first commit

tools/bootstrap.php

@@ -0,0 +1,17 @@
+<?php
+
+/**
+ * @file tools/bootstrap.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup tools
+ *
+ * @brief application-specific configuration common to all tools (corresponds
+ *  to index.php for web requests).
+ */
+
+define('INDEX_FILE_LOCATION', dirname(__FILE__, 2) . '/index.php');
+require dirname(__FILE__, 2) . '/lib/pkp/classes/cliTool/CommandLineTool.php';

tools/cleanReviewerInterests.php

@@ -0,0 +1,144 @@
+<?php
+
+/**
+ * @file tools/cleanReviewerInterests.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class ReviewerInterestsDeletionTool
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool to remove user interests that are not referenced by any user accounts.
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+use PKP\cliTool\CommandLineTool;
+use PKP\controlledVocab\ControlledVocabDAO;
+use PKP\controlledVocab\ControlledVocabEntryDAO;
+use PKP\db\DAORegistry;
+use PKP\user\InterestDAO;
+
+class ReviewerInterestsDeletionTool extends CommandLineTool
+{
+    public array $parameters;
+
+    /**
+     * Constructor.
+     *
+     * @param array $argv command-line arguments
+     */
+    public function __construct($argv = [])
+    {
+        parent::__construct($argv);
+
+        if (!sizeof($this->argv)) {
+            $this->usage();
+            exit(1);
+        }
+
+        $this->parameters = $this->argv;
+    }
+
+    /**
+     * Print command usage information.
+     */
+    public function usage()
+    {
+        echo "Permanently removes user interests that are not referenced by any user accounts.  USE WITH CARE.\n"
+            . "Usage:\n"
+            . "\t{$this->scriptName} --show : Display user interests not referenced\n"
+            . "\t{$this->scriptName} --remove  : Permanently delete user interests not referenced\n";
+    }
+
+    /**
+     * Remove user interests that are not referenced by any user account
+     */
+    public function execute()
+    {
+        $orphans = $this->_getOrphanVocabInterests();
+        if (!count($orphans)) {
+            echo "No user interests to remove.\n";
+            exit(0);
+        }
+
+        $command = $this->parameters[0];
+        switch ($command) {
+            case '--show':
+                $interests = array_map(function ($entry) {
+                    return $entry->getData(InterestDAO::CONTROLLED_VOCAB_INTEREST);
+                }, $orphans);
+                echo "Below are the user interests that are not referenced by any user account.\n";
+                echo "\t" . join("\n\t", $interests) . "\n";
+                break;
+
+            case '--remove':
+                /** @var ControlledVocabEntryDAO */
+                $vocabEntryDao = DAORegistry::getDAO('ControlledVocabEntryDAO');
+                foreach ($orphans as $orphanVocab) {
+                    $vocabEntryDao->deleteObject($orphanVocab);
+                }
+                echo count($orphans) . " entries deleted\n";
+                break;
+
+            default:
+                echo "Invalid command.\n";
+                $this->usage();
+                exit(2);
+        }
+    }
+
+    /**
+     * Returns user interests that are not referenced
+     *
+     * @return array array of ControlledVocabEntry object
+     */
+    protected function _getOrphanVocabInterests()
+    {
+        /** @var InterestDAO */
+        $interestDao = DAORegistry::getDAO('InterestDAO');
+        /** @var ControlledVocabDAO */
+        $vocabDao = DAORegistry::getDAO('ControlledVocabDAO');
+        /** @var ControlledVocabEntryDAO */
+        $vocabEntryDao = DAORegistry::getDAO('ControlledVocabEntryDAO');
+
+        $interestVocab = $vocabDao->getBySymbolic(InterestDAO::CONTROLLED_VOCAB_INTEREST);
+        $vocabEntryIterator = $vocabEntryDao->getByControlledVocabId($interestVocab->getId());
+        $vocabEntryList = $vocabEntryIterator->toArray();
+
+        // list of vocab interests in db
+        $allInterestVocabIds = array_map(
+            function ($entry) {
+                return $entry->getId();
+            },
+            $vocabEntryList
+        );
+
+        // list of vocabs associated to users
+        $interests = $interestDao->getAllInterests();
+        $userInterestVocabIds = array_map(
+            function ($interest) {
+                return $interest->getId();
+            },
+            $interests->toArray()
+        );
+
+        // get the difference
+        $diff = array_diff($allInterestVocabIds, $userInterestVocabIds);
+
+        $orphans = array_filter(
+            $vocabEntryList,
+            function ($entry) use ($diff) {
+                return in_array($entry->getId(), $diff);
+            }
+        );
+
+        return $orphans;
+    }
+}
+
+$tool = new ReviewerInterestsDeletionTool($argv ?? []);
+$tool->execute();

