WIKINDX / Discussion / Help: Upgrade 5.8.2 to 5.9.1

Roger Appleby - 2020-01-26

Hi,
When upgrading form 5.8.2 to 5.9.1 (and to latest version) I get the fellowing error message:
#0 MESSAGES->internaltext(collection, patent) called at [/home/mraths48/public_html/reports/core/messages/MESSAGES.php:49] #1 MESSAGES->text(collection, patent) called at [/home/mraths48/public_html/reports/core/navigation/MENU.php:1201] #2 MENU->publisherArray() called at [/home/mraths48/public_html/reports/core/navigation/MENU.php:472] #3 MENU->configure() called at [/home/mraths48/public_html/reports/core/navigation/MENU.php:248] #4 MENU->menus() called at [/home/mraths48/public_html/reports/core/display/CLOSE.php:138] #5 CLOSE->__construct() called at [/home/mraths48/public_html/reports/core/startup/FACTORY.php:976] #6 FACTORY_CLOSE::getInstance() called at [/home/mraths48/public_html/reports/index.php:199]

Message patent not found in section collection of MESSAGES class.

The update fails and I am unsure how to troubleshoot please advise.

Regards
RogerA

(Edited for the appearrance only)

Last edit: Stéphane Aulery 2020-01-26

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- Stéphane Aulery - 2020-01-26
  
  Hi Roger,
  
  Please use 6.0.2 for your upgrade since we fixed a lot of errors from 5.9.1.
  
  If already done I will check this resource type.
  
  Regards,
  
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  - Roger Appleby - 2020-01-26
    
    Hi Stéphane,
    
    I will try 6.0.2 in fact I was in the process of trying 6.0.1 when the error
    first appeared but I decide to track back to 5.9.1 in case it was occurring
    there also.
    
    I will let you know.
    
    Regards
    
    Roger
    
    (Edit: remove useless part)
    
    Last edit: Stéphane Aulery 2020-01-26
    
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Mark Grimshaw - 2020-01-26

Hi Roger,

Sorry about that. Yes, as Stéphane says, you should use 6.0.2.

However, that message is indeed missing even in 6.0.2. I've added it to SVN but, once you have downloaded and extracted 6.0.2, add the following to core/messages/MESSAGES.php in the "collection" array somewhere after line 1147:

"patent" => dgettext($domain, "Patent"),

That should fix it.

Regards,

Mark
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- Stéphane Aulery - 2020-01-26
  
  Is there no shortage of other entries for the collections?
  
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- Roger Appleby - 2020-01-26
  
  Hi Mark,
  
  Thanks for prompt reply!
  
  That’s great I will give it a go later.
  
  I was in fact trying to install 6.0.1 when the error first appeared! The alert form Sourceforge for 6.0.2 appeared just after I finished. I went back to 5.9 just in case!
  
  Regards
  
  Roger
  
  From: Mark Grimshaw sirfragalot@users.sourceforge.net
  Sent: 26 January 2020 13:34
  To: [wikindx:discussion] 326884@discussion.wikindx.p.re.sourceforge.net
  Subject: [wikindx:discussion] Upgrade 5.8.2 to 5.9.1
  
  Hi Roger,
  
  Sorry about that. Yes, as Stéphane says, you should use 6.0.2.
  
  However, that message is indeed missing even in 6.0.2. I've added it to SVN but, once you have downloaded and extracted 6.0.2, add the following to core/messages/MESSAGES.php in the "collection" array somewhere after line 1147:
  
  "patent" => dgettext($domain, "Patent"),
  
  That should fix it.
  
  Regards,
  
  Mark
  
  Upgrade 5.8.2 to 5.9.1 https://sourceforge.net/p/wikindx/discussion/326884/thread/d67db706b5/?limit=25#3877
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/wikindx/discussion/326884/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  Last edit: Roger Appleby 2020-01-26
  
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Mark Grimshaw - 2020-01-26

Since moving to the new localization system, I've been picking up a number of missing messages leading to errors. These messages were missing in the old system but that system gracefully ignored anything missing. I think this was by mistake ;) and so I'd never noticed the problem.

