Merge pull request #15 from BiodataMiningGroup/largo

Rename module to biigle/largo

README.md

@@ -1,16 +1,16 @@
-# Biigle Ate Module
+# Biigle Largo Module
 
 Install the module:
 
 Add the following to the repositories array of your `composer.json`:
 ```
 {
   "type": "vcs",
-  "url": "https://github.com/BiodataMiningGroup/biigle-ate.git"
+  "url": "https://github.com/BiodataMiningGroup/biigle-largo.git"
 }
 ```
 
-1. Run `php composer.phar require biigle/ate`.
-2. Add `'Biigle\Modules\Ate\AteServiceProvider'` to the `providers` array in `config/app.php`.
-3. Run `php artisan ate:publish` to refresh the public assets of this package. Do this for every update of the package.
-4. Create a directory `storage/ate_patches` which is read-/writable for the application. To change the path, run `php artisan ate:config` and edit `patch_storage` in `config/ate.php`.
+1. Run `php composer.phar require biigle/largo`.
+2. Add `'Biigle\Modules\Largo\LargoServiceProvider'` to the `providers` array in `config/app.php`.
+3. Run `php artisan largo:publish` to refresh the public assets of this package. Do this for every update of the package.
+4. Create a directory `storage/largo_patches` which is read-/writable for the application. To change the path, run `php artisan largo:config` and edit `patch_storage` in `config/largo.php`.

composer.json

@@ -1,5 +1,5 @@
 {
-    "name": "biigle/ate",
+    "name": "biigle/largo",
     "require": {
         "biigle/volumes": "~1.1",
         "intervention/image": "~2.1",
@@ -9,7 +9,7 @@
     },
     "autoload": {
         "psr-4": {
-            "Biigle\\Modules\\Ate\\": "src"
+            "Biigle\\Modules\\Largo\\": "src"
         }
     }
 }

gulpfile.js

@@ -2,7 +2,7 @@
 
 var gulp = require('gulp');
 var h = require('gulp-helpers');
-var publish = h.publish('Biigle\\Modules\\Ate\\AteServiceProvider', 'public');
+var publish = h.publish('Biigle\\Modules\\Largo\\LargoServiceProvider', 'public');
 
 h.paths.sass = 'src/resources/assets/sass/';
 h.paths.js = 'src/resources/assets/js/';
@@ -19,24 +19,24 @@ gulp.task('sass-annotations', function () {
 gulp.task('sass', ['sass-main', 'sass-annotations']);
 
 gulp.task('js-main', function (cb) {
-   h.angular('ate/**/*.js', 'main.js', cb);
+   h.angular('largo/**/*.js', 'main.js', cb);
 });
 
-gulp.task('js-project-ate', function (cb) {
-   h.angular('project-ate/**/*.js', 'project-ate.js', cb);
+gulp.task('js-project-largo', function (cb) {
+   h.angular('project-largo/**/*.js', 'project-largo.js', cb);
 });
 
 gulp.task('js-annotations', function (cb) {
    h.angular('annotations/**/*.js', 'annotations.js', cb);
 });
 
-gulp.task('js', ['js-main', 'js-project-ate', 'js-annotations']);
+gulp.task('js', ['js-main', 'js-project-largo', 'js-annotations']);
 
 gulp.task('watch', function () {
     gulp.watch(h.paths.sass + 'main.scss', ['sass-main']);
     gulp.watch(h.paths.sass + 'annotations.scss', ['sass-annotations']);
-    gulp.watch(h.paths.js + 'ate/**/*.js', ['js-main']);
-    gulp.watch(h.paths.js + 'project-ate/**/*.js', ['js-project-ate']);
+    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 + 'annotations/**/*.js', ['js-annotations']);
     gulp.watch(h.paths.public + '**/*', publish);
 });

package.json

@@ -1,5 +1,5 @@
 {
-  "name": "biigle-ate",
+  "name": "biigle-largo",
   "version": "0.0.1",
   "directories": {
     "test": "tests"

src/Console/Commands/Config.php

@@ -1,9 +1,9 @@
 <?php
 
-namespace Biigle\Modules\Ate\Console\Commands;
+namespace Biigle\Modules\Largo\Console\Commands;
 
 use Illuminate\Console\Command;
-use Biigle\Modules\Ate\AteServiceProvider as ServiceProvider;
+use Biigle\Modules\Largo\LargoServiceProvider as ServiceProvider;
 
 class Config extends Command {
 
@@ -12,7 +12,7 @@ class Config extends Command {
      *
      * @var string
      */
-    protected $name = 'ate:config';
+    protected $name = 'largo:config';
 