tools/deleteSubmissions.php

@@ -0,0 +1,69 @@
+<?php
+
+/**
+ * @file tools/deleteSubmissions.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class SubmissionDeletionTool
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool to delete submissions
+ */
+
+use APP\facades\Repo;
+use PKP\cliTool\CommandLineTool;
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+class SubmissionDeletionTool extends CommandLineTool
+{
+    public array $parameters;
+
+    /**
+     * Constructor.
+     *
+     * @param array $argv command-line arguments
+     */
+    public function __construct($argv = [])
+    {
+        parent::__construct($argv);
+
+        if (!sizeof($this->argv)) {
+            $this->usage();
+            exit(1);
+        }
+
+        $this->parameters = $this->argv;
+    }
+
+    /**
+     * Print command usage information.
+     */
+    public function usage()
+    {
+        echo "Permanently removes submission(s) and associated information.  USE WITH CARE.\n"
+            . "Usage: {$this->scriptName} submission_id [...]\n";
+    }
+
+    /**
+     * Delete submission data and associated files
+     */
+    public function execute()
+    {
+        foreach ($this->parameters as $articleId) {
+            $article = Repo::submission()->get($articleId);
+            if (!isset($article)) {
+                printf("Error: Skipping {$articleId}. Unknown submission.\n");
+                continue;
+            }
+            Repo::submission()->delete($article);
+        }
+    }
+}
+
+$tool = new SubmissionDeletionTool($argv ?? []);
+$tool->execute();

tools/importExport.php

@@ -0,0 +1,83 @@
+<?php
+
+/**
+ * @file tools/importExport.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class importExport
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool to perform import/export tasks
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+use PKP\cliTool\CommandLineTool;
+use PKP\plugins\ImportExportPlugin;
+use PKP\plugins\PluginRegistry;
+
+class importExport extends CommandLineTool
+{
+    public $command;
+    /** @var ImportExportPlugin */
+    public $plugin;
+    public $parameters;
+
+    /**
+     * Constructor.
+     *
+     * @param array $argv command-line arguments (see usage)
+     */
+    public function __construct($argv = [])
+    {
+        parent::__construct($argv);
+        $this->command = array_shift($this->argv);
+        $this->parameters = $this->argv;
+    }
+
+    /**
+     * Print command usage information.
+     */
+    public function usage()
+    {
+        echo "Command-line tool for import/export tasks\n"
+            . "Usage:\n"
+            . "\t{$this->scriptName} list: List available plugins\n"
+            . "\t{$this->scriptName} [pluginName] usage: Display usage information for a plugin\n"
+            . "\t{$this->scriptName} [pluginName] [params...]: Invoke a plugin\n";
+    }
+
+    /**
+     * Parse and execute the import/export task.
+     */
+    public function execute()
+    {
+        $plugins = PluginRegistry::loadCategory('importexport');
+        if ($this->command === 'list') {
+            echo "Available plugins:\n";
+            if (empty($plugins)) {
+                echo "\t(None)\n";
+            } else {
+                foreach ($plugins as $plugin) {
+                    if ($plugin->supportsCLI()) {
+                        echo "\t" . $plugin->getName() . "\n";
+                    }
+                }
+            }
+            return;
+        }
+        /** @var ImportExportPlugin $plugin */
+        if ($this->command == 'usage' || $this->command == 'help' || $this->command == '' || ($plugin = PluginRegistry::getPlugin('importexport', $this->command)) === null || !$plugin->supportsCLI()) {
+            $this->usage();
+            return;
+        }
+        return $plugin->executeCLI($this->scriptName, $this->parameters);
+    }
+}
+
+$tool = new importExport($argv ?? []);
+$tool->execute();

