multiple author affiliations

pkp · Dec 6, 2024 · 639dca7 · 639dca7
1 parent 1f1bb3f
commit 639dca7
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Showing 15 changed files with 222 additions and 74 deletions.
diff --git a/api/v1/rors/index.php b/api/v1/rors/index.php
@@ -0,0 +1,19 @@
+<?php
+
+/**
+ * @defgroup api_v1_rors Ror API requests
+ */
+
+/**
+ * @file api/v1/rors/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_rors
+ *
+ * @brief Handle API requests for rors.
+ */
+
+return new \PKP\handler\APIHandler(new \PKP\API\v1\rors\PKPRorController());
diff --git a/dbscripts/xml/install.xml b/dbscripts/xml/install.xml
@@ -3,8 +3,8 @@
 <!--
   * dbscripts/xml/install.xml
   *
-  * Copyright (c) 2014-2021 Simon Fraser University
-  * Copyright (c) 2003-2021 John Willinsky
+  * Copyright (c) 2014-2024 Simon Fraser University
+  * Copyright (c) 2003-2024 John Willinsky
   * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
   *
   * Installation descriptor file.
@@ -39,6 +39,8 @@
 	<migration class="PKP\migration\install\TombstoneMigration" />
 	<migration class="PKP\migration\install\DoiMigration" />
 	<migration class="PKP\migration\install\InstitutionsMigration" />
+	<migration class="PKP\migration\install\AffiliationsMigration" />
+	<migration class="PKP\migration\install\RorsMigration" />
 
 	<migration class="APP\migration\install\OJSMigration" />
 

diff --git a/dbscripts/xml/upgrade.xml b/dbscripts/xml/upgrade.xml
@@ -3,8 +3,8 @@
 <!--
   * dbscripts/xml/upgrade.xml
   *
-  * Copyright (c) 2014-2021 Simon Fraser University
-  * Copyright (c) 2003-2021 John Willinsky
+  * Copyright (c) 2014-2024 Simon Fraser University
+  * Copyright (c) 2003-2024 John Willinsky
   * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
   *
   * Upgrade descriptor file.
@@ -151,6 +151,8 @@
         <migration class="PKP\migration\upgrade\v3_5_0\I9771_OrcidMigration"/>
 		<migration class="APP\migration\upgrade\v3_5_0\I5885_RenameReviewReminderSettingsName"/>
 		<migration class="PKP\migration\upgrade\v3_5_0\COA75_AddUserRoleEndEmail"/>
+		<migration class="PKP\migration\upgrade\v3_5_0\I7135_CreateAuthorAffiliationsTables"/>
+		<migration class="PKP\migration\upgrade\v3_5_0\I7135_CreateNewRorRegistryCacheTables"/>
 	</upgrade>
 
 	<!-- update plugin configuration - should be done as the final upgrade task -->

diff --git a/pages/article/ArticleHandler.php b/pages/article/ArticleHandler.php
@@ -3,8 +3,8 @@
 /**
  * @file pages/article/ArticleHandler.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class ArticleHandler
@@ -357,6 +357,12 @@ public function view($args, $request)
                 $templateMgr->assign('purchaseArticleEnabled', true);
             }
 
+            // ror icon
+            $rorIdIcon = 'ROR';
+            if (file_exists('templates/images/ror-org-logo-icon.svg'))
+                $rorIdIcon = file_get_contents('templates/images/ror-org-logo-icon.svg');
+            $templateMgr->assign('rorIdIcon', $rorIdIcon);
+
             if (!Hook::call('ArticleHandler::view', [&$request, &$issue, &$article, $publication])) {
                 $templateMgr->display('frontend/pages/article.tpl');
                 event(new UsageEvent(Application::ASSOC_TYPE_SUBMISSION, $context, $article, null, null, $this->issue));

