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Issue upgrading from 2.1.1 to 2.3.7

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Issue upgrading from 2.1.1 to 2.3.7

Postby rdnorris » Wed Jun 20, 2012 5:47 am

A database error has occurred: Data truncated for column 'comment_title' at row 35

Hello,
We are trying to migrate from 2.1.1 to 2.3.7 using the full download method..IE download the whole new version and copy config.inc.php and public to new version folder and change installed to off. I keep getting the error above during the database upgrade. I thought there was an issue with the data in line 35..but after restoring the database from backup and then deleting the line and rerunning the upgrade ...the same error occurs but it just moved to row 34 ..and if I delete row 34 it goes to 33. I have no idea why this is happening. Any help would be appreciated.

Also I should say that we are running on a Windows 2008 R2 server. I know it was recommend to use gnu32win to patch to the latest level ...But I am unable to figure out exactly how you do that. It would be a great video tutorial in the future. Thanks -Richard
rdnorris
 
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Re: Issue upgrading from 2.1.1 to 2.3.7

Postby ramon » Wed Jun 20, 2012 12:04 pm

Hello Richard,

By copying the config.inc.php of 2.1.1 to 2.3.7 you mean just editing 2.3.7 version, by adding your previous configuration, with the database info, right?
Is your database in UTF-8? If not, you may have to convert it first to UTF-8 before attempting the upgrade.
You may also be running into a timeout issue of some kind (browser, server, MySQL).
Have you checked your logs and timeout settings?
Are you upgrading via command line?
I'm not sure how, but if you have PHP CLI enabled and installed, you should try upgrading via command line. It's safer.
Although I'm not an expert in Windows environments, I'm pretty sure it can be done.

At least you have a db backup...
ramon
 
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Re: Issue upgrading from 2.1.1 to 2.3.7

Postby rdnorris » Wed Jun 20, 2012 12:35 pm

Ramon,
Thanks for the post. I just tried changing the database to utf8 but sadly got the same error. I am using verbose mode so it is showing me the error..and quickly so it is not timing out but failing on the truncated data ..which is located under article_comments>comments_title ...it says line 37 but if I delete it and retry it then says line 36 is the issue...even if I delete 1-37..it fails at line 2..which is weird since there is no line 2. I willing to try php_cli if someone out there can help me by telling me how. Again thanks for the response. -Richard
rdnorris
 
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Re: Issue upgrading from 2.1.1 to 2.3.7

Postby ramon » Wed Jun 20, 2012 1:20 pm

Hello Richard,

Try editing a dump of your database, if possible, to check for any invalid characters.
If your database was not in UTF-8 and then changed to UTF-8 at some point, you may have garbage saved in some fields.
Some special characters may have been double encoded, which may break the query as well.
Sometimes PHPMyAdmin, which comes bundled in many servers, does not provide adequate tools, and sometimes masks these problems.

If it's a database issue, PHP CLI will not help or improve your situation...

_______________________________
Ramón Martins Sodoma da Fonseca
Analista em C&T
Coordenação de Tecnologias de Informação
Instituto Brasileiro de Informação em Ciência e Tecnologia - IBICT
Ministério da Ciência e Tecnologia - MCT
ramon
 
Posts: 940
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Location: Brasí­lia/DF - Brasil

Re: Issue upgrading from 2.1.1 to 2.3.7

Postby rdnorris » Thu Jun 21, 2012 6:00 am

Ramon,
Thanks for the idea. I tried to look for bad characters but I can't seem to find any. I even tried changing the comment to say just test1 and nothing else and I get the error. I have also deleted all of the comments because I could see that causing an error but it still gives the same error. In fact I tried changing everything about the row and it still gives the same error. Only if I delete the row will it not give an error in that line but it errors on the next one down. Could it be database corruption? Here is the details under the error
1265: Data truncated for column 'comment_title' at row 36

ADOConnection._Execute(ALTER TABLE article_comments MODIFY COLUMN comment_title VARCHAR(90) NOT NULL, false) % line 864, file: adodb.inc.php
ADOConnection.Execute(ALTER TABLE article_comments MODIFY COLUMN comment_title VARCHAR(90) NOT NULL) % line 435, file: Installer.inc.php
Installer.executeSQL(ALTER TABLE article_comments MODIFY COLUMN comment_title VARCHAR(90) NOT NULL) % line 430, file: Installer.inc.php
Installer.executeSQL(Array[579]) % line 378, file: Installer.inc.php
Installer.executeAction(Array[3]) % line 268, file: Installer.inc.php




Here is an output of the line it gives the error on.

36 2 256 100 100 1 RADIOGRAPHIC OBSERVATIONS ON THE USE OF TWO ... "Dear Peter Galgut,



The three reviewers were not unanimous in their assessment of your submitted

work. However, I have decided that it can be acceptable after you have

revised the article, taking into account each of the points raised by the

reviewers.



Note that I am not requiring that the author have to agree with all of the

review comments. If there is reason to disagree with any of the suggested

corrections that are technical in nature, please attempt to clarify the

text, and give an explanation in an e-mail message accompanying the revised

version.



Reviewer C raises a fascinating point that maybe, at some point in the

future, our journal should require that every submitted article should

represent a greater degree of completion, statistical proof, and substantial

nature. We have decided that we are happy to waive such expectations,

especially in the present case, since this breif article gives a glimpse of

an application of cellulose that may be quite unexpected and revealing for

many of our readers.



Please use colored text or highlighting to indicate new or changed items in

the revised version, when it is sent to hubbe@ncsu.edu.



