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OrcidProfilePlugin.inc.php
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OrcidProfilePlugin.inc.php
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<?php
/**
* @file plugins/generic/orcidProfile/OrcidProfilePlugin.inc.php
*
* Copyright (c) 2015-2019 University of Pittsburgh
* Copyright (c) 2014-2019 Simon Fraser University
* Copyright (c) 2003-2019 John Willinsky
* Distributed under the GNU GPL v2. For full terms see the file docs/COPYING.
*
* @class OrcidProfilePlugin
* @ingroup plugins_generic_orcidProfile
*
* @brief ORCID Profile plugin class
*/
import('lib.pkp.classes.plugins.GenericPlugin');
define('ORCID_URL', 'https://orcid.org/');
define('ORCID_URL_SANDBOX', 'https://sandbox.orcid.org/');
define('ORCID_API_URL_PUBLIC', 'https://pub.orcid.org/');
define('ORCID_API_URL_PUBLIC_SANDBOX', 'https://pub.sandbox.orcid.org/');
define('ORCID_API_URL_MEMBER', 'https://api.orcid.org/');
define('ORCID_API_URL_MEMBER_SANDBOX', 'https://api.sandbox.orcid.org/');
define('ORCID_API_VERSION_URL', 'v2.1/');
define('ORCID_API_SCOPE_PUBLIC', '/authenticate');
define('ORCID_API_SCOPE_MEMBER', '/activities/update');
define('OAUTH_TOKEN_URL', 'oauth/token');
define('ORCID_EMPLOYMENTS_URL', 'employments');
define('ORCID_PROFILE_URL', 'person');
define('ORCID_EMAIL_URL', 'email');
define('ORCID_WORK_URL', 'work');
class OrcidProfilePlugin extends GenericPlugin {
const PUBID_TO_ORCID_EXT_ID = [ "doi" => "doi", "other::urn" => "urn"];
const USERGROUP_TO_ORCID_ROLE = [ "Author" => "AUTHOR", "Translator" => "CHAIR_OR_TRANSLATOR"];
private $submissionIdToBePublished;
private $currentContextId;
/**
* @copydoc Plugin::register()
*/
function register($category, $path, $mainContextId = null) {
$success = parent::register($category, $path, $mainContextId);
if (!Config::getVar('general', 'installed') || defined('RUNNING_UPGRADE')) return true;
if ($success && $this->getEnabled($mainContextId)) {
// Register callback for Smarty filters; add CSS
HookRegistry::register('TemplateManager::display', array($this, 'handleTemplateDisplay'));
// Add "Connect ORCID" button to PublicProfileForm
HookRegistry::register('User::PublicProfile::AdditionalItems', array($this, 'handleUserPublicProfileDisplay'));
// Display additional ORCID access information and checkbox to send e-mail to authors in the AuthorForm
HookRegistry::register('authorform::display', array($this, 'handleFormDisplay'));
// Send email to author, if the added checkbox was ticked
HookRegistry::register('authorform::execute', array($this, 'handleAuthorFormExecute'));
// Insert the OrcidHandler to handle ORCID redirects
HookRegistry::register('LoadHandler', array($this, 'setupCallbackHandler'));
// Handle ORCID on user registration
HookRegistry::register('registrationform::execute', array($this, 'collectUserOrcidId'));
// Send emails to authors without ORCID id upon submission
HookRegistry::register('submissionsubmitstep3form::execute', array($this, 'handleSubmissionSubmitStep3FormExecute'));
// Add more ORCiD fields to author DAO
HookRegistry::register('authordao::getAdditionalFieldNames', array($this, 'handleAdditionalFieldNames'));
// Add more ORCiD fields to UserDAO
HookRegistry::register('userdao::getAdditionalFieldNames', array($this, 'handleAdditionalFieldNames'));
// Send submission meta data upload to ORCID profiles on publication of an issue
HookRegistry::register('IssueGridHandler::publishIssue', array($this, 'handlePublishIssue'));
HookRegistry::register('issueentrypublicationmetadataform::execute', array($this, 'handleScheduleForPublication'));
// Send emails to authors without authorised ORCID access on promoting a submission to production
HookRegistry::register('EditorAction::recordDecision', array($this, 'handleEditorAction'));
}
return $success;
}
/**
* Get page handler path for this plugin.