tools/install.php

@@ -0,0 +1,39 @@
+<?php
+
+/**
+ * @file tools/install.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class OJSInstallTool
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool for installing OJS.
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+class OJSInstallTool extends \PKP\cliTool\InstallTool
+{
+    /**
+     * Read installation parameters from stdin.
+     * FIXME: May want to implement an abstract "CLIForm" class handling input/validation.
+     * FIXME: Use readline if available?
+     */
+    public function readParams()
+    {
+        printf("%s\n", __('installer.appInstallation'));
+
+        parent::readParams();
+
+        $this->readParamBoolean('install', 'installer.installApplication');
+
+        return $this->params['install'];
+    }
+}
+
+$tool = new OJSInstallTool($argv ?? []);
+$tool->execute();

tools/jsonlint-exclusions.txt

@@ -0,0 +1,7 @@
+./lib/pkp/lib
+./plugins/paymethod/paypal/vendor
+./plugins/generic/citationStyleLanguage/lib
+./plugins/generic/plagiarism/vendor
+./node_modules
+./lib/ui-library/node_modules
+./lib/pkp/js/lib

tools/mergeUsers.php

@@ -0,0 +1,20 @@
+<?php
+
+/**
+ * @file tools/mergeUsers.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class mergeUsers
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool for merging two user accounts.
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+$tool = new \PKP\cliTool\MergeUsersTool($argv ?? []);
+$tool->execute();

tools/rebuildSearchIndex.php

@@ -0,0 +1,89 @@
+<?php
+
+/**
+ * @file tools/rebuildSearchIndex.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class rebuildSearchIndex
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool to rebuild the article keyword search database.
+ */
+
+require dirname(__FILE__) . '/bootstrap.php';
+
+use APP\core\Application;
+use APP\journal\JournalDAO;
+use PKP\cliTool\CommandLineTool;
+use PKP\config\Config;
+use PKP\db\DAORegistry;
+use PKP\plugins\Hook;
+
+class rebuildSearchIndex extends CommandLineTool
+{
+    /**
+     * Print command usage information.
+     */
+    public function usage(): void
+    {
+        echo "Script to rebuild article search index\n"
+            . "Usage: {$this->scriptName} [options] [journal_path]\n\n"
+            . "options: The standard index implementation does\n"
+            . "         not support any options. For other\n"
+            . "         implementations please see the corresponding\n"
+            . "         plugin documentation (e.g. 'plugins/generic/\n"
+            . "         lucene/README').\n";
+    }
+
+    /**
+     * Rebuild the search index for all articles in all journals.
+     */
+    public function execute(): void
+    {
+        // Check whether we have (optional) switches.
+        $switches = [];
+        while (count($this->argv) && substr($this->argv[0], 0, 1) === '-') {
+            $switches[] = array_shift($this->argv);
+        }
+
+        // If we have another argument that this must be a journal path.
+        $journal = null;
+        if (count($this->argv)) {
+            $journalPath = array_shift($this->argv);
+            /** @var JournalDAO */
+            $journalDao = DAORegistry::getDAO('JournalDAO');
+            $journal = $journalDao->getByPath($journalPath);
+            if (!$journal) {
+                exit(__('search.cli.rebuildIndex.unknownJournal', ['journalPath' => $journalPath]) . "\n");
+            }
+        }
+
+        // Register a router hook so that we can construct
+        // useful URLs to journal content.
+        Hook::add('Request::getBaseUrl', [$this, 'callbackBaseUrl']);
+
+        // Let the search implementation re-build the index.
+        $articleSearchIndex = Application::getSubmissionSearchIndex();
+        $articleSearchIndex->rebuildIndex(true, $journal, $switches);
+    }
+
+    /**
+     * Callback to patch the base URL which will be required
+     * when constructing galley/supp file download URLs.
+     *
+     * @see \APP\core\Request::getBaseUrl()
+     */
+    public function callbackBaseUrl(string $hookName, array $params): bool
+    {
+        $baseUrl = & $params[0];
+        $baseUrl = Config::getVar('general', 'base_url');
+        return Hook::ABORT;
+    }
+}
+
+$tool = new rebuildSearchIndex($argv ?? []);
+$tool->execute();

