From 39812e9e261b1557eb2edd412d0383902376ceec Mon Sep 17 00:00:00 2001
From: Kaitlin Newson <kaitlin.newson@gmail.com>
Date: Wed, 7 Aug 2024 16:44:04 -0300
Subject: [PATCH 1/3] pkp/pkp-lib#8564 order export by issue ordering in pubmed
 plugin

---
 .../pubmed/PubMedExportPlugin.php             | 24 ++++++++++++-------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/plugins/importexport/pubmed/PubMedExportPlugin.php b/plugins/importexport/pubmed/PubMedExportPlugin.php
index a8b9f63e634..a1a42fa07a5 100644
--- a/plugins/importexport/pubmed/PubMedExportPlugin.php
+++ b/plugins/importexport/pubmed/PubMedExportPlugin.php
@@ -3,8 +3,8 @@
 /**
  * @file plugins/importexport/pubmed/PubMedExportPlugin.php
  *
- * Copyright (c) 2014-2022 Simon Fraser University
- * Copyright (c) 2003-2022 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 PubMedExportPlugin
@@ -187,14 +187,22 @@ public function exportIssues($issueIds, $context, $user)
         $pubmedExportFilters = $filterDao->getObjectsByGroup('article=>pubmed-xml');
         assert(count($pubmedExportFilters) == 1); // Assert only a single serialization filter
         $exportFilter = array_shift($pubmedExportFilters);
-        $submissions = Repo::submission()
-            ->getCollector()
-            ->filterByContextIds([$context->getId()])
-            ->filterByIssueIds($issueIds)
-            ->getMany();
+        $input = [];
+
+        foreach ($issueIds as $issueId) {
+            $sections = Repo::section()->getByIssueId($issueId);
+            foreach ($sections as $section) {
+                $submissionsInSections = [];
+                $submissionsInSections[] = Repo::submission()->getInSections($issueId, $context->getId());
+                foreach ($submissionsInSections as $articles) {
+                    foreach ($articles[$section->getId()]['articles'] as $article) {
+                        $input[] = $article;
+                    }
+                }
+            }
+        }
 
         libxml_use_internal_errors(true);
-        $input = $submissions->toArray();
         $submissionXml = $exportFilter->execute($input, true);
         $xml = $submissionXml->saveXml();
         $errors = array_filter(libxml_get_errors(), function ($a) {

From 066c2e761fe6ff5db87afd2157c0a87d7808d483 Mon Sep 17 00:00:00 2001
From: Kaitlin Newson <kaitlin.newson@gmail.com>
Date: Thu, 29 Aug 2024 13:14:05 -0300
Subject: [PATCH 2/3] pkp/pkp-lib#8564 order export by issue ordering in pubmed
 plugin

---
 plugins/importexport/pubmed/PubMedExportPlugin.php | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/plugins/importexport/pubmed/PubMedExportPlugin.php b/plugins/importexport/pubmed/PubMedExportPlugin.php
index a1a42fa07a5..f15296f8311 100644
--- a/plugins/importexport/pubmed/PubMedExportPlugin.php
+++ b/plugins/importexport/pubmed/PubMedExportPlugin.php
@@ -191,13 +191,11 @@ public function exportIssues($issueIds, $context, $user)
 
         foreach ($issueIds as $issueId) {
             $sections = Repo::section()->getByIssueId($issueId);
+            $submissionsInSections = [];
+            $submissionsInSections[] = Repo::submission()->getInSections($issueId, $context->getId());
             foreach ($sections as $section) {
-                $submissionsInSections = [];
-                $submissionsInSections[] = Repo::submission()->getInSections($issueId, $context->getId());
                 foreach ($submissionsInSections as $articles) {
-                    foreach ($articles[$section->getId()]['articles'] as $article) {
-                        $input[] = $article;
-                    }
+                    $input = array_merge($input, $articles[$section->getId()]['articles']);
                 }
             }
         }

From d51cbc8c6c7291cf1f963f7913284b375964378a Mon Sep 17 00:00:00 2001
From: Kaitlin Newson <kaitlin.newson@gmail.com>
Date: Fri, 30 Aug 2024 09:41:26 -0300
Subject: [PATCH 3/3] pkp/pkp-lib#8564 order export by issue ordering in pubmed
 plugin

---
 plugins/importexport/pubmed/PubMedExportPlugin.php | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/plugins/importexport/pubmed/PubMedExportPlugin.php b/plugins/importexport/pubmed/PubMedExportPlugin.php
index f15296f8311..38601ea69e0 100644
--- a/plugins/importexport/pubmed/PubMedExportPlugin.php
+++ b/plugins/importexport/pubmed/PubMedExportPlugin.php
@@ -191,12 +191,9 @@ public function exportIssues($issueIds, $context, $user)
 
         foreach ($issueIds as $issueId) {
             $sections = Repo::section()->getByIssueId($issueId);
-            $submissionsInSections = [];
-            $submissionsInSections[] = Repo::submission()->getInSections($issueId, $context->getId());
+            $submissionsInSections = Repo::submission()->getInSections($issueId, $context->getId());
             foreach ($sections as $section) {
-                foreach ($submissionsInSections as $articles) {
-                    $input = array_merge($input, $articles[$section->getId()]['articles']);
-                }
+                $input = array_merge($input, $submissionsInSections[$section->getId()]['articles']);
             }
         }