* @return string Path to plugin's page handler
*/
function getHandlerPath() {
return $this->getPluginPath() . DIRECTORY_SEPARATOR . 'pages';
}
/**
* Hook callback: register pages for each sushi-lite method
* This URL is of the form: orcidapi/{$orcidrequest}
* @see PKPPageRouter::route()
*/
function setupCallbackHandler($hookName, $params) {
$page = $params[0];
if ($this->getEnabled() && $page == 'orcidapi') {
$this->import('pages/OrcidHandler');
define('HANDLER_CLASS', 'OrcidHandler');
return true;
}
return false;
}
/**
* Load a setting for a specific journal or load it from the config.inc.php if it is specified there.
*
* @param $contextId int The id of the journal from which the plugin settings should be loaded.
* @param $name string Name of the setting.
* @return mixed The setting value, either from the database for this context
* or from the global configuration file.
*/
function getSetting($contextId, $name)
{
switch ($name) {
case 'orcidProfileAPIPath':
$config_value = Config::getVar('orcid','api_url');
break;
case 'orcidClientId':
$config_value = Config::getVar('orcid','client_id');
break;
case 'orcidClientSecret':
$config_value = Config::getVar('orcid','client_secret');
break;
default:
return parent::getSetting($contextId, $name);
}
return $config_value ?: parent::getSetting($contextId, $name);
}
/**
* Check if there exist a valid orcid configuration section in the global config.inc.php of OJS.
* @return boolean True, if the config file has api_url, client_id and client_secret set in an [orcid] section
*/
function isGloballyConfigured() {
$apiUrl = Config::getVar('orcid','api_url');
$clientId = Config::getVar('orcid','client_id');
$clientSecret = Config::getVar('orcid','client_secret');
return isset($apiUrl) && trim($apiUrl) && isset($clientId) && trim($clientId) &&
isset($clientSecret) && trim($clientSecret);
}
/**
* Hook callback to handle form display.
* Registers output filter for public user profile and author form.
*
* @see Form::display()
*
* @param $hookName string
* @param $args Form[]
*
* @return bool
*/
function handleFormDisplay($hookName, $args) {
$request = PKPApplication::get()->getRequest();
$templateMgr = TemplateManager::getManager($request);
switch ($hookName) {
case 'authorform::display':
$authorForm =& $args[0];
$author = $authorForm->getAuthor();
if ($author) {
$authenticated = !empty($author->getData('orcidAccessToken'));
$templateMgr->assign( array(
'orcidAccessToken' => $author->getData('orcidAccessToken'),
'orcidAccessScope' => $author->getData('orcidAccessScope'),
'orcidAccessExpiresOn' => $author->getData('orcidAccessExpiresOn'),
'orcidAccessDenied' => $author->getData('orcidAccessDenied'),
'orcidAuthenticated' => $authenticated
));
}
$templateMgr->registerFilter("output", array($this, 'authorFormFilter'));
break;
}
return false;
}
/**
* Hook callback: register output filter for user registration and article display.
*
* @see TemplateManager::display()
*
* @param $hookName string
* @param $args array
* @return bool
*/
function handleTemplateDisplay($hookName, $args) {
$templateMgr =& $args[0];
$template =& $args[1];
$request = PKPApplication::get()->getRequest();
// Assign our private stylesheet, for front and back ends.
$templateMgr->addStyleSheet(
'orcidProfile',
$request->getBaseUrl() . '/' . $this->getStyleSheet(),
array(
'contexts' => array('frontend', 'backend')
)
);
switch ($template) {
case 'frontend/pages/userRegister.tpl':
$templateMgr->registerFilter("output", array($this, 'registrationFilter'));
break;
case 'frontend/pages/article.tpl':
//$templateMgr->assign('orcidIcon', $this->getIcon());
$script = 'var orcidIconSvg = $('. json_encode($this->getIcon()) .');';
$article = $templateMgr->getTemplateVars('article');
$authors = $article->getAuthors();
foreach ($authors as $author) {
if(!empty($author->getOrcid()) && !empty($author->getData('orcidAccessToken'))) {
$script .= '$("a[href=\"'.$author->getOrcid().'\"]").prepend(orcidIconSvg);';
}
}
$templateMgr->addJavaScript('orcidIconDisplay', $script, ['inline' => true]);
break;
}
return false;
}
/**
* Return the OAUTH path (prod or sandbox) based on the current API configuration
*
* @return string
*/
function getOauthPath() {
return $this->getOrcidUrl() . 'oauth/';
}
/**
* Return the ORCID website url (prod or sandbox) based on the current API configuration
*
* @return string
*/
function getOrcidUrl() {
$request = Application::get()->getRequest();
$context = $request->getContext();
$contextId = ($context == null) ? 0 : $context->getId();
$apiPath = $this->getSetting($contextId, 'orcidProfileAPIPath');
if ($apiPath == ORCID_API_URL_PUBLIC || $apiPath == ORCID_API_URL_MEMBER) {
return ORCID_URL;
} else {
return ORCID_URL_SANDBOX;
}
}
/**
* Return an ORCID OAuth authorization link with
*
* @param $handlerMethod string containting a valid method of the OrcidHandler
* @param $redirectParams Array associative array with additional request parameters for the redirect URL
*/
function buildOAuthUrl($handlerMethod, $redirectParams) {
$request = PKPApplication::get()->getRequest();
$context = $request->getContext();
// This should only ever happen within a context, never site-wide.