tools/release.sh

@@ -0,0 +1,114 @@
+#!/bin/bash
+
+#
+# tools/release.sh
+#
+# Copyright (c) 2014-2021 Simon Fraser University
+# Copyright (c) 2003-2021 John Willinsky
+# Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+#
+# Script to create an automated (incremental) release of OJS.
+#
+# Usage: release.sh <stable-branch> <distrib dir> <github access token>
+#  <stable_branch>: the stable branch to release from (e.g. ojs-stable-2_4_5)
+#  <distrib dir>: a directory containing prior tarballs to use in generating
+#    patches
+#  <github access token>: an API token from
+#    https://github.com/settings/applications
+#
+# NOTE: This script CANNOT currently be used to release a first build of a
+# revision (i.e. a -0 build). It can only be used to release -1 and subsequent
+# builds of a revision.
+
+# Fail on first error
+set -e
+
+# Check for proper usage
+if [ -z "$3" ]; then
+	echo "Usage: $0 <stable-branch> <distrib dir> <github access token>";
+	exit 1;
+fi
+BRANCH=$1
+DISTRIBDIR=$2
+ACCESSTOKEN=$3
+
+# Make sure we're at the head of the stable branch
+git checkout ${BRANCH}
+git pull
+cd lib/pkp
+git checkout ${BRANCH}
+git pull
+cd ../..
+
+# Determine the tag of the last release on this branch (e.g. ojs-2_4_5-0)
+LASTTAG=`git describe --tags --abbrev=0 $BRANCH`
+
+# Parse the version number information from the tag
+[[ $LASTTAG =~ ([a-z]+)-([0-9]+)_([0-9]+)_([0-9]+)-([0-9]+) ]] && APPLICATION="${BASH_REMATCH[1]}" && MAJOR="${BASH_REMATCH[2]}" && MINOR="${BASH_REMATCH[3]}" && REVISION="${BASH_REMATCH[4]}" && LASTBUILD="${BASH_REMATCH[5]}"
+THISBUILD=$((LASTBUILD+1))
+
+# Calculate the tag of the next release (e.g. ojs-2_4_5-1
+THISTAG=`echo $LASTTAG | sed -r 's/(.*-)([0-9]+)/echo \1$((\2+1))/ge'`
+
+# Other useful bits and pieces
+BUILDDATE=`date +%Y-%m-%d`
+APPLICATION_UPPER=`echo ${APPLICATION} | tr '[:lower:]' '[:upper:]'`
+
+# Update the version descriptor
+LASTPATCHSUFFIX="${MAJOR}.${MINOR}.${REVISION}"
+[[ ${LASTBUILD} -ne "" ]] && LASTPATCHSUFFIX="${LASTPATCHSUFFIX}-${LASTBUILD}"
+sed -i	-e "s/<tag>.*<\/tag>/<tag>${THISTAG}<\/tag>/" \
+	-e "s/<release>.*<\/release>/<release>${MAJOR}.${MINOR}.${REVISION}.${THISBUILD}<\/release>/" \
+	-e "s/<date>.*<\/date>/<date>${BUILDDATE}<\/date>/" \
+	-e "s/<package>.*<\/package>/<package>http:\/\/pkp.sfu.ca\/${APPLICATION}\/download\/${APPLICATION}-${MAJOR}.${MINOR}.${REVISION}-${THISBUILD}.tar.gz<\/package>/" \
