Merge branch 'develop'

.github/workflows/test.yml

@@ -2,7 +2,7 @@ name: test
 
 on:
   push:
-    branches: [main, develop]
+    branches: [main, develop, fix-test-action]
   pull_request:
     branches: [main, develop]
 
@@ -14,9 +14,9 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04]
-        php: ["7.4"]
+        php: ["8.2"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Create config files
         run: |

.gitignore

@@ -6,6 +6,8 @@ tmp
 vendor
 webroot/theme/node_modules
 webroot/scss/*.css
+webroot/js/node_modules/
+!webroot/js/node_modules/mermaid/dist/
 .vscode
 docker/run/
 .phpunit.result.cache

config/Migrations/20231012000007_SGExtend.php

@@ -0,0 +1,34 @@
+<?php
+declare(strict_types=1);
+
+use Migrations\AbstractMigration;
+use Phinx\Db\Adapter\MysqlAdapter;
+
+final class SGExtend extends AbstractMigration
+{
+    public $autoId = false; // turn off automatic `id` column create. We want it to be `int(10) unsigned`
+
+    /**
+     * Change Method.
+     *
+     * Write your reversible migrations using this method.
+     *
+     * More information on writing migrations is available here:
+     * https://book.cakephp.org/phinx/0/en/migrations.html#the-change-method
+     *
+     * Remember to call "create()" or "update()" and NOT "save()" when working
+     * with the Table class.
+     */
+    public function change(): void
+    {
+        $table = $this->table('sgo');
+        $exists = $table->hasColumn('extend');
+        if (!$exists) {
+            $table
+                ->addColumn('extend', 'boolean', [
+                    'default' => 0,
+                    'null' => false,
+                ])->update();
+        }
+    }
+}

config/app.php

@@ -178,7 +178,6 @@
      */
     'Error' => [
         'errorLevel' => E_ALL,
-        'exceptionRenderer' => ExceptionRenderer::class,
         'skipLog' => [],
         'log' => true,
         'trace' => true,

config/bootstrap.php

@@ -194,6 +194,11 @@
 
     return $detector->isTablet();
 });
+ServerRequest::addDetector('csv', [
+    'accept' => ['text/csv',],
+    'param' => '_ext',
+    'value' => 'csv',
+]);
 
 /*
  * You can set whether the ORM uses immutable or mutable Time types.

config/routes.php

@@ -45,7 +45,7 @@
 /** @var \Cake\Routing\RouteBuilder $routes */
 $routes->setRouteClass(DashedRoute::class);
 $routes->scope('/', function (RouteBuilder $builder) {
-    $builder->setExtensions(['json']);
+    $builder->setExtensions(['json', 'csv']);
     // Register scoped middleware for in scopes.
     $builder->registerMiddleware('csrf', new CsrfProtectionMiddleware([
         'httponly' => true,

phpunit.xml.dist

@@ -20,6 +20,9 @@
         <testsuite name="api">
             <directory>./tests/TestCase/Api</directory>
         </testsuite>
+        <testsuite name="e2e">
+            <directory>./tests/TestCase/Integration</directory>
+        </testsuite>
     </testsuites>
 
     <extensions>

plugins/Tags/src/View/Helper/TagHelper.php

@@ -106,7 +106,7 @@ public function tag($tag, array $options = [])
             $deleteButton = $this->Bootstrap->button([
                 'size' => 'sm',
                 'icon' => 'times',
-                'class' => ['ms-1', 'border-0', "text-${textColour}"],
+                'class' => ['ms-1', 'border-0', "text-$textColour"],
                 'variant' => 'text',
                 'title' => __('Delete tag'),
                 'onclick' => sprintf('deleteTag(\'%s\', \'%s\', this)',

