After upgrading to 3.3.0.8 error 500 on Trying to Import Issues/Articles - Native XML Plugin

Trying to import issues/articles to OJS like other times, but now this happen:
2022-02-24 10.03.30 tesztojs.bibl.u-szeged.hu dc7451350fd8

We are using xml based on an exported article from another journal.

This is the console:
2022-02-24 10.08.22 tesztojs.bibl.u-szeged.hu e041d4a435ee

And this is the error log:

[23-Feb-2022 10:24:31 Europe/Budapest] PHP Notice:  Undefined offset: 0 in /var/www/html/ojs-3.3.0-8/lib/pkp/classes/submission/PKPSubmission.inc.php on line 163
[23-Feb-2022 10:24:44 Europe/Budapest] PHP Notice:  Undefined variable: newFileId in /var/www/html/ojs-3.3.0-8/lib/pkp/plugins/importexport/native/filter/NativeXmlSubmissionFileFilter.inc.php on line 323
[23-Feb-2022 10:24:44 Europe/Budapest] PHP Fatal error:  Uncaught PDOException: SQLSTATE[HY000]: General error: 1364 Field 'file_id' doesn't have a default value in /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOStatement.php:115
Stack trace:
#0 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOStatement.php(115): PDOStatement->execute(NULL)
#1 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(464): Doctrine\DBAL\Driver\PDOStatement->execute()
#2 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(664): Illuminate\Database\Connection->Illuminate\Database\{closure}('insert into `su...', Array)
#3 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(631): Illuminate\Database\Connection->runQueryCallback('insert into `su...', Array, Object(Closure))
#4 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connec in /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php on line 671
[23-Feb-2022 10:25:42 Europe/Budapest] ojs2: 404 Not Found
[23-Feb-2022 10:25:52 Europe/Budapest] PHP Notice:  Undefined offset: 0 in /var/www/html/ojs-3.3.0-8/lib/pkp/classes/submission/PKPSubmission.inc.php on line 163
[23-Feb-2022 10:25:52 Europe/Budapest] PHP Notice:  Undefined offset: 0 in /var/www/html/ojs-3.3.0-8/lib/pkp/classes/submission/PKPSubmission.inc.php on line 163

We have no idea that where should be this "Field ‘file_id’ doesn’t have a default value in "

Hi @molnart,

The likeliest cause for this is that a file is missing, or couldn’t be downloaded. You can specify files in one of several ways:

  • <href src="http://some-url-here" />
  • <href src="/absolute/path/to/file" />
  • <href src="relative/path/to/file" /> (relative to the current directory when running a command-line import)
  • <embed encoding="base64">base64_embedded_file_content_here</embed>

Check how you’re specifying your files, and ensure that all of them are present where they’re supposed to be. (I understand that this is a pretty useless error message – if we can confirm that this is the problem, we can file an issue to improve it.)

Regards,
Alec Smecher
Public Knowledge Project Team

Thank you @asmecher,
At the previous versions we got experience in using this plugin for importing files and metadata. We have a multi-journal system, and the part of it came from archives by importing.
We have tried to import from another url and from base64 content too. I copy here the two samples which gives the error message.
XML importing from url:

<?xml version="1.0" ?> 
<articles xmlns="http://pkp.sfu.ca" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
	<article date_submitted="2021-04-01" status="3" submission_progress="0" current_publication_id="33000" stage="production" >
		<id type="internal" advice="ignore">43800</id>
		<submission_file xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" created_at="2021-04-01" stage="proof" id="51000" xsi:schemaLocation="http://pkp.sfu.ca native.xsd" genre="Article Text" viewable="false" uploader="admin" file_id="31000">
            <name locale="en_US">journal_geo_014_001-002_015-023.pdf</name> 
			<file id="31000">
				<href src="http://acta.bibl.u-szeged.hu/73888/1/journal_geo_014_001-002_015-023.pdf" />
			</file>
        </submission_file>
		<publication xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" locale="en_US" version="1" status="3" url_path="" seq="1" date_published="2021-04-01" section_ref="ART" access_status="0" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
			<id type="internal" advice="ignore">33000</id>
			<title locale="en_US">XML Test Title</title>		
			<abstract locale="en_US">XML Test abstract</abstract>
			<authors xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
			  <author include_in_browse="true" user_group_ref="Author" seq="1" id="65000">
				  <givenname locale="en_US">Givenname</givenname>
				  <familyname locale="en_US">Familyname</familyname>	
				  <email>teszt@email.hu</email> 
			  </author>
			</authors>
			<article_galley xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" locale="en_US" url_path="" approved="false" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
				<id type="internal" advice="ignore">43000</id>
				<name locale="en_US">PDF</name>
				<seq>0</seq>
				<submission_file_ref id="51000"/>
			</article_galley>
				<issue_identification>
				<volume>100</volume>
				<number>100</number>
				<year>100</year>
			</issue_identification>
			<pages>1-50</pages>
		</publication>
	</article>
</articles>

