From e60349f975045aa2084654ff29615d3395d302a8 Mon Sep 17 00:00:00 2001
From: Erik Hanson <erik@erikhanson.dev>
Date: Fri, 6 Oct 2023 14:05:01 -0700
Subject: [PATCH] pkp/pkp-lib#9771 Move ORCID functionality into core
 application

---
 api/v1/orcid/index.php                        |  20 +++
 classes/orcid/OrcidReview.php                 | 134 ++++++++++++++++++
 classes/orcid/OrcidWork.php                   | 116 +++++++++++++++
 .../orcid/actions/SendSubmissionToOrcid.php   |  44 ++++++
 dbscripts/xml/upgrade.xml                     |   1 +
 jobs/orcid/PublishReviewerWorkToOrcid.php     | 121 ++++++++++++++++
 pages/article/ArticleHandler.php              |   2 +
 plugins/themes/default/styles/index.less      |   2 +
 registry/emailTemplates.xml                   |   2 +
 registry/uiLocaleKeysBackend.json             |   6 +
 10 files changed, 448 insertions(+)
 create mode 100644 api/v1/orcid/index.php
 create mode 100644 classes/orcid/OrcidReview.php
 create mode 100644 classes/orcid/OrcidWork.php
 create mode 100644 classes/orcid/actions/SendSubmissionToOrcid.php
 create mode 100644 jobs/orcid/PublishReviewerWorkToOrcid.php

diff --git a/api/v1/orcid/index.php b/api/v1/orcid/index.php
new file mode 100644
index 00000000000..9e3bc82e2d3
--- /dev/null
+++ b/api/v1/orcid/index.php
@@ -0,0 +1,20 @@
+<?php
+
+/**
+ * @defgroup api_v1_orcid ORCID API requests
+ */
+
+/**
+ * @file api/v1/orcid/index.php
+ *
+ * Copyright (c) 2024 Simon Fraser University
+ * Copyright (c) 2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup api_v1_orcid
+ *
+ * @brief Handle requests for ORCID API functions.
+ *
+ */
+
+return new \PKP\handler\APIHandler(new \PKP\API\v1\orcid\OrcidController());
diff --git a/classes/orcid/OrcidReview.php b/classes/orcid/OrcidReview.php
new file mode 100644
index 00000000000..02f7183d965
--- /dev/null
+++ b/classes/orcid/OrcidReview.php
@@ -0,0 +1,134 @@
+<?php
+
+/**
+ * @file classes/orcid/OrcidReview.php
+ *
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class OrcidReview
+ *
+ * @brief Builds ORCID review object for deposit
+ */
+
+namespace APP\orcid;
+
+use APP\core\Application;
+use APP\submission\Submission;
+use Carbon\Carbon;
+use PKP\context\Context;
+use PKP\doi\Doi;
+use PKP\i18n\LocaleConversion;
+use PKP\orcid\OrcidManager;
+use PKP\submission\reviewAssignment\ReviewAssignment;
+
+class OrcidReview
+{
+    private array $data;
+
+    public function __construct(
+        private Submission $submission,
+        private ReviewAssignment $review,
+        private Context $context,
+    ) {
+        $this->data = $this->build();
+    }
+
+    /**
+     * Returns ORCID review data as an associative array, ready for deposit.
+     */
+    public function toArray(): array
+    {
+        return $this->data;
+    }
+
+    /**
+     * Builds the internal structure for the ORCID review.