Martin Hubbe

BioResources

NC State University

(919) 513-3022





------------------------------------------------------

Reviewer A:

Review of Peter N. Galgut Article:



Radiographic Observations on the Use of Two Different Regeneration Materials

in a Single Subject: Case Study



The above article provides a compelling study on the use of cellulose,

specifically oxidized cellulose, as an adjuvant for periodontal recovery in

aggravated bone loss patients. It is a remarkably concise, albeit

abbreviated study, that should provide fodder for future studies. As such

it will need to have the following elements in it to be considered for

publication:



1. Why is this approach valid? What did you choose oxidized cellulose?

What is about it that makes it attractive for this application and what

characteristics does it possess that enhance its overall value for this

procedure? In other words, does the surface chemistry or physical

parameters merit more study? A recent study by Kong et al. (PNAS 2005,

article attached as supplementary information) indicated that a relationship

between the mechanical rigidity of the medium and the phenotype of the cell

existed. Perhaps this article can lend clarity to your discussion?

2. I would certainly be much clearer in the use of terms that have no

meaning to the typical reader; in other words, please indicate what the

meaning of “bioglasses” and “GTR,” and “oxidized cellulose.”

How are they made? Any characterization necessary?

3. The radiographs should be labeled to avoid confusion on identification of

specific teeth. In fact, there is a disconnect between the mentioned teeth

(page 5) and the Figure 2a teeth enumerated. Please check and confirm the

teeth indicated.

4. I would combine the Results and Discussion of Results section into one

big “Results and Discussion” section which is the typical formatting

style of this journal.



This is an interesting article that was very well written and offers a lot

of good seed for future work. I would follow the suggestions above to

improve the article, use the appended article for reference and support, and

clarify the work to ensure that all readers can understand it.



------------------------------------------------------



------------------------------------------------------

Reviewer B:

The manuscript compared the effects of tissue regeneration for treating

infrabony defects caused by periodontal diseases at different sites in the

same individual using two different materials, oxidized cellulose mesh and

bioglass with radiographic results. The author previously has done a lot of

work in bone re-growth. This work is the continuing contribution. The paper

can be considered for publication in this journal. However, several

questions need to be addressed.

1.The radiographs were shown before and 15 months after treatment. What will

happen for the treated defects after 15 months on the calcification and bone

re-growth?

2.The difference between pre and post-treatment is not very clear only from

radiographs. More results are required to demonstrate the points in the

manuscript.

3.Why the author selected the person? Which type of patient he can

represent? It is hard to reach any conclusion from single case study.



------------------------------------------------------



------------------------------------------------------

Reviewer C:

This manuscript describes a clinical study aimed at investigating the use of

oxidized cellulose and bioglass for the regeneration of bone tissue in

periodontal defects.

The subject itself is still relevant since no widely efficient solutions

exist, and it also consists in a clinical study in a human subject, which is

always relevant.

However, the present study is disappointing since it based on results

obtained from only one patient, and the analyses are only based on

radiographs. Although this later aspect can be debatable due to the

limitations in experiments that can be done in human subjects, the former

aspect constitutes a serious drawback of this study, as is correctly pointed

out by the author himself. Also, additional analyses could be carried out,

besides radiography, to characterize the implants along the time of the

experiment.

Not surprisingly, results are not conclusive since almost no differences

were found between the two different materials. Maybe a larger sampling

could provide more insights.

This manuscript raises more issues. After 15 months, no regeneration was

found and the non-specialized reader does not understand if this is to be

expected in a 50 years old healthy male or whether if the regeneration

materials are delaying the regeneration process. It seems also confusing for

the reader how can one compare the implantation of a mesh (cellulose;

positioned in incremental layers over the defect) with that of a

powder/granules (?) (bioglass) to fill-in a defect? Also, oxidized cellulose

has been widely described as bioresorbable, but no mention to it is made in

the manuscript. Could the materials have been degraded to fast?

Overall, I consider that this work is interesting but should be complemented

with additional analyses and, especially, with more results.



------------------------------------------------------

Lucian A. Lucia and Martin A. Hubbe, Co-Editors,

BioResources; lucian.lucia@ncsu.edu; hubbe@ncsu.edu;

http://152.1.192.20/index.php/BioRes;

http://ncsu.edu/bioresources
Lucian A. Lucia and Martin A. Hubbe, Co-Editors,

BioResources; lucian.lucia@ncsu.edu; hubbe@ncsu.edu;

http://152.1.192.20/index.php/BioRes;

http://ncsu.edu/bioresources" 11/14/2007 22:48 NULL 1
rdnorris
 
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Joined: Wed Jun 20, 2012 5:22 am

Re: Issue upgrading from 2.1.1 to 2.3.7

Postby ramon » Thu Jun 21, 2012 8:04 am

Hello Richard,

The “Results and Discussion” and similar are characters that are probably breaking your SQL commands, and they may be occurring in other places as well.
You have to make sure you are editing in UTF-8 (view and saving), so you are sure the character is not garbled because of the display.

Have you tried with charset_normalization = Off in your config.inc.php? This tends to relax a little bit mixed charsets.

Alec has pointed out in other posts about running the mysqldump into myconv, but I can't find anything related to myconv on the web.
It he meant iconv, which is a Linux application, I've tested it and results where not satisfactory.
I had to manually search and fix all characters that were garbled.
I used VIM for this, as you can use regular expressions to search and replace text.

I haven't tested RJ TextEd fully, but I looked up its search capabilities and it also has regular expressions.
It may help editing your SQL file in it to fix garbled characters.

_______________________________
Ramón Martins Sodoma da Fonseca
Analista em C&T
Coordenação de Tecnologias de Informação
Instituto Brasileiro de Informação em Ciência e Tecnologia - IBICT
Ministério da Ciência e Tecnologia - MCT
ramon
 
Posts: 940
Joined: Wed Oct 15, 2003 6:15 am
Location: Brasí­lia/DF - Brasil


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