     /**
      * The console command description.

src/Console/Commands/Publish.php

@@ -1,9 +1,9 @@
 <?php
 
-namespace Biigle\Modules\Ate\Console\Commands;
+namespace Biigle\Modules\Largo\Console\Commands;
 
 use Illuminate\Console\Command;
-use Biigle\Modules\Ate\AteServiceProvider as ServiceProvider;
+use Biigle\Modules\Largo\LargoServiceProvider as ServiceProvider;
 
 class Publish extends Command {
 
@@ -12,7 +12,7 @@ class Publish extends Command {
      *
      * @var string
      */
-    protected $name = 'ate:publish';
+    protected $name = 'largo:publish';
 
     /**
      * The console command description.

src/Http/Controllers/Api/AteController.php → src/Http/Controllers/Api/LargoController.php

@@ -1,6 +1,6 @@
 <?php
 
-namespace Biigle\Modules\Ate\Http\Controllers\Api;
+namespace Biigle\Modules\Largo\Http\Controllers\Api;
 
 use DB;
 use Biigle\Role;
@@ -12,11 +12,11 @@
 use Illuminate\Http\Request;
 use Illuminate\Contracts\Auth\Guard;
 use Biigle\Http\Controllers\Api\Controller;
-use Biigle\Modules\Ate\Jobs\RemoveAnnotationPatches;
+use Biigle\Modules\Largo\Jobs\RemoveAnnotationPatches;
 use Illuminate\Auth\Access\AuthorizationException;
 use Symfony\Component\HttpFoundation\File\Exception\FileNotFoundException;
 
-class AteController extends Controller
+class LargoController extends Controller
 {
     /**
      * Show the patch image of an annotation
@@ -36,9 +36,9 @@ public function showPatch($id)
         $annotation = Annotation::with('image')->findOrFail($id);
         $this->authorize('access', $annotation);
 
-        $file = config('ate.patch_storage').'/'.
+        $file = config('largo.patch_storage').'/'.
             $annotation->image->volume_id.'/'.
-            $annotation->id.'.'.config('ate.patch_format');
+            $annotation->id.'.'.config('largo.patch_format');
 
         try {
             return response()->download($file);
@@ -49,11 +49,11 @@ public function showPatch($id)
 
 
     /**
-     * Save changes of an ATE session for a volume
+     * Save changes of an Largo session for a volume
      *
-     * @api {post} volumes/:id/ate Save ATE session
-     * @apiGroup ATE
-     * @apiName VolumesStoreATE
+     * @api {post} volumes/:id/largo Save Largo session
+     * @apiGroup Largo
+     * @apiName VolumesStoreLargo
      * @apiParam {Number} id The volume ID.
      * @apiPermission projectEditor
      * @apiDescription From the `dismissed` map only annotation labels that were attached by the requesting user will be detached. If the map contains annotation labels that were not attached by the user, the information will be ignored. From the `changed` map, new annotation labels will be created. If, after detaching `dismissed` annotation labels and attaching `changed` annotation labels, there is an annotation whithout any label, the annotation will be deleted. All affected annotations must belong to the same volume. If the user is not allowed to edit in this volume, the whole request will be denied.
@@ -83,7 +83,7 @@ public function saveVolume(Request $request, Guard $auth, $id)
     {
         $volume = Volume::findOrFail($id);
         $this->authorize('edit-in', $volume);
-        $this->validateAteInput($request);
+        $this->validateLargoInput($request);
 
