Merge pull request #13 from BiodataMiningGroup/annotation-sessions

Annotation sessions
biigle · Oct 20, 2016 · e9e67f7 · e9e67f7
2 parents 76adf4c + 96567cb
commit e9e67f7
Show file tree

Hide file tree

Showing 11 changed files with 128 additions and 42 deletions.
diff --git a/composer.json b/composer.json
@@ -1,7 +1,7 @@
 {
     "name": "dias/ate",
     "require": {
-        "dias/transects": "~1.0",
+        "dias/transects": "~1.1",
         "intervention/image": "~2.1"
     },
     "require-dev": {

diff --git a/src/AteServiceProvider.php b/src/AteServiceProvider.php
@@ -45,7 +45,7 @@ public function boot(Modules $modules, Router $router)
         $modules->addMixin('ate', 'annotationsStyles');
         $modules->addMixin('ate', 'annotationsSidebar');
         $modules->addMixin('ate', 'annotationsSettings');
-        $modules->addMixin('ate', 'projectsShow');
+        $modules->addMixin('ate', 'projectsShowToolbar');
     }
 
     /**

diff --git a/src/Http/Controllers/Api/AteController.php b/src/Http/Controllers/Api/AteController.php
@@ -26,7 +26,7 @@ class AteController extends Controller
      * @apiName ShowAnnotationPatch
      * @apiParam {Number} id The annotation ID.
      * @apiPermission projectMember
-     * @apiDescription Responds with an image file
+     * @apiDescription Responds with an image file. If there is an active annotation session, access to annotations hidden by the session is denied.
      *
      * @param  int  $id
      * @return \Illuminate\Http\Response

diff --git a/src/Http/Controllers/Api/ProjectsAnnotationsController.php b/src/Http/Controllers/Api/ProjectsAnnotationsController.php
@@ -35,17 +35,14 @@ public function filter(Request $request, $pid, $lid)
         $take = $request->input('take');
 
         return Annotation::join('annotation_labels', 'annotations.id', '=', 'annotation_labels.annotation_id')
-            ->whereIn('annotations.image_id', function ($query) use ($pid) {
-                $query->select('id')
-                    ->from('images')
-                    ->whereIn('transect_id', function ($query) use ($pid) {
-                        $query->select('transect_id')
-                            ->from('project_transect')
-                            ->where('project_id', $pid);
-                    });
+            ->join('images', 'annotations.image_id', '=', 'images.id')
+            ->whereIn('images.transect_id', function ($query) use ($pid) {
+                $query->select('transect_id')
+                    ->from('project_transect')
+                    ->where('project_id', $pid);
             })
             ->where('annotation_labels.label_id', $lid)
-            ->when($take !== null, function ($query) use ($take) {
+            ->when(!is_null($take), function ($query) use ($take) {
                 return $query->orderBy('annotations.created_at', 'desc')
                     ->take($take);
             })

diff --git a/src/Http/Controllers/Api/TransectsAnnotationsController.php b/src/Http/Controllers/Api/TransectsAnnotationsController.php
@@ -5,6 +5,7 @@
 use Dias\Transect;
 use Dias\Annotation;
 use Illuminate\Http\Request;
+use Illuminate\Contracts\Auth\Guard;
 use Dias\Http\Controllers\Api\Controller;
 
 class TransectsAnnotationsController extends Controller
@@ -19,28 +20,38 @@ class TransectsAnnotationsController extends Controller
      * @apiParam {Number} lit The Label ID
      * @apiParam (Optional arguments) {Number} take Number of annotations to return. If this parameter is present, the most recent annotations will be returned first. Default is unlimited and unordered.
      * @apiPermission projectMember
-     * @apiDescription Returns a list of annotation IDs
+     * @apiDescription Returns a list of annotation IDs. If there is an active annotation session, images with annotations hidden by the session are not returned.
      *
      * @param Request $request
+     * @param Guard $auth
      * @param  int  $tid Transect ID
      * @param int $lid Label ID
      * @return \Illuminate\Http\Response
      */
-    public function filter(Request $request, $tid, $lid)
+    public function filter(Request $request, Guard $auth, $tid, $lid)
     {
         $transect = Transect::findOrFail($tid);
         $this->authorize('access', $transect);
         $this->validate($request, ['take' => 'integer']);
         $take = $request->input('take');
 
