Missing supplementary files after upgrading to 3.1.0-1


We have upgraded to 3.1.0-1 from 2.4.8-1 and noticed that the supplementary files do not display.

I modified the db and set file_stage field from 10 to 2 and viewable field from 0 to 1 and I can now see the supplementary file under the submissions tab but of course I can’t download the file as the file stage is wrong.

Is there a way to display supplementary files in the submissions tab? Is there a setting i’m not seeing?


Hi @jhennig,

By default the supplementary files should have been migrated to galley files and displayed automatically during the OJS 2.x to 3.x migration process. Is that something you specifically prevented from happening? (There are a few relevant threads and some instructions for doing so on the forum, which is why I ask.)

Alec Smecher
Public Knowledge Project Team

I’m specifically looking at files yet to be published. I can’t see the supplementary files even if I send it to be published.

Hi @jhennig,

How are you sending these files for publication? (Screenshots might help.)

Alec Smecher
Public Knowledge Project Team

So this file exists on ojs 2.4.8

The file doesn’t exist here:


I can’t select it here:

It doesn’t exist in copy editing either:

My point is not that I can’t send it to production, but I can’t see it anywhere except for when it was in ojs 2.4.8

Am I missing something?

To clarify @jhennig’s comments, what seems to be happening is that “additional files” uploaded at various workflow stages in OJS 2 seem to disappear from the UI in the upgrade process and aren’t showing up in OJS 3. These include both supplementary files submitted by the author during the initial submission, and files that were added in later stages, like review. The common denominator seems to be that these are “additional files.”

Specific cases we’ve identified so far:

  • supplementary files uploaded by an author during a submission are not accessible or visible anywhere in the workflow.
  • an editor added 2 review files, but only one of those files is visible in the workflow - the second file uploaded is not visible anywhere in the workflow.
  • an author uploaded a revision file and a second document along with the revision - the second file is not visible anywhere in the workflow.

This is only affecting submissions that were upgraded. Multiple files are behaving as expected for all newly uploaded content.

Any thoughts on what might be happening here?

Hi @sfbetz,

I wonder if you’re running into supplementary files migration · Issue #3016 · pkp/pkp-lib · GitHub – there’s an SQL query there that should help you identify whether the missing files are accounted for by that bug. (Tagging @bozana, who can probably confirm whether it’s the same issue.)

Alec Smecher
Public Knowledge Project Team

Hi all,

If you were upgrading directly from OJS 2.4.8-1.x to OJS 3.1.0-1 there should not be the problem @asmecher pointed above – this problems appears only for the upgrade 3.0.x to 3.1.x, I think.

Thus, actually your supp files should be migrated to the article production stage, galleys grid. Do you not see them there either?
Do you see those files in the DB table submission_files and in the files folder (note that the name has probably be changed during the migration)?

Regarding other files (review and revision files): I will take a look what is happening i.e. if I can find something that is leading to the problem and if we maybe already heard of something similar… and then I will come back to you…

Else, did you have any warnings/errors during the upgrade?


Hi all,

We aren’t seeing any of the supp files in any stage of production at all. I’ll ask @jhennig to respond if they are in the DB submission_files and in the file folder or if we had any errors / warnings during the upgrade.

In our most recent migration, embedded images and figures in the HTML articles are also gone (moved?).

For example this article View of Identifying Research Support Needs of Members of the Canadian Health Libraries Association / Association des bibliothèques de la santé du Canada | Journal of the Canadian Health Libraries Association / Journal de l'Association des bibliothèques de la santé du Canada

Originally had these files embedded:





But the location of those files has changed and we don’t know where! I think we must be missing some obvious step in our configuration or upgrade process. Any help would be appreciated!

Hi @sfbetz

Ah, this was my bug in the upgrade form an earlier OJS 3 to the 3.1.1 :frowning:
We could try to repair the files together – they should still be there, just moved, I think.

I will come to you soon with a few SQLs, that you could then execute, so that we figure out what files are these and where to look for them and how to repair them…


Ah, @sfbetz, now I realize that you are pointing to the HTML galleys with embedded images… – Those are maybe not exactly the same as supplementary files…
From which to which OJS version did you upgraded? It seems like you upgraded from OJS 2 to OJS 3.1.0-1, correct?
I’ll see to test it locally, what is happening during the migration when having a HTML galley with embedded images…

Hi @sfbetz,

Hmm… I’ve just tested it and everything worked fine for me – the HTML galleys with images were migrated correctly.
Could you go to the backend of the submission 29354 from the example above, then to the Production tag, to Galleys grid there, expand the arrow close to the HTML galley 21439 there, and then click on Edit action link. Do you see the images listed there?

Also, what does it mean “In our most recent migration” in your last post?

Concerning other files that are missing, from the older posts in this thread: maybe we would need to go one by one i.e. step by step i.e. example by example, to figure out what is going on.
As I said no failure should be there when upgrading from OJS 2 – the supp files should be migrated to the Production stage and be visible as galleys, in the Galleys grid.
Did you also have some other upgrades, after the first upgrade from OJS 2 to OJS 3?


Hi Bozana,

Yes the images are there and they work. See image below.
“In our most recent migration” means we have upgraded a number of other journals to version 3. This one is the most recent. We upgraded from to 3.1.1


These were the only errors:

WARNING: Unable to find a match for “22718-55832-1-PB.pdf” in “/journals-data/uploads/jchla/journals/76//articles/22718/”. Skipping this file.

PHP Warning: Element ‘<ahref|target><em><strong><cite><code><ul><ol><li><dl><dt><dd><b><i><u><imgsrc|alt><sup><sub><br><p>’ is not supported (for information on implementing this, see the support forums) in /var/www/sites/jchla/lib/pkp/lib/vendor/ezyang/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php on line 311

ERROR: Reviewer files with ID 70533 from review assignment 11776 could not be found in the database table submission_files

Hi Bozana, This sounds exactly like the issue we are experiencing: Upgrade OJS to supplementary files lost for activ submissions · Issue #3744 · pkp/pkp-lib · GitHub

Is it resolved in the newest release?