assert($context != null);
$contextId = $context->getId();
if ( $this->isMemberApiEnabled($contextId) ) {
$scope = ORCID_API_SCOPE_MEMBER;
}
else {
$scope = ORCID_API_SCOPE_PUBLIC;
}
// We need to construct a page url, but the request is using the component router.
// Use the Dispatcher to construct the url and set the page router.
$redirectUrl = $request->getDispatcher()->url($request, ROUTE_PAGE, null, 'orcidapi',
$handlerMethod, null, $redirectParams);
return $this->getOauthPath() . 'authorize?' . http_build_query(array(
'client_id' => $this->getSetting($contextId, 'orcidClientId'),
'response_type' => 'code',
'scope' => $scope,
'redirect_uri' => $redirectUrl));
}
/**
* Output filter adds ORCiD interaction to registration form.
*
* @param $output string
* @param $templateMgr TemplateManager
* @return string
*/
function registrationFilter($output, $templateMgr) {
if (preg_match('/<form[^>]+id="register"[^>]+>/', $output, $matches, PREG_OFFSET_CAPTURE)) {
$match = $matches[0][0];
$offset = $matches[0][1];
$request = Application::get()->getRequest();
$context = $request->getContext();
$contextId = ($context == null) ? 0 : $context->getId();
$targetOp = 'register';
$templateMgr->assign(array(
'targetOp' => $targetOp,
'orcidUrl' => $this->getOrcidUrl(),
'orcidOAuthUrl' => $this->buildOAuthUrl('orcidAuthorize', array('targetOp' => $targetOp)),
'orcidIcon' => $this->getIcon(),
));
$newOutput = substr($output, 0, $offset+strlen($match));
$newOutput .= $templateMgr->fetch($this->getTemplateResource('orcidProfile.tpl'));
$newOutput .= substr($output, $offset+strlen($match));
$output = $newOutput;
$templateMgr->unregisterFilter('output', array($this, 'registrationFilter'));
}
return $output;
}
/**
* Renders additional content for the PublicProfileForm.
*
* Called by @see lib/pkp/templates/user/publicProfileForm.tpl
*
* @param $output string
* @param $templateMgr TemplateManager
* @return bool
*/
function handleUserPublicProfileDisplay($hookName, $params) {
$templateMgr =& $params[1];
$output =& $params[2];
$request = Application::get()->getRequest();
$context = $request->getContext();
$user = $request->getUser();
$contextId = ($context == null) ? 0 : $context->getId();
$targetOp = 'profile';
$templateMgr->assign(array(
'targetOp' => $targetOp,
'orcidUrl' => $this->getOrcidUrl(),
'orcidOAuthUrl' => $this->buildOAuthUrl('orcidAuthorize', array('targetOp' => $targetOp)),
'orcidClientId' => $this->getSetting($contextId, 'orcidClientId'),
'orcidIcon' => $this->getIcon(),
'orcidAuthenticated' => !empty($user->getData('orcidAccessToken')),
));
$output = $templateMgr->fetch($this->getTemplateResource('orcidProfile.tpl'));
return true;
}
/**
* Output filter adds ORCiD interaction to contributors metadata add/edit form.
*
* @param $output string
* @param $templateMgr TemplateManager
* @return string
*/
function authorFormFilter($output, $templateMgr) {
if (preg_match('/<input[^>]+name="submissionId"[^>]*>/', $output, $matches, PREG_OFFSET_CAPTURE)) {
$match = $matches[0][0];
$offset = $matches[0][1];
$templateMgr->assign('orcidIcon', $this->getIcon());
$newOutput = substr($output, 0, $offset+strlen($match));
$newOutput .= $templateMgr->fetch($this->getTemplateResource('authorFormOrcid.tpl'));
$newOutput .= substr($output, $offset+strlen($match));
$output = $newOutput;
$templateMgr->unregisterFilter('output', array($this, 'authorFormFilter'));
}
return $output;
}
/**
* handleAuthorFormexecute sends an e-mail to the author if a specific checkbox was ticked in the author form.
*
* @see AuthorForm::execute() The function calling the hook.
