pkp/pkp-lib#13447 Allow automatic DOI assignment on item creation

classes/components/listPanels/DoiListPanel.php

@@ -52,6 +52,15 @@ protected function setAppConfig(array &$config): void
                 ]
             ]
         ];
-
+        $config['filters'][] = [
+            'heading' => __('manager.dois.filters.workflow'),
+            'filters' => [
+                [
+                    'title' => __('manager.dois.filters.inEditingOrPublished'),
+                    'param' => 'inEditingOrPublished',
+                    'value' => '1',
+                ],
+            ],
+        ];
     }
 }

classes/doi/DAO.php

@@ -18,6 +18,7 @@
 
 namespace APP\doi;
 
+use APP\core\Application;
 use APP\facades\Repo;
 use Illuminate\Database\Query\Builder;
 use Illuminate\Support\Collection;
@@ -38,62 +39,66 @@ class DAO extends \PKP\doi\DAO
     public function getAllDepositableSubmissionIds(Context $context): Collection
     {
         $enabledDoiTypes = $context->getData(Context::SETTING_ENABLED_DOI_TYPES) ?? [];
+        $doiVersioning = (bool) $context->getData(Context::SETTING_DOI_VERSIONING);
 
         $q = DB::table($this->table, 'd')
+            // Minor versions share their major version's DOIs, so a DOI can match several publications/objects
             ->leftJoin('publications as p', 'd.doi_id', '=', 'p.doi_id')
-            ->leftJoin('submissions as s', 'p.publication_id', '=', 's.current_publication_id')
+            ->leftJoin('submission_chapters as cd', 'd.doi_id', '=', 'cd.doi_id')
+            ->leftJoin('publications as cp', 'cd.publication_id', '=', 'cp.publication_id')
+            ->leftJoin('publication_formats as pfd', 'd.doi_id', '=', 'pfd.doi_id')
+            ->leftJoin('publications as pfp', 'pfd.publication_id', '=', 'pfp.publication_id')
+            ->leftJoin('submission_files as sfd', 'd.doi_id', '=', 'sfd.doi_id')
             ->where('d.context_id', '=', $context->getId())
-            ->where(function (Builder $q) use ($enabledDoiTypes) {
+            ->where(function (Builder $q) use ($enabledDoiTypes, $doiVersioning) {
                 // Publication DOIs
-                $q->when(in_array(Repo::doi()::TYPE_PUBLICATION, $enabledDoiTypes), function (Builder $q) {
-                    $q->whereIn('d.doi_id', function (Builder $q) {
+                $q->when(in_array(Repo::doi()::TYPE_PUBLICATION, $enabledDoiTypes), function (Builder $q) use ($doiVersioning) {
+                    $q->whereIn('d.doi_id', function (Builder $q) use ($doiVersioning) {
                         $q->select('p.doi_id')
                             ->from('publications', 'p')
-                            ->leftJoin('submissions as s', 'p.publication_id', '=', 's.current_publication_id')
-                            ->whereColumn('p.publication_id', '=', 's.current_publication_id')
                             ->whereNotNull('p.doi_id')
                             ->where('p.status', '=', PKPPublication::STATUS_PUBLISHED);
+                        $this->whereDepositablePublication($q, $doiVersioning);
                     });
                 });
                 // Chapter DOIs
-                $q->when(in_array(Repo::doi()::TYPE_CHAPTER, $enabledDoiTypes), function (Builder $q) {
-                    $q->orWhereIn('d.doi_id', function (Builder $q) {
+                $q->when(in_array(Repo::doi()::TYPE_CHAPTER, $enabledDoiTypes), function (Builder $q) use ($doiVersioning) {
+                    $q->orWhereIn('d.doi_id', function (Builder $q) use ($doiVersioning) {
                         $q->select('spc.doi_id')
                             ->from('submission_chapters', 'spc')
                             ->join('publications as p', 'spc.publication_id', '=', 'p.publication_id')