+	-e "s/\(<patch .*_to_\).*\(\.patch\.gz.*\)/\1${MAJOR}.${MINOR}.${REVISION}-${THISBUILD}.patch.gz/" \
+	dbscripts/xml/version.xml
+git add dbscripts/xml/version.xml
+
+# Update the upgrade and install descriptors
+sed -i	-e "s/<install version=\".*\">/<install version=\"${MAJOR}.${MINOR}.${REVISION}.${THISBUILD}\">/" \
+	dbscripts/xml/upgrade.xml dbscripts/xml/install.xml
+git add dbscripts/xml/upgrade.xml dbscripts/xml/install.xml
+
+# Update the README.md
+sed -i	-e "s/=== Version: .*/=== Version: ${MAJOR}.${MINOR}.${REVISION}-${THISBUILD}/" \
+	-e "s/=== GIT tag: .*/=== GIT tag: ${THISTAG}/" \
+	-e "s/=== Release date: .*/=== Release date: ${BUILDDATE}/" \
+	docs/README.md
+git add docs/README.md
+
+# Update the Doxygen config file
+sed -i	-e "s/^\(PROJECT_NUMBER.*= \).*/\1${MAJOR}.${MINOR}.${REVISION}-${THISBUILD}/" \
+	docs/dev/*.doxygen
+
+# Generate the release notes
+echo -n "Generating release notes"
+echo "
+Automated Build ${MAJOR}-${MINOR}-${REVISION}.${THISBUILD}
+-----------------------
+This automated build adds the following fixes to the base release of ${APPLICATION_UPPER} ${MAJOR}.${MINOR}.${REVISION}:
+" >> docs/RELEASE
+
+# Get the bug IDs and titles for issues referenced in this release
+for ISSUENUM in `(git log --pretty=oneline ${LASTTAG}..HEAD && cd lib/pkp && git log --pretty=oneline ${LASTTAG}..HEAD) | sed -n -e "s/.*pkp\/pkp-lib#\([0-9]\+\).*/\1/p" | sort -n | uniq`; do
+	ISSUETITLE=`wget --auth-no-challenge --user=${ACCESSTOKEN} --password=x-oauth-basic -q -O - "https://api.github.com/repos/pkp/pkp-lib/issues/${ISSUENUM}" | php -r "echo trim(json_decode(file_get_contents('php://stdin'))->title);"`
+	echo "	#${ISSUENUM}: ${ISSUETITLE}" >> docs/RELEASE
+	echo -n "." # Status
+done
+RELEASE_ALTCOPY="docs/release-notes/README-${MAJOR}.${MINOR}.${REVISION}"
+cp docs/RELEASE ${RELEASE_ALTCOPY}
+git add docs/RELEASE ${RELEASE_ALTCOPY}
+echo " Done."
+
+# Commit the last changes
+git add lib/pkp
+git commit -m "Automated commits for ${APPLICATION_UPPER} ${MAJOR}.${MINOR}.${REVISION}-${THISBUILD}"
+cd lib/pkp
+git tag ${THISTAG}
+git push --tags
+cd ../..
+git tag ${THISTAG}
+git push --tags
+
+# Build the package
+bash tools/buildpkg.sh ${MAJOR}.${MINOR}.${REVISION}-${THISBUILD} ${THISTAG} ${DISTRIBDIR}

