How to replace all dataset configs with MartEditor "Upload All"

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

How to replace all dataset configs with MartEditor "Upload All"

Leandro Hermida-2
Hi,

I am having trouble using the "Upload All" functionality in MartEditor
to replace all the dataset configs in my mart with new dataset xmls.
It doesn't seem to let me use multiple dataset config xml files or a
single file with multiple dataset configs.  How do I do this?

best,
Leandro
Reply | Threaded
Open this post in threaded view
|

Re: How to replace all dataset configs with MartEditor "Upload All"

Syed Haider
Hi Leandro,

please select the template XML file and all dataset files as
multiSelect, it should be able to pick. Let us know how you get on with
this ?

thanks
Syed

On 21/10/2010 09:57, Leandro Hermida wrote:
> Hi,
>
> I am having trouble using the "Upload All" functionality in MartEditor
> to replace all the dataset configs in my mart with new dataset xmls.
> It doesn't seem to let me use multiple dataset config xml files or a
> single file with multiple dataset configs.  How do I do this?
>
> best,
> Leandro
suo
Reply | Threaded
Open this post in threaded view
|

meta_conf__user__dm' doesn't exist

suo
In reply to this post by Leandro Hermida-2
Hello all:

I am installing biomart0.7 on MySQL5 on RHEL5. There is some problem when issuing:

perl bin/configure.pl -r conf/myRegistry.xml

Here is the error message:

DBD::mysql::st execute failed: Table 'mymart.meta_conf__user__dm' doesn't exist at /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm line 210.

ERROR something wrong with your registry: DBD::mysql::st execute failed: Table 'mymart.meta_conf__user__dm' doesn't exist at /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm line 210.


Here is my myRegistry.xml:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>

<MartDBLocation
                    name         = "my_mart"
                    displayName  = "My BioMart Database"
                    databaseType = "mysql"
                    host         = "127.0.0.1"
                    port         = "3306"
                    database     = "mymart"
                    schema       = "mymart"
                    user         = "root"
                    password     = "******"
                    visible      = "1"
                    default      = ""
                    includeDatasets = ""
                    martUser     = ""
/>
</MartRegistry>




     
Reply | Threaded
Open this post in threaded view
|

Re: meta_conf__user__dm' doesn't exist

Syed Haider
Hi Suo,

please execute the following perl code on your machine.

##############################
#!/usr/bin/perl
use strict;
use DBI;

my $conString =
"dbi:mysql:database=ensembl_mart_52;host=martdb.ensembl.org;port=5316;user=anonymous";

my $dbh = DBI->connect($conString) or die "Couldn't connect to database:
" . DBI->errstr;

##############################

let me know what you see,

thanks,
Syed



On 21/10/2010 19:28, suo wrote:

> Hello all:
>
> I am installing biomart0.7 on MySQL5 on RHEL5. There is some problem when issuing:
>
> perl bin/configure.pl -r conf/myRegistry.xml
>
> Here is the error message:
>
> DBD::mysql::st execute failed: Table 'mymart.meta_conf__user__dm' doesn't exist at /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm line 210.
>
> ERROR something wrong with your registry: DBD::mysql::st execute failed: Table 'mymart.meta_conf__user__dm' doesn't exist at /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm line 210.
>
>
> Here is my myRegistry.xml:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>
> <MartDBLocation
>                      name         = "my_mart"
>                      displayName  = "My BioMart Database"
>                      databaseType = "mysql"
>                      host         = "127.0.0.1"
>                      port         = "3306"
>                      database     = "mymart"
>                      schema       = "mymart"
>                      user         = "root"
>                      password     = "******"
>                      visible      = "1"
>                      default      = ""
>                      includeDatasets = ""
>                      martUser     = ""
> />
> </MartRegistry>
>
>
>
>
>
Reply | Threaded
Open this post in threaded view
|

Re: How to replace all dataset configs with MartEditor "Upload All"

Leandro Hermida-2
In reply to this post by Syed Haider
Hi Syed,

This works thank you... I selected all the <dataset_name>.xml and
<dataset_name>.template.xml pair of XML files to reload the entire
configuration.

best,
Leandro

On Thu, Oct 21, 2010 at 3:26 PM, Syed Haider <[hidden email]> wrote:

> Hi Leandro,
>
> please select the template XML file and all dataset files as multiSelect, it
> should be able to pick. Let us know how you get on with this ?
>
> thanks
> Syed
>
> On 21/10/2010 09:57, Leandro Hermida wrote:
>>
>> Hi,
>>
>> I am having trouble using the "Upload All" functionality in MartEditor
>> to replace all the dataset configs in my mart with new dataset xmls.
>> It doesn't seem to let me use multiple dataset config xml files or a
>> single file with multiple dataset configs.  How do I do this?
>>
>> best,
>> Leandro
>
suo
Reply | Threaded
Open this post in threaded view
|

Re: meta_conf__user__dm' doesn't exist

suo
In reply to this post by Syed Haider
Hello Syed:

Thanks for your quick response.
I ran your perl code and it went through. There is NO any message including error.

--- On Thu, 10/21/10, Syed Haider <[hidden email]> wrote:

> From: Syed Haider <[hidden email]>
> Subject: Re: [mart-dev] meta_conf__user__dm' doesn't exist
> To: "suo" <[hidden email]>
> Cc: "[hidden email]" <[hidden email]>
> Date: Thursday, October 21, 2010, 12:03 PM
> Hi Suo,
>
> please execute the following perl code on your machine.
>
> ##############################
> #!/usr/bin/perl
> use strict;
> use DBI;
>
> my $conString =
> "dbi:mysql:database=ensembl_mart_52;host=martdb.ensembl.org;port=5316;user=anonymous";
>
> my $dbh = DBI->connect($conString) or die "Couldn't
> connect to database:
> " . DBI->errstr;
>
> ##############################
>
> let me know what you see,
>
> thanks,
> Syed
>
>
>
> On 21/10/2010 19:28, suo wrote:
> > Hello all:
> >
> > I am installing biomart0.7 on MySQL5 on RHEL5. There
> is some problem when issuing:
> >
> > perl bin/configure.pl -r conf/myRegistry.xml
> >
> > Here is the error message:
> >
> > DBD::mysql::st execute failed: Table
> 'mymart.meta_conf__user__dm' doesn't exist at
> /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm
> line 210.
> >
> > ERROR something wrong with your registry:
> DBD::mysql::st execute failed: Table
> 'mymart.meta_conf__user__dm' doesn't exist at
> /root/biomart-perl/bin/../lib/BioMart/Configuration/MartDBLocation.pm
> line 210.
> >
> >
> > Here is my myRegistry.xml:
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <!DOCTYPE MartRegistry>
> > <MartRegistry>
> >
> > <MartDBLocation
> >               
>       name     
>    = "my_mart"
> >               
>       displayName  = "My BioMart
> Database"
> >               
>       databaseType = "mysql"
> >               
>       host     
>    = "127.0.0.1"
> >               
>       port     
>    = "3306"
> >               
>       database     =
> "mymart"
> >               
>       schema       =
>

> >               
>       user     
>    = "root"
> >               
>       password     =
> "******"
> >               
>       visible      = "1"
> >               
>       default      = ""
> >               
>       includeDatasets = ""
> >               
>       martUser     = ""
> > />
> > </MartRegistry>
> >
> >
> >
> >
> >
>