General code issues

[jonasraoni]

Describe the bug
The problems below were found while skimming through the code and are currently not covered by the linked PRs (which are fixing other random issues):

pkp-lib

• The methods getMetadataSchema() and getApplicationEntityIdFromMetadataDescription() are not declared at the class:

  • pkp-lib/classes/metadata/MetadataRecord.php

    Line 46 in 87e018e

    $recordMetadataSchema = $this->getMetadataSchema();

  • pkp-lib/classes/metadata/MetadataRecord.php

    Line 53 in 87e018e

    $applicationEntityId = $this->getApplicationEntityIdFromMetadataDescription($metadataDescription);

• Given the JWT::decode() seems to return an object, it's curious to have it inside a json_decode() or being used as a string (there are similar cases at the application repository).

  • pkp-lib/classes/notification/PKPNotificationOperationManager.php

    Line 404 in 87e018e

    $jwt = json_decode(JWT::decode($token, $secret, ['HS256']));

  • pkp-lib/classes/security/authorization/internal/ApiTokenDecodingMiddleware.php

    Lines 83 to 84 in 87e018e

    	if (substr($apiToken, 0, 2) === '""') {
    	$apiToken = json_decode($apiToken);

OJS

• Calls to non-existent methods getSetting()/updateSetting():

  • https://github.com/pkp/ojs/blob/9fa385a2b795985f3b745577a6400414c89016c4/classes/payment/ojs/OJSPaymentManager.php#L233
  • https://github.com/pkp/ojs/blob/9fa385a2b795985f3b745577a6400414c89016c4/classes/payment/ojs/OJSPaymentManager.php#L245
  • https://github.com/pkp/ojs/blob/ecadfa2a654efe544d2c0d155936ee89ff5b72da/pages/issue/IssueHandler.php#L279

  ⚠ Before updating the code to setData()/getData(), it's probably needed to check if the field is part of the schema, otherwise it will be ignored.

• Another JWT::decode() vs string

  • https://github.com/pkp/ojs/blob/9fa385a2b795985f3b745577a6400414c89016c4/pages/article/ArticleHandler.php#L81-L86
  • https://github.com/pkp/ojs/blob/9fa385a2b795985f3b745577a6400414c89016c4/pages/oai/OAIHandler.php#L68-L74

• The method exportArticles() doesn't exist:
  https://github.com/pkp/ojs/blob/9fa385a2b795985f3b745577a6400414c89016c4/plugins/importexport/pubmed/PubMedExportPlugin.php#L232

OMP

• Not sure if it's a bug, but the OMP doesn't have the "Distribution > Access" interface

• The method getInsertData() isn't defined at the parent class
  https://github.com/pkp/omp/blob/2cfbb90c67d374016450bc40b07520dd5a090288/classes/statistics/TemporaryItemInvestigationsDAO.php#L31

• The method getInsertData() isn't defined at the parent class
  https://github.com/pkp/omp/blob/2cfbb90c67d374016450bc40b07520dd5a090288/classes/statistics/TemporaryItemRequestsDAO.php#L32

• The method _getNotificationRequestOptions() isn't defined at the parent class
  https://github.com/pkp/omp/blob/2cfbb90c67d374016450bc40b07520dd5a090288/pages/authorDashboard/AuthorDashboardHandler.php#L110

• The methods $submission->setUserId() and $submissionFile->setDateUploaded() do not exist.
  https://github.com/pkp/omp/blob/690e2be1e0a879be57ca659f47acf51a3466a470/plugins/importexport/csv/CSVImportExportPlugin.php#L158
  https://github.com/pkp/omp/blob/690e2be1e0a879be57ca659f47acf51a3466a470/plugins/importexport/csv/CSVImportExportPlugin.php#L247

OPS

• The OPSPaymentManager is missing.

• The UserImportExportPlugin is missing.

• tests\plugins\importexport\PubObjectCacheTest.php has several issues.

PRs

• Bugfix/main/8845 general fixes #8846
• Bugfix/main/8845 general fixes ojs#3853
• Bugfix/main/8845 general fixes omp#1380
• Bugfix/main/8845 general fixes ops#504