*
* @param $hookname string
* @param $args AuthorForm[]
*/
function handleAuthorFormExecute($hookname, $args) {
$form =& $args[0];
$form->readUserVars(array('requestOrcidAuthorization', 'deleteOrcid'));
$requestAuthorization = $form->getData('requestOrcidAuthorization');
$deleteOrcid = $form->getData('deleteOrcid');
$author = $form->getAuthor();
if ($author && $requestAuthorization) {
$this->sendAuthorMail($author);
}
if ($author && $deleteOrcid) {
$author->setOrcid(null);
$this->removeOrcidAccessToken($author, false);
}
}
/**
* Collect the ORCID when registering a user.
*
* @param $hookName string
* @param $params array
* @return bool
*/
function collectUserOrcidId($hookName, $params) {
$form = $params[0];
$user = $form->user;
$form->readUserVars(array('orcid'));
$user->setOrcid($form->getData('orcid'));
return false;
}
/**
* Output filter adds ORCiD interaction to the 3rd step submission form.
*
* @param $output string
* @param $templateMgr TemplateManager
* @return bool
*/
function handleSubmissionSubmitStep3FormExecute($hookName, $params) {
$form = $params[0];
// Have to use global Request access because request is not passed to hook
$authors = $form->submission->getAuthors();
$request = Application::get()->getRequest();
$user = $request->getUser();
//error_log("OrcidProfilePlugin: authors[0] = " . var_export($authors[0], true));
//error_log("OrcidProfilePlugin: user = " . var_export($user, true));
if($authors[0]->getOrcid() === $user->getOrcid()) {
// if the author and user share the same ORCID id
// copy the access token from the user
error_log("OrcidProfilePlugin: user->orcidAccessToken = " . $user->getData('orcidAccessToken'));
$authors[0]->setData('orcidAccessToken', $user->getData('orcidAccessToken'));
$authors[0]->setData('orcidAccessScope', $user->getData('orcidAccessScope'));
$authors[0]->setData('orcidRefreshToken', $user->getData('orcidRefreshToken'));
$authors[0]->setData('orcidAccessExpiresOn', $user->getData('orcidAccessExpiresOn'));
$authors[0]->setData('orcidSandbox', $user->getData('orcidSandbox'));
$authorDao = DAORegistry::getDAO('AuthorDAO');
$authorDao->updateObject($authors[0]);
error_log("OrcidProfilePlugin: author = " . var_export($authors[0], true));
}
return false;
}
/**
* Add additional ORCID specific fields to the Author and User objects
*
* @param $hookName string
* @param $params array
*
* @return bool
*/
function handleAdditionalFieldNames($hookName, $params) {
$fields =& $params[1];
$fields[] = 'orcidSandbox';
$fields[] = 'orcidAccessToken';
$fields[] = 'orcidAccessScope';
$fields[] = 'orcidRefreshToken';
$fields[] = 'orcidAccessExpiresOn';
$fields[] = 'orcidAccessDenied';
if ($hookName === 'authordao::getAdditionalFieldNames') {
// holds a one time hash string generated before sending the ORCID authorization e-mail
$fields[] = 'orcidEmailToken';
// holds the id of the added work entry in the corresponding ORCID profile for updates
$fields[] = 'orcidWorkPutCode';
}
return false;
}
/**
* @copydoc Plugin::getDisplayName()
*/
function getDisplayName() {
return __('plugins.generic.orcidProfile.displayName');
}
/**
* @copydoc Plugin::getDescription()
*/
function getDescription() {
return __('plugins.generic.orcidProfile.description');
}
/**
* @see PKPPlugin::getInstallEmailTemplatesFile()
*/
function getInstallEmailTemplatesFile() {
return ($this->getPluginPath() . '/emailTemplates.xml');
}
/**
* @see PKPPlugin::getInstallEmailTemplateDataFile()
*/
function getInstallEmailTemplateDataFile() {
return ($this->getPluginPath() . '/locale/{$installedLocale}/emailTemplates.xml');
}
/**
* Extend the {url ...} smarty to support this plugin.
