Bug on version 2.2.1

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Victor Tavares

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May 11, 2016, 6:43:50 AM5/11/16
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Hi every one!


I have two problems with my AToM installed.


When I migrate to version 2.2.1 I preserve the 2.2.0 version on atom_old directory with database outdated.


1 - The instance with the 2.2.1 version does not load completely after two weeks of upgrade. Only the first "Browse by" menu, without loading css and javascript. But in other parts of the site it loads normally, only the first page got this error.


- Because of this error, I did a downgrade to version 2.2.0 and then came to database outdated. I create a third directory with the database of instance 2.2.1 and the directory of the version 2.2.0, and them problem two:


2 - When running the command elastic search (./symfony search: populate) got the following message:

Could not find object information (id: 15988).


I see that problem two occurs on version 2.2.1 too. 

I think is a problem on database. I see that was a lot of bugs on MySQL version 5.5 , ASAP I will perform a database upgrade to MySQL version 5.7.


See my list of applications and versions required and mandatory to AToM:


Application

Version

Status

Required

Sistema Operacional: Debian 7.8  64bits

7.8 64bits

ok

Apache: Apache/2.2.22

2.2.22

ok

Elasticsearch: 1.7.5

1.7.5

ok

Java: OpenJDK Runtime Environment (IcedTea6 1.13.8) (6b36-1.13.8-1~deb7u1) 64-bit

1.13.8 64bits

ok

MySQL: 5.5.47

5.5.47

ok

PHP: 5.4.45

5.4.45

ok

Memcached: 1.4.13

1.4.13

ok

German job server - Installed

 

ok

Mandatory

cURL (php5-curl)  = OK 7.26.0

7.26.0

ok

JSON (php5-json) = Adicionado por padrão... Sem informações

NA

ERR

APC (php-apc, or php5-apcu in PHP 5.5) = OK  3.1.13

3.1.13

ok

PDO and PDO-MySQL (php5-mysql) = OK 5.5.44

5.5.44

ok

XSL (php5-xsl) = OK 1.1.26

1.1.26

ok



Did you guys know how to solve this problems?

Regards,

Victor Tavares.





Dan Gillean

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May 11, 2016, 3:42:47 PM5/11/16
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Hi Victor,

I'm not a developer, but I have a couple of initial thoughts.

I will mention first that you are using Debian, with Apache as your webserver - we know of other users out there using a similar set-up, but we at Artefactual do not test beyond our recommended installation parameters - currently Ubuntu 14.04 with an Nginx webserver for AtoM 2.2. So there may be issues we have not come across resulting from this?

For example, I noticed that you do not have php5-json installed. I'm not sure if the package is available on Debian, you might have to look around. All of the php extensions in our documentation are required.

For the issue with the CSS on the homepage - you can try recompiling the CSS with the following instructions, to see if it resolves the issue:
  • cd plugins/arDominionPlugin
  • make
  • cd ../..

You'll probably want to clear your cache and restart php5-fpm after:

  • php symfony cc
  • sudo service php5-fpm restart


The "could not find information object" error you encountered when trying to populate the search index may indicate that you have corrupt data? This can occur if you have attempted  large requests via the browser that have timed out - for example, imports. I can ask our developers to take a look at this thread and see if they have suggestions to resolve this, or how best to investigate further.

Regards,


Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Dan Gillean

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May 11, 2016, 5:43:09 PM5/11/16
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Hello again!

Another thought to deal with issue 2 (problems with populating the search index):

Sometimes the data corruption can be as small as a missing slug, or a broken nested set. So I don't know if it will work, but you might try using the CLI tasks to generate missing slugs rebuild the nested set to see if it might help resolve that issue.

Generate slugs:

Build nested set:

I would also then clear the cache and restart your services (webserver, php5-fpm, etc).

We have some video tutorials that will show you the basic use of these CLI tasks - video 5 in this series should cover them both:

Let us know if these suggestions help!


Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Victor Tavares

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May 12, 2016, 9:16:04 AM5/12/16
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Hi Dan.

After run your procedure, problem of indexing search still persists.

Thanks in advance,

Victor Tavares.

Dan Gillean

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May 12, 2016, 2:34:05 PM5/12/16
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Hi Victor,

I posted this on Letwatle's thread about a similar issue, but I will post it here as well:

If the solutions above don't work, it may be because of data corruption - some process (like an import, creation, etc) that halted mid-process and left incomplete data in the system. The most common case is when the publication status is missing in the database. You will have to add it directly via SQL queries in this case - see the following thread for some advice:

For more details, and if the above solution doesn't work, please see this thread - it includes a query that should help you identify problem rows in the database, as well as a proposed query to resolve a much more rare issue:

Note that in AtoM 2.3, we will be introducing the use of transactions, to try to prevent data corruption - essentially, if a request times out mid-process, AtoM will automatically roll back to the last database state, instead of leaving corrupted data in the system.

Good luck!




Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

Victor Hase.


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Victor Tavares

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May 19, 2016, 12:40:32 PM5/19/16
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Hi Dan,

I move all website content to a server with UBUNTU 14.04, NGINX, MYSQL 5.7 and all mandatory resquisits.