And this is for base64 file import:

<?xml version="1.0" ?> 
<articles xmlns="http://pkp.sfu.ca" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
	<article date_submitted="2021-04-01" status="3" submission_progress="0" current_publication_id="33000" stage="production" >
		<id type="internal" advice="ignore">43800</id>
		<submission_file xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" created_at="2021-04-01" stage="proof" id="51000" xsi:schemaLocation="http://pkp.sfu.ca native.xsd" genre="Article Text" viewable="false" uploader="admin" file_id="31000">
            <name locale="en_US">journal_014_001-002_015-023.pdf</name> 
			<file id="31000" extension="pdf">
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NjgKPj4Kc3RhcnR4cmVmCjYyMTMKJSVFT0YK</embed>
			</file>
        </submission_file>
		<publication xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" locale="en_US" version="1" status="3" url_path="" seq="1" date_published="2021-04-01" section_ref="ART" access_status="0" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
			<id type="internal" advice="ignore">33000</id>
			<title locale="en_US">XML Test Title</title>		
			<abstract locale="en_US">XML Test abstract</abstract>
			<authors xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
			  <author include_in_browse="true" user_group_ref="Author" seq="1" id="65000">
				  <givenname locale="en_US">Givenname</givenname>
				  <familyname locale="en_US">Familyname</familyname>	
				  <email>teszt@email.hu</email> 
			  </author>
			</authors>
			<article_galley xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" locale="en_US" url_path="" approved="false" xsi:schemaLocation="http://pkp.sfu.ca native.xsd">
				<id type="internal" advice="ignore">43000</id>
				<name locale="en_US">PDF</name>
				<seq>0</seq>
				<submission_file_ref id="51000"/>
			</article_galley>
				<issue_identification>
				<volume>100</volume>
				<number>100</number>
				<year>100</year>
			</issue_identification>
			<pages>1-50</pages>
		</publication>
	</article>
</articles>

We are preferring the import from URL option.
Thank you in advances!

Hi @molnart,

I’m afraid that doesn’t give me much to go on; the XML looks OK but obviously a file is failing to import. Is it possible that the file permissions are set in your files directory such that the import is not able to place files there? The file permission details will depend on your server and how you’re attempting to import the files – e.g. web-based, or command line.

Regards,
Alec Smecher
Public Knowledge Project Team

I’m sorry.
There is a log line. It could still belong here.
[16-Mar-2022 09:33:27 UTC] PHP Notice: Undefined variable: newFileId in /path to ojs//lib/pkp/plugins/importexport/native/filter/NativeXmlSubmissionFileFilter.inc.php on line 323

And then he comes.

[16-Mar-2022 09:33:27 UTC] PHP Fatal error: Uncaught PDOException: SQLSTATE[HY000]: General error: 1364 Field ‘file_id’ doesn’t have a default value in /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOStatement.php:115
Stack trace:
#0 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOStatement.php(115): PDOStatement->execute(NULL)
#1 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(464): Doctrine\DBAL\Driver\PDOStatement->execute()
#2 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(664): Illuminate\Database\Connection->Illuminate\Database{closure}(‘insert into su...', Array) #3 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(631): Illuminate\Database\Connection->runQueryCallback('insert into su…’, Array, Object(Closure))
#4 /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connec in /var/www/html/ojs-3.3.0-8/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php on line 671

The first is just a NOTICE

Hi @mauser1,

That’s part of the same issue but unfortunately doesn’t shed more light on the problem.

Were you able to check for the potential permissions issue suggested above?

Regards,
Alec Smecher
Public Knowledge Project Team

Yes, we also tried 775 and 777 for the files folder.

Hi @mauser1,

At a glance, it looks like your XML is missing the filesize attribute to the <file> element; try specifying the file size there. That previously would have caused a more helpful warning message, but it appears that our addition of a FOREIGN KEY constraint is obscuring that warning with a fatal error; I’ll fix that for the next release.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher ,

We added the filesize attribute to the xml, and the import is worked on this way.

Thank you very much for your help.

1 Like

(Issue filed to improve this behaviour: Import XML missing filesize attribute to file node causes confusing fatal error · Issue #7773 · pkp/pkp-lib · GitHub)