*/
function smartyPluginUrl($params, $smarty) {
$path = array($this->getCategory(), $this->getName());
if (is_array($params['path'])) {
$params['path'] = array_merge($path, $params['path']);
} elseif (!empty($params['path'])) {
$params['path'] = array_merge($path, array($params['path']));
} else {
$params['path'] = $path;
}
if (!empty($params['id'])) {
$params['path'] = array_merge($params['path'], array($params['id']));
unset($params['id']);
}
return $smarty->smartyUrl($params, $smarty);
}
/**
* @see Plugin::getActions()
*/
function getActions($request, $actionArgs) {
$router = $request->getRouter();
import('lib.pkp.classes.linkAction.request.AjaxModal');
return array_merge(
$this->getEnabled()?array(
new LinkAction(
'settings',
new AjaxModal(
$router->url(
$request,
null,
null,
'manage',
null,
array(
'verb' => 'settings',
'plugin' => $this->getName(),
'category' => 'generic'
)
),
$this->getDisplayName()
),
__('manager.plugins.settings'),
null
),
):array(),
parent::getActions($request, $actionArgs)
);
}
/**
* @see Plugin::manage()
*/
function manage($args, $request) {
switch ($request->getUserVar('verb')) {
case 'settings':
$context = $request->getContext();
$contextId = ($context == null) ? 0 : $context->getId();
$templateMgr = TemplateManager::getManager();
$templateMgr->registerPlugin('function', 'plugin_url', array($this, 'smartyPluginUrl'));
$apiOptions = [
ORCID_API_URL_PUBLIC => 'plugins.generic.orcidProfile.manager.settings.orcidProfileAPIPath.public',
ORCID_API_URL_PUBLIC_SANDBOX => 'plugins.generic.orcidProfile.manager.settings.orcidProfileAPIPath.publicSandbox',
ORCID_API_URL_MEMBER => 'plugins.generic.orcidProfile.manager.settings.orcidProfileAPIPath.member',
ORCID_API_URL_MEMBER_SANDBOX => 'plugins.generic.orcidProfile.manager.settings.orcidProfileAPIPath.memberSandbox'
];
$templateMgr->assign('orcidApiUrls', $apiOptions);
$templateMgr->assign('logLevelOptions', [
'ERROR' => 'plugins.generic.orcidProfile.manager.settings.logLevel.error',
'ALL' => 'plugins.generic.orcidProfile.manager.settings.logLevel.all'
]);
$this->import('OrcidProfileSettingsForm');
$form = new OrcidProfileSettingsForm($this, $contextId);
if ($request->getUserVar('save')) {
$form->readInputData();
if ($form->validate()) {
$form->execute();
return new JSONMessage(true);
}
} else {
$form->initData();
}
return new JSONMessage(true, $form->fetch($request));
}
return parent::manage($args, $request);
}
/**
* Return the location of the plugin's CSS file
*
* @return string
*/
function getStyleSheet() {
return $this->getPluginPath() . '/css/orcidProfile.css';
}
/**
* Return a string of the ORCiD SVG icon
*
* @return string
*/
function getIcon() {
$path = Core::getBaseDir() . '/' . $this->getPluginPath() . '/templates/images/orcid.svg';
return file_exists($path) ? file_get_contents($path) : '';
}
/**
* Instantiate a MailTemplate
*
* @param string $emailKey
* @param Context $context
*
* @return MailTemplate
*/
function getMailTemplate($emailKey, $context = null) {
import('lib.pkp.classes.mail.MailTemplate');
return new MailTemplate($emailKey, null, $context, false);
}
/**
* Send mail with ORCID authorization link to the e-mail address of the supplied Author object.
*
* @param Author $author
* @param bool $updateAuthor If true update the author fields in the database.
* Use this only if not called from a function, which does this anyway.
*/
public function sendAuthorMail($author, $updateAuthor = false)
{
$request = PKPApplication::get()->getRequest();
$context = $request->getContext();
// This should only ever happen within a context, never site-wide.
assert($context != null);
$contextId = $context->getId();
if ( $this->isMemberApiEnabled($contextId) ) {
$mailTemplate = 'ORCID_REQUEST_AUTHOR_AUTHORIZATION';
}
else {
$mailTemplate = 'ORCID_COLLECT_AUTHOR_ID';
}
$mail = $this->getMailTemplate($mailTemplate, $context);
$emailToken = md5(microtime().$author->getEmail());
$author->setData('orcidEmailToken', $emailToken);
$articleDao = DAORegistry::getDAO('ArticleDAO');
$article = $articleDao->getById($author->getSubmissionId());
$oauthUrl = $this->buildOAuthUrl('orcidVerify', array('token' => $emailToken, 'articleId' => $author->getSubmissionId()));
$aboutUrl = $request->getDispatcher()->url($request, ROUTE_PAGE, null, 'orcidapi', 'about', null);
// Set From to primary journal contact
$mail->setFrom($context->getData('contactEmail'), $context->getData('contactName'));
// Send to author
$mail->setRecipients(array(array('name' => $author->getFullName(), 'email' => $author->getEmail())));
// Send the mail with parameters
$mail->sendWithParams(array(
'orcidAboutUrl' => $aboutUrl,
'authorOrcidUrl' => $oauthUrl,
'authorName' => $author->getFullName(),
'articleTitle' => $article->getLocalizedTitle(),
));
if ($updateAuthor) {
$authorDao = DAORegistry::getDAO('AuthorDAO');
$authorDao->updateLocaleFields($author);
}
}
/**
* handlePublishIssue sends all submissions for which the authors hava an ORCID and access token
* to ORCID. This hook will be called on publication of a new issue.
