Pubmed plugin exports articles out of order compared to issue order

[jnugent]

Describe the bug
The generated XML that the PubMed plugin generates when exporting an issue does not sort the articles according to how they appear in an issue's table of contents. This used to happen in older versions of OJS but is no longer the case. This is probably due to the plugin using the submission service's getMany method since the old way of doing this with the PublishedArticleDAO is no longer possible. Restoring the order of content is important to some of our largest medical journal clients.

To Reproduce
Steps to reproduce the behavior:

1. Export an issue using the PubMed plugin
2. Examine the elements and compare them to the issue's table of contents.

What application are you using?
OJS 3.3.0.13

[mgscano]

Just to add a note here, since I'm the client impacted, also I hope I'm not the only one.
This one's really a painful thing to work around, since when a journal is under periodic publishing it becomes necessary to have PubMed IDs in the correct page order.
Reordering the XML code manually is definitely prone to error, and becomes an unnecessary long task.

[kaitlinnewson]

PRs ready for review:

• 3_3_0: pkp/pkp-lib#8564 order export by issue ordering in pubmed plugin ojs#4388
• 3_4_0: pkp/pkp-lib#8564 order export by issue ordering in pubmed plugin ojs#4389
• main: pkp/pkp-lib#8564 order export by issue ordering in pubmed plugin ojs#4390

@bozana could you review these?

[bozana]

Hi @kaitlinnewson, the plugin does not consider the section ordering, and the publication sequence is currently only per section. Thus, I think some more work is needed -- similar to how the articles are displayed on the issue TOC page, we would need to consider the sections (and their order) too.
Depending on how the issue #8998 is going to be fixed, this plugin will maybe need to be adapted as well, but lets fix it now as if that other issue would not exists :-)

[kaitlinnewson]

Hi @bozana, I've updated the PRs above, can you take another look?

[bozana]

Hi @kaitlinnewson, I left a few comments for the PR for the main branch, but they can be applied to other PRs/branches as well. Thanks!

[kaitlinnewson]

Hi @bozana, I've updated the PRs above, ready for another check!

[bozana]

Hi @kaitlinnewson, one more comment in the PR for stable-3_3_0, but relevant for all :-)
Thanks!

[kaitlinnewson]

Hi @bozana, PRs updated and hopefully ready to merge now!

[bozana]

All merged, thus closing