[BioMart Users] materializing an existing database

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[BioMart Users] materializing an existing database

andrea_bio
Hi

I am trying to materialize a dataset based on the ensembl core database.
It doesn't seem to be working.
I have called the dataset gene. This is what happens when i click
materialize

target database: gene
target_schema: gene
martrunner host:localhost
port: 9005
database server: ensembldb.ensembl.org
database port: 5306


NOthing seems to happen. When i click refresh the job is still pink but
the 'start job' button is active again. If i look in the terminal where
martrunner is running there is this error

[Thread-3] ERROR martrunner -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
for user 'anonymous'@'%' to database 'gene'
ERROR [Thread-3] (Log.java:197) -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
for user 'anonymous'@'%' to database 'gene'


I have created a database called gene and given the anonymous user full
access to this database on the local server.

andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$ mysql -u
anonymous


mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| gene               |
+--------------------+
2 rows in set (0.00 sec)

mysql> use gene;
Database changed


I thought perhaps there might be some confusion because my database is
called gene and I was using gene as the main table in the ensembl core
database so i renamed my local database to gene_test and then i got this
error instead

andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$
./martrunner.sh 9005
Starting MartRunner please wait ....
...martrunner started.
[Thread-3] ERROR martrunner -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
database 'gene_test'
ERROR [Thread-3] (Log.java:197) -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
database 'gene_test'


but the database does exist


mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| gene_test          |
+--------------------+
2 rows in set (0.00 sec)

mysql> use gene_test;
Database changed

thanks a lot


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Re: [BioMart Users] materializing an existing database

Joachim Baran-2
Hello,

On 11-03-25 5:22 PM, "Andrea Edwards" <[hidden email]> wrote:
>mysql> use gene;
>Database changed
  Have you given your user permissions to create databases and tables too?

>I thought perhaps there might be some confusion because my database is
>called gene and I was using gene as the main table in the ensembl core
>database so i renamed my local database to gene_test and then i got this
>error instead
  The database and table can be called the same. However, I am curious how
you renamed the database, because that functionality was only available in
MySQL for a brief time before it was removed again. If you did the
renaming on the filesystem, then you might have broken something. Try to
re-create your database afresh.

Joachim

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Re: [BioMart Users] materializing an existing database

Yong Liang
In reply to this post by andrea_bio
Hi Andrea,

Biomart doesn't support materialize data into different servers. The source
data and the mart have to be in the same machine. You cannot do the
materialize unless your have the write permit with ensembldb.ensembl.org.

Yong

On 11-03-25 5:22 PM, "Andrea Edwards" <[hidden email]> wrote:

> Hi
>
> I am trying to materialize a dataset based on the ensembl core database.
> It doesn't seem to be working.
> I have called the dataset gene. This is what happens when i click
> materialize
>
> target database: gene
> target_schema: gene
> martrunner host:localhost
> port: 9005
> database server: ensembldb.ensembl.org
> database port: 5306
>
>
> NOthing seems to happen. When i click refresh the job is still pink but
> the 'start job' button is active again. If i look in the terminal where
> martrunner is running there is this error
>
> [Thread-3] ERROR martrunner -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
> for user 'anonymous'@'%' to database 'gene'
> ERROR [Thread-3] (Log.java:197) -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
> for user 'anonymous'@'%' to database 'gene'
>
>
> I have created a database called gene and given the anonymous user full
> access to this database on the local server.
>
> andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$ mysql -u
> anonymous
>
>
> mysql> show databases;
> +--------------------+
> | Database           |
> +--------------------+
> | information_schema |
> | gene               |
> +--------------------+
> 2 rows in set (0.00 sec)
>
> mysql> use gene;
> Database changed
>
>
> I thought perhaps there might be some confusion because my database is
> called gene and I was using gene as the main table in the ensembl core
> database so i renamed my local database to gene_test and then i got this
> error instead
>
> andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$
> ./martrunner.sh 9005
> Starting MartRunner please wait ....
> ...martrunner started.
> [Thread-3] ERROR martrunner -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
> database 'gene_test'
> ERROR [Thread-3] (Log.java:197) -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
> database 'gene_test'
>
>
> but the database does exist
>
>
> mysql> show databases;
> +--------------------+
> | Database           |
> +--------------------+
> | information_schema |
> | gene_test          |
> +--------------------+
> 2 rows in set (0.00 sec)
>
> mysql> use gene_test;
> Database changed
>
> thanks a lot
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users



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Re: [BioMart Users] materializing an existing database

Yong Liang
In reply to this post by andrea_bio
Hi Andrea,

Why you want to materialize ensembl data? If you just want to query the
data, you can deploy your server and query through virtual mart. Or you can
add a mart from martdb.ensembl.org, or URL.

Hope this helps.

Yong


On 11-03-25 5:22 PM, "Andrea Edwards" <[hidden email]> wrote:

> Hi
>
> I am trying to materialize a dataset based on the ensembl core database.
> It doesn't seem to be working.
> I have called the dataset gene. This is what happens when i click
> materialize
>
> target database: gene
> target_schema: gene
> martrunner host:localhost
> port: 9005
> database server: ensembldb.ensembl.org
> database port: 5306
>
>
> NOthing seems to happen. When i click refresh the job is still pink but
> the 'start job' button is active again. If i look in the terminal where
> martrunner is running there is this error
>
> [Thread-3] ERROR martrunner -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
> for user 'anonymous'@'%' to database 'gene'
> ERROR [Thread-3] (Log.java:197) -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied
> for user 'anonymous'@'%' to database 'gene'
>
>
> I have created a database called gene and given the anonymous user full
> access to this database on the local server.
>
> andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$ mysql -u
> anonymous
>
>
> mysql> show databases;
> +--------------------+
> | Database           |
> +--------------------+
> | information_schema |
> | gene               |
> +--------------------+
> 2 rows in set (0.00 sec)
>
> mysql> use gene;
> Database changed
>
>
> I thought perhaps there might be some confusion because my database is
> called gene and I was using gene as the main table in the ensembl core
> database so i renamed my local database to gene_test and then i got this
> error instead
>
> andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$
> ./martrunner.sh 9005
> Starting MartRunner please wait ....
> ...martrunner started.
> [Thread-3] ERROR martrunner -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
> database 'gene_test'
> ERROR [Thread-3] (Log.java:197) -
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown
> database 'gene_test'
>
>
> but the database does exist
>
>
> mysql> show databases;
> +--------------------+
> | Database           |
> +--------------------+
> | information_schema |
> | gene_test          |
> +--------------------+
> 2 rows in set (0.00 sec)
>
> mysql> use gene_test;
> Database changed
>
> thanks a lot
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users




_______________________________________________
Users mailing list
[hidden email]
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