The problem persists, but I discover what causing the problem 1. When user input another traduction to a field, the site become unstable and problem 1 occurs and even the traduction don't change.

To solve this problem I recover to last state database.

My default language on this version was pt_BR.


I discover other problem. When user deletes authority records   freezes any adding option.


Regards,

Victor Tavares.

Dan Gillean

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May 19, 2016, 1:03:07 PM5/19/16
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Hi Victor,

Interesting... thank you for sharing this.

Did you try running the fixes mentioned above? If there are data corruption issues, this may still cause problems even if you have moved your data to a new site following the recommended installation.

Assuming you have - is this error occurring when you try to translate the content (your data), or the user interface (by using the translation bar at the bottom of the page)?

I think we will need to see if we can get more information about the error. First, take a look at the webserver error logs after repeating the problem - please share any useful output about the error you find there. If you are using Nginx in this installation and have followed our recommended installation, here is where you can find the error logs:

You might also try putting the application in Debug mode while repeating the errors, to see if there is any useful information. See:

This video tutorial will show you both of the above steps - how to access the Nginx error logs, and how to enable Debug mode:

Hopefully more information about the errors will help us diagnose the issue.

Thanks,


Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

On Thu, May 19, 2016 at 9:35 AM, Victor Tavares <victo...@gmail.com> wrote:
Hi Dan,

I move all website content to a server with UBUNTU 14.04, NGINX, MYSQL 5.7 and all mandatory resquisits.

The problem persists, but I discover what causing the problem 1. When user input another traduction to a field, the site become unstable and problem 1 occurs even the traduction don't change.

To solve this problem I recover to last state database.

My default language on this version was pt_BR.


I discover other problem. When user deletes authority records   freezes any adding option.


Regards,

Victor Tavares.

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victor hase

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May 19, 2016, 3:37:51 PM5/19/16
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Hi Dan.
I just remove the data which are currupted and $ php symfony search:populate works.
I save the data for future adding.

I think the problem are another.

Thanks,

Victor Tavares.

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Dan Gillean

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May 19, 2016, 8:01:40 PM5/19/16
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Hi Victor,

Can you please check the error logs as described in my last post, and try Debug mode, and see if you can get any more information about the errors?

Thanks!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

Victor Tavares

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May 20, 2016, 1:15:31 PM5/20/16
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I run all fixes you mentioned. 

The debug mode are enabled and log too.

I have other problem when try to read some publications. blank page appears...

This is the log page when try to read the page:

2016/05/20 14:00:00 [error] 11781#0: *4498 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Call to a member function __toString() on a non-object in /usr/share/nginx/atom/plugins/sfIsadPlugin/lib/sfIsadPlugin.class.php on line 47" while reading response header from upstream, client: CLIENT-IP, server: _, request: "GET /index.php/PAGE TRY TO READ HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.atom.sock:", host: "DNS RESOLUTION NAME", referrer: "http://SERVER-IP/index.php/informationobject/browse?levels=27688&limit=10&sort=lastUpdated&topLod=1"

I remove on database this object: 27688. on all tables are mentioned and nothing change. 

Now the  authority records are ok to delete.

Regards,

Victor Tavares.

Mike G

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May 20, 2016, 2:35:21 PM5/20/16
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Hi Victor,

Did you keep database backups for your MySQL database? If so, can you revert back to the start? Then, drop this file I'm attaching into your AtoM directory and run from the console "php symfony tools:run fix_15988.php". If the script doesn't complain, please retry the task you were running into problems with.

cheers
fix_15988.php

Victor Tavares

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May 23, 2016, 7:04:38 AM5/23/16
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Hi Mike. 

I run for object 15988 and no output appears and it works, but the problem isn't in just this object there are more 2 with this problem.
I create another file and edit the line who are pointing to id 15988 and put the new object 27619, which are in error.
And run again php symfony tools:run fix_27619.php
And message error appears. "Could not fetch information object 27619"

Thanks for help,

Victor.

Victor Tavares

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May 23, 2016, 8:55:19 AM5/23/16
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Hi again.

I was reviewing all threads and see all relationship databases, and are two tables missing information: status and object, now the error 2 of first topic are ok.

My steps are:
- inserts on tables status, object 
- run "$ php symfony propel:generate-slugs" "$ php symfony propel:build-nested-set". 

I think it's very important create a topic to speak to users all relationship databases, like one database diagram to clarify any problems on missing objects.

If you guys have this relationship database diagram I will thank you.

I try to create on reverse engineering, but can't create the relationship.

Thanks in advance,

Victor.

Dan Gillean

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May 24, 2016, 2:13:23 PM5/24/16
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Hi Victor,

I'm glad to hear that you're making progress! Hopefully the addition of transactions in 2.3 will prevent this database corruption you've encountered from happening again.

In terms of a database relationship diagram, I am sharing some older versions I have currently - the most recent I have is from January 2016, while 2.3 was in development. There may have been a few changes since then, but most major entities and relationships should be included.

I'm also attaching 2 older versions, from 2014 - while 2.1 was in development - for comparison.

When we have a stable release candidate for 2.3, I will ask our developers if they can generate a newer version for 2.3, and I will put it on the wiki for reference.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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