Fatal Error while uploading a File with special Characters

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Fatal Error while uploading a File with special Characters

Matthias Enders
Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character  (ä / ü / ö / ß). This resulted in the following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
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Re: Fatal Error while uploading a File with special Characters

Dannon Baker-2
You should definitely not have to purge a user to fix this (not that it should happen in the first place).  Was it the file with special characters, or the name of the file?



On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <[hidden email]> wrote:
Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character  (ä / ü / ö / ß). This resulted in the following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Fatal Error while uploading a File with special Characters

Matthias Enders

It was the name of the File:

 

Blühzeitpunkt.txt

 

(for example)

 

Von: Dannon Baker [mailto:[hidden email]]
Gesendet: Thursday, September 10, 2015 4:12 PM
An: Matthias Enders <[hidden email]>
Cc: [hidden email]
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

 

You should definitely not have to purge a user to fix this (not that it should happen in the first place).  Was it the file with special characters, or the name of the file?

 

 

 

On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <[hidden email]> wrote:

Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character  (ä / ü / ö / ß). This resulted in the following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Fatal Error while uploading a File with special Characters

Dannon Baker-2
Thanks.  Can you specify exactly which release (or even the exact changeset) of the galaxy revision you're running, and what encoding the database is currently set to?  I've reproduced the error with the latest galaxy release, mysql 5.6.26 (utf8 encoding) and will get a fix out shortly, but I want to make sure I'm testing your situation as well.

On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders <[hidden email]> wrote:

It was the name of the File:

 

Blühzeitpunkt.txt

 

(for example)

 

Von: Dannon Baker [mailto:[hidden email]]
Gesendet: Thursday, September 10, 2015 4:12 PM
An: Matthias Enders <[hidden email]>
Cc: [hidden email]
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

 

You should definitely not have to purge a user to fix this (not that it should happen in the first place).  Was it the file with special characters, or the name of the file?

 

 

 

On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <[hidden email]> wrote:

Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character  (ä / ü / ö / ß). This resulted in the following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: Fatal Error while uploading a File with special Characters

Matthias Enders

Hi,

 

MySQL:

Server version: 5.5.44-0ubuntu0.14.04.1 (Ubuntu)

 

MySQL-GalaxyDB Encoding: UTF8

 

Galaxy: Where can I find the current release und changeset of my Galaxy Instance?

 

Mit freundlichen Grüßen

Matthias Enders

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GERMAN SEED ALLIANCE GmbH

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Mobil: +49 (0)151/ 14247360

 

Email: [hidden email]

 

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Amtsgericht Köln, HRB 73844

 

Von: Dannon Baker [mailto:[hidden email]]
Gesendet: Thursday, September 10, 2015 4:53 PM
An: Matthias Enders <[hidden email]>
Cc: [hidden email]
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

 

Thanks.  Can you specify exactly which release (or even the exact changeset) of the galaxy revision you're running, and what encoding the database is currently set to?  I've reproduced the error with the latest galaxy release, mysql 5.6.26 (utf8 encoding) and will get a fix out shortly, but I want to make sure I'm testing your situation as well.

 

On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders <[hidden email]> wrote:

It was the name of the File:

 

Blühzeitpunkt.txt

 

(for example)

 

Von: Dannon Baker [mailto:[hidden email]]
Gesendet: Thursday, September 10, 2015 4:12 PM
An: Matthias Enders <
[hidden email]>
Cc:
[hidden email]
Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

 

You should definitely not have to purge a user to fix this (not that it should happen in the first place).  Was it the file with special characters, or the name of the file?

 

 

 

On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <[hidden email]> wrote:

Dear Galaxy Community,

a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character  (ä / ü / ö / ß). This resulted in the following status (only for the given user):

- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"


This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!

We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?

Thanks in advance!

Matthias
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 
http://galaxyproject.org/search/mailinglists/

 

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/