OJS 3.3.0.10 PKP PN Bad Request Error (Take 2)

shaun · May 22, 2022, 7:08am

I previously posted about getting a bad request error on PKP PN: https://forum.pkp.sfu.ca/t/ojs-3-3-0-10-pkp-pn-bad-request-error/73058

At the end of that thread I thought it was fixed but it turns I was wrong. We thought that the error might be due to the journal not being public. And on 10 May I republished the the issues as public and reset the deposit.

My log files from 10 May show that the main deposits I’m concerned about were OK:

[2022-05-10 07:08:32] [Notice] Task process started.
[2022-05-10 07:08:32] [Notice] PLN Depositor executeActions started
[2022-05-10 07:08:32] [Notice] Depositor processing for Neuroanatomy and Behaviour.
[2022-05-10 07:08:32] [Notice] Getting service document.
[2022-05-10 07:08:35] [Notice] Processing deposit status updates.
[2022-05-10 07:08:35] [Notice] Trying status update for 6 (Issue: 6) (Local Status: [Transferred], Processing Status: [Sent to LOCKSS], Lockss Status: [Unknown])
[2022-05-10 07:08:37] [Notice] Processing status got for 6 -> (deposited)
[2022-05-10 07:08:37] [Notice] Deposit 6 has unknown LOCKSS state inProgress
[2022-05-10 07:08:37] [Notice] Processing updated content.
[2022-05-10 07:08:37] [Notice] Processing new content.
[2022-05-10 07:08:37] [Notice] Packaging content for deposit.
[2022-05-10 07:08:37] [Notice] Sending deposits to the PKP PN.
[2022-05-10 07:08:37] [Notice] Depositor processing for Journal for Reproducibility in Neuroscience.
[2022-05-10 07:08:37] [Notice] Getting service document.
[2022-05-10 07:08:37] [Notice] Processing deposit status updates.
[2022-05-10 07:08:37] [Notice] Processing updated content.
[2022-05-10 07:08:37] [Notice] Processing new content.
[2022-05-10 07:08:37] [Notice] Packaging content for deposit.
[2022-05-10 07:08:37] [Notice] Sending deposits to the PKP PN.
[2022-05-10 07:08:37] [Notice] Task process stopped.

However, I noticed that after a few days that the journal wasn’t showing up on the nightly list. So I checked the plugin status again and it was showing the “PKP PLN does not know about this journal yet” error. I then reset the deposits and now I’m back to square 1 with the bad request errors:
2022-05-22-PKPPN-JRN-Status

The Ts&Cs have all been accepted:
2022-05-22-PKPPN-JRN

I have a Cloudflare firewall rule to let the PKP PN bot bypass their security:
2022-05-22-PKPPN-Bypass

But I’m still getting the same errors:

[2022-05-16 08:15:00] [Notice] Task process started.
[2022-05-16 08:15:00] [Notice] PLN Depositor executeActions started
[2022-05-16 08:15:00] [Notice] Depositor processing for Neuroanatomy and Behaviour.
[2022-05-16 08:15:00] [Notice] Getting service document.
[2022-05-16 08:15:02] [Notice] Processing deposit status updates.
[2022-05-16 08:15:02] [Notice] Trying status update for 6 (Issue: 6) (Local Status: [Transferred], Processing Status: [Sent to LOCKSS], Lockss Status: [Unknown])
[2022-05-16 08:15:03] [Notice] Processing status got for 6 -> (deposited)
[2022-05-16 08:15:03] [Notice] Deposit 6 has unknown LOCKSS state inProgress
[2022-05-16 08:15:03] [Notice] Processing updated content.
[2022-05-16 08:15:03] [Notice] Processing new content.
[2022-05-16 08:15:03] [Notice] Packaging content for deposit.
[2022-05-16 08:15:03] [Notice] Sending deposits to the PKP PN.
[2022-05-16 08:15:03] [Notice] Depositor processing for Journal for Reproducibility in Neuroscience.
[2022-05-16 08:15:03] [Notice] Getting service document.
[2022-05-16 08:15:03] [Notice] Processing deposit status updates.
[2022-05-16 08:15:03] [Notice] Processing updated content.
[2022-05-16 08:15:03] [Notice] Processing new content.
[2022-05-16 08:15:03] [Notice] Packaging content for deposit.
[2022-05-16 08:15:03] [Notice] Trying package deposit 4 (Issue: 4) (Local Status: [New], Processing Status: [Unknown], Lockss Status: [Unknown])
[2022-05-16 08:15:05] [Notice] Packaging for deposit 4 succeeded
[2022-05-16 08:15:05] [Notice] Trying package deposit 5 (Issue: 5) (Local Status: [New], Processing Status: [Unknown], Lockss Status: [Unknown])
[2022-05-16 08:15:06] [Notice] Packaging for deposit 5 succeeded
[2022-05-16 08:15:06] [Notice] Sending deposits to the PKP PN.
[2022-05-16 08:15:06] [Notice] Trying transfer deposit 4 (Issue: 4) (Local Status: [Packaged], Processing Status: [Unknown], Lockss Status: [Unknown])
[2022-05-16 08:15:06] [Notice] Posting the Atom file to staging server for deposit 4 (Local Status: [Packaged], Processing Status: [Unknown], Lockss Status: [Unknown]) - (Url: [http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD], AtomPath: [/var/www/files/journals/4/pln/140E2B1C-D0F3-47E1-90EF-8B5A5BBABF4A/140E2B1C-D0F3-47E1-90EF-8B5A5BBABF4A.xml], Method: [PostFile])
[2022-05-16 08:15:07] [Notice] Posting the Atom file to staging server for deposit 4 failed (Error: [Client error: `POST http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD` resulted in a `400 Bad Request` response:
<?xml version="1.0" encoding="utf-8"?>
<sword:error xmlns="http://www.w3.org/2005/Atom"
       xmlns:sword="http://purl. (truncated...)
 - []])
[2022-05-16 08:15:07] [Notice] Network error Client error: `POST http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD` resulted in a `400 Bad Request` response:
<?xml version="1.0" encoding="utf-8"?>
<sword:error xmlns="http://www.w3.org/2005/Atom"
       xmlns:sword="http://purl. (truncated...)
 connecting to the PKP PN to send the deposit.
[2022-05-16 08:15:07] [Notice] Trying transfer deposit 5 (Issue: 5) (Local Status: [Packaged], Processing Status: [Unknown], Lockss Status: [Unknown])
[2022-05-16 08:15:07] [Notice] Posting the Atom file to staging server for deposit 5 (Local Status: [Packaged], Processing Status: [Unknown], Lockss Status: [Unknown]) - (Url: [http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD], AtomPath: [/var/www/files/journals/4/pln/E71FFA89-C1E2-44CA-9FE5-D9AA5AA813F4/E71FFA89-C1E2-44CA-9FE5-D9AA5AA813F4.xml], Method: [PostFile])
[2022-05-16 08:15:07] [Notice] Posting the Atom file to staging server for deposit 5 failed (Error: [Client error: `POST http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD` resulted in a `400 Bad Request` response:
<?xml version="1.0" encoding="utf-8"?>
<sword:error xmlns="http://www.w3.org/2005/Atom"
       xmlns:sword="http://purl. (truncated...)
 - []])
[2022-05-16 08:15:07] [Notice] Network error Client error: `POST http://pkp-pln.lib.sfu.ca/api/sword/2.0/col-iri/54960F22-A02D-4480-97B7-374EA389EDDD` resulted in a `400 Bad Request` response:
<?xml version="1.0" encoding="utf-8"?>
<sword:error xmlns="http://www.w3.org/2005/Atom"
       xmlns:sword="http://purl. (truncated...)
 connecting to the PKP PN to send the deposit.
[2022-05-16 08:15:07] [Notice] Task process stopped.

I’ve tried resetting the deposits again, but no effect. Any ideas?

jonasraoni · May 30, 2022, 1:40pm

Hi @shaun,

On our end looks like your journal still hasn’t accepted the terms, so I’ve manually updated it. Could you try to reset again?

Best,
Jonas

shaun · May 31, 2022, 10:05am

Hi @jonasraoni

Thanks for checking that. I’ve reset the deposits and we’ll see if that works.
reset-pkppn

shaun · June 1, 2022, 9:32pm

Hi @jonasraoni

Unfortunately we’re still getting the same error. Not sure what to do next

morebadrequests

jonasraoni · June 2, 2022, 8:18am

Hi!

I’ve just re-checked and the “terms accepted” was reset to “No” again. I guess that’s because your journal isn’t public.

Private journals aren’t going to be preserved until we release some updates to OJS or the plugin (if you’re skilled enough, you might temporarily apply these updates to your plugin, then it should work: Enable external access to the plugin URLs for private journals · Issue #19 · pkp/pln · GitHub).

Also, ensure the output of the URL https://epistemehealth.com/index.php/jrn/gateway/plugin/PLNGatewayPlugin includes the text <terms termsAccepted="yes"> (if you’re retrieving the content using the browser you’ll need to click with the right button, then select View page source).

Best,
Jonas

shaun · June 3, 2022, 12:55am

Thanks @jonasraoni

That’s strange because the PLNGatewayPlugin does include <terms termsAccepted="yes">. I’ve also made the journal public so I don’t know why it’s doing that.