         $user = $auth->user();
 
@@ -143,14 +143,14 @@ public function saveVolume(Request $request, Guard $auth, $id)
     }
 
     /**
-     * Save changes of an ATE session for a project
+     * Save changes of an Largo session for a project
      *
-     * @api {post} projects/:id/ate Save ATE session
-     * @apiGroup ATE
-     * @apiName ProjectsStoreATE
+     * @api {post} projects/:id/largo Save Largo session
+     * @apiGroup Largo
+     * @apiName ProjectsStoreLargo
      * @apiParam {Number} id The project ID.
      * @apiPermission projectEditor
-     * @apiDescription see the 'Save ATE session' endpoint for a volume for more information
+     * @apiDescription see the 'Save Largo session' endpoint for a volume for more information
      *
      * @apiParam (Optional arguments) {Object} dismissed Map from a label ID to a list of IDs of annotations from which this label should be detached.
      * @apiParam (Optional arguments) {Object} changed Map from annotation ID to a label ID that should be attached to the annotation.
@@ -164,7 +164,7 @@ public function saveProject(Request $request, Guard $auth, $id)
     {
         $project = Project::findOrFail($id);
         $this->authorize('edit-in', $project);
-        $this->validateAteInput($request);
+        $this->validateLargoInput($request);
 
         $volumeIds = $project->volumes()->pluck('id');
 
@@ -210,11 +210,11 @@ public function saveProject(Request $request, Guard $auth, $id)
     }
 
     /**
-     * Validates the input for saving an ATE session
+     * Validates the input for saving an Largo session
      *
      * @param Request $request
      */
-    protected function validateAteInput(Request $request)
+    protected function validateLargoInput(Request $request)
     {
         $this->validate($request, [
             'dismissed' => 'array',
@@ -270,7 +270,7 @@ protected function getRequiredLabelTrees($changed)
     }
 
     /**
-     * Apply the changes of an ATE 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

@@ -1,6 +1,6 @@
 <?php
 
-namespace Biigle\Modules\Ate\Http\Controllers\Api;
+namespace Biigle\Modules\Largo\Http\Controllers\Api;
 
 use Biigle\Project;
 use Biigle\Volume;

src/Http/Controllers/Api/VolumesAnnotationsController.php

@@ -1,6 +1,6 @@
 <?php
 
-namespace Biigle\Modules\Ate\Http\Controllers\Api;
+namespace Biigle\Modules\Largo\Http\Controllers\Api;
 
 use Biigle\Volume;
 use Biigle\Annotation;

src/Http/Controllers/Views/AteController.php → src/Http/Controllers/Views/LargoController.php

@@ -1,6 +1,6 @@
 <?php
 
-namespace Biigle\Modules\Ate\Http\Controllers\Views;
+namespace Biigle\Modules\Largo\Http\Controllers\Views;
 
 use DB;
 use Biigle\Role;
@@ -11,10 +11,10 @@
 use Illuminate\Contracts\Auth\Guard;
 use Biigle\Http\Controllers\Views\Controller;
 
-class AteController extends Controller
+class LargoController extends Controller
 {
     /**
-     * Show the the ATE view for a volume
+     * Show the the Largo view for a volume
      *
      * @param Guard $auth
      * @param int $id Volume ID
@@ -53,7 +53,7 @@ public function indexVolume(Guard $auth, $id)
             })
             ->get();
 
-        return view('ate::index', [
+        return view('largo::index', [
             'user' => $user,
             'volume' => $volume,
             'projects' => $projects,
@@ -62,7 +62,7 @@ public function indexVolume(Guard $auth, $id)
     }
 
     /**
-     * Show the ATE view for a project
+     * Show the Largo view for a project
      *
      * @param Guard $auth
      * @param int $id Project ID
@@ -79,7 +79,7 @@ public function indexProject(Guard $auth, $id)
             ->select('id', 'name')
             ->get();
 
-        return view('ate::project', [
+        return view('largo::project', [
             'user' => $user,
             'project' => $project,
             'labelTrees' => $labelTrees,