I10692 fixes

api/v1/citations/PKPCitationController.php

@@ -22,6 +22,9 @@
 use Illuminate\Http\Request;
 use Illuminate\Http\Response;
 use Illuminate\Support\Facades\Route;
+use PKP\citation\pid\Arxiv;
+use PKP\citation\pid\Doi;
+use PKP\citation\pid\Handle;
 use PKP\core\PKPBaseController;
 use PKP\core\PKPRequest;
 use PKP\plugins\Hook;
@@ -173,6 +176,19 @@ public function edit(Request $illuminateRequest): JsonResponse
 
         $params = $this->convertStringsToSchema(PKPSchemaService::SCHEMA_CITATION, $illuminateRequest->input());
 
+        $arxiv = Arxiv::extractFromString($params['arxiv']);
+        if(!empty($arxiv)){
+            $params['arxiv'] = $arxiv;
+        }
+        $doi = Doi::extractFromString($params['doi']);
+        if(!empty($doi)){
+            $params['doi'] = $doi;
+        }
+        $handle = Handle::extractFromString($params['handle']);
+        if(!empty($handle)){
+            $params['handle'] = $handle;
+        }
+
         $readOnlyErrors = $this->getWriteDisabledErrors(PKPSchemaService::SCHEMA_CITATION, $params);
         if (!empty($readOnlyErrors)) {
             return response()->json($readOnlyErrors, Response::HTTP_BAD_REQUEST);

api/v1/submissions/PKPSubmissionController.php

@@ -121,8 +121,8 @@ class PKPSubmissionController extends PKPBaseController
         'changeVersion',
         'getNextAvailableVersion',
         'importAdditionalCitations',
-        'editCitationsMetadataLookup',
         'deleteCitationsByPublicationId',
+        'reprocessCitationsByPublicationId'
     ];
 
     /** @var array Handlers that must be authorized to write to a publication */
@@ -371,17 +371,17 @@ public function getGroupRoutes(): void
                 Role::ROLE_ID_AUTHOR,
             ]),
         ])->group(function () {
-            Route::put('{submissionId}/publications/{publicationId}/citations/metadataLookup', $this->editCitationsMetadataLookup(...))
-                ->name('submission.citations.import')
-                ->whereNumber(['submissionId', 'publicationId']);
-
             Route::post('{submissionId}/publications/{publicationId}/citations/importAdditionalCitations', $this->importAdditionalCitations(...))
                 ->name('submission.citations.import')
                 ->whereNumber(['submissionId', 'publicationId']);
 
             Route::delete('{submissionId}/publications/{publicationId}/citations/deleteCitationsByPublicationId', $this->deleteCitationsByPublicationId(...))
                 ->name('submission.citations.delete')
                 ->whereNumber(['submissionId', 'publicationId']);
+
+            Route::post('{submissionId}/publications/{publicationId}/citations/reprocessCitationsByPublicationId', $this->reprocessCitationsByPublicationId(...))
+                ->name('submission.citations.reprocess')
+                ->whereNumber(['submissionId', 'publicationId']);
         });
     }
 
@@ -2335,9 +2335,9 @@ protected function validateVersionIsMinor(Request $illuminateRequest): ?bool
     }
 
     /**
-     * Update citationsMetadataLookup of a publication, reprocess citations if enabled.
+     * Import / add citations from a raw citation string of a publication.
      */
-    protected function editCitationsMetadataLookup(Request $illuminateRequest): JsonResponse
+    protected function importAdditionalCitations(Request $illuminateRequest): JsonResponse
     {
         $publication = Repo::publication()->get((int)$illuminateRequest->route('publicationId'));
 
@@ -2365,39 +2365,17 @@ protected function editCitationsMetadataLookup(Request $illuminateRequest): Json
             ], Response::HTTP_FORBIDDEN);
         }
 