*
* @see
*
* @param $hookName string
* @param $args Issue[] Issue object that will be published
*
**/
public function handlePublishIssue($hookName, $args) {
$issue =& $args[0];
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
$authorDao = DAORegistry::getDAO('AuthorDAO');
$publishedArticles = $publishedArticleDao->getPublishedArticles($issue->getId());
$request = PKPApplication::get()->getRequest();
$journal = $request->getContext();
foreach ($publishedArticles as $publishedArticle) {
$articleId = $publishedArticle->getId();
$this->sendSubmissionToOrcid($articleId, $request, $issue);
}
}
/**
* handleScheduleForPublication is a hook called during the "Schedule for publication" step
* from the production stage of a submission. It registers another hook, because at the time of calling this hook,
* the issue
*
* @param $hookName string The name the hook was registered as.
* @param $args array Hook arguments, $form, $request, &$returner
*
* @see IssueEntryPublicationMetadataForm::execute() The function calling the hook.
*/
public function handleScheduleForPublication($hookName, $args) {
$form = $args[0];
$submissionId = $form->getSubmission()->getId();
$this->submissionIdToBePublished = $submissionId;
HookRegistry::register('ArticleSearchIndex::articleChangesFinished',
[$this, 'handleScheduleForPublicationFinished']);
}
/**
* handleScheduleForPublicationFinished is a hook registered by handleScheduleForPublication and sends the
* submission data to orcid. The hook will be called at the end of IssueEntryPublicationMetadataForm::execute()
*
* @param $hookName string The name the hook was registered as.
* @param $args array Hook arguments
*
* @see IssueEntryPublicationMetadataForm::execute() The function calling the hook.
*/
public function handleScheduleForPublicationFinished($hookName, $args) {
if ( $this->submissionIdToBePublished ) {
$request = PKPApplication::get()->getRequest();
$this->sendSubmissionToOrcid($this->submissionIdToBePublished, $request);
$this->submissionIdToBePublished = null;
}
}
/**
* handleEditorAction handles promoting a submission to production.
*
* @param $hookName string Name the hook was registered with
* @param $args array Hook arguments, &$submission, &$editorDecision, &$result, &$recommendation.
*
* @see EditorAction::recordDecision() The function calling the hook.
*/
public function handleEditorAction($hookName, $args) {
$submission =& $args[0];
$authorDao = DAORegistry::getDAO('AuthorDAO');
$authors = $authorDao->getBySubmissionId($submission->getId());
foreach ($authors as $author) {
$orcidAccessExpiresOn = Carbon\Carbon::parse($author->getData('orcidAccessExpiresOn'));
if ( $author->getData('orcidAccessToken') == null || $orcidAccessExpiresOn->isPast()) {
$this->sendAuthorMail($author, true);
}
}
}
/**
* Check if the submission with the supplied id is actually published.
* @param int $submissionId Id of the submission/article to check.
* @return boolean True, if the article is part of a published issue. False otherwise.
*/
public function isSubmissionPublished($submissionId) {
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
$article = $publishedArticleDao->getByArticleId($submissionId);
if ( $article === null ) {
return false;
}
$issue = DAORegistry::getDAO('IssueDAO')->getById($article->getIssueId());
if ( $issue === null || !$issue->getPublished()) {
return false;
}
return true;
}
/**
* sendSubmissionToOrcid posts JSON consisting of submission, journal and issue meta data
* to ORCID profiles of submission authors.
*
* @see https://github.com/ORCID/ORCID-Source/tree/master/orcid-model/src/main/resources/record_2.1
* for documentation and examples of the ORCID JSON format.
