[BioMart Users] Biomart local setup - load source problem

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[BioMart Users] Biomart local setup - load source problem

zhilianghu
I have setup a local copy of the Biomart 0.8.  With martconfigurator.sh
I can load  multiple data sources for "snp".  When I try to load
"Ensembl", I could load only 1 species relatively quickly.  However, when
I try to load more than 1 species, or add 1 species after a successful
load (1 species), it would take *forever* (I waited at times over couple
hours), regardless if I choose to let it calculate links between species
not not.  Some console messagee are like:

[Thread-6] ERROR martconfigurator - Checking importable
ERROR [Thread-6] (Log.java:197) - Checking importable
[Thread-6] ERROR martconfigurator - checking filter
ERROR [Thread-6] (Log.java:197) - checking filter
[Thread-6] ERROR martconfigurator - Checking exportable
ERROR [Thread-6] (Log.java:197) - Checking exportable
[Thread-6] ERROR martconfigurator - Done
ERROR [Thread-6] (Log.java:197) - Done

Any advice?

Zhiliang

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Re: [BioMart Users] Biomart local setup - load source problem

Joachim Baran-2
Hi!

On 11-04-26 1:00 PM, "Zhiliang" <[hidden email]> wrote:
>I have setup a local copy of the Biomart 0.8.  With martconfigurator.sh
>I can load  multiple data sources for "snp".  When I try to load
>"Ensembl", I could load only 1 species relatively quickly.  However, when
>I try to load more than 1 species, or add 1 species after a successful
>load (1 species), it would take *forever* (I waited at times over couple
>hours), regardless if I choose to let it calculate links between species
>not not.

  Can you please describe how you click through the interface so that we
can replicate the problem?

  For example, you could say: "Click on 'Add Source', select Type: 'URL',
..."

Thanks,
Joachim

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Re: [BioMart Users] Biomart local setup - load source problem

zhilianghu
In reply to this post by zhilianghu
On Tue, 26 Apr 2011, Joachim Baran wrote:

> Date: Tue, 26 Apr 2011 13:11:08 -0400
> From: Joachim Baran <[hidden email]>
> To: Zhiliang <[hidden email]>, "[hidden email]" <[hidden email]>
> Subject: Re: [BioMart Users] Biomart local setup - load source problem
>
> Hi!
>
> On 11-04-26 1:00 PM, "Zhiliang" <[hidden email]> wrote:
>> I have setup a local copy of the Biomart 0.8.  With martconfigurator.sh
>> I can load  multiple data sources for "snp".  When I try to load
>> "Ensembl", I could load only 1 species relatively quickly.  However, when
>> I try to load more than 1 species, or add 1 species after a successful
>> load (1 species), it would take *forever* (I waited at times over couple
>> hours), regardless if I choose to let it calculate links between species
>> not not.
>
>  Can you please describe how you click through the interface so that we
> can replicate the problem?
>
>  For example, you could say: "Click on 'Add Source', select Type: 'URL',
> ..."
>
> Thanks,
> Joachim

(1) In "File" window, under *Source, click "+Add Source"
    -> An "add data source" window pop up
(2) In "Add Data Source" window, under "Marts", click select "ensembl"
    -> A list of species appear on the right column "Datasets"
(3) In "Add Data Source" window, under "Datasets", click unselect
not-wanted species [a suggestion: could the default be all 'un-selected'?]
    -> if I select 1 species, it loads, and I can start the server etc
    -> if I select 2 or more species, it "runs" forever
    -> if after a successful load of a species, I select 1 speciess, it
"runs" forever

I hope these details are sufficient?

Thank you,
Zhiliang

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Re: [BioMart Users] Biomart local setup - load source problem

Yong Liang
Hi Zhiliang,

Do you still have the problem? I followed your steps and selected multiple
species for "URL" mart. It worked fine for me. Could you let me know what
species you are choosing? In the "add data source" dialog, do you choose
"URL" or "RDBMS"?

>(3) In "Add Data Source" window, under "Datasets", click unselect
> not-wanted species [a suggestion: could the default be all 'un-selected'?]
In the new release, you can do select/un-select all.

Thanks,

Yong


On 11-04-26 1:25 PM, "Zhiliang" <[hidden email]> wrote:

> On Tue, 26 Apr 2011, Joachim Baran wrote:
>
>> Date: Tue, 26 Apr 2011 13:11:08 -0400
>> From: Joachim Baran <[hidden email]>
>> To: Zhiliang <[hidden email]>, "[hidden email]" <[hidden email]>
>> Subject: Re: [BioMart Users] Biomart local setup - load source problem
>>
>> Hi!
>>
>> On 11-04-26 1:00 PM, "Zhiliang" <[hidden email]> wrote:
>>> I have setup a local copy of the Biomart 0.8.  With martconfigurator.sh
>>> I can load  multiple data sources for "snp".  When I try to load
>>> "Ensembl", I could load only 1 species relatively quickly.  However, when
>>> I try to load more than 1 species, or add 1 species after a successful
>>> load (1 species), it would take *forever* (I waited at times over couple
>>> hours), regardless if I choose to let it calculate links between species
>>> not not.
>>
>>  Can you please describe how you click through the interface so that we
>> can replicate the problem?
>>
>>  For example, you could say: "Click on 'Add Source', select Type: 'URL',
>> ..."
>>
>> Thanks,
>> Joachim
>
> (1) In "File" window, under *Source, click "+Add Source"
>     -> An "add data source" window pop up
> (2) In "Add Data Source" window, under "Marts", click select "ensembl"
>     -> A list of species appear on the right column "Datasets"
> (3) In "Add Data Source" window, under "Datasets", click unselect
> not-wanted species [a suggestion: could the default be all 'un-selected'?]
>     -> if I select 1 species, it loads, and I can start the server etc
>     -> if I select 2 or more species, it "runs" forever
>     -> if after a successful load of a species, I select 1 speciess, it
> "runs" forever
>
> I hope these details are sufficient?
>
> Thank you,
> Zhiliang
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users