+     */
+    private function build(): array
+    {
+        $publicationUrl = Application::get()->getDispatcher()->url(
+            Application::get()->getRequest(),
+            Application::ROUTE_PAGE,
+            $this->context->getPath(),
+            'article',
+            'view',
+            $this->submission->getId(),
+            urlLocaleForPage: '',
+        );
+
+        $submissionLocale = $this->submission->getData('locale');
+        $currentPublication = $this->submission->getCurrentPublication();
+
+        if (empty($this->review->getData('dateCompleted')) || empty($this->context->getData('onlineIssn'))) {
+            return [];
+        }
+
+        $reviewCompletionDate = Carbon::parse($this->review->getData('dateCompleted'));
+
+        $orcidReview = [
+            'reviewer-role' => 'reviewer',
+            'review-type' => 'review',
+            'review-completion-date' => [
+                'year' => [
+                    'value' => $reviewCompletionDate->format('Y')
+                ],
+                'month' => [
+                    'value' => $reviewCompletionDate->format('m')
+                ],
+                'day' => [
+                    'value' => $reviewCompletionDate->format('d')
+                ]
+            ],
+            'review-group-id' => 'issn:' . $this->context->getData('onlineIssn'),
+
+            'convening-organization' => [
+                'name' => $this->context->getData('publisherInstitution'),
+                'address' => [
+                    'city' => OrcidManager::getCity($this->context),
+                    'country' => OrcidManager::getCountry($this->context),
+
+                ]
+            ],
+            'review-identifiers' => ['external-id' => [
+                [
+                    'external-id-type' => 'source-work-id',
+                    'external-id-value' => $this->review->getData('reviewRoundId'),
+                    'external-id-relationship' => 'part-of']
+            ]]
+        ];
+        if ($this->review->getReviewMethod() == ReviewAssignment::SUBMISSION_REVIEW_METHOD_OPEN) {
+            $orcidReview['subject-url'] = ['value' => $publicationUrl];
+            $orcidReview['review-url'] = ['value' => $publicationUrl];
+            $orcidReview['subject-type'] = 'journal-article';
+            $orcidReview['subject-name'] = [
+                'title' => ['value' => $this->submission->getCurrentPublication()->getLocalizedData('title') ?? '']
+            ];
+
+            if (!empty($currentPublication->getDoi())) {
+                /** @var Doi $doiObject */
+                $doiObject = $currentPublication->getData('doiObject');
+                $externalIds = [
+                    'external-id-type' => 'doi',
+                    'external-id-value' => $doiObject->getDoi(),
+                    'external-id-url' => [
+                        'value' => $doiObject->getResolvingUrl(),
+                    ],
+                    'external-id-relationship' => 'self'
+
+                ];
+                $orcidReview['subject-external-identifier'] = $externalIds;
+            }
+        }
+
+        $allTitles = $currentPublication->getData('title');
+        foreach ($allTitles as $locale => $title) {
+            if ($locale !== $submissionLocale) {
+                $orcidReview['subject-name']['translated-title'] = ['value' => $title, 'language-code' => LocaleConversion::getIso1FromLocale($locale)];
+            }
+        }
+
+        return $orcidReview;
+    }
+}
diff --git a/classes/orcid/OrcidWork.php b/classes/orcid/OrcidWork.php
new file mode 100644
index 00000000000..74b27469a3e
--- /dev/null
+++ b/classes/orcid/OrcidWork.php
@@ -0,0 +1,116 @@
+<?php
+
+/**
+ * @file classes/orcid/OrcidWork.php
+ *
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class OrcidWork
+ *
+ * @brief Builds ORCID work object for deposit
+ */
+
+namespace APP\orcid;
+
+use APP\core\Application;
+use APP\issue\Issue;
+use APP\plugins\generic\citationStyleLanguage\CitationStyleLanguagePlugin;
+use APP\plugins\PubIdPlugin;
+use APP\publication\Publication;
+use APP\submission\Submission;
+use PKP\context\Context;
+use PKP\orcid\PKPOrcidWork;
+use PKP\plugins\PluginRegistry;
+