src/Command/ImporterCommand.php

@@ -136,7 +136,7 @@ private function marshalData($table, $data, $config, $primary_key=null)
                 $entity = null;
                 if (isset($item[$primary_key])) {
                     $query = $table->find('all')
-                        ->where(["${primary_key}" => $item[$primary_key]]);
+                        ->where(["$primary_key" => $item[$primary_key]]);
                     $entity = $query->first();
                 }
                 if (is_null($entity)) {

src/Controller/AuditLogsController.php

@@ -40,5 +40,4 @@ public function filtering()
     {
         $this->CRUD->filtering();
     }
-
 }

src/Controller/Component/ACLComponent.php

@@ -107,14 +107,16 @@ public function initialize(array $config): void
             'viewTags' => ['*']
         ],
         'Instance' => [
+            'downloadTopology' => ['perm_admin'],
             'home' => ['*'],
             'migrate' => ['perm_admin'],
             'migrationIndex' => ['perm_admin'],
             'rollback' => ['perm_admin'],
             'saveSetting' => ['perm_admin'],
             'searchAll' => ['*'],
             'settings' => ['perm_admin'],
-            'status' => ['*']
+            'status' => ['*'],
+            'topology' => ['perm_admin'],
         ],
         'LocalTools' => [
             'action' => ['perm_admin'],

src/Controller/Component/CRUDComponent.php

@@ -19,7 +19,7 @@
 
 class CRUDComponent extends Component
 {
-    public $components = ['RestResponse'];
+    public $components = ['RestResponse', 'APIRearrange'];
 
     public function initialize(array $config): void
     {
@@ -102,12 +102,12 @@ public function index(array $options): void
 
         if (!$this->Controller->ParamHandler->isRest()) {
             $this->setRequestedEntryAmount();
-        } else if (!empty($this->request->getQuery('limit'))) {
+        } else if (empty($this->request->getQuery('limit'))) {
             $this->Controller->paginate['limit'] = PHP_INT_MAX; // Make sure to download the entire filtered table
         }
         $data = $this->Controller->paginate($query, $this->Controller->paginate ?? []);
         $totalCount = $this->Controller->getRequest()->getAttribute('paging')[$this->TableAlias]['count'];
-        if ($this->Controller->ParamHandler->isRest()) {
+        if ($this->Controller->ParamHandler->isRest() || $this->request->is('csv')) {
             if (isset($options['hidden'])) {
                 $data->each(function($value, $key) use ($options) {
                     $hidden = is_array($options['hidden']) ? $options['hidden'] : [$options['hidden']];
@@ -138,9 +138,21 @@ public function index(array $options): void
                     return $this->attachMetaTemplatesIfNeeded($value, $metaTemplates);
                 });
             }
-            $this->Controller->restResponsePayload = $this->RestResponse->viewData($data, 'json', false, false, false, [
-                'X-Total-Count' => $totalCount,
-            ]);
+            if ($this->request->is('csv')) {
+                require_once(ROOT . '/src/Lib/Tools/CsvConverter.php');
+                $rearranged = $this->APIRearrange->rearrangeForAPI($data, ['smartFlattenMetafields' => true]);
+                $rearranged = $rearranged->map(function($e) {
+                    return $e->toArray();
+                })->toList();
+                $data = \App\Lib\Tools\CsvConverter::flattenJSON($rearranged, []);
+                $this->Controller->restResponsePayload = $this->RestResponse->viewData($data, 'csv', false, false, false, [
+                    'X-Total-Count' => $totalCount,
+                ]);
+            } else {
+                $this->Controller->restResponsePayload = $this->RestResponse->viewData($data, 'json', false, false, false, [
+                    'X-Total-Count' => $totalCount,
+                ]);
+            }
         } else {
             $this->Controller->setResponse($this->Controller->getResponse()->withHeader('X-Total-Count', $totalCount));
             if (isset($options['afterFind'])) {
@@ -281,7 +293,7 @@ public function getFilterFieldsName(): array
      */
     public function getResponsePayload()
     {
-        if ($this->Controller->ParamHandler->isRest()) {
+        if ($this->Controller->ParamHandler->isRest() || $this->request->is('csv')) {
             return $this->Controller->restResponsePayload;
         } else if ($this->Controller->ParamHandler->isAjax() && $this->request->is(['post', 'put'])) {
             return $this->Controller->ajaxResponsePayload;
@@ -1305,6 +1317,7 @@ protected function setFilters($params, \Cake\ORM\Query $query, array $options):
             }
             $query = $this->setMetaFieldFilters($query, $filteringMetaFields);
         }
+        $activeFilters['_here'] = $this->request->getRequestTarget();
 
