Re: [base] Stopping Base after MySQL crash

[Nicklas Nordborg]

Marie Mooney wrote:
 Hi.

I don't know much about BASE 1.2 but I think that you must have the 
MySQL running for stopBase.php to work. And you must also have MySQL 
running to be able to upgrade from 1.2.14 to 1.2.17. So you have to find 
a way to start the MySQL server again.

/Nicklas

 
 I am an extremely (completely) new user to BASE, and I was tasked with
 migrating from Base 1.2.14 to BASE2. Unfortunately, it seems, I started by
 installing BASE2, and doing all the other system upgrades necessary for
 that, which included updating MySQL from 4.1 to 5.0.27. When I did this, I
 had stopped the 4.1 version, which I had problems restarting. However, to
 do the migration in BASE, I apparently have to update to 1.2.17 first,
 then do the migration to BASE2, and to do the first upgrade, I need to
 stop the old version of BASE 1.2.14  (Does all this sound correct so
 far?), which won't stop on this error:
 
 # stopBase.php
 PHP Warning:  mysql_pconnect(): Can't connect to local MySQL server
 through socket '/var/lib/mysql/mysql.sock' (13) in
 /usr/local/base-1.2.14/include/drivers/mysql.inc.php on line 86
 mysql_pconnect() failed: Can't connect to local MySQL server through
 socket '/var/lib/mysql/mysql.sock' (13)
 Could not connect to database 'base' at host 'localhost' as user 'apache'
 BASE appears to be running, but connecting to the database failed.
 
 My question then is whether there is a way to stop BASE without having
 access to the old version of MySQL, or is there a way to make BASE 1.2.14
 run on the new version of MySQL without stopping it?
 
 I tried changing the 'base' db BaseControl table to have startscripts = 0,
 as mentioned in the forums for after someone else had a problem where
 MySQL went down before BASE was stopped, but this didn't give me any
 different results.
 
 Any suggestions from anyone would be greatly appreciated.
 
 


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Re: [base] Problem importing into ReporterLists

[Nicklas Nordborg]

Reha Yildirimman wrote:
 Hello,
 
 I am trying to import Reporter into a new reporter list inside a 
 fresh,new base2 installation, getting the following error:
 
 Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in 
 'field list'

Can you please submit the entire stacktrace and also a step-by-step 
description of how to reproduce the error. Also include information 
about which version of BASE you are using, which database you are using, 
the Java version, and any other information that you think is important. 
All of this should be available in the About box or on the error message 
page.

/Nicklas

 
 I cannot find the column 'reporterda0_.' inside any mysql table or 
 inside extended-properties.xml/raw-data-types.xml ...
 When I try to access the - empty - Reporters part I get the following error:
 
 could not execute query using scroll
 
 
 Does anybody have a clue ? The file containing the list of reporters is 
 a tab-delimited file with 6 columns, the first with the ID,
 the other 5 columns with annotations
 
 Thanks alot in advance for your help.
 
 Cheers,
 
 Reha
 
 ---
 Reha Yildirimman
 Max-Planck-Institute for Molecular Genetics
 Department Lehrach (Vertebrate Genomics)
 Ihnestr. 73
 14195 Berlin
 Germany
 ---
 
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