-                            ->leftJoin('submissions as s', 'p.publication_id', '=', 's.current_publication_id')
-                            ->whereColumn('p.publication_id', '=', 's.current_publication_id')
                             ->whereNotNull('spc.doi_id')
                             ->where('p.status', '=', PKPPublication::STATUS_PUBLISHED);
+                        $this->whereDepositablePublication($q, $doiVersioning, false);
                     });
                 });
                 // Publication format DOIs
-                $q->when(in_array(Repo::doi()::TYPE_REPRESENTATION, $enabledDoiTypes), function (Builder $q) {
-                    $q->orWhereIn('d.doi_id', function (Builder $q) {
+                $q->when(in_array(Repo::doi()::TYPE_REPRESENTATION, $enabledDoiTypes), function (Builder $q) use ($doiVersioning) {
+                    $q->orWhereIn('d.doi_id', function (Builder $q) use ($doiVersioning) {
                         $q->select('pf.doi_id')
                             ->from('publication_formats', 'pf')
                             ->join('publications as p', 'pf.publication_id', '=', 'p.publication_id')
-                            ->leftJoin('submissions as s', 'p.publication_id', '=', 's.current_publication_id')
-                            ->whereColumn('p.publication_id', '=', 's.current_publication_id')
                             ->whereNotNull('pf.doi_id')
                             ->where('p.status', '=', PKPPublication::STATUS_PUBLISHED);
+                        $this->whereDepositablePublication($q, $doiVersioning, false);
                     });
                 });
-                // Submission file DOIs
-                $q->when(in_array(Repo::doi()::TYPE_SUBMISSION_FILE, $enabledDoiTypes), function (Builder $q) {
-                    $q->orWhereIn('d.doi_id', function (Builder $q) {
+                // Submission file DOIs, of the proof files of a publication format
+                $q->when(in_array(Repo::doi()::TYPE_SUBMISSION_FILE, $enabledDoiTypes), function (Builder $q) use ($doiVersioning) {
+                    $q->orWhereIn('d.doi_id', function (Builder $q) use ($doiVersioning) {
                         $q->select('sf.doi_id')
                             ->from('submission_files', 'sf')
-                            ->join('submissions as s', 's.submission_id', '=', 'sf.submission_id')
-                            ->leftJoin('publications as p', 's.current_publication_id', '=', 'p.publication_id')
-                            ->whereColumn('p.publication_id', '=', 's.current_publication_id')
+                            ->join('publication_formats as pf', 'sf.assoc_id', '=', 'pf.publication_format_id')
+                            ->join('publications as p', 'pf.publication_id', '=', 'p.publication_id')
+                            ->where('sf.assoc_type', '=', Application::ASSOC_TYPE_PUBLICATION_FORMAT)
                             ->where('sf.file_stage', '=', SubmissionFile::SUBMISSION_FILE_PROOF)
                             ->whereNotNull('sf.doi_id')
                             ->where('p.status', '=', PKPPublication::STATUS_PUBLISHED);
+                        $this->whereDepositablePublication($q, $doiVersioning, false);
                     });
                 });
             })
             ->whereIn('d.status', [Doi::STATUS_UNREGISTERED, Doi::STATUS_ERROR, Doi::STATUS_STALE]);
-        return $q->get(['s.submission_id', 'd.doi_id']);
+        return $q->distinct()->get([DB::raw('COALESCE(p.submission_id, cp.submission_id, pfp.submission_id, sfd.submission_id) AS submission_id'), 'd.doi_id']);
     }
 }

classes/doi/Repository.php

@@ -113,61 +113,12 @@ public function mintSubmissionFileDoi(SubmissionFile $submissionFile, Submission
 
