Minor bugs

GaziYucel · Feb 27, 2024 · da5b7ae · da5b7ae
1 parent ca59eb6
commit da5b7ae
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Showing 11 changed files with 46 additions and 54 deletions.
diff --git a/classes/External/ApiAbstract.php b/classes/External/ApiAbstract.php
@@ -50,6 +50,9 @@ public function apiRequest(string $method, string $url, array $options): array
     {
         if ($method !== 'POST' && $method !== 'GET') return [];
 
+        $response = null;
+        $result = null;
+
         try {
             $response = $this->httpClient->request($method, $url, $options);
 
@@ -67,6 +70,7 @@ public function apiRequest(string $method, string $url, array $options): array
             return $result;
 
         } catch (GuzzleException $e) {
+            LogHelper::logDebug([$method, $url, $options, $response, $result]);
             error_log(__METHOD__ . ' ' . $e->getMessage());
         }
 

diff --git a/classes/External/OpenAlex/Api.php b/classes/External/OpenAlex/Api.php
@@ -52,6 +52,6 @@ public function getWork(string $doi): array
     {
         if(empty($doi)) return [];
 
-        return $this->apiRequest('GET', '/' . 'works/doi:' . $doi, []);
+        return $this->apiRequest('GET', $this->url . '/works/doi:' . $doi, []);
     }
 }
diff --git a/classes/External/Wikidata/Deposit.php b/classes/External/Wikidata/Deposit.php
@@ -92,7 +92,7 @@ public function execute(Context             $context,
         foreach ($publication->getData('authors') as $id => $authorLC) {
             /* @var Author $authorLC */
             $author = (array)$authorLC;
-            $metadata = json_decode($author['_data'][CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR], true);
+            $metadata = json_decode($authorLC->getData(CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR), true);
             $metadata = ClassHelper::getClassWithValuesAssigned(new MetadataAuthor(), $metadata);
             if (empty($metadata)) $metadata = new MetadataAuthor();
             $author['_data'][CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR] = $metadata;
@@ -114,7 +114,7 @@ public function execute(Context             $context,
             /* @var CitationModel $citation */
             $citation = Classhelper::getClassWithValuesAssigned(new CitationModel(), $citations[$i]);
 
-            if (empty($citation->wikidata_id))
+            if ($citation->isProcessed && empty($citation->wikidata_id))
                 $citation->wikidata_id = $this->processCitedArticle($locale, $citation);
 
             $citations[$i] = $citation;

diff --git a/classes/Handlers/DepositHandler.php b/classes/Handlers/DepositHandler.php
@@ -18,8 +18,9 @@
 use APP\plugins\generic\citationManager\classes\Db\PluginDAO;
 use APP\plugins\generic\citationManager\classes\External\OpenCitations\Deposit as OpenCitationsDeposit;
 use APP\plugins\generic\citationManager\classes\External\Wikidata\Deposit as WikidataDeposit;
-use Application;
+use APP\core\Application;
 use Exception;
+use PKP\plugins\PluginRegistry;
 
 class DepositHandler
 {
@@ -38,9 +39,10 @@ class DepositHandler
     /** @var array|null */
     private ?array $authors = [];
 
-    /** @param CitationManagerPlugin $plugin */
-    public function __construct(CitationManagerPlugin $plugin)
+    public function __construct()
     {
+        /** @var CitationManagerPlugin $plugin */
+        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
         $this->plugin = $plugin;
     }
 

diff --git a/classes/Handlers/PluginAPIHandler.php b/classes/Handlers/PluginAPIHandler.php
@@ -16,7 +16,6 @@
 import('lib.pkp.classes.security.authorization.PolicySet');
 import('lib.pkp.classes.security.authorization.RoleBasedHandlerOperationPolicy');
 
-use APP\plugins\generic\citationManager\CitationManagerPlugin;
 use APP\plugins\generic\citationManager\classes\DataModels\Metadata\MetadataPublication;
 use APP\plugins\generic\citationManager\classes\Helpers\ClassHelper;
 use APIResponse;
@@ -29,9 +28,6 @@
 
 class PluginAPIHandler extends APIHandler
 {
-    /** @var CitationManagerPlugin */
-    protected CitationManagerPlugin $plugin;
-
     /** @var array Structure of the response body */
     private array $responseBody = [
         'status' => 'ok',
@@ -45,10 +41,8 @@ class PluginAPIHandler extends APIHandler
 
     private array $roles = [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SUB_EDITOR, Role::ROLE_ID_ASSISTANT, Role::ROLE_ID_REVIEWER, Role::ROLE_ID_AUTHOR];
 