-        $citationsMetadataLookup = (bool)$illuminateRequest->input('citationsMetadataLookup');
-
-        $processCitation = false;
-        if ($citationsMetadataLookup && !$publication->getData('citationsMetadataLookup')) {
-            $processCitation = true;
-        }
-
-        /** @var Citation $citation */
-        foreach ($publication->getData('citations') as &$citation) {
-            $citation->setIsProcessed(!$processCitation);
-            if ($processCitation) {
-                Repo::citation()->reprocessCitation($citation);
-            }
-        }
-        unset($citation);
-
-        $publication->setData('citationsMetadataLookup', $citationsMetadataLookup);
-        Repo::publication()->edit($publication, []);
+        $rawCitations = (string)$illuminateRequest->input('rawCitations');
 
-        $publication = Repo::publication()->get($publication->getId());
+        $result = Repo::citation()->importAdditionalCitations($publication->getId(), $rawCitations);
 
-        return response()->json(
-            [
-                'citationsMetadataLookup' => $publication->getData('citationsMetadataLookup')
-            ],
-            Response::HTTP_OK
-        );
+        return response()->json($result, Response::HTTP_OK);
     }
 
     /**
-     * Import / add citations from a raw citation string of a publication.
+     * Delete a publication's citations.
      */
-    protected function importAdditionalCitations(Request $illuminateRequest): JsonResponse
+    protected function deleteCitationsByPublicationId(Request $illuminateRequest): JsonResponse
     {
         $publication = Repo::publication()->get((int)$illuminateRequest->route('publicationId'));
 
@@ -2425,17 +2403,24 @@ protected function importAdditionalCitations(Request $illuminateRequest): JsonRe
             ], Response::HTTP_FORBIDDEN);
         }
 
-        $rawCitations = (string)$illuminateRequest->input('rawCitations');
+        $existingCitations = [];
+        /** @var Citation $citation */
+        foreach ($publication->getData('citations') as $citation) {
+            $existingCitations[] = Repo::citation()->getSchemaMap()->map($citation);
+        }
 
-        $result = Repo::citation()->importAdditionalCitations($publication->getId(), $rawCitations);
+        Repo::citation()->deleteByPublicationId($publication->getId());
 
-        return response()->json($result, Response::HTTP_OK);
+        return response()->json([
+            'itemsMax' => count($existingCitations),
+            'items' => $existingCitations
+        ], Response::HTTP_OK);
     }
 
     /**
-     * Delete a publication's citations.
+     * Reprocess a publication's citations.
      */
-    protected function deleteCitationsByPublicationId(Request $illuminateRequest): JsonResponse
+    protected function reprocessCitationsByPublicationId(Request $illuminateRequest): JsonResponse
     {
         $publication = Repo::publication()->get((int)$illuminateRequest->route('publicationId'));
 
@@ -2463,17 +2448,23 @@ protected function deleteCitationsByPublicationId(Request $illuminateRequest): J
             ], Response::HTTP_FORBIDDEN);
         }
 
-        $existingCitations = [];
-        /** @var Citation $citation */
-        foreach ($publication->getData('citations') as $citation) {
-            $existingCitations[] = Repo::citation()->getSchemaMap()->map($citation);
+        // Set all citations as not processed
+        $citations = $publication->getData('citations');
+        foreach ($citations as &$citation) {
+            $citation->setIsProcessed(false);
+            Repo::citation()->edit($citation, []);
         }
+        unset($citation);
 
-        Repo::citation()->deleteByPublicationId($publication->getId());
+        foreach ($citations as &$citation) {
+            Repo::citation()->reprocessCitation($citation);
+            $citation = Repo::citation()->getSchemaMap()->map($citation);
+        }
+        unset($citation);
 
         return response()->json([
-            'itemsMax' => count($existingCitations),
-            'items' => $existingCitations
+            'itemsMax' => count($citations),
+            'items' => $citations
         ], Response::HTTP_OK);
     }
 }