     public function getDoisForSubmission(int $submissionId): array
     {
-        $doiIds = Collection::make();
-
         $submission = Repo::submission()->get($submissionId);
-        /** @var Publication[] $publications */
-        $publications = [$submission->getCurrentPublication()];
-
-        /** @var PressDAO $contextDao */
-        $contextDao = Application::getContextDAO();
-        /** @var Press */
-        $context = $contextDao->getById($submission->getData('contextId'));
-
-        foreach ($publications as $publication) {
-            $publicationDoiId = $publication->getData('doiId');
-            if (!empty($publicationDoiId) && $context->isDoiTypeEnabled(self::TYPE_PUBLICATION)) {
-                $doiIds->add($publicationDoiId);
-            }
-
-            // Chapters
-            $chapters = $publication->getData('chapters');
-            foreach ($chapters as $chapter) {
-                $chapterDoiId = $chapter->getData('doiId');
-                if (!empty($chapterDoiId) && $context->isDoiTypeEnabled(self::TYPE_CHAPTER)) {
-                    $doiIds->add($chapterDoiId);
-                }
-            }
-
-            // Publication formats
-            $publicationFormats = $publication->getData('publicationFormats');
-            foreach ($publicationFormats as $publicationFormat) {
-                $publicationFormatDoiId
-                    = $publicationFormat->getData('doiId');
-                if (!empty($publicationFormatDoiId) && $context->isDoiTypeEnabled(self::TYPE_REPRESENTATION)) {
-                    $doiIds->add($publicationFormatDoiId);
-                }
-            }
-
-            // Submission files
-            if ($context->isDoiTypeEnabled(self::TYPE_SUBMISSION_FILE)) {
-                $submissionFiles = Repo::submissionFile()
-                    ->getCollector()
-                    ->filterBySubmissionIds([$publication->getData('submissionId')])
-                    ->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PROOF])
-                    ->getMany();
-
-                /** @var SubmissionFile $submissionFile */
-                foreach ($submissionFiles as $submissionFile) {
-                    $submissionFileDoiId = $submissionFile->getData('doiId');
-                    if (!empty($submissionFileDoiId)) {
-                        $doiIds->add($submissionFileDoiId);
-                    }
-                }
-            }
-        }
-
-        return $doiIds->unique()->toArray();
+        return collect($submission->getData('publications'))
+            ->flatMap(fn (Publication $publication) => $this->getDoisForPublication($publication))
+            ->unique()
+            ->values()
+            ->all();
     }
 
     /**
@@ -212,10 +163,13 @@ public function getDoisForPublication(Publication $publication): array
 
         // Submission files
         if ($context->isDoiTypeEnabled(self::TYPE_SUBMISSION_FILE)) {
-            $submissionFiles = Repo::submissionFile()
+            // Only the files of this version's publication formats
+            $publicationFormatIds = collect($publicationFormats)->map(fn (PublicationFormat $publicationFormat) => $publicationFormat->getId())->all();
+            $submissionFiles = empty($publicationFormatIds) ? [] : Repo::submissionFile()
                 ->getCollector()
                 ->filterBySubmissionIds([$publication->getData('submissionId')])
                 ->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PROOF])
+                ->filterByAssoc(Application::ASSOC_TYPE_PUBLICATION_FORMAT, $publicationFormatIds)
                 ->getMany();
 
             /** @var SubmissionFile $submissionFile */

classes/publication/DAO.php

@@ -16,8 +16,11 @@
 
 use APP\core\Application;
 use APP\monograph\ChapterDAO;
+use Illuminate\Database\Query\Builder;
+use Illuminate\Support\Facades\DB;
 use PKP\core\interfaces\CollectorInterface;
 use PKP\db\DAORegistry;
+use PKP\submissionFile\SubmissionFile;
 