-        return Annotation::join('annotation_labels', 'annotations.id', '=', 'annotation_labels.annotation_id')
+        $user = $auth->user();
+        $session = $transect->getActiveAnnotationSession($user);
+
+        if ($session) {
+            $query = Annotation::allowedBySession($session, $user);
+        } else {
+            $query = Annotation::query();
+        }
+
+        return $query->join('annotation_labels', 'annotations.id', '=', 'annotation_labels.annotation_id')
             ->whereIn('annotations.image_id', function ($query) use ($tid) {
                 $query->select('id')
                     ->from('images')
                     ->where('transect_id', $tid);
             })
             ->where('annotation_labels.label_id', $lid)
-            ->when($take !== null, function ($query) use ($take) {
+            ->when(!is_null($take), function ($query) use ($take) {
                 return $query->orderBy('annotations.created_at', 'desc')
                     ->take($take);
             })

diff --git a/src/Jobs/GenerateAnnotationPatch.php b/src/Jobs/GenerateAnnotationPatch.php
@@ -2,13 +2,13 @@
 
 namespace Dias\Modules\Ate\Jobs;
 
-use Dias\Annotation;
+use File;
 use Dias\Shape;
 use Dias\Jobs\Job;
+use Dias\Annotation;
+use InterventionImage as IImage;
 use Illuminate\Queue\InteractsWithQueue;
 use Illuminate\Contracts\Queue\ShouldQueue;
-use InterventionImage as IImage;
-use File;
 
 class GenerateAnnotationPatch extends Job implements ShouldQueue
 {

diff --git a/src/resources/views/index.blade.php b/src/resources/views/index.blade.php
@@ -19,20 +19,7 @@
 
 @section('navbar')
 <div class="navbar-text navbar-ate-breadcrumbs">
-    @if ($projects->count() > 1)
-        <span class="dropdown">
-            <a href="#" class="dropdown-toggle navbar-link">Projects <span class="caret"></span></a>
-            <ul class="dropdown-menu">
-                @foreach ($projects as $project)
-                    <li><a href="{{route('project', $project->id)}}">{{$project->name}}</a></li>
-                @endforeach
-            </ul>
-        </span>
-    @else
-        <a href="{{route('project', $projects->first()->id)}}" class="navbar-link" title="Show project {{$projects->first()->name}}">{{$projects->first()->name}}</a>
-    @endif
-    / <a href="{{route('transect', $transect->id)}}" title="Show transect {{$transect->name}}">{{$transect->name}}</a>
-    / <strong id="dismiss-mode-title">ATE - dismiss existing annotations</strong><strong id="re-labelling-mode-title" class="ng-hide">ATE - re-label dismissed annotations</strong> <small>(<span id="annotation-count">0</span>&nbsp;annotations)</small>
+    @include('transects::partials.projectsBreadcrumb') / <a href="{{route('transect', $transect->id)}}" title="Show transect {{$transect->name}}" class="navbar-link">{{$transect->name}}</a> / <strong id="dismiss-mode-title">ATE - dismiss existing annotations</strong><strong id="re-labelling-mode-title" class="ng-hide">ATE - re-label dismissed annotations</strong> <small>(<span id="annotation-count">0</span>&nbsp;annotations)</small> @include('transects::partials.annotationSessionIndicator')
 </div>
 @endsection
 

diff --git a/src/resources/views/projectsShow.blade.php b/src/resources/views/projectsShow.blade.php
diff --git a/src/resources/views/projectsShowToolbar.blade.php b/src/resources/views/projectsShowToolbar.blade.php
@@ -0,0 +1 @@
+<a href="{{route('projectsAte', $project->id)}}" class="btn btn-default" title="Perform ATE re-evaluation of annotations for this project"><span class="glyphicon glyphicon-check" aria-hidden="true"></span> ATE re-evaluation</a>
diff --git a/tests/Http/Controllers/Api/AteModuleHttpControllersApiProjectsAnnotationsControllerTest.php b/tests/Http/Controllers/Api/AteModuleHttpControllersApiProjectsAnnotationsControllerTest.php
@@ -1,6 +1,5 @@
 <?php
 