+class OrcidWork extends PKPOrcidWork
+{
+    public function __construct(
+        protected Publication $publication,
+        protected Context $context,
+        protected array $authors,
+        protected ?Issue $issue = null
+    ) {
+        parent::__construct($this->publication, $this->context, $this->authors);
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function getAppPubIdExternalIds(PubIdPlugin $plugin): array
+    {
+        $ids = [];
+
+        $pubIdType = $plugin->getPubIdType();
+        $pubId = $this->issue?->getStoredPubId($pubIdType);
+        if ($pubId) {
+            $ids[] = [
+                'external-id-type' => self::PUBID_TO_ORCID_EXT_ID[$pubIdType],
+                'external-id-value' => $pubId,
+                'external-id-url' => [
+                    'value' => $plugin->getResolvingURL($this->context->getId(), $pubId)
+                ],
+                'external-id-relationship' => 'part-of'
+            ];
+        }
+
+        return $ids;
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function getAppDoiExternalIds(): array
+    {
+        $ids = [];
+
+        $issueDoiObject = $this->issue->getData('doiObject');
+        if ($issueDoiObject) {
+            $ids[] = [
+                'external-id-type' => self::PUBID_TO_ORCID_EXT_ID['doi'],
+                'external-id-value' => $issueDoiObject->getData('doi'),
+                'external-id-url' => [
+                    'value' => $issueDoiObject->getResolvingUrl()
+                ],
+                'external-id-relationship' => 'part-of'
+            ];
+        }
+
+        return $ids;
+    }
+
+    /**
+     * @inheritDoc
+     */
+    protected function getOrcidPublicationType(): string
+    {
+        return 'journal-article';
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function getBibtexCitation(Submission $submission): string
+    {
+        $request = Application::get()->getRequest();
+        try {
+            PluginRegistry::loadCategory('generic');
+            /** @var CitationStyleLanguagePlugin $citationPlugin */
+            $citationPlugin = PluginRegistry::getPlugin('generic', 'citationstylelanguageplugin');
+            return trim(
+                strip_tags(
+                    $citationPlugin->getCitation(
+                        $request,
+                        $submission,
+                        'bibtex',
+                        $this->issue,
+                        $this->publication
+                    )
+                )
+            );
+        } catch (\Exception $exception) {
+            return '';
+        }
+    }
+}
diff --git a/classes/orcid/actions/SendSubmissionToOrcid.php b/classes/orcid/actions/SendSubmissionToOrcid.php
new file mode 100644
index 00000000000..bb7de09e32e
--- /dev/null
+++ b/classes/orcid/actions/SendSubmissionToOrcid.php
@@ -0,0 +1,44 @@
+<?php
+
+/**
+ * @file classes/orcid/actions/SendSubmissionToOrcid.php
+ *
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class SendSubmissionToOrcid
+ *
+ * @brief Compile and trigger deposits of submissions to ORCID.
+ */
+
+namespace APP\orcid\actions;
+
+use APP\facades\Repo;
+use APP\orcid\OrcidWork;
+use PKP\orcid\actions\PKPSendSubmissionToOrcid;
+use PKP\orcid\PKPOrcidWork;
+
+class SendSubmissionToOrcid extends PKPSendSubmissionToOrcid
+{
+    /**
+     * @inheritDoc
+     */
+    protected function getOrcidWork(array $authors): ?PKPOrcidWork
+    {
+        $issueId = $this->publication->getData('issueId');
+        if (isset($issueId)) {
+            $issue = Repo::issue()->get($issueId);
+        }
+
+        return new OrcidWork($this->publication, $this->context, $authors, $issue ?? null);
+    }
+
+    /**
+     * @inheritDoc
+     */
+    protected function canDepositSubmission(): bool
+    {
+        return true;
+    }
+}
diff --git a/dbscripts/xml/upgrade.xml b/dbscripts/xml/upgrade.xml
index c662a2df355..ffd6efbbaa3 100644
--- a/dbscripts/xml/upgrade.xml
+++ b/dbscripts/xml/upgrade.xml
@@ -133,6 +133,7 @@
 		<migration class="PKP\migration\upgrade\v3_5_0\I9809_ReviewCancelDate"/>
 		<migration class="PKP\migration\upgrade\v3_5_0\I9860_EditorialMastheadNavMenuItem"/>
 		<migration class="PKP\migration\upgrade\v3_5_0\I8826_AddMissingForeignKeys" />
