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plugins/generic/crossref/CrossrefExportPlugin.php

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+<?php
+
+/**
+ * @file plugins/generic/crossref/CrossrefExportPlugin.php
+ *
+ * Copyright (c) 2014-2022 Simon Fraser University
+ * Copyright (c) 2003-2022 John Willinsky
+ * Distributed under The MIT License. For full terms see the file LICENSE.
+ *
+ * @class CrossrefExportPlugin
+ *
+ * @brief Crossref/MEDLINE XML metadata export plugin
+ */
+
+namespace APP\plugins\generic\crossref;
+
+use APP\core\Application;
+use PKP\config\Config;
+use APP\facades\Repo;
+use APP\issue\Issue;
+use APP\journal\Journal;
+use APP\plugins\DOIPubIdExportPlugin;
+use APP\plugins\IDoiRegistrationAgency;
+use APP\submission\Submission;
+use Exception;
+use GuzzleHttp\Exception\GuzzleException;
+use GuzzleHttp\Exception\RequestException;
+use PKP\core\DataObject;
+use PKP\doi\Doi;
+use PKP\file\FileManager;
+use PKP\file\TemporaryFileManager;
+use PKP\plugins\Hook;
+use PKP\plugins\Plugin;
+
+class CrossrefExportPlugin extends DOIPubIdExportPlugin
+{
+    // The status of the Crossref DOI.
+    // any, notDeposited, and markedRegistered are reserved
+    public const CROSSREF_STATUS_FAILED = 'failed';
+    public const CROSSREF_API_DEPOSIT_OK = 200;
+    public const CROSSREF_API_DEPOSIT_ERROR_FROM_CROSSREF = 403;
+    public const CROSSREF_API_URL = 'https://api.crossref.org/v2/deposits';
+    //TESTING
+    public const CROSSREF_API_URL_DEV = 'https://test.crossref.org/v2/deposits';
+    public const CROSSREF_API_STATUS_URL = 'https://doi.crossref.org/servlet/submissionDownload';
+    //TESTING
+    public const CROSSREF_API_STATUS_URL_DEV = 'https://test.crossref.org/servlet/submissionDownload';
+    // The name of the setting used to save the registered DOI and the URL with the deposit status.
+    public const CROSSREF_DEPOSIT_STATUS = 'depositStatus';
+
+    public function __construct(protected IDoiRegistrationAgency|Plugin $agencyPlugin)
+    {
+        parent::__construct();
+    }
+
+    public function register($category, $path, $mainContextId = null)
+    {
+        $success = parent::register($category, $path, $mainContextId);
+        if ($success) {
+            // register hooks. This will prevent DB access attempts before the
+            // schema is installed.
+            if (Application::isUnderMaintenance()) {
+                return true;
+            }
+        }
+        return $success;
+    }
+
+    /**
+     * @copydoc Plugin::getName()
+     */
+    public function getName()
+    {
+        return 'CrossrefExportPlugin';
+    }
+
+    /**
+     * @copydoc Plugin::getDisplayName()
+     */
+    public function getDisplayName()
+    {
+        return __('plugins.importexport.crossref.displayName');
+    }
+
+    /**
+     * @copydoc Plugin::getDescription()
+     */
+    public function getDescription()
+    {
+        return __('plugins.importexport.crossref.description');
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getSubmissionFilter()
+     */
+    public function getSubmissionFilter()
+    {
+        return 'article=>crossref-xml';
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getIssueFilter()
+     */
+    public function getIssueFilter()
+    {
+        return 'issue=>crossref-xml';
+    }
+
+    /** Proxy to main plugin class's `getSetting` method */
+    public function getSetting($contextId, $name)
+    {
+        return $this->agencyPlugin->getSetting($contextId, $name);
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getStatusMessage()
+     */
+    public function getStatusMessage($request)
+    {
+        // Application is set to sandbox mode and will not run the features of plugin
+        if (Config::getVar('general', 'sandbox', false)) {
+            error_log('Application is set to sandbox mode and will not have any interaction with crossref external service');
+            return __('common.sandbox');
+        }
+        
+        // if the failure occurred on request and the message was saved
+        // return that message
+        $articleId = $request->getUserVar('articleId');
+        $article = Repo::submission()->get((int)$articleId);
+        $failedMsg = $article->getData('doiObject')->getData($this->getFailedMsgSettingName());
+        if (!empty($failedMsg)) {
+            return $failedMsg;
+        }
+
+        $context = $request->getContext();
+
+        $httpClient = Application::get()->getHttpClient();
+        try {
+            $response = $httpClient->request(
+                'POST',
+                $this->isTestMode($context) ? static::CROSSREF_API_STATUS_URL_DEV : static::CROSSREF_API_STATUS_URL,
+                [
+                    'form_params' => [
+                        'doi_batch_id' => $request->getUserVar('batchId'),
+                        'type' => 'result',
+                        'usr' => $this->getSetting($context->getId(), 'username'),
+                        'pwd' => $this->getSetting($context->getId(), 'password'),
+                    ]
+                ]
+            );
+        } catch (RequestException $e) {
+            $returnMessage = $e->getMessage();
+            if ($e->hasResponse()) {
+                $returnMessage = $e->getResponse()->getBody() . ' (' . $e->getResponse()->getStatusCode() . ' ' . $e->getResponse()->getReasonPhrase() . ')';
+            }
+            return __('plugins.importexport.common.register.error.mdsError', ['param' => $returnMessage]);
+        }
+
+        return (string) $response->getBody();
+    }
+
+    /**
+     * Get a list of additional setting names that should be stored with the objects.