-
 class AteModuleHttpControllersApiProjectsAnnotationsControllerTest extends ApiTestCase {
 
     public function testFilter() {

diff --git a/tests/Http/Controllers/Api/AteModuleHttpControllersApiTransectsAnnotationsControllerTest.php b/tests/Http/Controllers/Api/AteModuleHttpControllersApiTransectsAnnotationsControllerTest.php
@@ -1,5 +1,6 @@
 <?php
 
+use Carbon\Carbon;
 
 class AteModuleHttpControllersApiTransectsAnnotationsControllerTest extends ApiTestCase {
 
@@ -51,4 +52,102 @@ public function testFilter() {
         $this->assertResponseOk();
         $this->seeJsonEquals($expect3);
     }
+
+    public function testFilterAnnotationSession()
+    {
+        $id = $this->transect()->id;
+        $image = ImageTest::create(['transect_id' => $id]);
+
+        $a1 = AnnotationTest::create([
+            'image_id' => $image->id,
+            'created_at' => Carbon::yesterday(),
+        ]);
+
+        $a2 = AnnotationTest::create([
+            'image_id' => $image->id,
+            'created_at' => Carbon::today(),
+        ]);
+
+        $a3 = AnnotationTest::create([
+            'image_id' => $image->id,
+            'created_at' => Carbon::yesterday(),
+        ]);
+
+        $l1 = AnnotationLabelTest::create([
+            'annotation_id' => $a1->id,
+            'user_id' => $this->editor()->id,
+        ]);
+
+        $l2 = AnnotationLabelTest::create([
+            'annotation_id' => $a2->id,
+            'label_id' => $l1->label_id,
+            'user_id' => $this->editor()->id,
+        ]);
+
+        $l3 = AnnotationLabelTest::create([
+            'annotation_id' => $a3->id,
+            'label_id' => $l1->label_id,
+            'user_id' => $this->admin()->id,
+        ]);
+
+        $this->beEditor();
+
+        // test hide own
+        $session = AnnotationSessionTest::create([
+            'transect_id' => $id,
+            'starts_at' => Carbon::today(),
+            'ends_at' => Carbon::tomorrow(),
+            'hide_own_annotations' => true,
+            'hide_other_users_annotations' => false,
+        ]);
+
+        $session->users()->attach($this->editor());
+
+        $expect = [$a2->id, $a3->id];
+        if ($this->isSqlite()) {
+            $expect = array_map('strval', $expect);
+        }
+
+        $this->get("/api/v1/transects/{$id}/annotations/filter/label/{$l1->label_id}");
+        $this->assertResponseOk();
+        $this->seeJsonEquals($expect);
+
+        // test hide other
+        $session->hide_own_annotations = false;
+        $session->hide_other_users_annotations = true;
+        $session->save();
+
+        $expect = [$a1->id, $a2->id];
+        if ($this->isSqlite()) {
+            $expect = array_map('strval', $expect);
+        }
+
+        $this->get("/api/v1/transects/{$id}/annotations/filter/label/{$l1->label_id}");
+        $this->assertResponseOk();
+        $this->seeJsonEquals($expect);
+
+        // test hide both
+        $session->hide_own_annotations = true;
+        $session->save();
+
+        $expect = [$a2->id];
+        if ($this->isSqlite()) {
+            $expect = array_map('strval', $expect);
+        }
+
+        $this->get("/api/v1/transects/{$id}/annotations/filter/label/{$l1->label_id}");
+        $this->assertResponseOk();
+        $this->seeJsonEquals($expect);
+
+        $session->users()->detach($this->editor());
+
+        $expect = [$a1->id, $a2->id, $a3->id];
+        if ($this->isSqlite()) {
+            $expect = array_map('strval', $expect);
+        }
+
+        $this->get("/api/v1/transects/{$id}/annotations/filter/label/{$l1->label_id}");
+        $this->assertResponseOk();
+        $this->seeJsonEquals($expect);
+    }
 }