 class DAO extends \PKP\publication\DAO
 {
@@ -55,4 +58,34 @@ public function fromRow(object $row, array $ids, object $cache, ?CollectorInterf
         $publication->setData('chapters', $chapterDao->getByPublicationId($publication->getId())->toArray());
         return $publication;
     }
+
+    /**
+     * @copydoc \PKP\publication\DAO::whereHasDoi()
+     */
+    protected function whereHasDoi(Builder $q): Builder
+    {
+        return parent::whereHasDoi($q)
+            ->orWhereExists(
+                fn (Builder $q) => $q->select(DB::raw(1))
+                    ->from('submission_chapters as spc')
+                    ->whereColumn('spc.publication_id', '=', 'p.publication_id')
+                    ->whereNotNull('spc.doi_id')
+            )
+            ->orWhereExists(
+                fn (Builder $q) => $q->select(DB::raw(1))
+                    ->from('publication_formats as pf')
+                    ->whereColumn('pf.publication_id', '=', 'p.publication_id')
+                    ->where(
+                        fn (Builder $q) => $q->whereNotNull('pf.doi_id')
+                            ->orWhereExists(
+                                fn (Builder $q) => $q->select(DB::raw(1))
+                                    ->from('submission_files as sf')
+                                    ->where('sf.assoc_type', '=', Application::ASSOC_TYPE_PUBLICATION_FORMAT)
+                                    ->whereColumn('sf.assoc_id', '=', 'pf.publication_format_id')
+                                    ->where('sf.file_stage', '=', SubmissionFile::SUBMISSION_FILE_PROOF)
+                                    ->whereNotNull('sf.doi_id')
+                            )
+                    )
+            );
+    }
 }

classes/publication/Repository.php

@@ -38,6 +38,7 @@
 use PKP\db\DAORegistry;
 use PKP\doi\exceptions\DoiException;
 use PKP\notification\Notification;
+use PKP\observers\events\PublicationVersioned;
 use PKP\plugins\Hook;
 use PKP\publication\Collector;
 use PKP\publication\PKPPublication;
@@ -252,6 +253,8 @@ public function version(Publication $publication, ?VersionStage $versionStage =
             }
         }
 
+        event(new PublicationVersioned($this->get($newId), $publication, Repo::submission()->get($submissionId), $context));
+
         return $newId;
     }
 
@@ -483,6 +486,24 @@ public function makeThumbnail($filePath, $thumbFileName, $maxWidth, $maxHeight)
         imagedestroy($thumb);
     }
 
+    /**
+     * Assign DOIs to a publication's new chapters, formats or files, if DOIs are assigned on item creation
+     */
+    public function createDoisOnCreation(int $publicationId): void
+    {
+        $publication = $this->get($publicationId);
+        $submission = Repo::submission()->get($publication->getData('submissionId'));
+        // Objects added during the submission wizard get their DOIs on submit
+        if ($submission->getData('submissionProgress')) {
+            return;
+        }
+
+        $context = Application::getContextDAO()->getById($submission->getData('contextId'));
+        if (Repo::doi()->assignOnItemCreation($context)) {
+            $this->createDois($publication);
+        }
+    }
+
     /** @copydoc \PKP\publication\Repository::createDois() */
     public function createDois(Publication $publication): array
     {
@@ -544,11 +565,13 @@ public function createDois(Publication $publication): array
 
         // Submission files
         if ($context->isDoiTypeEnabled(Repo::doi()::TYPE_SUBMISSION_FILE)) {
-            // Get all submission files assigned to a publication format
-            $submissionFiles = Repo::submissionFile()
+            // Only the files of this version's publication formats
+            $publicationFormatIds = collect($publicationFormats)->map(fn (PublicationFormat $publicationFormat) => $publicationFormat->getId())->all();
+            $submissionFiles = empty($publicationFormatIds) ? [] : Repo::submissionFile()
                 ->getCollector()
                 ->filterBySubmissionIds([$publication->getData('submissionId')])
                 ->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PROOF])
+                ->filterByAssoc(Application::ASSOC_TYPE_PUBLICATION_FORMAT, $publicationFormatIds)
                 ->getMany();
 
             /** @var SubmissionFile $submissionFile */

classes/submission/Collector.php

@@ -131,12 +131,27 @@ protected function addHasDoisFilterToQuery(Builder $q)
 