diff --git a/plugins/generic/datacite/filter/DataciteXmlFilter.php b/plugins/generic/datacite/filter/DataciteXmlFilter.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/generic/datacite/filter/DataciteXmlFilter.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * 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 DataciteXmlFilter
@@ -307,8 +307,7 @@ public function createCreatorsNode($doc, $issue, $publication, $galley, $galleyF
                     $creators[] = [
                         'name' => $creator,
                         'orcid' => null,
-                        'affiliation' => null,
-                        'ror' => null
+                        'affiliations' => null
                     ];
                     break;
                 }
@@ -323,17 +322,15 @@ public function createCreatorsNode($doc, $issue, $publication, $galley, $galleyF
                     $creators[] = [
                         'name' => $author->getFullName(false, true, $publication->getData('locale')),
                         'orcid' => $author->getOrcid(),
-                        'affiliation' => $author->getLocalizedData('affiliation', $publication->getData('locale')),
-                        'ror' => $author->getData('rorId') ?? null
+                        'affiliations' => $author->getLocalizedAffiliations($publication->getData('locale'))
                     ];
                 }
                 break;
             case isset($issue):
                 $creators[] = [
                     'name' => $publisher,
                     'orcid' => null,
-                    'affiliation' => null,
-                    'ror' => null
+                    'affiliations' => null
                 ];
                 break;
         }
@@ -349,15 +346,17 @@ public function createCreatorsNode($doc, $issue, $publication, $galley, $galleyF
                 $node->setAttribute('nameIdentifierScheme', 'ORCID');
                 $creatorNode->appendChild($node);
             }
-            if ($creator['affiliation']) {
-                $node = $doc->createElementNS($deployment->getNamespace(), 'affiliation');
-                if ($creator['ror']) {
-                    $node->setAttribute('affiliationIdentifier', $creator['ror']);
-                    $node->setAttribute('affiliationIdentifierScheme', 'ROR');
-                    $node->setAttribute('schemeURI', 'https://ror.org');
+            if ($creator['affiliations']) {
+                foreach($creator['affiliations'] as $affiliation) {
+                    $node = $doc->createElementNS($deployment->getNamespace(), 'affiliation');
+                    if ($affiliation['ror']) {
+                        $node->setAttribute('affiliationIdentifier', $affiliation['ror']);
+                        $node->setAttribute('affiliationIdentifierScheme', 'ROR');
+                        $node->setAttribute('schemeURI', 'https://ror.org');
+                    }
+                    $node->appendChild($doc->createTextNode($affiliation['name']));
+                    $creatorNode->appendChild($node);
                 }
-                $node->appendChild($doc->createTextNode($creator['affiliation']));
-                $creatorNode->appendChild($node);
             }
             $creatorsNode->appendChild($creatorNode);
         }

diff --git a/plugins/importexport/doaj/filter/DOAJJsonFilter.php b/plugins/importexport/doaj/filter/DOAJJsonFilter.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/importexport/doaj/filter/DOAJJsonFilter.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * 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 DOAJJsonFilter
@@ -159,9 +159,9 @@ public function &process(&$pubObject)
 
             foreach ($articleAuthors as $articleAuthor) {
                 $author = ['name' => $articleAuthor->getFullName(false, false, $publicationLocale)];
-                $affiliation = $articleAuthor->getAffiliation($publicationLocale);
-                if (!empty($affiliation)) {
-                    $author['affiliation'] = $affiliation;
+                $affiliations = $articleAuthor->getLocalizedAffiliationNamesAsString($publicationLocale);
+                if (!empty($affiliations)) {
+                    $author['affiliations'] = $affiliations;
                 }
                 if ($orcid = $articleAuthor->getData('orcid')) {
                     $author['orcid_id'] = $orcid;

diff --git a/plugins/importexport/doaj/filter/DOAJXmlFilter.php b/plugins/importexport/doaj/filter/DOAJXmlFilter.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/importexport/doaj/filter/DOAJXmlFilter.php
  *
- * Copyright (c) 2014-2022 Simon Fraser University
- * Copyright (c) 2000-2022 John Willinsky
+ * 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 DOAJXmlFilter
@@ -245,8 +245,15 @@ public function createAuthorNode($doc, $publication, $author, $affilList)
         $deployment = $this->getDeployment();
         $authorNode = $doc->createElement('author');
         $authorNode->appendChild($node = $doc->createElement('name', htmlspecialchars($author->getFullName(false, false, $publication->getData('locale')), ENT_COMPAT, 'UTF-8')));
-        if (in_array($author->getAffiliation($publication->getData('locale')), $affilList) && !empty($affilList[0])) {
-            $authorNode->appendChild($node = $doc->createElement('affiliationId', htmlspecialchars(current(array_keys($affilList, $author->getAffiliation($publication->getData('locale')))), ENT_COMPAT, 'UTF-8')));
+        $affiliations = $author->getLocalizedAffiliationNames($publication->getData('locale'));
+        foreach ($affiliations as $affiliation) {
+            if (in_array($affiliation, $affilList) && !empty($affilList[0])) {
+                $authorNode->appendChild(
+                    $node = $doc->createElement('affiliationId',
+                        htmlspecialchars(current(array_keys($affilList, $affiliation)), ENT_COMPAT, 'UTF-8')
+                    )
+                );
+            }
         }
         if ($orcid = $author->getData('orcid')) {
             $authorNode->appendChild($doc->createElement('orcid_id'))->appendChild($doc->createTextNode($orcid));
@@ -266,8 +273,11 @@ public function createAffiliationsList($authors, $publication)
     {
         $affilList = [];
         foreach ($authors as $author) {
-            if (!in_array($author->getAffiliation($publication->getData('locale')), $affilList)) {
-                $affilList[] = $author->getAffiliation($publication->getData('locale')) ;
+            $affiliations = $author->getLocalizedAffiliationNames($publication->getData('locale'));
+            foreach ($affiliations as $affiliation) {
+                if (!in_array($affiliation, $affilList)) {
+                    $affilList[] = $affiliation;;
+                }
             }
         }
         return $affilList;

