Merge pull request #19 from BiodataMiningGroup/develop

Develop

composer.json

@@ -1,7 +1,8 @@
 {
     "name": "biigle/largo",
     "require": {
-        "biigle/volumes": "~1.1",
+        "biigle/label-trees": "~1.3",
+        "biigle/volumes": "~1.5",
         "intervention/image": "~2.1",
         "intervention/imagecache": "~2.1"
     },

gulpfile.js

@@ -19,24 +19,19 @@ gulp.task('sass-annotations', function () {
 gulp.task('sass', ['sass-main', 'sass-annotations']);
 
 gulp.task('js-main', function (cb) {
-   h.angular('largo/**/*.js', 'main.js', cb);
-});
-
-gulp.task('js-project-largo', function (cb) {
-   h.angular('project-largo/**/*.js', 'project-largo.js', cb);
+   h.angular('vue/**/*.js', 'main.js', cb);
 });
 
 gulp.task('js-annotations', function (cb) {
    h.angular('annotations/**/*.js', 'annotations.js', cb);
 });
 
-gulp.task('js', ['js-main', 'js-project-largo', 'js-annotations']);
+gulp.task('js', ['js-main', 'js-annotations']);
 
 gulp.task('watch', function () {
-    gulp.watch(h.paths.sass + 'main.scss', ['sass-main']);
+    gulp.watch(h.paths.sass + '**/*.scss', ['sass-main']);
     gulp.watch(h.paths.sass + 'annotations.scss', ['sass-annotations']);
-    gulp.watch(h.paths.js + 'largo/**/*.js', ['js-main']);
-    gulp.watch(h.paths.js + 'project-largo/**/*.js', ['js-project-largo']);
+    gulp.watch(h.paths.js + 'vue/**/*.js', ['js-main']);
     gulp.watch(h.paths.js + 'annotations/**/*.js', ['js-annotations']);
     gulp.watch(h.paths.public + '**/*', publish);
 });

src/Console/Commands/Config.php

@@ -5,8 +5,8 @@
 use Illuminate\Console\Command;
 use Biigle\Modules\Largo\LargoServiceProvider as ServiceProvider;
 
-class Config extends Command {
-
+class Config extends Command
+{
     /**
      * The console command name.
      *

src/Console/Commands/Publish.php

@@ -5,8 +5,8 @@
 use Illuminate\Console\Command;
 use Biigle\Modules\Largo\LargoServiceProvider as ServiceProvider;
 
-class Publish extends Command {
-
+class Publish extends Command
+{
     /**
      * The console command name.
      *

src/Http/Controllers/Api/LargoController.php

@@ -19,7 +19,7 @@
 class LargoController extends Controller
 {
     /**
-     * Show the patch image of an annotation
+     * Show the patch image of an annotation.
      *
      * @api {get} annotations/:id/patch Get an annotation patch
      * @apiGroup Annotations
@@ -47,9 +47,8 @@ public function showPatch($id)
         }
     }
 
-
     /**
-     * Save changes of an Largo session for a volume
+     * Save changes of an Largo session for a volume.
      *
      * @api {post} volumes/:id/largo Save Largo session
      * @apiGroup Largo
@@ -143,7 +142,7 @@ public function saveVolume(Request $request, Guard $auth, $id)
     }
 
     /**
-     * Save changes of an Largo session for a project
+     * Save changes of an Largo session for a project.
      *
      * @api {post} projects/:id/largo Save Largo session
      * @apiGroup Largo
@@ -210,7 +209,7 @@ public function saveProject(Request $request, Guard $auth, $id)
     }
 
     /**
-     * Validates the input for saving an Largo session
+     * Validates the input for saving an Largo session.
      *
      * @param Request $request
      */
@@ -223,7 +222,7 @@ protected function validateLargoInput(Request $request)
     }
 
     /**
-     * Get a list of unique annotation IDs that are either dismissed or changed
+     * Get a list of unique annotation IDs that are either dismissed or changed.
      *
      * @param array $dismissed Array of all dismissed annotation IDs for each label
      * @param array $changed Array of IDs of changed annotations
@@ -240,7 +239,7 @@ protected function getAffectedAnnotations($dismissed, $changed)
     }
 
     /**
-     * Check if all given annotations belong to the given volumes
+     * Check if all given annotations belong to the given volumes.
      *
      * @param array $annotations Annotation IDs
      * @param array $volumes Volume IDs
@@ -256,7 +255,7 @@ protected function anotationsBelongToVolumes($annotations, $volumes)
     }
 
     /**
-     * Returns the IDs of all label trees that must be available to apply the changes
+     * Returns the IDs of all label trees that must be available to apply the changes.
      *
      * @param array $changed Array of IDs of changed annotations
      *
@@ -270,7 +269,7 @@ protected function getRequiredLabelTrees($changed)
     }
 