tools/resolveAgencyDuplicates.php

@@ -0,0 +1,185 @@
+<?php
+
+use Illuminate\Database\Query\Builder;
+use Illuminate\Support\Collection;
+use Illuminate\Support\Facades\DB;
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+class resolveAgencyDuplicates extends \PKP\cliTool\CommandLineTool
+{
+    private string|null $command = null;
+    private string|null $agency_name = null;
+    private bool $forceFlag = false;
+    /**
+     * List of potential agencies to choose from along with related fields for resolution.
+     *
+     * Array shape should look like:
+     * `['agency_name' => [
+     *      'status' => 'agency_name::status',
+     *      'additionalFields': [...],
+     *      ]
+     * ]`
+     */
+    private array $agencies = [
+        'crossref' => [
+            'status' => 'crossref::status',
+            'additionalFields' => [
+                'crossref::registeredDoi',
+                'crossref::batchId',
+                'crossref::failedMsg',
+            ],
+        ],
+        'datacite' => [
+            'status' => 'datacite::status',
+            'additionalFields' => [
+                'datacite::registeredDoi',
+            ],
+        ],
+        'medra' => [
+            'status' => 'medra::status',
+            'additionalFields' => [
+                'medra::registeredDoi',
+            ],
+        ],
+    ];
+
+    public function __construct($argv = [])
+    {
+        parent::__construct($argv);
+
+        $forceFlagIndex = array_search('--force', $this->argv);
+        if ($forceFlagIndex) {
+            $this->forceFlag = true;
+            array_splice($this->argv, $forceFlagIndex, 1);
+        }
+
+        if (sizeof($this->argv) == 0) {
+            $this->exitWithUsageMessage();
+        }
+        $this->command = array_shift($this->argv);
+        $this->agency_name = array_shift($this->argv);
+
+        if (
+            $this->command === 'resolve' &&
+            ($this->agency_name === null || !in_array($this->agency_name, array_keys($this->agencies)))
+        ) {
+            $this->exitWithUsageMessage();
+        }
+    }
+
+    public function usage()
+    {
+        $agencies = implode(', ', array_keys($this->agencies));
+        echo "Script to resolve DOI registration agency duplication pre-3.4.\n"
+            . "NB: If a conflict exists for a submission, the corresponding publication objects (galleys, etc.) will also be cleaned up.\n\n"
+            . "Usage:\n"
+            . "{$this->scriptName} resolve [agency_name] --force : Remove conflicting DOI registration info, keeping agency_name.\n"
+            . "{$this->scriptName} test : Returns list of conflicting items\n\n"
+            . "Options:\n"
+            . "agency_name      One of: {$agencies}.\n"
+            . "--force          Force resolve operation. Will not delete data without it.\n";
+    }
+
+    public function execute(): void
+    {
+        switch ($this->command) {
+            case 'resolve':
+                $this->resolve();
+                break;
+            case 'test':
+                $this->test();
+                break;
+            default:
+                $this->exitWithUsageMessage();
+                break;
+        }
+    }
+
+    private function resolve(): void
+    {
+        if (!$this->forceFlag) {
+            $this->print('Warning! This is a destructive operation. Ensure you have a database backup and re-run this command with the `--force` flag.');
+            exit(0);
+        }
+
+        $agencies = array_filter($this->agencies, fn ($key) => $key !== $this->agency_name, ARRAY_FILTER_USE_KEY);
+        $this->print('Removing duplicate registration info for ' . implode(', ', array_keys($agencies)) . '...');
+
+        $agencyFields = array_reduce($agencies, fn ($carry, $item) => array_merge($carry, [$item['status']], $item['additionalFields']), []);
+        $submissionIds = $this->getSubmissionIds();
+        $galleyIds = $this->getGalleyIds();
+        $issueIds = $this->getIssueIds();
+
+        DB::table('submission_settings')
+            ->whereIn('setting_name', $agencyFields)
+            ->whereIn('submission_id', $submissionIds)
+            ->delete();
+        $this->print("Removed duplicates for {$submissionIds->count()} submission(s)");
+
+        DB::table('publication_galley_settings')
+            ->whereIn('setting_name', $agencyFields)
+            ->whereIn('galley_id', $galleyIds)
+            ->delete();
+        $this->print("Removed duplicates for {$galleyIds->count()} galley(s)");
+
+        DB::table('issue_settings')
+            ->whereIn('setting_name', $agencyFields)
+            ->whereIn('issue_id', $issueIds)
+            ->delete();
+        $this->print("Removed duplicates for {$issueIds->count()} issues(s)");
+    }
+
+    private function test(): void
+    {
+        $this->print('IDs with duplicate DOI registration metadata:');
+        $this->print("Submissions: {$this->getSubmissionIds()}");
+        $this->print("Galleys: {$this->getGalleyIds()}");
+        $this->print("Issues: {$this->getIssueIds()}");
+    }
+
+    private function getSubmissionIds(): Collection
+    {
+        return DB::table('submission_settings')
+            ->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
+            ->groupBy('submission_id')
+            ->havingRaw('COUNT(submission_id) > 1')
+            ->pluck('submission_id');
+    }
+
+    /**
+     * Gets galley IDs that have duplicates OR are associated with submissions with conflicts
+     */
+    private function getGalleyIds(): Collection
+    {
+        return DB::table('publication_galley_settings')
+            ->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
+            ->orWhereIn('galley_id', function (Builder $q) {
+                $q->select('pg.galley_id')
+                    ->from('publication_galleys', 'pg')
+                    ->leftJoin('publications as p', 'pg.publication_id', '=', 'p.publication_id')
+                    ->leftJoin('submissions as s', 'p.submission_id', '=', 's.submission_id')
+                    ->whereIn('s.submission_id', $this->getSubmissionIds());
+            })
+            ->groupBy('galley_id')
+            ->havingRaw('COUNT(galley_id) > 1')
+            ->pluck('galley_id');
+    }
+
+    private function getIssueIds(): Collection
+    {
+        return DB::table('issue_settings')
+            ->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
+            ->groupBy('issue_id')
+            ->havingRaw('COUNT(issue_id) > 1')
+            ->pluck('issue_id');
+    }
+
+    protected function print(string $message): void
+    {
+        echo $message . PHP_EOL;
+    }
+}
+
+$tool = new resolveAgencyDuplicates($argv ?? []);
+$tool->execute();