*
* @param $submissionId integer Id of the article for which the data will be sent to ORCID
* @return void
*
**/
public function sendSubmissionToOrcid($submissionId, $request, $issue = null) {
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
$article = $publishedArticleDao->getByArticleId($submissionId);
if ( $article === null ) {
$this->logError("No PublishedArticle found for id $submissionId");
return false;
}
if ( $issue === null ) {
$issue = DAORegistry::getDAO('IssueDAO')->getById($article->getIssueId());
}
if ( $issue === null || !$issue->getPublished()) {
// Issue not yet published, do not send
return false;
}
$journal = $request->getContext();
$this->currentContextId = $journal->getId();
if (!$this->isMemberApiEnabled($journal->getId())) {
// Sending to ORCID only works with the member API
return false;
}
$authorDao = DAORegistry::getDAO('AuthorDAO');
$authors = $authorDao->getBySubmissionId($submissionId);
// Collect valid ORCID ids and access tokens from submission contributors
$authorsWithOrcid = [];
foreach ($authors as $author) {
if ($author->getOrcid() && $author->getData('orcidAccessToken') ) {
$orcidAccessExpiresOn = Carbon\Carbon::parse($author->getData('orcidAccessExpiresOn'));
if ($orcidAccessExpiresOn->isFuture()) {
# Extract only the ORCID from the stored ORCID uri
$orcid = basename(parse_url($author->getOrcid(), PHP_URL_PATH));
$authorsWithOrcid[$orcid] = $author;
}
else {
$this->logError("Token expired on $orcidAccessExpiresOn for author ". $author->getId() .
", deleting orcidAccessToken!");
$this->removeOrcidAccessToken($author);
}
}
}
if ( empty($authorsWithOrcid) ) {
$this->logInfo('No contributor with ORICD id or valid access token for submission ' . $submissionId);
return false;
}
$orcidWork = $this->buildOrcidWork($article, $journal, $authors, $issue, $request);
$this::logInfo("Request body (without put-code): " . json_encode($orcidWork));
$requestsSuccess = [];
foreach ($authorsWithOrcid as $orcid => $author) {
$url = $this->getSetting($journal->getId(), 'orcidProfileAPIPath') . ORCID_API_VERSION_URL . $orcid . '/'
. ORCID_WORK_URL;
$method = "POST";
if ( $putCode = $author->getData('orcidWorkPutCode')) {
// Submission has already been sent to ORCID. Use PUT to update meta data
$url .= '/' . $putCode;
$method = "PUT";
$orcidWork['put-code'] = $putCode;
}
else {
// Remove put-code from body because the work has not yet been sent
unset($orcidWork['put-code']);
}
$orcidWorkJson = json_encode($orcidWork);
$header = [
'Content-Type: application/vnd.orcid+json',
'Content-Length: ' . strlen($orcidWorkJson),
'Accept: application/json',
'Authorization: Bearer ' . $author->getData('orcidAccessToken')
];
$this->logInfo("$method $url");
$this->logInfo("Header: " . var_export($header, true));
$ch = curl_init($url);
curl_setopt_array($ch, [
CURLOPT_CUSTOMREQUEST => $method,
CURLOPT_POSTFIELDS => $orcidWorkJson,
CURLOPT_RETURNTRANSFER => true,
CURLOPT_HTTPHEADER => $header
]);
// Use proxy if configured
if ($httpProxyHost = Config::getVar('proxy', 'http_host')) {
curl_setopt($ch, CURLOPT_PROXY, $httpProxyHost);
curl_setopt($ch, CURLOPT_PROXYPORT, Config::getVar('proxy', 'http_port', '80'));
if ($username = Config::getVar('proxy', 'username')) {
curl_setopt($ch, CURLOPT_PROXYUSERPWD, $username . ':' . Config::getVar('proxy', 'password'));
}
}
$responseHeaders = [];
// Needed to correctly process response headers.
// This function is called by curl for each received line of the header.
// Code from StackOverflow answer here: https://stackoverflow.com/a/41135574/8938233
// Thanks to StackOverflow user Geoffrey.
curl_setopt($ch, CURLOPT_HEADERFUNCTION,
function($curl, $header) use (&$responseHeaders)
{
$len = strlen($header);
$header = explode(':', $header, 2);
if (count($header) < 2) {
// ignore invalid headers
return $len;
}
$name = strtolower(trim($header[0]));
if (!array_key_exists($name, $responseHeaders)) {
$responseHeaders[$name] = [trim($header[1])];
}
else {
$responseHeaders[$name][] = trim($header[1]);
}
return $len;
}
);
$result = curl_exec($ch);
if (curl_error($ch)) {
$this->logError('Unable to post to ORCID API, curl error: ' . curl_error($ch));
curl_close($ch);
return false;
}
$httpstatus = curl_getinfo($ch, CURLINFO_HTTP_CODE);
curl_close($ch);
$this->logInfo("Response status: $httpstatus");
switch ($httpstatus) {
case 200:
// Work updated
$this->logInfo("Work updated in profile, putCode: $putCode");
$requestsSuccess[$orcid] = true;
break;
case 201:
$location = $responseHeaders['location'][0];
// Extract the ORCID work put code for updates/deletion.