-    /** @param CitationManagerPlugin $plugin */
-    public function __construct(CitationManagerPlugin $plugin)
+    public function __construct()
     {
-        $this->plugin = $plugin;
         $this->_handlerPath = CITATION_MANAGER_PLUGIN_NAME;
 
         // Configure API endpoints
@@ -107,7 +101,7 @@ public function process(SlimRequest $slimRequest, APIResponse $response, array $
         if (empty($submissionId) || empty($publicationId) || empty($citationsRaw))
             return $response->withJson($this->responseBody, 200);
 
-        $process = new ProcessHandler($this->plugin);
+        $process = new ProcessHandler();
         $process->execute($submissionId, $publicationId, $citationsRaw);
 
         $this->responseBody['message-type'] = 'process';
@@ -143,7 +137,7 @@ public function deposit(SlimRequest $slimRequest, APIResponse $response, array $
         if (empty($submissionId) || empty($publicationId) || empty($publicationMetadata) || empty($citations))
             return $response->withJson($this->responseBody, 200);
 
-        $depositor = new DepositHandler($this->plugin);
+        $depositor = new DepositHandler();
         $depositor->execute(
             $submissionId,
             $publicationId,

diff --git a/classes/Handlers/ProcessHandler.php b/classes/Handlers/ProcessHandler.php
@@ -24,7 +24,8 @@
 use APP\plugins\generic\citationManager\classes\PID\Handle;
 use APP\plugins\generic\citationManager\classes\PID\Url;
 use APP\plugins\generic\citationManager\classes\PID\Urn;
-use Application;
+use APP\core\Application;
+use PKP\plugins\PluginRegistry;
 use Publication;
 use Submission;
 use Exception;
@@ -37,9 +38,10 @@ class ProcessHandler
     /** @var array|null [ { CitationModel }, ... ] */
     private ?array $citations = null;
 
-    /** @param CitationManagerPlugin $plugin */
-    public function __construct(CitationManagerPlugin $plugin)
+    public function __construct()
     {
+        /** @var CitationManagerPlugin $plugin */
+        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
         $this->plugin = $plugin;
     }
 

diff --git a/classes/Helpers/ClassHelper.php b/classes/Helpers/ClassHelper.php
@@ -19,6 +19,7 @@ class ClassHelper
 {
     /**
      * Get public properties of an object and assign null values.
+     *
      * @param object $class The object for which properties are retrieved and assigned null values.
      * @return array An associative array with property names as keys and null values.
      */
@@ -29,6 +30,7 @@ public static function getClassAsArrayNullAssigned(object $class): array
 
     /**
      * Get public properties of an object and assign provided values.
+     *
      * @param object $class  The object for which properties are retrieved and values assigned.
      * @param ?array  $values An associative array with property names as keys and corresponding values.
      * @return array An associative array with property names as keys and assigned values.
@@ -53,12 +55,15 @@ public static function getClassAsArrayWithValuesAssigned(object $class, ?array $
 
     /**
      * Get a class instance with public properties assigned values.
+     *
      * @param object $class  The class instance to be populated.
-     * @param array  $values An associative array with property names as keys and corresponding values.
+     * @param array|null  $values An associative array with property names as keys and corresponding values.
      * @return object An instance of the class with properties assigned values.
      */
-    public static function getClassWithValuesAssigned(object $class, array $values): object
+    public static function getClassWithValuesAssigned(object $class, ?array $values): object
     {
+        if(empty($values)) return new $class();
+
         $object = new $class();
 
         $reflect = new ReflectionClass($class);
@@ -75,6 +80,7 @@ public static function getClassWithValuesAssigned(object $class, array $values):
 
     /**
      * Get public properties of an object as an array
+     *
      * @param object $class The object for which properties are retrieved.
      * @return array A with property names as keys.
      */
@@ -94,6 +100,7 @@ public static function getClassPropertiesAsArray(object $class): array
 
     /**
      * Get class public properties as a csv, e.g. "id","title","pub_date"
+     *
      * @param object $class
      * @return string
      */

diff --git a/classes/ScheduledTasks/DepositTask.php b/classes/ScheduledTasks/DepositTask.php
@@ -12,42 +12,33 @@
 
 namespace APP\plugins\generic\citationManager\classes\ScheduledTasks;
 
-// import('lib.pkp.classes.scheduledTask.ScheduledTask');
-
-use APP\plugins\generic\citationManager\CitationManagerPlugin;
 use APP\plugins\generic\citationManager\classes\Handlers\DepositHandler;
-use PluginRegistry;
-use ScheduledTask;
-use ScheduledTaskHelper;
+use PKP\plugins\PluginRegistry;
+use PKP\scheduledTask\ScheduledTask;
+use PKP\scheduledTask\ScheduledTaskHelper;
 
 class DepositTask extends ScheduledTask
 {
-    /** @var CitationManagerPlugin */
-    var CitationManagerPlugin $plugin;
-
     /** @copydoc ScheduledTask::__construct */
     function __construct($args)
     {
-        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
-
-        /** @var CitationManagerPlugin $plugin */
-        $this->plugin = $plugin;
-
         parent::__construct($args);
     }
 