classes/citation/Repository.php

@@ -221,7 +221,6 @@ public function importCitations(int $publicationId, ?string $rawCitationList): v
             $importedCitations = [];
             $this->deleteByPublicationId($publicationId);
             if (is_array($citationStrings) && !empty($citationStrings)) {
-                $publication = Repo::publication()->get($publicationId);
                 foreach ($citationStrings as $seq => $rawCitationString) {
                     if (!empty($rawCitationString)) {
                         $citation = new Citation();
@@ -231,8 +230,7 @@ public function importCitations(int $publicationId, ?string $rawCitationList): v
                         $citation->setIsProcessed(false);
                         $newCitationId = $this->dao->insert($citation);
                         $citation->setId($newCitationId);
-                        if ($publication->getData('citationsMetadataLookup') ||
-                            (is_null($publication->getData('citationsMetadataLookup')) && $this->request->getContext()->getData('citationsMetadataLookup'))) {
+                        if ($this->request->getContext()->getData('citationsMetadataLookup')) {
                             $this->reprocessCitation($citation);
                         }
                         $importedCitations[] = $citation;
@@ -256,7 +254,6 @@ public function importAdditionalCitations(int $publicationId, ?string $rawCitati
 
         $rejectedCitations = [];
         if (is_array($citationStrings) && !empty($citationStrings)) {
-            $publication = Repo::publication()->get($publicationId);
             foreach ($citationStrings as $rawCitationString) {
                 if (!empty($rawCitationString)) {
                     if (!$this->existsRawCitation($publicationId, $rawCitationString)) {
@@ -268,8 +265,7 @@ public function importAdditionalCitations(int $publicationId, ?string $rawCitati
                         $citation->setIsProcessed(false);
                         $newCitationId = $this->dao->insert($citation);
                         $citation->setId($newCitationId);
-                        if ($publication->getData('citationsMetadataLookup') ||
-                            (is_null($publication->getData('citationsMetadataLookup')) && $this->request->getContext()->getData('citationsMetadataLookup'))) {
+                        if ($this->request->getContext()->getData('citationsMetadataLookup')) {
                             $this->reprocessCitation($citation);
                         }
                     } else {

classes/citation/enum/CitationSourceType.php

@@ -0,0 +1,28 @@
+<?php
+
+/**
+ * @file classes/citation/enum/CitationSourceType.php
+ *
+ * Copyright (c) 2025 Simon Fraser University
+ * Copyright (c) 2025 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class CitationSourceType
+ *
+ * @ingroup citation
+ *
+ * @brief Enumeration for citation source types.
+ */
+
+namespace PKP\citation\enum;
+
+enum CitationSourceType: string
+{
+    case BOOK_SERIES = 'book series';
+    case CONFERENCE = 'conference';
+    case EBOOK_PLATFORM = 'ebook platform';
+    case JOURNAL = 'journal';
+    case METADATA = 'metadata';
+    case OTHER = 'other';
+    case REPOSITORY = 'repository';
+}

classes/citation/enum/CitationType.php

@@ -0,0 +1,60 @@
+<?php
+
+/**
+ * @file classes/citation/enum/CitationType.php
+ *
+ * Copyright (c) 2025 Simon Fraser University
+ * Copyright (c) 2025 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class CitationType
+ *
+ * @ingroup citation
+ *
+ * @brief Enumeration for citation types.
+ */
+
+namespace PKP\citation\enum;
+
+enum CitationType: string
+{
+    case BOOK = 'book';
+    case BOOK_CHAPTER = 'book-chapter';
+    case BOOK_PART = 'book-part';
+    case BOOK_SECTION = 'book-section';
+    case BOOK_SERIES = 'book-series';
+    case BOOK_SET = 'book-set';
+    case BOOK_TRACK = 'book-track';
+    case COMPONENT = 'component';
+    case DATABASE = 'database';
+    case DATASET = 'dataset';
+    case DISSERTATION = 'dissertation';
+    case EDITED_BOOK = 'edited-book';
+    case EDITORIAL = 'editorial';
+    case ERRATUM = 'erratum';
+    case GRANT = 'grant';
+    case JOURNAL = 'journal';
+    case JOURNAL_ARTICLE = 'journal-article';
+    case JOURNAL_ISSUE = 'journal-issue';
+    case JOURNAL_VOLUME = 'journal-volume';
+    case LETTER = 'letter';
+    case LIBGUIDES = 'libguides';
+    case MONOGRAPH = 'monograph';
+    case OTHER = 'other';
+    case PARATEXT = 'paratext';
+    case PEER_REVIEW = 'peer-review';
+    case POSTED_CONTENT = 'posted-content';
+    case PREPRINT = 'preprint';
+    case PROCEEDINGS = 'proceedings';
+    case PROCEEDINGS_ARTICLE = 'proceedings-article';
+    case PROCEEDINGS_SERIES = 'proceedings-series';
+    case REFERENCE_BOOK = 'reference-book';
+    case REFERENCE_ENTRY = 'reference-entry';
+    case REPORT = 'report';
+    case REPORT_COMPONENT = 'report-component';
+    case REPORT_SERIES = 'report-series';
+    case RETRACTION = 'retraction';
+    case REVIEW = 'review';
+    case STANDARD = 'standard';
+    case SUPPLEMENTARY_MATERIALS = 'supplementary-materials';
+}