$putCode = intval(basename(parse_url($location, PHP_URL_PATH)));
$this->logInfo("Work added to profile, putCode: $putCode");
$author->setData('orcidWorkPutCode', $putCode);
$authorDao->updateLocaleFields($author);
$requestsSuccess[$orcid] = true;
break;
case 401:
// invalid access token, token was revoked
$error = json_decode($result);
if ($error->error === 'invalid_token') {
$this->logError("$error->error_description, deleting orcidAccessToken from author");
$this->removeOrcidAccessToken($author);
}
$requestsSuccess[$orcid] = false;
break;
case 404:
// a work has been deleted from a ORCID record. putCode is no longer valid.
if ($method === 'PUT') {
$this->logError("Work deleted from ORCID record, deleting putCode form author");
$author->setData('orcidWorkPutCode', null);
$authorDao->updateLocaleFields($author);
$requestsSuccess[$orcid] = false;
}
else {
$this->logError("Unexpected status $httpstatus response, body: $result");
$requestsSuccess[$orcid] = false;
}
break;
case 409:
$this->logError('Work already added to profile, response body: '. $result);
$requestsSuccess[$orcid] = false;
break;
default:
$this->logError("Unexpected status $httpstatus response, body: $result");
$requestsSuccess[$orcid] = false;
}
}
if (array_product($requestsSuccess) ) {
return true;
}
else {
return $requestsSuccess;
}
}
/**
* Build an associative array with submission meta data, which can be encoded to a valid ORCID work JSON structure.
*
* @see https://github.com/ORCID/ORCID-Source/blob/master/orcid-model/src/main/resources/record_2.1/samples/write_sample/bulk-work-2.1.json
* Example of valid ORCID JSON for adding works to an ORCID record.
* @param Article $article extract data from this Article
* @param Journal $journal Journal (context) object the Article is part of
* @param Author[] $authors Array of Author objects, the contributors of the article
* @param Issue $issue Issue the Article is part of
* @param Request $request the current request
* @return array an associative array with article meta data corresponding to ORCID work JSON structure
*/
public function buildOrcidWork($article, $journal, $authors, $issue, $request) {
$articleLocale = $article->getLocale();
$titles = $article->getTitle($articleLocale);
$citationPlugin = PluginRegistry::getPlugin('generic', 'citationstylelanguageplugin');
$bibtexCitation = trim(strip_tags($citationPlugin->getCitation($request, $article, 'bibtex')));
$articleUrl = $request->getDispatcher()->url($request, ROUTE_PAGE, null, 'article', 'view', $article->getBestArticleId());
$orcidWork = [
'title' => [
'title' => [
'value' => $article->getLocalizedTitle($articleLocale)
],
'subtitle' => [
'value' => $article->getSubtitle($articleLocale)
]
],
'journal-title' => [
'value' => $journal->getName('en_US')
],
'short-description' => trim(strip_tags($article->getAbstract('en_US'))),
'type' => 'JOURNAL_ARTICLE',
'external-ids' => [ 'external-id' => $this->buildOrcidExternalIds($article, $journal, $issue, $articleUrl)],
'publication-date' => $this->buildOrcidPublicationDate($issue),
'url' => $articleUrl,
'citation' => [
'citation-type' => 'BIBTEX',
'citation-value' => $bibtexCitation
],
'language-code' => substr($articleLocale, 0, 2),
'contributors' => [ 'contributor' => $this->buildOrcidContributors($authors, $journal->getId()) ]
];
if ($articleLocale !== 'en_US') {
$orcidWork['title']['translated-title'] = [
'value' => $article->getTitle('en_US'),
'language-code' => 'en'
];
}
return $orcidWork;
}
/**
* Parse issue year and publication date and use the older on of the two as
* the publication date of the ORCID work.
*
* @return array Associative array with year, month and day or only year
*/
private function buildOrcidPublicationDate($issue) {
$issuePublicationDate = Carbon\Carbon::parse($issue->getDatePublished());
return [
'year' => [ 'value' => $issuePublicationDate->format("Y")],
'month' => [ 'value' => $issuePublicationDate->format("m")],
'day' => [ 'value' => $issuePublicationDate->format("d")]
];
}
/**
* Build the external identifiers ORCID JSON structure from article, journal and issue meta data.
*
* @see https://pub.orcid.org/v2.0/identifiers Table of valid ORCID identifier types.
*
* @param Article $article The Article object for which the external identifiers should be build.
* @param Journal $journal Journal the Article is part of.