     /** @copydoc ScheduledTask::executeActions() */
     public function executeActions(): bool
     {
-        $plugin = $this->plugin;
+        /** @var \APP\plugins\generic\citationManager\CitationManagerPlugin $plugin */
+        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
+
         if (!$plugin->getEnabled()) {
             $this->addExecutionLogEntry(
                 __METHOD__ . '->pluginEnabled=false [' . date('Y-m-d H:i:s') . ']',
                 ScheduledTaskHelper::SCHEDULED_TASK_MESSAGE_TYPE_WARNING);
             return false;
         }
 
-        $depositor = new DepositHandler($this->plugin);
+        $depositor = new DepositHandler();
         $result = $depositor->batchExecute();
 
         if (!$result) {

diff --git a/classes/ScheduledTasks/ProcessTask.php b/classes/ScheduledTasks/ProcessTask.php
@@ -12,41 +12,33 @@
 
 namespace APP\plugins\generic\citationManager\classes\ScheduledTasks;
 
-import('lib.pkp.classes.scheduledTask.ScheduledTask');
-
-use APP\plugins\generic\citationManager\CitationManagerPlugin;
 use APP\plugins\generic\citationManager\classes\Handlers\ProcessHandler;
-use PluginRegistry;
-use ScheduledTask;
-use ScheduledTaskHelper;
+use PKP\plugins\PluginRegistry;
+use PKP\scheduledTask\ScheduledTask;
+use PKP\scheduledTask\ScheduledTaskHelper;
 
 class ProcessTask extends ScheduledTask
 {
-    /** @var CitationManagerPlugin */
-    var CitationManagerPlugin $plugin;
-
     /** @copydoc ScheduledTask::__construct */
     function __construct($args)
     {
-        /* @var CitationManagerPlugin $plugin */
-        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
-        $this->plugin = $plugin;
-
         parent::__construct($args);
     }
 
     /** @copydoc ScheduledTask::executeActions() */
     public function executeActions(): bool
     {
-        $plugin = $this->plugin;
+        /** @var \APP\plugins\generic\citationManager\CitationManagerPlugin $plugin */
+        $plugin = PluginRegistry::getPlugin('generic',  strtolower(CITATION_MANAGER_PLUGIN_NAME));
+
         if (!$plugin->getEnabled()) {
             $this->addExecutionLogEntry(
                 __METHOD__ . '->pluginEnabled=false [' . date('Y-m-d H:i:s') . ']',
                 ScheduledTaskHelper::SCHEDULED_TASK_MESSAGE_TYPE_WARNING);
             return false;
         }
 
-        $process = new ProcessHandler($this->plugin);
+        $process = new ProcessHandler();
         $result = $process->batchExecute();
 
         if (!$result) {

diff --git a/classes/Settings/Manage.php b/classes/Settings/Manage.php
@@ -53,7 +53,7 @@ public function execute($args, $request): JSONMessage
                 $form->initData();
                 return new JSONMessage(true, $form->fetch($request));
             case 'batch_process':
-                $process = new ProcessHandler($this->plugin);
+                $process = new ProcessHandler();
                 $process->batchExecute();
                 $notificationManager = new NotificationManager();
                 $notificationManager->createTrivialNotification(
@@ -62,7 +62,7 @@ public function execute($args, $request): JSONMessage
                     array('contents' => __('plugins.generic.citationManager.settings.process.notification')));
                 return DAO::getDataChangedEvent();
             case 'batch_deposit':
-                $deposit = new DepositHandler($this->plugin);
+                $deposit = new DepositHandler();
                 $deposit->batchExecute();
                 $notificationManager = new NotificationManager();
                 $notificationManager->createTrivialNotification(

diff --git a/classes/Workflow/WorkflowTab.php b/classes/Workflow/WorkflowTab.php
@@ -83,7 +83,7 @@ public function execute(string $hookName, array $args): void
         foreach ($publication->getData('authors') as $id => $authorLC) {
             /* @var Author $authorLC */
             $author = (array)$authorLC;
-            $metadata = json_decode($author['_data'][CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR], true);
+            $metadata = json_decode($authorLC->getData(CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR), true);
             $metadata = ClassHelper::getClassWithValuesAssigned(new MetadataAuthor(), $metadata);
             if (empty($metadata)) $metadata = new MetadataAuthor();
             $author['_data'][CitationManagerPlugin::CITATION_MANAGER_METADATA_AUTHOR] = $metadata;