It's difficult to know what's missing until the error message pops up.

Regards,

Mark

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- Stéphane Aulery - 2020-01-26
  
  Ok, I can release, again, to unbreak.
  
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  - Mark Grimshaw - 2020-01-26
    
    Yes, let’s do that.
    
    I suspect there may well be other missing messages but it is very difficult if not impossible to test for all possible message combinations.
    
    Regards,
    
    Mark
    
    On 26 Jan 2020, at 15.39, Stéphane Aulery lkppo@users.sourceforge.net wrote:
    
    Ok, I can release, again, to unbreak.
    
    Upgrade 5.8.2 to 5.9.1 https://sourceforge.net/p/wikindx/discussion/326884/thread/d67db706b5/?limit=250#7863/8954
    Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/wikindx/discussion/326884/ https://sourceforge.net/p/wikindx/discussion/326884/
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    alternate
    
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Roger Appleby - 2020-01-26

Hi Mark and Stephane,
I installed 6.0.2 with the new MESSAGES.php and I did get some warnings see attached. However it did install but now strangely none of the resources are displaying although they are clearly all still there. So if I go to Search->Browse->Types and select Books then the screen shows empty records apart from hwo and when they were created but if I select one and view it all the information is there.

Again any help welcome.

Regards

Roger

Wikindx_warnings_6.0.2

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- Stéphane Aulery - 2020-01-26
  
  All errors are related to the styles folder, you should delete if yet presents.
  
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Hi Roger,

What type of document is the attached file? I ccan't open it.

Regards,

Mark

Just a text file without extension.

Warning: scandir(styles/bibliography/._abnt): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._apa): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._britishmedicaljournal): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._cfb): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._chicago): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._harvard): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._ieee): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._mla): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._turabian): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

Warning: scandir(styles/bibliography/._wikindx): failed to open dir: Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: scandir(): (errno 20): Not a directory in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2603

Warning: Invalid argument supplied for foreach() in /home/mraths48/public_html/reports/core/startup/UPDATEDATABASE.php on line 2604

In WIKINDX 5.10, component locations have been changed and are installed in components/languages, components/plugins, components/styles, components/templates, and components/vendor folders. If you created custom components or changed the configuration of the official components, the code for the old components remained in place. You have to migrate them manually according to the documentation then delete the languages, plugins, styles, and vendor folders.

Upgrade the Database

MAX EXECUTION TIME: 120 secs
ELAPSED TIME (stage6): 0 secs.
Database queries: 13
MEMORY LIMIT: 128M
MEMORY USED: 1.238992MB

`stage6` of 1 finished. Please click on the button to continue the upgrade.  Do not click until each script has finished.

Roger Appleby - 2020-01-26

Hi Mark and Stephanie,
The styles folder is indeed empty as I have not added any styles to it yet. A bigger concern was that the resources were not visible.
I see 6.0.3 is released and so will try that.

Regards

Roger

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Roger Appleby - 2020-01-26

Hi Mark and Stephanie,
OK updated to 6.0.3 still got the sam problem see attached . The resources are there but noy displayed. I hovered over "View Details" for the screen dump but you will see title author etc are all missing on the top line.
Regards

Roger

PS I did not go back to 5.9 before installing 6.0.3.

screen_dump.docx

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Mark Grimshaw - 2020-01-26

Hi Roger,

Sorry you're still having problems. Did you do a clean install with 6.0.3 or did you install over the failed 5.9.3 installation. If the latter, could you try a clean install removing any existing folders within wikindx/ (or the top level folder). If you have attachments, you can copy these back to data/attachments/ and any cached attachments to cache/attachments/ when done and before running wikindx.

If you still get the issue, what happens if you turn on error reporting from the Admin|COnfigure menu?