         $this->Controller->set('activeFilters', $activeFilters);
         return $query;
@@ -1489,7 +1502,7 @@ private function prefixConditions(string $prefix, array $conditions)
     {
         $prefixedConditions = [];
         foreach ($conditions as $condField => $condValue) {
-            $prefixedConditions["${prefix}.${condField}"] = $condValue;
+            $prefixedConditions["$prefix.$condField"] = $condValue;
         }
         return $prefixedConditions;
     }
@@ -1613,13 +1626,13 @@ private function getFilteringContextFromField($field)
                     [sprintf('%s.id = %s.%s', $this->Table->getAlias(), $associatedTable->getAlias(), $association->getForeignKey())]
                 )
                     ->where([
-                        ["${field} IS NOT" => NULL]
+                        ["$field IS NOT" => NULL]
                     ]);
             } else if ($associationType == 'manyToOne') {
                 $fieldToExtract = sprintf('%s.%s', Inflector::singularize(strtolower($model)), $subField);
                 $query = $this->Table->find()->contain($model);
             } else {
-                throw new Exception("Association ${associationType} not supported in CRUD Component");
+                throw new Exception("Association $associationType not supported in CRUD Component");
             }
         } else {
             $fieldToExtract = $field;

src/Controller/Component/Navigation/OrgGroups.php

@@ -8,7 +8,7 @@ class OrgGroupsNavigation extends BaseNavigation
     public function addLinks()
     {
         $controller = 'OrgGroups';
-        if (empty($this->viewVars['canEdit'])) {
+        if (empty($this->viewVars['canEditDefinition'])) {
             $this->bcf->removeLink($controller, 'view', $controller, 'edit');
             $this->bcf->removeLink($controller, 'edit', $controller, 'edit');
         }
@@ -17,9 +17,10 @@ public function addLinks()
     public function addActions()
     {
         $controller = 'OrgGroups';
-        if (empty($this->viewVars['canEdit'])) {
+        if (empty($this->viewVars['canEditDefinition'])) {
             $this->bcf->removeAction($controller, 'view', $controller, 'delete');
             $this->bcf->removeAction($controller, 'edit', $controller, 'delete');
+            $this->bcf->removeAction($controller, 'view', $controller, 'add');
         }
     }
 }

src/Controller/Component/Navigation/sidemenu.php

@@ -113,6 +113,11 @@ public function get(): array
                     'label' => __('Instance'),
                     'icon' => $this->iconTable['Instance'],
                     'children' => [
+                        'Topology' => [
+                            'label' => __('Topology'),
+                            'url' => '/instance/topology',
+                            'icon' => 'project-diagram',
+                        ],
                         'Settings' => [
                             'label' => __('Settings'),
                             'url' => '/instance/settings',

src/Controller/Component/RestResponseComponent.php

@@ -4,6 +4,7 @@
 
 use Cake\Controller\Component;
 use Cake\Core\Configure;
+use Cake\Utility\Hash;
 use Cake\Utility\Inflector;
 
 class RestResponseComponent extends Component
@@ -390,7 +391,7 @@ public function getApiInfo($relative_path)
         return '[]';
     }
 