+     *
+     * @return array
+     */
+    protected function _getObjectAdditionalSettings()
+    {
+        return array_merge(parent::_getObjectAdditionalSettings(), [
+            $this->getDepositBatchIdSettingName(),
+            $this->getFailedMsgSettingName(),
+            $this->getSuccessMsgSettingName(),
+        ]);
+    }
+
+    /**
+     * @copydoc ImportExportPlugin::getPluginSettingsPrefix()
+     */
+    public function getPluginSettingsPrefix()
+    {
+        return 'crossrefplugin';
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getSettingsFormClassName()
+     */
+    public function getSettingsFormClassName()
+    {
+        throw new Exception('DOI settings no longer managed via plugin settings form.');
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getExportDeploymentClassName()
+     */
+    public function getExportDeploymentClassName()
+    {
+        return (string) \APP\plugins\generic\crossref\CrossrefExportDeployment::class;
+    }
+
+    public function exportAndDeposit($context, $objects, $filter, string &$responseMessage, $noValidation = null): bool
+    {
+        $fileManager = new FileManager();
+        $resultErrors = [];
+
+        assert($filter != null);
+        // Errors occurred will be accessible via the status link
+        // thus do not display all errors notifications (for every article),
+        // just one general.
+        // Warnings occurred when the registration was successful will however be
+        // displayed for each article.
+        $errorsOccurred = false;
+        // The new Crossref deposit API expects one request per object.
+        // On contrary the export supports bulk/batch object export, thus
+        // also the filter expects an array of objects.
+        // Thus the foreach loop, but every object will be in an one item array for
+        // the export and filter to work.
+        foreach ($objects as $object) {
+            // Get the XML
+            // Supply an exportErrors array because otherwise exportXML() will echo out export errors
+            $exportErrors = [];
+            $exportXml = $this->exportXML([$object], $filter, $context, $noValidation, $exportErrors);
+            // Write the XML to a file.
+            // export file name example: crossref-20160723-160036-articles-1-1.xml
+            $objectFileNamePart = $this->_getObjectFileNamePart($object);
+            $exportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.xml');
+            $fileManager->writeFile($exportFileName, $exportXml);
+            // Deposit the XML file.
+            $result = $this->depositXML($object, $context, $exportFileName);
+            if (!$result) {
+                $errorsOccurred = true;
+            }
+            if (is_array($result)) {
+                $resultErrors[] = $result;
+            }
+            // Remove all temporary files.
