CMap - oracle dumps of Gramene maps?

[Gregory Brown]

Ken,

On the Gramene ftp site there are 3 types of files with map data. I  
first found the tabbed files named by map set.  If I understand  
correctly, these files can be loaded into any database (mysql, oracle,  
postgres) as long as the tables are defined and the map set is manually  
defined via the CMap web interface.  I actually forgot where I found  
these files.

The second file is cmap16.dmp.gz  which is the mysql version 4.1.7  
export of all the current CMap data.  I loaded this file simply and  
fairly quickly with something like  "mysql -u gregb -p CMAP <  
cmap16.dmp.sql" after first removing some mysql version 4.1 specific  
statements.  This type of file is what I was looking for to load into  
an oracle database. This file is found at  
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/database_dump/ 
mysql-dumps/

The third file type I found at Gramene was the complete CMap table  
dumps that can be loaded using MySQL's "mysqlimport" command you  
mention below.  This is the cmap16.tgz file at  
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/database_dump/ 
mysql-dumps/

I just noticed that Mysql version 4.1 has support for "mysqldump  
--compatible=oracle ..." exports.  Supposedly I could export my mysql  
CMap db in an oracle compatible format and then import that file into  
oracle.  I have to upgrade to the newest version of mysql first and  
then I will try that.  Has anyone any experience with this new export  
option?

gb

On Mar 30, 2005, at 8:37 AM, Ken Youens-Clark wrote:

> On Mar 29, 2005, at 11:14 AM, Gregory Brown wrote:
>
>> I was able to get CMap version .13 running using mysql on a mac g5  
>> osX system.  I found the mysql dumps for the Gramene CMap maps and  
>> loaded those successfully.  Now I would like to switch my CMap  
>> database to Oracle (version 10g) and load the Gramene CMap data.   
>> Unfortunately I cannot find any oracle dump files on the gramene ftp  
>> site.  I have found the tab separated gramene CMap data.  I need  
>> advice on how to actually load this CMap data into an oracle db.
>
> When you say the tab-delimited CMap data, do you mean the files that  
> are named by the map sets, or are there tab files that are named like  
> table names (e.g., "cmap_feature")?  If not the latter, then I would  
> say we need to be dumping tab-delimited files of every table in our  
> databases for loading with MySQL's "mysqlimport" or the LOAD FILE  
> command (which is much faster to use than parsing the default CREATE  
> and INSERT statements from "mysqldump").  Additionally, it would  
> probably make it easier for non-MySQL users to import given simple  
> things like how MySQL and Oracle each escape embedded quotes, etc.
>
> Shuly or Greg, Oracle can import tab files if the fielded data is in  
> the same order as the column definitions in the table, right?
>
> ky
>