Here’s the output from the PLNGatewayPlugin:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plnplugin SYSTEM "ping.dtd"> 
<plnplugin>
	<ojsInfo>
		<release>3.3.0.10</release>
	</ojsInfo>
	<pluginInfo>
		<release>2.0.4.2</release>
		<releaseDate>2020-07-21</releaseDate>
		<current>1</current>
		<prerequisites>
			<phpVersion>7.4.29</phpVersion>
			<curlVersion>not required</curlVersion>
			<zipInstalled>yes</zipInstalled>
			<tarInstalled>yes</tarInstalled>
			<acron>yes</acron>
			<tasks></tasks>
		</prerequisites>
		<terms termsAccepted="yes">
						<term key="pkp:plugins.generic.pln.terms_of_use.jm_has_authority" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I have the authority to include this journal&#039;s content in a secure preservation network and, if and when necessary, to make the content accessible in the PKP-PLN and its successors.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.pkp_can_use_address" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I agree to allow the PKP-PLN to include this journal&#039;s title and ISSN, and the email address of the Primary Contact, with the preserved journal content.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.licensing_is_current" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I confirm that licensing information pertaining to articles in this journal is accurate at the time of publication.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.terms_may_be_revised" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I acknowledge these terms may be revised from time to time and will supersede all previous versions. I will be asked to review them and to agree to them in order to continue to include this journal’s content in the PKP-PLN.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.jm_will_not_violate" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I agree not to intentionally violate any laws and regulations that may be applicable to the content.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.trigger_events" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I agree to make every reasonable effort to inform the PKP-PLN in the event this journal ceases publication. I acknowledge that PKP-PLN will also employ automated techniques to detect a potential trigger event and contact the journal to confirm their publication status.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.pkp_may_not_preserve" updated="2015-11-30 18:34:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            I agree that the PKP-PLN reserves the right not to preserve or make content accessible.
        </term>
						<term key="pkp:plugins.generic.pln.terms_of_use.use_aggregated_content" updated="2015-12-04 16:53:43+00:00" accepted="2022-05-31T09:52:50+00:00">
            PKP reserves the right to use the aggregated content in the PKP-PLN for research and reporting purposes and will adhere to the norms of standard research procedures.
        </term>
					</terms>
	</pluginInfo>
	<journalInfo>
		<title>Journal for Reproducibility in Neuroscience</title>
		<articles count="12">
						<article pubDate="2020-02-23">A platform for reproducibility</article>
						<article pubDate="2022-02-15">Barriers to reproducibility: misalignment of career incentives and open science best practices</article>
						<article pubDate="2020-08-13">Have we reproduced Rat Park? Conceptual but not direct replication of the protective effects of social and environmental enrichment in addiction</article>
						<article pubDate="2020-08-13">Reproducibility of behavioral phenotypes in mouse models - a short history with critical and practical notes</article>
						<article pubDate="2020-08-13">Anticompulsive-like effect of nitric oxide synthase inhibitors in marble-burying test</article>
						<article pubDate="2020-11-24">Kinin B1 receptor is involved in mechanical nociception in a fibromyalgia-like model in mice</article>
						<article pubDate="2020-12-04">How research reproducibility challenges librarians’ skill sets. A French librarian’s perspective</article>
						<article pubDate="2020-12-30">Preprints: a tool and a vehicle towards greater reproducibility in the life sciences</article>
						<article pubDate="2021-01-19">We need another 3R rule: repeat, repeat, repeat!</article>
						<article pubDate="2021-03-24">Five best practices for fMRI research: Towards a biologically grounded understanding of mental phenomena</article>
						<article pubDate="2021-08-12">Science communication of reproducibility</article>
						<article pubDate="2022-01-04">A compact guide to the systematic review and meta-analysis of the literature in neuroscience</article>
					</articles>
	</journalInfo>
</plnplugin>

jonasraoni · June 3, 2022, 6:45am

Great, the output seems to be right, but when I access the link it’s still requiring me to login.

If you really disabled the login requirement at “Users & Roles > Site Access Options”, then perhaps it could be a cache issue, you can try to clear it at the “Administration” menu (the “Clear Data Caches” should be enough).

Best,
Jonas

shaun · June 3, 2022, 7:09am

Thanks - I had missed that one and been toggling the settings under Distribution > Access > “The journal will provide open access to its contents.”

Have checked the Users & Roles option and reset the deposits. Will see how that goes tomorrow.

jonasraoni · June 10, 2022, 2:18pm

Looks like everything is fine on our side now, but I see there’s no deposits yet. Do you still see errors there?

Best,
Jonas

shaun · June 13, 2022, 7:32pm

Hi, yes, I see the status of the journal has updated but even though the deposit is marked complete, there is nothing in the PKP PN journal list.

complete

I have reset the deposits again and we’ll see if it works this time

jonasraoni · June 13, 2022, 8:22pm

I’m not sure about what happened there, but you might try to reset the deposits through the blue arrow next to them.

Best,
Jonas

jonasraoni · June 14, 2022, 7:33am

Hi!

I see the deposits appeared, so I’m closing the topic.
I’ll leave a note to simulate the problem that you had (completed deposits which were not even sent).

Best,
Jonas