+        <migration class="PKP\migration\upgrade\v3_5_0\I9771_OrcidMigration"/>
 	</upgrade>
 
 	<!-- update plugin configuration - should be done as the final upgrade task -->
diff --git a/jobs/orcid/PublishReviewerWorkToOrcid.php b/jobs/orcid/PublishReviewerWorkToOrcid.php
new file mode 100644
index 00000000000..d5b1ae46edf
--- /dev/null
+++ b/jobs/orcid/PublishReviewerWorkToOrcid.php
@@ -0,0 +1,121 @@
+<?php
+
+/**
+ * @file jobs/doi/PublishReviewerWorkToOrcid.php
+ *
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class PublishReviewerWorkToOrcid
+ *
+ * @ingroup jobs
+ *
+ * @brief Job to deposit peer review contribution to reviewer's ORCID profile
+ */
+
+namespace APP\jobs\orcid;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use APP\orcid\OrcidReview;
+use APP\submission\Submission;
+use Carbon\Carbon;
+use GuzzleHttp\Exception\ClientException;
+use PKP\config\Config;
+use PKP\context\Context;
+use PKP\jobs\BaseJob;
+use PKP\orcid\OrcidManager;
+use PKP\submission\reviewAssignment\ReviewAssignment;
+
+class PublishReviewerWorkToOrcid extends BaseJob
+{
+    public function __construct(
+        private Submission $submission,
+        private Context $context,
+        private ReviewAssignment $reviewAssignment,
+    ) {
+        parent::__construct();
+    }
+
+    /**
+     * @inheritDoc
+     */
+    public function handle()
+    {
+        // If the application is set to sandbox mode, it will not reach out to external services
+        if (Config::getVar('general', 'sandbox', false)) {
+            $this->fail('Application is set to sandbox mode and will not interact with the ORCID service');
+            return;
+        }
+
+        if (!OrcidManager::isMemberApiEnabled($this->context)) {
+            return;
+        }
+
+        if (!OrcidManager::getCity($this->context) || !OrcidManager::getCountry($this->context)) {
+            return;
+        }
+
+        $reviewer = Repo::user()->get($this->reviewAssignment->getData('reviewerId'));
+
+        if ($reviewer->getOrcid() && $reviewer->getData('orcidAccessToken')) {
+            $orcidAccessExpiresOn = Carbon::parse($reviewer->getData('orcidAccessExpiresOn'));
+            if ($orcidAccessExpiresOn->isFuture()) {
+                # Extract only the ORCID from the stored ORCID uri
+                $orcid = basename(parse_url($reviewer->getOrcid(), PHP_URL_PATH));
+
+                $orcidReview = new OrcidReview($this->submission, $this->reviewAssignment, $this->context);
+
+                $uri = OrcidManager::getApiPath($this->context) . OrcidManager::ORCID_API_VERSION_URL . $orcid . '/' . OrcidManager::ORCID_REVIEW_URL;
+                $method = 'POST';
+                if ($putCode = $reviewer->getData('orcidReviewPutCode')) {
+                    $uri .= '/' . $putCode;
+                    $method = 'PUT';
+                    $orcidReview['put-code'] = $putCode;
+                }
+                $headers = [
+                    'Content-Type' => ' application/vnd.orcid+json; qs=4',
+                    'Accept' => 'application/json',
+                    'Authorization' => 'Bearer ' . $reviewer->getData('orcidAccessToken')
+                ];
+                $httpClient = Application::get()->getHttpClient();
+
+                try {
+                    $response = $httpClient->request(
+                        $method,
+                        $uri,
+                        [
+                            'headers' => $headers,
+                            'json' => $orcidReview->toArray(),
+                        ]
+                    );
+
+                    $httpStatus = $response->getStatusCode();
+                    OrcidManager::logInfo("Response status: {$httpStatus}");
+                    $responseHeaders = $response->getHeaders();
+                    switch ($httpStatus) {
+                        case 200:
+                            OrcidManager::logInfo("Review updated in profile, putCode: {$putCode}");
+                            break;
+                        case 201:
+                            $location = $responseHeaders['Location'][0];
+                            // Extract the ORCID work put code for updates/deletion.