tools/runScheduledTasks.php

@@ -0,0 +1,24 @@
+<?php
+
+/**
+ * @file tools/runScheduledTasks.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class runScheduledTasks
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool to execute a set of scheduled tasks.
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+class runScheduledTasks extends \PKP\cliTool\ScheduledTaskTool
+{
+}
+
+$tool = new runScheduledTasks($argv ?? []);
+$tool->execute();

tools/startSubmodulesTRAVIS.sh

@@ -0,0 +1,123 @@
+#!/bin/bash
+
+parseRepositoryName () {
+    local url=$1
+    if [ -z "$url" ]; then
+        echo "You should pass a URL" >&2
+        exit 2;
+    fi;
+
+    echo $(basename "${url}" .git)
+}
+
+getSubmodulesList () {
+    local option=$1
+    if [ -z "$option" ]; then
+        echo "You should select an option" >&2
+        exit 2;
+    fi;
+
+    echo $(git config --file .gitmodules --get-regexp ${option} | awk '{ print $2 }');
+}
+
+existsFork () {
+    local username=$1
+    local repository=$2
+    local branch=$3
+    if [ -z "$username" ]
+    then
+        echo "Username should be pass as first parameter." >&2
+        exit 2;
+    fi;
+
+    if [ -z "$repository" ]
+    then
+        echo "Repository should be pass as second parameter." >&2
+        exit 2;
+    fi;
+
+    if [ -z "$branch" ]
+    then
+        echo "Branch should be pass as third parameter." >&2
+        exit 2;
+    fi;
+
+    result=$(git ls-remote --quiet --exit-code -h https://github.com/${username}/${repository} ${branch});
+
+    if [ ! -z "$result" ]
+     then
+        echo 1;
+     else
+        echo 0;
+    fi;
+}
+
+git config --global user.email "pkp@mailinator.com"
+git config --global user.name "PKP"
+echo "1 - Retrieving git user:"
+gitUser=$(cat .git/config | grep -A2 "remote \"origin\"" | grep "url" | cut -f2 -d":" | cut -f4 -d"/")
+echo "    Gituser: $gitUser"
+echo "2 - Verifying if we have a merge commit in HEAD:"
+isMergeCommit=$(git log -m --pretty=oneline -n1 | grep -P "Merge [0-9a-z]{40} into [0-9a-z]{40}")
+echo "    Merge commit message: $isMergeCommit"
+if [ \( -n "$isMergeCommit" \) -a \( "$gitUser" = "pkp" \) ]; then
+	commitHash=$(git log -m --pretty=oneline -n2 | sed -n 2p | grep -Po "^[0-9a-z]{40}")
+	echo "    HEAD points to a merge commit."
+	echo "    HEAD^ points to a common commit with hash $commitHash"
+else
+	commitHash=$(git log -m --pretty=oneline -n1 | grep -Po "^[0-9a-z]{40}")
+	echo "    HEAD points to a common commit with hash $commitHash"
+fi
+echo "3 - Verifying if last non merge commit is a subproject commit:"
+libModuleHashes=$(git show "$commitHash" | grep "+Subproject commit" | cut -f3 -d" ")
+strLength=${#libModuleHashes}
+echo "    Subproject commit hash: $libModuleHashes"
+if [ \( -n "$libModuleHashes" \) -a \( "$strLength" -ge 40 \) ]; then
+	echo "    Last non merge commit is subproject commit."
+	echo "4 - Trying to get user and branch from commit message:"