classes/citation/externalServices/openAlex/Inbound.php

@@ -63,6 +63,9 @@ public function getWork(Citation $citation): ?Citation
                         $newValue[] = $this->getAuthor($authorship);
                     }
                     break;
+                case 'type':
+                    $newValue = !empty($response[$mappedKey]) ? $response[$mappedKey] : $response['type'];
+                    break;
                 default:
                     if (is_array($mappedKey)) {
                         $newValue = ExternalServicesHelper::getValueFromArrayPath($response, $mappedKey);

classes/citation/externalServices/openAlex/Mapping.php

@@ -34,7 +34,7 @@ public static function getWork(): array
         return [
             'title' => 'title',
             'date' => 'publication_date',
-            'type' => 'type_crossref',
+            'type' => 'type_crossref', // use 'type' if empty
             'volume' => ['biblio', 'volume'],
             'issue' => ['biblio', 'issue'],
             'firstPage' => ['biblio', 'first_page'],

classes/citation/pid/Arxiv.php

@@ -19,33 +19,20 @@
 class Arxiv extends BasePid
 {
     /** @copydoc AbstractPid::regex */
-    public const regex = '%\b(([\w-]+://?|www[.])[^\s()<>]+(?:\([\w\d]+\)|([^[:punct:]\s]|/)))%s';
-
-    /** @copydoc AbstractPid::prefix */
-    public const prefix = 'https://arxiv.org/abs';
-
-    /** @copydoc AbstractPid::prefixInCorrect */
-    public const prefixInCorrect = [
-        'arxiv:'
+    public const regexes = [
+        '/arxiv:\s*\d{4}\.\d{4,5}(v\d+)?/i', // arxiv:2025.12345v2
+        '/https?:\/\/arxiv.org\/(?:abs|pdf)\/(?:\d+.\d+|[a-z-]+.\d+)/i' // https://arxiv.org/abs/2025.12345
     ];
 
-    /** @copydoc AbstractPid::extractFromString() */
-    public static function extractFromString(?string $string): string
-    {
-        $string = parent::extractFromString($string);
-
-        $class = get_called_class();
-
-        // check if prefix found in extracted string
-        $prefixes = $class::prefixInCorrect;
-        $prefixes[] = $class::prefix;
+    /** @copydoc AbstractPid::prefix */
+    public const prefix = 'arxiv:';
 
-        foreach ($prefixes as $prefix) {
-            if (str_contains($string, $prefix)) {
-                return $string;
-            }
-        }
+    /** @copydoc AbstractPid::urlPrefix */
+    public const urlPrefix = 'https://arxiv.org/abs/';
 
-        return '';
-    }
+    /** @copydoc AbstractPid::alternatePrefixes */
+    public const alternatePrefixes = [
+        'arxiv',
+        'https://arxiv.org/pdf/'
+    ];
 }