     /**
-     * Apply the changes of an Largo session
+     * Apply the changes of an Largo session.
      *
      * Removes the dismissed annotation labels and creates the changed annotation labels.
      *

src/Http/Controllers/Api/ProjectsAnnotationsController.php

@@ -3,15 +3,14 @@
 namespace Biigle\Modules\Largo\Http\Controllers\Api;
 
 use Biigle\Project;
-use Biigle\Volume;
 use Biigle\Annotation;
 use Illuminate\Http\Request;
 use Biigle\Http\Controllers\Api\Controller;
 
 class ProjectsAnnotationsController extends Controller
 {
     /**
-     * Show all annotations of the project that have a specific label attached
+     * Show all annotations of the project that have a specific label attached.
      *
      * @api {get} projects/:tid/annotations/filter/label/:lid Get annotations with a specific label
      * @apiGroup Projects
@@ -48,5 +47,4 @@ public function filter(Request $request, $pid, $lid)
             })
             ->pluck('annotations.id');
     }
-
 }

src/Http/Controllers/Api/VolumesAnnotationsController.php

@@ -11,7 +11,7 @@
 class VolumesAnnotationsController extends Controller
 {
     /**
-     * Show all annotations of the volume that have a specific label attached
+     * Show all annotations of the volume that have a specific label attached.
      *
      * @api {get} volumes/:tid/annotations/filter/label/:lid Get annotations with a specific label
      * @apiGroup Volumes
@@ -57,5 +57,4 @@ public function filter(Request $request, Guard $auth, $tid, $lid)
             })
             ->pluck('annotations.id');
     }
-
 }

src/Http/Controllers/Views/LargoController.php

@@ -2,19 +2,17 @@
 
 namespace Biigle\Modules\Largo\Http\Controllers\Views;
 
-use DB;
 use Biigle\Role;
 use Biigle\Project;
 use Biigle\Volume;
 use Biigle\LabelTree;
-use Biigle\Annotation;
 use Illuminate\Contracts\Auth\Guard;
 use Biigle\Http\Controllers\Views\Controller;
 
 class LargoController extends Controller
 {
     /**
-     * Show the the Largo view for a volume
+     * Show the the Largo view for a volume.
      *
      * @param Guard $auth
      * @param int $id Volume ID
@@ -53,7 +51,7 @@ public function indexVolume(Guard $auth, $id)
             })
             ->get();
 
-        return view('largo::index', [
+        return view('largo::show', [
             'user' => $user,
             'volume' => $volume,
             'projects' => $projects,
@@ -62,7 +60,7 @@ public function indexVolume(Guard $auth, $id)
     }
 
     /**
-     * Show the Largo view for a project
+     * Show the Largo view for a project.
      *
      * @param Guard $auth
      * @param int $id Project ID

src/Http/routes.php

@@ -2,7 +2,7 @@
 
 $router->group([
     'namespace' => 'Views',
-    'middleware' => 'auth'
+    'middleware' => 'auth',
 ], function ($router) {
     $router->get('volumes/{id}/largo', [
         'as'   => 'largo',

src/Jobs/GenerateAnnotationPatch.php

@@ -16,7 +16,7 @@ class GenerateAnnotationPatch extends Job implements ShouldQueue
     use InteractsWithQueue;
 
     /**
-     * The ID of the annotation to generate a patch for
+     * The ID of the annotation to generate a patch for.
      *
      * @var int
      */

src/Jobs/RemoveAnnotationPatches.php

@@ -15,14 +15,14 @@ class RemoveAnnotationPatches extends Job implements ShouldQueue
     use InteractsWithQueue, SerializesModels;
 
     /**
-     * The volume ID of which the annotation patches should be removed
+     * The volume ID of which the annotation patches should be removed.
      *
      * @var int
      */
     private $volumeId;
 
     /**
-     * The annotation IDs whose patches should be removed
+     * The annotation IDs whose patches should be removed.
      *
      * @var array
      */

src/LargoServiceProvider.php

@@ -7,8 +7,8 @@
 use Biigle\Modules\Largo\Listeners\ImagesCleanupListener;
 use Biigle\Services\Modules;
 
-class LargoServiceProvider extends ServiceProvider {
-
+class LargoServiceProvider extends ServiceProvider
+{
     /**
      * Bootstrap the application events.
      *
@@ -40,7 +40,7 @@ public function boot(Modules $modules, Router $router)
 
         \Event::listen('images.cleanup', ImagesCleanupListener::class);
 
-        $modules->addMixin('largo', 'volumesMenubar');
+        $modules->addMixin('largo', 'volumesSidebar');
         $modules->addMixin('largo', 'annotationsScripts');
         $modules->addMixin('largo', 'annotationsStyles');
         $modules->addMixin('largo', 'annotationsSidebar');

src/Observers/AnnotationObserver.php

@@ -9,11 +9,10 @@
 
 class AnnotationObserver
 {
-
     use DispatchesJobs;
 
     /**
-     * Handle the event of creating/saving a single annotation
+     * Handle the event of creating/saving a single annotation.
      *
      * @param Annotation $annotation
      */
@@ -25,7 +24,7 @@ public function saved(Annotation $annotation)
     }
 
     /**
-     * Handle the event of deleting a single annotation
+     * Handle the event of deleting a single annotation.
      *
      * @param Annotation $annotation
      * @return bool