diff --git a/plugins/importexport/pubmed/filter/ArticlePubMedXmlFilter.php b/plugins/importexport/pubmed/filter/ArticlePubMedXmlFilter.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/importexport/pubmed/filter/ArticlePubMedXmlFilter.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * 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 ArticlePubMedXmlFilter
@@ -215,7 +215,18 @@ public function generateAuthorNode($doc, $journal, $issue, $submission, $author)
             $authorElement->appendChild($doc->createElement('FirstName'))->appendChild($doc->createTextNode(ucfirst($author->getLocalizedGivenName())));
             $authorElement->appendChild($doc->createElement('LastName'))->appendChild($doc->createTextNode(ucfirst($author->getLocalizedFamilyName())));
         }
-        $authorElement->appendChild($doc->createElement('Affiliation'))->appendChild($doc->createTextNode($author->getLocalizedAffiliation()));
+        foreach($author->getLocalizedAffiliations() as $affiliation) {
+            if(!empty($affiliation['name']) || !empty($affiliation['ror'])) {
+                $affiliationInfoElement = $doc->createElement('AffiliationInfo');
+                if(!empty($affiliation['name'])) {
+                    $affiliationInfoElement->appendChild($doc->createElement('Affiliation'))->appendChild($doc->createTextNode($affiliation['name']));
+                }
+                if(!empty($affiliation['ror'])) {
+                    $affiliationInfoElement->appendChild($doc->createElement('Identifier'))->appendChild($doc->createTextNode($affiliation['ror']));
+                }
+                $authorElement->appendChild($affiliationInfoElement);
+            }
+        }
         // We're storing the ORCID with a URL (http://orcid.org/{$ID}), but the XML expects just the ID
         $orcidId = explode('/', trim($author->getData('orcid') ?? '', '/'));
         $orcidId = array_pop($orcidId);

diff --git a/plugins/oaiMetadataFormats/dc/tests/OAIMetadataFormat_DCTest.php b/plugins/oaiMetadataFormats/dc/tests/OAIMetadataFormat_DCTest.php
@@ -1,13 +1,14 @@
 <?php
+
 /**
  * @defgroup plugins_oaiMetadataFormats_dc_tests Dublin Core OAI Plugin
  */
 
 /**
  * @file plugins/oaiMetadataFormats/dc/tests/OAIMetadataFormat_DCTest.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * 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 OAIMetadataFormat_DCTest
@@ -88,7 +89,14 @@ public function testToXml()
         $author = new Author();
         $author->setGivenName('author-firstname', 'en');
         $author->setFamilyName('author-lastname', 'en');
-        $author->setAffiliation('author-affiliation', 'en');
+        $author->setAffiliations([
+            Repo::affiliation()->newDataObject([
+                "id" => 1,
+                "authorId" => 1,
+                "ror" => 'https://ror.org/05ek4tb53',
+                "name" => ['en' => 'author-affiliation']
+            ])
+        ]);
         $author->setEmail('someone@example.com');
 