+            $fileManager->deleteByPath($exportFileName);
+        }
+        // Prepare response message and return status
+        if (empty($resultErrors)) {
+            if ($errorsOccurred) {
+                $responseMessage = 'plugins.importexport.crossref.register.error.mdsError';
+                return false;
+            } else {
+                $responseMessage = $this->getDepositSuccessNotificationMessageKey();
+                return true;
+            }
+        } else {
+            $responseMessage = 'api.dois.400.depositFailed';
+            return false;
+        }
+    }
+
+    /**
+     * Exports and stores XML as a TemporaryFile
+     *
+     *
+     * @throws Exception
+     */
+    public function exportAsDownload(\PKP\context\Context $context, array $objects, string $filter, string $objectsFileNamePart, ?bool $noValidation = null, ?array &$exportErrors = null): ?int
+    {
+        $fileManager = new TemporaryFileManager();
+
+        $exportErrors = [];
+        $exportXml = $this->exportXML($objects, $filter, $context, $noValidation, $exportErrors);
+
+        $exportFileName = $this->getExportFileName($this->getExportPath(), $objectsFileNamePart, $context, '.xml');
+
+        $fileManager->writeFile($exportFileName, $exportXml);
+
+        $user = Application::get()->getRequest()->getUser();
+
+        return $fileManager->createTempFileFromExisting($exportFileName, $user->getId());
+    }
+
+    /**
+     * @param Submission $objects
+     * @param Journal $context
+     * @param string $filename Export XML filename
+     *
+     * @throws GuzzleException
+     *
+     * @see PubObjectsExportPlugin::depositXML()
+     *
+     */
+    public function depositXML($objects, $context, $filename)
+    {
+        // Application is set to sandbox mode and will not run the features of plugin
+        if (Config::getVar('general', 'sandbox', false)) {
+            error_log('Application is set to sandbox mode and will not have any interaction with crossref external service');
+            return false;
+        }
+
+        $status = null;
+        $msgSave = null;
+
+        $httpClient = Application::get()->getHttpClient();
+        assert(is_readable($filename));
+
+        try {
+            $response = $httpClient->request(
+                'POST',
+                $this->isTestMode($context) ? static::CROSSREF_API_URL_DEV : static::CROSSREF_API_URL,
+                [
+                    'multipart' => [
+                        [
+                            'name' => 'usr',
+                            'contents' => $this->getSetting($context->getId(), 'username'),
+                        ],
+                        [
+                            'name' => 'pwd',
+                            'contents' => $this->getSetting($context->getId(), 'password'),
+                        ],
+                        [
+                            'name' => 'operation',
+                            'contents' => 'doMDUpload',
+                        ],
+                        [
+                            'name' => 'mdFile',
+                            'contents' => fopen($filename, 'r'),
+                        ],
+                    ]
+                ]
+            );
+        } catch (RequestException $e) {
+            $returnMessage = $e->getMessage();
+            if ($e->hasResponse()) {
+                $eResponseBody = $e->getResponse()->getBody();
+                $eStatusCode = $e->getResponse()->getStatusCode();
+                if ($eStatusCode == static::CROSSREF_API_DEPOSIT_ERROR_FROM_CROSSREF) {
+                    $xmlDoc = new \DOMDocument('1.0', 'utf-8');
+                    $xmlDoc->loadXML($eResponseBody);
+                    $batchIdNode = $xmlDoc->getElementsByTagName('batch_id')->item(0);
+                    $msg = $xmlDoc->getElementsByTagName('msg')->item(0)->nodeValue;
+                    $msgSave = $msg . PHP_EOL . $eResponseBody;
+                    $status = Doi::STATUS_ERROR;
+                    $this->updateDepositStatus($context, $objects, $status, $batchIdNode->nodeValue, $msgSave);
+                    $returnMessage = $msg . ' (' . $eStatusCode . ' ' . $e->getResponse()->getReasonPhrase() . ')';
+                } else {
+                    $returnMessage = $eResponseBody . ' (' . $eStatusCode . ' ' . $e->getResponse()->getReasonPhrase() . ')';
+                    $this->updateDepositStatus($context, $objects, Doi::STATUS_ERROR, null, $returnMessage);
+                }
+            }
+            return [['plugins.importexport.common.register.error.mdsError', $returnMessage]];
+        }
+
+        // Get DOMDocument from the response XML string
+        $xmlDoc = new \DOMDocument('1.0', 'utf-8');
+        $xmlDoc->loadXML($response->getBody());
+        $batchIdNode = $xmlDoc->getElementsByTagName('batch_id')->item(0);