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Re: [BioMart Users] Biomart local setup - load source problem

zhilianghu
In reply to this post by zhilianghu
Thanks Yong,

I used "URL" in the "add data source" window (if I choose "RDBMS" I got
"database connection error" - with anonymous/myEmail_pass).

How is your "new release" available - should I wait for next release
version or i can get it somewhere?

Yes my previously describe problem still persists.

Zhiliang

> Date: Tue, 26 Apr 2011 14:27:03 -0400
> From: Yong Liang <[hidden email]>
> To: Zhiliang <[hidden email]>, Joachim Baran <[hidden email]>
> Cc: "[hidden email]" <[hidden email]>
> Subject: Re: [BioMart Users] Biomart local setup - load source problem
>
> Hi Zhiliang,
>
> Do you still have the problem? I followed your steps and selected multiple
> species for "URL" mart. It worked fine for me. Could you let me know what
> species you are choosing? In the "add data source" dialog, do you choose
> "URL" or "RDBMS"?
>
>> (3) In "Add Data Source" window, under "Datasets", click unselect
>> not-wanted species [a suggestion: could the default be all 'un-selected'?]
> In the new release, you can do select/un-select all.
>
> Thanks,
>
> Yong
>
>
> On 11-04-26 1:25 PM, "Zhiliang" <[hidden email]> wrote:
>
>> On Tue, 26 Apr 2011, Joachim Baran wrote:
>>
>>> Date: Tue, 26 Apr 2011 13:11:08 -0400
>>> From: Joachim Baran <[hidden email]>
>>> To: Zhiliang <[hidden email]>, "[hidden email]"
> <[hidden email]>
>>> Subject: Re: [BioMart Users] Biomart local setup - load source problem
>>>
>>> Hi!
>>>
>>> On 11-04-26 1:00 PM, "Zhiliang" <[hidden email]> wrote:
>>>> I have setup a local copy of the Biomart 0.8.  With martconfigurator.sh
>>>> I can load  multiple data sources for "snp".  When I try to load
>>>> "Ensembl", I could load only 1 species relatively quickly.  However, when
>>>> I try to load more than 1 species, or add 1 species after a successful
>>>> load (1 species), it would take *forever* (I waited at times over couple
>>>> hours), regardless if I choose to let it calculate links between species
>>>> not not.
>>>
>>>  Can you please describe how you click through the interface so that we
>>> can replicate the problem?
>>>
>>>  For example, you could say: "Click on 'Add Source', select Type: 'URL',
>>> ..."
>>>
>>> Thanks,
>>> Joachim
>>
>> (1) In "File" window, under *Source, click "+Add Source"
>>     -> An "add data source" window pop up
>> (2) In "Add Data Source" window, under "Marts", click select "ensembl"
>>     -> A list of species appear on the right column "Datasets"
>> (3) In "Add Data Source" window, under "Datasets", click unselect
>> not-wanted species [a suggestion: could the default be all 'un-selected'?]
>>     -> if I select 1 species, it loads, and I can start the server etc
>>     -> if I select 2 or more species, it "runs" forever
>>     -> if after a successful load of a species, I select 1 speciess, it
>> "runs" forever
>>
>> I hope these details are sufficient?
>>
>> Thank you,
>> Zhiliang
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>
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suo
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[BioMart Users] Biomart 0.7 martview fails to start

suo
In reply to this post by zhilianghu
Dear all,

I followed "BioMart 0.7 Quick Install Guide" to set up my biomart
with RHEL5 built-in Apache 2.0 and mod_perl 2.0.4.
There were no errors reported during the process. However, after issuing "/my/chosen/Apache/binary -d $PWD -f $PWD/conf/httpd.conf", the MartView does not start (checked via either web browser or httpd status).

Any suggestions would be appreciated.
Thanks in advance.
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Re: [BioMart Users] Biomart 0.7 martview fails to start

Joachim Baran-2
Hi!

On 11-04-26 11:23 PM, "suo" <[hidden email]> wrote:
>There were no errors reported during the process. However, after issuing
>"/my/chosen/Apache/binary -d $PWD -f $PWD/conf/httpd.conf", the MartView
>does not start (checked via either web browser or httpd status).
  Have you had a look at the error log-file of Apache? You can post an
excerpt of the file here for us to investigate if you like.

Joachim

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