Regards,

Mark

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Roger Appleby - 2020-01-26

Hi Mark,
I installed it over 5.9.1 so I will go back and do a clean install. I have no attachments so straight forward.

I will let you know what happens.

Regards

Roger

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Roger Appleby - 2020-01-26

Hi Mark,
I did a clean install. I reset the database to 5.9.1 and then updated it in the normal way. Still got the same problem. Switched PHP errors on and got the attached.

Regards

Roger

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- Stéphane Aulery - 2020-01-26
  
  Ok, you need to enable PHP error display and SQL queries display in admin. Maybe we will see some query that fail.
  
  Could you edit the resource and post screenshots of the complete edit screen? You probably define something/some data that is not well handled in case of a patent but is ok for others resources.
  
  What is displayed by a view of a resource of an other type?
  
  Last edit: Stéphane Aulery 2020-01-26
  
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- Mark Grimshaw - 2020-01-26
  
  The first line:
  
  Warning: fopen(components/styles/ieee/ieee.xml): failed to open stream: No such file or directory in /home/mraths48/public_html/reports/core/bibcitation/PARSEXML.php on line 74
  
  Notice: Undefined index: fallback in /home/mraths48/public_html/reports/core/bibcitation/BIBFORMAT.php on line 147
  
  Notice: Undefined index: citationStyle in /home/mraths48/public_html/reports/core/bibcitation/CITEFORMAT.php on line 2894
  
  Notice: Undefined index: template in /home/mraths48/public_html/reports/core/bibcitation/CITEFORMAT.php on line 248
  
  Notice: Undefined index: followCreatorTemplate in /home/mraths48/public_html/reports/core/bibcitation/CITEFORMAT.php on line 263
  
  Notice: Undefined index: consecutiveCreatorTemplate in /home/mraths48/public_html/reports/core/bibcitation/CITEFORMAT.php on line 280
  
  Notice: Undefined index: subsequentCreatorTemplate in /home/mraths48/public_html/reports/core/bibcitation/CITEFORMAT.php on line 297
  
  is the problem.
  
  Can you check if there is indeed an ieee.xml file in components/styles/ieee/ or even the ieee/ folder?
  
  In your Admin menu, there is an item called Components. It's the new system for disabling/enabling/installing/updating components such as plugins, templates and, in this case, bibliographic styles. If IEEE style is not installed, install and enable it.
  
  I suspect something in our swtich to the new components administration has not set the default style to the pre-installed APA style when upgrading.
  
  Regards,
  
  Mark
  
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  - Stéphane Aulery - 2020-01-26
    
    I suspect something in our swtich to the new components administration has not set the default style to the pre-installed APA style when upgrading.
    
    The preferred style is not overwritten. If not available, the default style must be applyed. Strange.
    
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Roger Appleby - 2020-01-26

Here is the extended error file with SQL clicked. I will check the IEEE style now.

Regards

Roger

Plus SQL errors.docx

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- Mark Grimshaw - 2020-01-26
  
  Either that ieee file/folder doesn't exist or it can't be read. Everything else stems from that.
  
  Mark
  
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Mark Grimshaw - 2020-01-26

Hi again Roger,

I'm looking at an example of a patent on your system and notice you are using custom fields for things such as granted date and attorney. I'm curious why you don't use the pre-supplied fields that are part of the patent template when creating a new resource?

Regards,

Mark

Screenshot 2020-01-26 at 18.34.41.png

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Mark Grimshaw - 2020-01-26

I can see it working now!

Was it because IEEE was not installed (and so file and folder did not exist) or did they exist but were not readable?

Regards,

Mark

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Upgrade 5.8.2 to 5.9.1

Virtual Research Environment / On-line Bibliography Manager

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Upgrade 5.8.2 to 5.9.1

Upgrade 5.8.2 to 5.9.1

Virtual Research Environment / On-line Bibliography Manager

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