+        $submissionIdNode = $xmlDoc->getElementsByTagName('submission_id')->item(0);
+        $successMessage = __('plugins.generic.crossref.successMessage', ['submissionId' => $submissionIdNode->nodeValue]);
+
+        // Get the DOI deposit status
+        // If the deposit failed
+        $failureCountNode = $xmlDoc->getElementsByTagName('failure_count')->item(0);
+        $failureCount = (int) $failureCountNode->nodeValue;
+        if ($failureCount > 0) {
+            $status = Doi::STATUS_ERROR;
+            $result = false;
+        } else {
+            // Deposit was received
+            $status = Doi::STATUS_REGISTERED;
+            $result = true;
+
+            // If there were some warnings, display them
+            $warningCountNode = $xmlDoc->getElementsByTagName('warning_count')->item(0);
+            $warningCount = (int) $warningCountNode->nodeValue;
+            if ($warningCount > 0) {
+                $result = [['plugins.importexport.crossref.register.success.warning', htmlspecialchars($response->getBody())]];
+            }
+            // A possibility for other plugins (e.g. reference linking) to work with the response
+            Hook::run('crossrefexportplugin::deposited', [[$this, $response->getBody(), $objects]]);
+        }
+
+        // Update the status
+        if ($status) {
+            $this->updateDepositStatus($context, $objects, $status, $batchIdNode->nodeValue, $msgSave, $successMessage);
+        }
+
+        return $result;
+    }
+
+    /**
+     * Check the Crossref APIs, if deposits and registration have been successful
+     *
+     * @param Journal $context
+     * @param DataObject $object The object getting deposited
+     * @param int $status
+     * @param string $batchId
+     * @param string $failedMsg (optional)
+     * @param null|mixed $successMsg
+     */
+    public function updateDepositStatus($context, $object, $status, $batchId = null, $failedMsg = null, $successMsg = null)
+    {
+        assert($object instanceof Submission || $object instanceof Issue);
+        if ($object instanceof Submission) {
+            $doiIds = Repo::doi()->getDoisForSubmission($object->getId());
+        } else {
+            $doiIds = Repo::doi()->getDoisForIssue($object->getId(), true);
+        }
+
+        foreach ($doiIds as $doiId) {
+            $doi = Repo::doi()->get($doiId);
+
+            $editParams = [
+                'status' => $status,
+                // Sets new failedMsg or resets to null for removal of previous message
+                $this->getFailedMsgSettingName() => $failedMsg,
+                $this->getDepositBatchIdSettingName() => $batchId,
+                $this->getSuccessMsgSettingName() => $successMsg,
+            ];
+
+            if ($status === Doi::STATUS_REGISTERED) {
+                $editParams['registrationAgency'] = $this->getName();
+            }
+
+            Repo::doi()->edit($doi, $editParams);
+        }
+    }
+
+    /**
+     * @copydoc DOIPubIdExportPlugin::markRegistered()
+     */
+    public function markRegistered($context, $objects)
+    {
+        foreach ($objects as $object) {
+            // Get all DOIs for each object
+            // Check if submission or issue
+            if ($object instanceof Submission) {
+                $doiIds = Repo::doi()->getDoisForSubmission($object->getId());
+            } else {
+                $doiIds = Repo::doi()->getDoisForIssue($object->getId, true);
+            }
+
+            foreach ($doiIds as $doiId) {
+                Repo::doi()->markRegistered($doiId);
+            }
+        }
+    }
+
+    /**
+     * Get request failed message setting name.
+     * NB: Changed as of 3.4
+     *
+     * @return string
+     */
+    public function getFailedMsgSettingName()
+    {
+        return $this->getPluginSettingsPrefix() . '_failedMsg';
+    }
+
+    /**
+     * Get deposit batch ID setting name.
+     * NB Changed as of 3.4
+     *
+     * @return string
+     */
+    public function getDepositBatchIdSettingName()
+    {
+        return $this->getPluginSettingsPrefix() . '_batchId';
+    }
+
+    public function getSuccessMsgSettingName(): string
+    {
+        return $this->getPluginSettingsPrefix() . '_successMsg';
+    }
+
+    /**
+     * @copydoc PubObjectsExportPlugin::getDepositSuccessNotificationMessageKey()
+     */
+    public function getDepositSuccessNotificationMessageKey()
+    {
+        return 'plugins.importexport.common.register.success';
+    }
+
+    /**
+     * @param Submission|Issue $object
+     *
+     */
+    private function _getObjectFileNamePart(DataObject $object): string
+    {
+        if ($object instanceof Submission) {
+            return 'articles-' . $object->getId();
+        } elseif ($object instanceof Issue) {
+            return 'issues-' . $object->getId();
+        } else {
+            return '';
+        }
+    }
+}