+                            $putCode = basename(parse_url($location, PHP_URL_PATH));
+                            $reviewer->setData('orcidReviewPutCode', $putCode);
+                            Repo::user()->edit($reviewer, ['orcidReviewPutCode']);
+                            OrcidManager::logInfo("Review added to profile, putCode: {$putCode}");
+                            break;
+                        default:
+                            OrcidManager::logError("Unexpected status {$httpStatus} response, body: " . json_encode($responseHeaders));
+                    }
+                } catch (ClientException $exception) {
+                    $reason = $exception->getResponse()->getBody();
+                    OrcidManager::logError("Publication fail: {$reason}");
+
+                    $this->fail($exception);
+                }
+            }
+        }
+    }
+}
diff --git a/pages/article/ArticleHandler.php b/pages/article/ArticleHandler.php
index 18de5d32962..57ae0b93020 100644
--- a/pages/article/ArticleHandler.php
+++ b/pages/article/ArticleHandler.php
@@ -34,6 +34,7 @@
 use PKP\core\PKPApplication;
 use PKP\core\PKPJwt as JWT;
 use PKP\db\DAORegistry;
+use PKP\orcid\OrcidManager;
 use PKP\plugins\Hook;
 use PKP\plugins\PluginRegistry;
 use PKP\security\authorization\ContextRequiredPolicy;
@@ -307,6 +308,7 @@ public function view($args, $request)
             'copyrightYear' => $publication->getData('copyrightYear'),
             'pubIdPlugins' => PluginRegistry::loadCategory('pubIds', true),
             'keywords' => $publication->getData('keywords'),
+            'orcidIcon' => OrcidManager::getIcon(),
         ]);
 
         // Fetch and assign the galley to the template
diff --git a/plugins/themes/default/styles/index.less b/plugins/themes/default/styles/index.less
index 52eea2223f7..5b82741f955 100644
--- a/plugins/themes/default/styles/index.less
+++ b/plugins/themes/default/styles/index.less
@@ -20,6 +20,8 @@
 @import "../../../../lib/pkp/styles/variables.less";
 @import "../../../../lib/pkp/styles/utils.less";
 @import "../../../../lib/pkp/styles/helpers.less";
+// General ORCID styles
+@import '../../../../lib/pkp/styles/orcid.less';
 
 // Styles unique to this theme
 @import "variables.less";
diff --git a/registry/emailTemplates.xml b/registry/emailTemplates.xml
index 33a38623f5c..5fac37ce923 100644
--- a/registry/emailTemplates.xml
+++ b/registry/emailTemplates.xml
@@ -76,4 +76,6 @@
 	<email key="SUBMISSION_SAVED_FOR_LATER" name="mailable.submissionSavedForLater.name" subject="emails.submissionSavedForLater.subject" body="emails.submissionSavedForLater.body"/>
 	<email key="SUBMISSION_NEEDS_EDITOR" name="mailable.submissionNeedsEditor.name" subject="emails.submissionNeedsEditor.subject" body="emails.submissionNeedsEditor.body"/>
 	<email key="PAYMENT_REQUEST_NOTIFICATION" name="mailable.paymentRequest.name" subject="emails.paymentRequestNotification.subject" body="emails.paymentRequestNotification.body"/>
+    <email key="ORCID_COLLECT_AUTHOR_ID" name="orcidProfile.orcidCollectAuthorId.name" subject="emails.orcidCollectAuthorId.subject" body="emails.orcidCollectAuthorId.body"/>
+    <email key="ORCID_REQUEST_AUTHOR_AUTHORIZATION" name="orcidProfile.orcidRequestAuthorAuthorization.name"  subject="emails.orcidRequestAuthorAuthorization.subject" body="emails.orcidRequestAuthorAuthorization.body"/>
 </emails>
diff --git a/registry/uiLocaleKeysBackend.json b/registry/uiLocaleKeysBackend.json
index 3763c71436a..ce214ec322f 100644
--- a/registry/uiLocaleKeysBackend.json
+++ b/registry/uiLocaleKeysBackend.json
@@ -126,6 +126,12 @@
   "manager.dois.update.partialFailure",
   "manager.dois.update.success",
   "navigation.backTo",
+  "orcid.field.authorEmailModal.message",
+  "orcid.field.authorEmailModal.title",
+  "orcid.field.deleteOrcidModal.message",
+  "orcid.field.deleteOrcidModal.title",
+  "orcid.field.verification.request",
+  "orcid.field.verification.requested",
   "publication.jats.autoCreatedMessage",
   "publication.jats.confirmDeleteFileButton",
   "publication.jats.confirmDeleteFileMessage",