokens->first()->can('delete'));
-        $this->assertFalse($user->fresh()->tokens->first()->can('read'));
-        $this->assertFalse($user->fresh()->tokens->first()->can('missing-permission'));
+        $this->assertTrue($user->fresh()->tokens->first()->can('project:delete'));
+        $this->assertFalse($user->fresh()->tokens->first()->can('project:read'));
+        $this->assertFalse($user->fresh()->tokens->first()->can('project:missing-permission'));
     }
 }