         // Publication

diff --git a/plugins/oaiMetadataFormats/marc/templates/record.tpl b/plugins/oaiMetadataFormats/marc/templates/record.tpl
@@ -1,8 +1,8 @@
 {**
  * plugins/oaiMetadataFormats/marc/record.tpl
  *
- * Copyright (c) 2013-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2013-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * MARC-formatted metadata record for an article
@@ -34,8 +34,10 @@
 	{foreach from=$authors item=author}
 		<varfield id="{if $authors|@count==1}100{else}720{/if}" i1="1" i2=" ">
 			<subfield label="a">{$author->getFullName(false, true, $journal->getPrimaryLocale())|escape}</subfield>
-			{assign var=affiliation value=$author->getAffiliation($journal->getPrimaryLocale())}
-			{if $affiliation}<subfield label="u">{$affiliation|escape}</subfield>{/if}
+			{foreach from=$author->getLocalizedAffiliations() item=$affiliation}
+			{if $affiliation['ror']}<subfield code="u">{$affiliation['ror']|escape}</subfield>
+			{elseif $affiliation['name']}<subfield code="u">{$affiliation['name']|escape}</subfield>{/if}
+			{/foreach}
 			{if $author->getUrl()}<subfield label="0">{$author->getUrl()|escape}</subfield>{/if}
 			{if $author->getData('orcid')}<subfield label="0">{$author->getData('orcid')|escape}</subfield>{/if}
 		</varfield>

diff --git a/plugins/oaiMetadataFormats/marcxml/templates/record.tpl b/plugins/oaiMetadataFormats/marcxml/templates/record.tpl
@@ -1,8 +1,8 @@
 {**
  * plugins/oaiMetadataFormats/marcxml/record.tpl
  *
- * Copyright (c) 2013-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2013-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * MARCXML-formatted metadata record for an article
@@ -43,8 +43,10 @@
 	{foreach from=$authors item=author}
 		<datafield tag="{if $authors|@count==1}100{else}720{/if}" ind1="1" ind2=" ">
 			<subfield code="a">{$author->getFullName(false, true, $journal->getPrimaryLocale())|escape}</subfield>
-			{assign var=affiliation value=$author->getAffiliation($journal->getPrimaryLocale())}
-			{if $affiliation}<subfield code="u">{$affiliation|escape}</subfield>{/if}
+			{foreach from=$author->getLocalizedAffiliations() item=$affiliation}
+			{if $affiliation['ror']}<subfield code="u">{$affiliation['ror']|escape}</subfield>
+			{elseif $affiliation['name']}<subfield code="u">{$affiliation['name']|escape}</subfield>{/if}
+			{/foreach}
 			{if $author->getUrl()}<subfield code="0">{$author->getUrl()|escape}</subfield>{/if}
 			{if $author->getData('orcid')}<subfield code="0">{$author->getData('orcid')|escape}</subfield>{/if}
 		</datafield>

diff --git a/plugins/oaiMetadataFormats/rfc1807/OAIMetadataFormat_RFC1807.php b/plugins/oaiMetadataFormats/rfc1807/OAIMetadataFormat_RFC1807.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/oaiMetadataFormats/rfc1807/OAIMetadataFormat_RFC1807.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class OAIMetadataFormat_RFC1807
@@ -58,12 +58,7 @@ public function toXml($record, $format = null)
         // Format creators
         $creators = [];
         foreach ($publication->getAuthors() as $author) {
-            $authorName = $author->getFullName(false, true);
-            $affiliation = $author->getLocalizedAffiliation();
-            if (!empty($affiliation)) {
-                $authorName .= '; ' . $affiliation;
-            }
-            $creators[] = $authorName;
+            $creators[] = $author->getFullName(false, true);
         }
 
         // Subject

diff --git a/plugins/reports/articles/ArticleReportPlugin.php b/plugins/reports/articles/ArticleReportPlugin.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/reports/articles/ArticleReportPlugin.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class ArticleReportPlugin
@@ -175,7 +175,7 @@ public function display($args, $request)
                         $author->getLocalizedFamilyName(),
                         $author->getData('orcid'),
                         $author->getData('country'),
-                        $author->getLocalizedData('affiliation'),
+                        $author->getLocalizedAffiliationNamesAsString(),
                         $author->getData('email'),
                         $author->getData('url'),
                         html_entity_decode(strip_tags($author->getLocalizedData('biography'))),
@@ -195,7 +195,7 @@ public function display($args, $request)
                 'url' => $request->url(null, 'workflow', 'access', $submission->getId()),
                 'doi' => $submission->getStoredPubId('doi'),
                 'dateSubmitted' => $submission->getData('dateSubmitted'),
-                'lastModified' => $submission->getLastModified(),
+                'lastModified' => $submission->getData['lastModified'],
                 'firstPublished' => $submission->getOriginalPublication()?->getData('datePublished') ?? '',
                 'editors' => $editors,
                 'decisions' => $editDecisions->toArray(),