     /**
      * APP-specific filtering for submissions that should be listed on the DOI management page.
-     * Those are:
-     * submissions in the workflow editing and production stage,
-     * submissions that have a published publication, and
-     * submissions whose sub objects have a DOI.
+     * Those are all submitted submissions that have not been declined, and all submissions in the
+     * copyediting or production stage, with a published publication or with a DOI. The latter
+     * can also be listed on their own (inEditingOrPublished).
      */
     protected function addOnDoiPageFilterToQuery(Builder $q)
+    {
+        $q->where('s.submission_progress', '');
+        if ($this->inEditingOrPublished) {
+            $this->addInEditingPublishedOrWithDoisToQuery($q);
+        } else {
+            $q->where(function (Builder $q) {
+                $q->where('s.status', '!=', Submission::STATUS_DECLINED)
+                    ->orWhere(fn (Builder $q) => $this->addInEditingPublishedOrWithDoisToQuery($q));
+            });
+        }
+    }
+
+    /**
+     * Submissions in the copyediting or production stage, with a published publication or with a DOI
+     */
+    protected function addInEditingPublishedOrWithDoisToQuery(Builder $q): void
     {
         $q->where(function (Builder $q) {
             $q->whereIn('s.stage_id', [WORKFLOW_STAGE_ID_EDITING, WORKFLOW_STAGE_ID_PRODUCTION])

classes/submission/Repository.php

@@ -116,11 +116,13 @@ public function createDois(Submission $submission): array
 
         // Submission files
         if ($context->isDoiTypeEnabled(Repo::doi()::TYPE_SUBMISSION_FILE)) {
-            // Get all submission files assigned to a publication format
-            $submissionFiles = Repo::submissionFile()
+            // Only the files of this version's publication formats
+            $publicationFormatIds = collect($publicationFormats)->map(fn (PublicationFormat $publicationFormat) => $publicationFormat->getId())->all();
+            $submissionFiles = empty($publicationFormatIds) ? [] : Repo::submissionFile()
                 ->getCollector()
                 ->filterBySubmissionIds([$publication->getData('submissionId')])
                 ->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PROOF])
+                ->filterByAssoc(Application::ASSOC_TYPE_PUBLICATION_FORMAT, $publicationFormatIds)
                 ->getMany();
 
             /** @var SubmissionFile $submissionFile */

classes/submissionFile/Repository.php

@@ -53,6 +53,28 @@ public function getCollector(): Collector
         return App::makeWith(Collector::class, ['dao' => $this->dao]);
     }
 
+    /** @copydoc SubmissionFileRepository::add() */
+    public function add(SubmissionFile $submissionFile): int
+    {
+        $submissionFileId = parent::add($submissionFile);
+
+        // Only proof files of a publication format get a DOI
+        if (
+            !$submissionFile->getData('doiId')
+            && $submissionFile->getData('fileStage') == SubmissionFile::SUBMISSION_FILE_PROOF
+            && $submissionFile->getData('assocType') == Application::ASSOC_TYPE_PUBLICATION_FORMAT
+        ) {
+            $publicationId = DB::table('publication_formats')
+                ->where('publication_format_id', '=', $submissionFile->getData('assocId'))
+                ->value('publication_id');
+            if ($publicationId) {
+                Repo::publication()->createDoisOnCreation($publicationId);
+            }
+        }
+
+        return $submissionFileId;
+    }
+
     public function getFileStages(): array
     {
         $stages = [

controllers/grid/catalogEntry/form/PublicationFormatForm.php

@@ -284,6 +284,8 @@ public function execute(...$functionParams)
                 'publicationFormatName' => $publicationFormat->getData('name')
             ]);
             Repo::eventLog()->add($logEntry);
+
+            Repo::publication()->createDoisOnCreation($this->getPublication()->getId());
         }
 
         return $representationId;

controllers/grid/users/chapter/form/ChapterForm.php

@@ -347,6 +347,9 @@ public function execute(...$functionParams)
             $this->getChapter()->getId()
         );
 
+        // Also when its page is enabled later, as only chapters with a page get a DOI
+        Repo::publication()->createDoisOnCreation($this->getPublication()->getId());
+
         return true;
     }
 }