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Errors upgrading beyond 2.3.6

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Errors upgrading beyond 2.3.6

Postby tdonnelly » Tue Apr 30, 2013 10:28 am

I am trying to bring our OJS install up to date (currently at 2.2.0) and am running into issues when I go beyond 2.3.6.

These issues manifest as browsers being unable to display pdf files and pages getting into a loop where clicking a link just brings a user back to the same page they started on.

My system:

OS platform Linux
PHP version 5.1.6
Apache version Apache/2.2.3 (CentOS)
Database driver mysql
Database server version 5.0.95

In the apache error logs I see:

Code: Select all
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: WARNING: Missing argument 1 for PaymentManager::PaymentManager(), called in /www/docs/ojs/classes/payment/ojs/OJSPaymentManager.inc.php on line 35 and defined\n  In file: /www/docs/ojs/lib/pkp/classes/payment/PaymentManager.inc.php\n  At line: 22\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'a' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'em' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'strong' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'cite' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'code' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'ul' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'ol' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'li' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'dl' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'dt' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'dd' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'b' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'i' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'u' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'sup' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'sub' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'br' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] ojs2 has produced an error\n  Message: USER WARNING: Attribute '' in element 'p' not supported (for information on implementing this, see the support forums) \n  In file: /www/docs/ojs/lib/pkp/lib/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php\n  At line: 324\n  Stacktrace: \n  Server info:\n   OS: Linux\n   PHP Version: 5.1.6\n   Apache Version: Apache/2.2.3 (CentOS)\n   DB Driver: mysql\n   DB server version: 5.0.95, referer: http://collaborativelibrarianship.org/index.php/jocl/article/view/212/187
[Tue Apr 30 10:44:52 2013] [error] [client 192.168.13.99] File does not exist: /www/docs/ojs/favicon.ico


By Google'ing I found this post viewtopic.php?f=8&t=8758 suggesting that the html tags are not being allowed by the HTML purifier.

My config.inc.php file heowever seems to allows all the tags mentioned in the error_log:

Code: Select all
; Security Settings ;
;;;;;;;;;;;;;;;;;;;;;

[security]

; Force SSL connections site-wide
force_ssl = Off

; Force SSL connections for login only
force_login_ssl = Off

; This check will invalidate a session if the user's IP address changes.
; Enabling this option provides some amount of additional security, but may
; cause problems for users behind a proxy farm (e.g., AOL).
session_check_ip = On

; The encryption (hashing) algorithm to use for encrypting user passwords
; Valid values are: md5, sha1
; Note that sha1 requires PHP >= 4.3.0
encryption = sha1

; Allowed HTML tags for fields that permit restricted HTML.
; For PHP 5.0.5 and greater, allowed attributes must be specified individually
; e.g. <img src|alt> to allow "src" and "alt" attributes. Unspecified
; attributes will be stripped. For PHP below 5.0.5 attributes may not be
; specified in this way.
allowed_html = "<a> <em> <strong> <cite> <code> <ul> <ol> <li> <dl> <dt> <dd> <b> <i> <u> <img src|alt> <sup> <sub> <br> <p>"

; Prevent VIM from attempting to highlight the rest of the config file
; with unclosed tags:
; </p></sub></sup></u></i></b></dd></dt></dl></li></ol></ul></code></cite></strong></em></a>


;Is implicit authentication enabled or not

;implicit_auth = On

;Implicit Auth Header Variables

;implicit_auth_header_first_name = HTTP_TDL_GIVENNAME
;implicit_auth_header_last_name = HTTP_TDL_SN
;implicit_auth_header_email = HTTP_TDL_MAIL
;implicit_auth_header_phone = HTTP_TDL_TELEPHONENUMBER
;implicit_auth_header_initials = HTTP_TDL_METADATA_INITIALS
;implicit_auth_header_mailing_address = HTTP_TDL_METADATA_TDLHOMEPOSTALADDRESS
;implicit_auth_header_uin = HTTP_TDL_TDLUID

; A space delimited list of uins to make admin
;implicit_auth_admin_list = "100000040@tdl.org 85B7FA892DAA90F7@utexas.edu 100000012@tdl.org"

; URL of the implicit auth 'Way Finder' page. See pages/login/LoginHandler.inc.php for usage.

;implicit_auth_wayf_url = "/Shibboleth.sso/wayf"


I've tried going directly from 2.2.0 to 2.4.2 and ran into the same problem. By doing each upgrade step-by-step I have been able to narrow it down to 2.3.7.

How can I resolve this?

