help: can't connect to external mysql atabase

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help: can't connect to external mysql atabase

wenqing zhang-2
Hi;
 
the mysql databse is installed inside drupal in local server.
the mysql path location is  /opt/drupal-6.16-0/mysql/bin/mysql.
 
when I tried to connect Galaxy to mysql database by modifying database_connection in file universe_wsgi.ini as following
database_connection =  /opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase
I fialed to do it. and ArgumentError: could not parse rfc1738URL from string '/opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase'
 
someone can help me?
 
thanks. 


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Re: help: can't connect to external mysql atabase

Greg Von Kuster
<base href="x-msg://135/">Hello,

The problem is that the connection string is a URL, it shouldn't have the path to the mysql binary in it (should just be "<a href="mysql://tiger:goDB@localhost/mydatabase">mysql://tiger:goDB@localhost/mydatabase")  Also, Galaxy and drupal are different and unrelated pieces of software, and Galaxy should have its own dedicated database.  Galaxy should work with mysql, but we highly recommend postgres.


On Jun 9, 2010, at 6:55 PM, wenqing zhang wrote:

Hi;
 
the mysql databse is installed inside drupal in local server.
the mysql path location is  /opt/drupal-6.16-0/mysql/bin/mysql.
 
when I tried to connect Galaxy to mysql database by modifying database_connection in file universe_wsgi.ini as following
database_connection =  /opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase 
I fialed to do it. and ArgumentError: could not parse rfc1738URL from string '/opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase'
 
someone can help me?
 
thanks. 


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Re: help: can't connect to external mysql atabase

Greg Von Kuster
<base href="x-msg://371/">Probably a data problem - the traceback is probably stating that some history or data cannot be located or something, which means that the data in your database is corrupted.

On Jun 11, 2010, at 10:59 AM, wenqing zhang wrote:

Hi,
thanks for your response.
 
we changed the database path connection to mysql database in drupal as following
database_connection=mysql://tiger:goDB@localhost/mydatabase?unix_socket=/opt/drupal-6.16-0/mysql/tmp/mysql.sock
 
it starts to run, but when we take a look at it through the web browser(127.0.0.1:8080), the right column (history panel) of galaxy is not work normally, showing  error traceback. is it still connection problem, or database broplem?
 
thanks in advance for your more help.
 
  

 

Subject: Re: [galaxy-dev] help: can't connect to external mysql atabase
From: [hidden email]
Date: Thu, 10 Jun 2010 18:36:26 -0400
CC: [hidden email]
To: [hidden email]

Hello,

The problem is that the connection string is a URL, it shouldn't have the path to the mysql binary in it (should just be "mysql://tiger:goDB@localhost/mydatabase")  Also, Galaxy and drupal are different and unrelated pieces of software, and Galaxy should have its own dedicated database.  Galaxy should work with mysql, but we highly recommend postgres.


On Jun 9, 2010, at 6:55 PM, wenqing zhang wrote:

Hi;
 
the mysql databse is installed inside drupal in local server.
the mysql path location is  /opt/drupal-6.16-0/mysql/bin/mysql.
 
when I tried to connect Galaxy to mysql database by modifying database_connection in file universe_wsgi.ini as following
database_connection =  /opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase 
I fialed to do it. and ArgumentError: could not parse rfc1738URL from string '/opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase'
 
someone can help me?
 
thanks. 


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Greg Von Kuster
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Re: help: can't connect to external mysql atabase

Greg Von Kuster
<base href="x-msg://396/">Again, make sure Galaxy has it's own dedicated database.  Also make sure you are running the latest Galaxy code - see getgalaxy.org for instructions on getting the latest code as your traceback infers that you have database tables that are out of sync with your Galaxy code.

If you are attempting a new install, drop all of the tables in the database, and start up your Galaxy instance with:

%sh run.sh

Galaxy will automatically create all of the tables for you, and everything should be fine.


On Jun 11, 2010, at 12:03 PM, wenqing zhang wrote:

Hi
 
we just modify the path of databse connection in file universe_wsgi.ini without to change anything else, the path connection is to the local database mydatabase, which is new one not without any table inside. the histoy panel shows error traceback, which is operational error (1054, "unknown column 'published' in 'field list' ") u 'insert into histroy (creat_time, update_time,  and more ...  
 
does it mean we need to setup tables in our local database for history or something else?
 
does "the data inyour database is corrupted" you mentioned mean data of database in galaxy engine is corrupted or the data in our local database is corrupted ?
 
thanks again.  
 

Subject: Re: [galaxy-dev] help: can't connect to external mysql atabase
From: [hidden email]
Date: Fri, 11 Jun 2010 11:11:58 -0400
CC: [hidden email]
To: [hidden email]

Probably a data problem - the traceback is probably stating that some history or data cannot be located or something, which means that the data in your database is corrupted.

On Jun 11, 2010, at 10:59 AM, wenqing zhang wrote:

Hi,
thanks for your response.
 
we changed the database path connection to mysql database in drupal as following
database_connection=mysql://tiger:goDB@localhost/mydatabase?unix_socket=/opt/drupal-6.16-0/mysql/tmp/mysql.sock
 
it starts to run, but when we take a look at it through the web browser(127.0.0.1:8080), the right column (history panel) of galaxy is not work normally, showing  error traceback. is it still connection problem, or database broplem?
 
thanks in advance for your more help.
 
  

 

Subject: Re: [galaxy-dev] help: can't connect to external mysql atabase
From: [hidden email]
Date: Thu, 10 Jun 2010 18:36:26 -0400
CC: [hidden email]
To: [hidden email]

Hello,

The problem is that the connection string is a URL, it shouldn't have the path to the mysql binary in it (should just be "mysql://tiger:goDB@localhost/mydatabase")  Also, Galaxy and drupal are different and unrelated pieces of software, and Galaxy should have its own dedicated database.  Galaxy should work with mysql, but we highly recommend postgres.


On Jun 9, 2010, at 6:55 PM, wenqing zhang wrote:

Hi;
 
the mysql databse is installed inside drupal in local server.
the mysql path location is  /opt/drupal-6.16-0/mysql/bin/mysql.
 
when I tried to connect Galaxy to mysql database by modifying database_connection in file universe_wsgi.ini as following
database_connection =  /opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase 
I fialed to do it. and ArgumentError: could not parse rfc1738URL from string '/opt/drupal-6.16-0/mysql/bin/mysql://tiger:godatabase@localhost/mydatabase'
 
someone can help me?
 
thanks. 


The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. _______________________________________________
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Greg Von Kuster
Galaxy Development Team





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Greg Von Kuster
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