+	userAndBranch=$(git log --pretty=oneline -1 "$commitHash" | grep -o "##.*##" | sed "s:^##\(.*\)##$:\1:")
+	gitUser=$(echo "$userAndBranch" | cut -f1 -d"/")
+	branch=$(echo "$userAndBranch" | cut -f2- -d"/")
+	echo "    User and branch: $userAndBranch - User: $gitUser - Branch: $branch"
+	if [ \( -n "$gitUser" \) -a \( -n "$branch" \) ]; then
+		echo "    Found user and branch in commit message."
+		echo "5 - Reseting the subproject commit in application."
+		git reset --hard "$commitHash"^
+		echo "6 - Initializing and updating submodule from official."
+		git submodule update --init --recursive
+        submoduleList=$(getSubmodulesList path)
+
+        declare -A submodulesArr
+        for submodule in $submoduleList
+        do
+            rawUrl=$(getSubmodulesList "submodule.${submodule}.url")
+            submodulesArr[$submodule]=$(parseRepositoryName $rawUrl)
+        done;
+
+        rootDir=$(pwd)
+        currentSubmoduleIteration=1
+
+        for submoduleName in ${!submodulesArr[@]};
+        do
+            submoduleUrlBasename=${submodulesArr[${submoduleName}]};
+            submoduleLocalPath=$submoduleName
+            printf "\nThis is the submodule: ${submoduleName}\n"
+            printf "\tLocal path for repository should be %s\n" "${submoduleLocalPath}"
+            printf "\tURL path for repository should be %s\n" "${submoduleUrlBasename}"
+            printf "\tExists fork for it?\n"
+            existsForkForSubmodule=$(existsFork ${gitUser} ${submoduleUrlBasename} ${branch})
+            if [[ $existsForkForSubmodule == 1 ]]
+                then
+                    echo "7 - Updating $submoduleLocalPath with code from $gitUser repository, $branch branch."
+                    cd ${submoduleLocalPath}
+                    git remote add "$gitUser" https://github.com/"$gitUser"/"$submoduleUrlBasename"
+                    git reset --hard HEAD
+                    git pull --rebase "$gitUser" "$branch"
+                    cd ${rootDir}
+                    ((currentSubmoduleIteration=currentSubmoduleIteration+1))
+            fi;
+        done
+		exit 0
+	fi
+fi
+git submodule update --init --recursive

tools/upgrade.php

@@ -0,0 +1,22 @@
+<?php
+
+/**
+ * @file tools/upgrade.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class upgradeTool
+ *
+ * @ingroup tools
+ *
+ * @brief CLI tool for upgrading OJS.
+ *
+ * Note: Some functions require fopen wrappers to be enabled.
+ */
+
+require(dirname(__FILE__) . '/bootstrap.php');
+
+$tool = new \PKP\cliTool\UpgradeTool($argv ?? []);
+$tool->execute();

tools/xmllint-exclusions.txt

@@ -0,0 +1,14 @@
+./files/
+./tests/
+./lib/pkp/tests/phpunit.xml
+./lib/pkp/lib
+./lib/pkp/tests/classes/xslt
+./lib/pkp/js/lib
+./plugins/generic/citationStyleLanguage/lib/vendor
+./plugins/oaiMetadataFormats/dc/tests/expectedResult.xml
+./plugins/importexport/users/sample.xml
+./plugins/paymethod/paypal/vendor
+./lib/pkp/tests
+./node_modules
+./lib/ui-library/node_modules
+./cypress/fixtures/export-issues.xml