Thanks
tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am

Re: Errors upgrading beyond 2.3.6

Postby asmecher » Tue Apr 30, 2013 10:32 am

Hi tdonnelly,

There are several things happening there and I think a few of them are red herrings. The looping problem is probably unrelated to HTMLPurifier or your allowed HTML tags. During the database upgrade process, do you receive any errors?

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8345
Joined: Wed Aug 10, 2005 12:56 pm

Re: Errors upgrading beyond 2.3.6

Postby tdonnelly » Tue Apr 30, 2013 11:32 am

Thanks for the quick reply,

No errors during the database upgrade:

Code: Select all
[root@collib ojs]# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 2.3.7.0]
[schema: lib/pkp/xml/schema/signoff.xml]
[schema: lib/pkp/xml/schema/common.xml]
[schema: lib/pkp/xml/schema/groups.xml]
[schema: lib/pkp/xml/schema/announcements.xml]
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
[schema: lib/pkp/xml/schema/metadata.xml]
[schema: lib/pkp/xml/schema/reviews.xml]
[schema: lib/pkp/xml/schema/reviewForms.xml]
[schema: lib/pkp/xml/schema/controlledVocab.xml]
[schema: lib/pkp/xml/schema/submissions.xml]
[schema: lib/pkp/xml/schema/comments.xml]
[schema: lib/pkp/xml/schema/notes.xml]
[schema: dbscripts/xml/ojs_schema.xml]
[code: Installer Installer::migrateReviewingInterests2]
[data: dbscripts/xml/upgrade/2.3.7_update.xml]
[data: registry/citationAssistantData.xml]
[code: Installer Installer::removeAuthorRevisedFilesFromSignoffs]
[note: docs/release-notes/README-2.3.7]
[code: Installer Installer::addPluginVersions]
[post-install]

tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am

Re: Errors upgrading beyond 2.3.6

Postby asmecher » Tue Apr 30, 2013 12:02 pm

Hi tdonnelly,

To clarify your work narrowing this down to a particular version: an upgrade to 2.3.6 works, but an upgrade to 2.3.7 results in the looping behavior you described?

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8345
Joined: Wed Aug 10, 2005 12:56 pm

Re: Errors upgrading beyond 2.3.6

Postby tdonnelly » Tue Apr 30, 2013 12:15 pm

Correct 2.3.7 or above.

One thing I forgot to mention. When logged into the site as the superadmin user everything works fine. It only misbehaves when logged out or logged in as any other role.
tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am

Re: Errors upgrading beyond 2.3.6

Postby asmecher » Tue Apr 30, 2013 2:03 pm

Hi tdonnelly,

This may be due to a database inconsistency. Can you check the value of the "status" column in the articles table for one of the articles that you're having trouble viewing?

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8345
Joined: Wed Aug 10, 2005 12:56 pm

Re: Errors upgrading beyond 2.3.6

Postby tdonnelly » Tue Apr 30, 2013 2:15 pm

Looks like status is "1".

The one that seems to work is "3".
tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am

Re: Errors upgrading beyond 2.3.6

Postby asmecher » Tue Apr 30, 2013 2:23 pm

Hi tdonnelly,

That's correct -- these constants are defined in classes/article/Article.inc.php.

A value of 1 is STATUS_QUEUED; a value of 3 is STATUS_PUBLISHED. You want STATUS_PUBLISHED.

Older versions (say OJS <2.2.4) occasionally introduced database problems like this; newer versions are much more consistent, hence the change in behavior.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8345
Joined: Wed Aug 10, 2005 12:56 pm

Re: Errors upgrading beyond 2.3.6

Postby tdonnelly » Wed May 01, 2013 6:43 am

BINGO! We have a winner!

Changing the status from 1 to 3 fixes it.

I'll make the changes in the data base and continue to upgrade to 2.4.2.

Thanks for your help on this.

**Edit for more information**

I do have a question though. Looking at the database for my 2.2.0 install, the status code is set at "1" for these articles and they load fine. Is there some change in the way that 2.2.0 and 2.3.7 handle this status?
tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am

Re: Errors upgrading beyond 2.3.6

Postby asmecher » Wed May 01, 2013 8:54 am

Hi tdonnelly,

The status for published articles should always be 3; previous releases, as you've seen, didn't properly set the status depending on what editorial process you were using, and an enforced check to the publishing front-end was only added recently.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8345
Joined: Wed Aug 10, 2005 12:56 pm

Re: Errors upgrading beyond 2.3.6

Postby tdonnelly » Wed May 01, 2013 9:15 am

Very good. This will give me an explanation I can pass on to the Journal owners.

Thanks again for your help.
tdonnelly
 
Posts: 6
Joined: Tue Apr 30, 2013 10:06 am


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