-    public function saveFailResponse($controller, $action, $id = false, $validationErrors, $format = false)
+    public function saveFailResponse($controller, $action, $id, $validationErrors, $format = false)
     {
         $this->autoRender = false;
         $response = array();

src/Controller/InstanceController.php

@@ -181,4 +181,21 @@ public function saveSetting()
             }
         }
     }
+
+    public function topology()
+    {
+        $this->set('title', __('Topology'));
+        $this->set('description', __('A list of all instances and local tools connected .'));
+        $this->set('data', $this->Instance->getTopology());
+    }
+
+    public function downloadTopology()
+    {
+        $topologyMd = $this->Instance->getTopology();
+        $response = $this->response;
+        $response = $response->withStringBody($topologyMd);
+        $response = $response->withType('text/markdown');
+        $response = $response->withDownload('topology.md');
+        return $response;
+    }
 }

src/Controller/OrgGroupsController.php

@@ -58,6 +58,7 @@ public function view($id)
             return $responsePayload;
         }
         $this->set('canEdit', $this->canEdit($id));
+        $this->set('canEditDefinition', $this->canEditDefinition($id));
     }
 
     public function edit($id)
@@ -136,6 +137,15 @@ private function canEdit($groupId): bool
         return false;
     }
 
+    private function canEditDefinition($groupId): bool
+    {
+        $currentUser = $this->ACL->getUser();
+        if ($currentUser['role']['perm_admin']) {
+            return true;
+        }
+        return false;
+    }
+
     // Listing should be available to all, it's purely informational
     public function listAdmins($groupId)
     {

src/Controller/SharingGroupsController.php

@@ -8,6 +8,7 @@
 use \Cake\Database\Expression\QueryExpression;
 use Cake\Error\Debugger;
 use Cake\Http\Exception\NotFoundException;
+use Cake\ORM\TableRegistry;
 
 class SharingGroupsController extends AppController
 {
@@ -171,9 +172,13 @@ public function addOrg($id)
                 $input['organisation_id'] = [$input['organisation_id']];
             }
             $result = true;
+            $this->SGO = TableRegistry::getTableLocator()->get('SGOs');
             foreach ($input['organisation_id'] as $org_id) {
-                $org = $this->SharingGroups->SharingGroupOrgs->get($org_id);
-                $result &= (bool)$this->SharingGroups->SharingGroupOrgs->link($sharingGroup, [$org]);
+                $additional_data = [];
+                if (!empty($input['extend'])) {
+                    $additional_data['extend'] = $input['extend'];
+                }
+                $result &= $this->SGO->attach($sharingGroup['id'], $org_id, $additional_data);
             }
             if ($result) {
                 $message = __('Organisation(s) added to the sharing group.');
@@ -216,8 +221,8 @@ public function removeOrg($id, $org_id)
             throw new NotFoundException(__('Invalid SharingGroup.'));
         }
         if ($this->request->is('post')) {
-            $org = $this->SharingGroups->SharingGroupOrgs->get($org_id);
-            $result = (bool)$this->SharingGroups->SharingGroupOrgs->unlink($sharingGroup, [$org]);
+            $this->SGO = TableRegistry::getTableLocator()->get('SGOs');
+            $result = (bool)$this->SharingGroups->SharingGroupOrgs->unlink($sharingGroup['id'], $org_id);
             if ($result) {
                 $message = __('Organisation(s) removed from the sharing group.');
             } else {
@@ -253,9 +258,10 @@ public function removeOrg($id, $org_id)
 
     public function listOrgs($id)
     {
-        $sharingGroup = $this->SharingGroups->get($id, [
-            'contain' => 'SharingGroupOrgs'
-        ]);
+        $sharingGroup = $this->SharingGroups->find()->where(['id' => $id])->contain(['SharingGroupOrgs'])->first();
+        foreach ($sharingGroup['sharing_group_orgs'] as $k => $org) {
+            $sharingGroup['sharing_group_orgs'][$k]['extend'] = $org['_joinData']['extend'];
+        }
         $params = $this->ParamHandler->harvestParams(['quickFilter']);
         if (!empty($params['quickFilter'])) {
             foreach ($sharingGroup['sharing_group_orgs'] as $k => $org) {