[BioMart Users] ICGC mart, queries never get to finish

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

[BioMart Users] ICGC mart, queries never get to finish

Jorge Zamora-2
Hello,

I'm experiencing that queries in the Quick Interface work but when I
query using the other two interfaces the query seems to run forever.
This happens when in query my local mart but not when I use other ICGC
marts.

This a example of one of the queries that never finish:


<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query client=""
processor="TSV" limit="-1" header="1"><Dataset name="snp_cnioCLL"
config="snp_3_1_1"><Attribute name="cancertype"/><Attribute
name="chromosome"/><Attribute
name="simple_somatic_mutation__dm_mutation_id"/><Attribute
name="donor_id"/></Dataset></Query>


anybody experiencing something similar? I'm using biomart 0.8 rc4

Thanks
Jorge

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC mart, queries never get to finish

Syed Haider
Hi Jorge,

please do

tail -f dist/logs/stdouterr.2011_02_09.log

and see what appears when you run this query, send me the contents,

Thanks
Syed

On 09/02/2011 10:46, Jorge Zamora wrote:

> Hello,
>
> I'm experiencing that queries in the Quick Interface work but when I
> query using the other two interfaces the query seems to run forever.
> This happens when in query my local mart but not when I use other ICGC
> marts.
>
> This a example of one of the queries that never finish:
>
>
> <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query client=""
> processor="TSV" limit="-1" header="1"><Dataset name="snp_cnioCLL"
> config="snp_3_1_1"><Attribute name="cancertype"/><Attribute
> name="chromosome"/><Attribute
> name="simple_somatic_mutation__dm_mutation_id"/><Attribute
> name="donor_id"/></Dataset></Query>
>
>
> anybody experiencing something similar? I'm using biomart 0.8 rc4
>
> Thanks
> Jorge
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC mart, queries never get to finish

Syed Haider
In reply to this post by Jorge Zamora-2
Hi Jorge,

We have managed to fix this and the patch should become available tomorrow.

Best,
Syed

On 09/02/2011 10:46, Jorge Zamora wrote:

> Hello,
>
> I'm experiencing that queries in the Quick Interface work but when I
> query using the other two interfaces the query seems to run forever.
> This happens when in query my local mart but not when I use other ICGC
> marts.
>
> This a example of one of the queries that never finish:
>
>
> <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query client=""
> processor="TSV" limit="-1" header="1"><Dataset name="snp_cnioCLL"
> config="snp_3_1_1"><Attribute name="cancertype"/><Attribute
> name="chromosome"/><Attribute
> name="simple_somatic_mutation__dm_mutation_id"/><Attribute
> name="donor_id"/></Dataset></Query>
>
>
> anybody experiencing something similar? I'm using biomart 0.8 rc4
>
> Thanks
> Jorge
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC mart, queries never get to finish

Syed Haider
Hi Jorge,

the patch is now available, please svn update your code, followed by ant.

You would need to start from icgc3 xml again and add your dataset.

Let us know how you get on with this,

thanks for your patience,
Syed

On 09/02/2011 22:59, Syed Haider wrote:

> Hi Jorge,
>
> We have managed to fix this and the patch should become available tomorrow.
>
> Best,
> Syed
>
> On 09/02/2011 10:46, Jorge Zamora wrote:
>> Hello,
>>
>> I'm experiencing that queries in the Quick Interface work but when I
>> query using the other two interfaces the query seems to run forever.
>> This happens when in query my local mart but not when I use other ICGC
>> marts.
>>
>> This a example of one of the queries that never finish:
>>
>>
>> <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query client=""
>> processor="TSV" limit="-1" header="1"><Dataset name="snp_cnioCLL"
>> config="snp_3_1_1"><Attribute name="cancertype"/><Attribute
>> name="chromosome"/><Attribute
>> name="simple_somatic_mutation__dm_mutation_id"/><Attribute
>> name="donor_id"/></Dataset></Query>
>>
>>
>> anybody experiencing something similar? I'm using biomart 0.8 rc4
>>
>> Thanks
>> Jorge
>>
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC mart, queries never get to finish

Jorge Zamora Berna
Hi Syed,

Thanks a lot for the patch!

If I understood it right I'll to configure the icgc3.xml from scratch, isn't it?

Jorge



--- El jue, 10/2/11, Syed Haider <[hidden email]> escribió:

> De: Syed Haider <[hidden email]>
> Asunto: Re: [BioMart Users] ICGC mart, queries never get to finish
> Para: "Jorge Zamora" <[hidden email]>
> CC: "[hidden email]" <[hidden email]>
> Fecha: jueves, 10 de febrero, 2011 22:07
> Hi Jorge,
>
> the patch is now available, please svn update your code,
> followed by ant.
>
> You would need to start from icgc3 xml again and add your
> dataset.
>
> Let us know how you get on with this,
>
> thanks for your patience,
> Syed
>
> On 09/02/2011 22:59, Syed Haider wrote:
> > Hi Jorge,
> >
> > We have managed to fix this and the patch should
> become available tomorrow.
> >
> > Best,
> > Syed
> >
> > On 09/02/2011 10:46, Jorge Zamora wrote:
> >> Hello,
> >>
> >> I'm experiencing that queries in the Quick
> Interface work but when I
> >> query using the other two interfaces the query
> seems to run forever.
> >> This happens when in query my local mart but not
> when I use other ICGC
> >> marts.
> >>
> >> This a example of one of the queries that never
> finish:
> >>
> >>
> >> <?xml version="1.0"
> encoding="UTF-8"?><!DOCTYPE Query><Query
> client=""
> >> processor="TSV" limit="-1"
> header="1"><Dataset name="snp_cnioCLL"
> >> config="snp_3_1_1"><Attribute
> name="cancertype"/><Attribute
> >> name="chromosome"/><Attribute
> >>
> name="simple_somatic_mutation__dm_mutation_id"/><Attribute
> >>
> name="donor_id"/></Dataset></Query>
> >>
> >>
> >> anybody experiencing something similar? I'm using
> biomart 0.8 rc4
> >>
> >> Thanks
> >> Jorge
> >>
> >> **NOTA DE CONFIDENCIALIDAD** Este correo
> electrónico, y en su caso los ficheros adjuntos, pueden
> contener información protegida para el uso exclusivo de su
> destinatario. Se prohíbe la distribución, reproducción o
> cualquier otro tipo de transmisión por parte de otra
> persona que no sea el destinatario. Si usted recibe por
> error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> >> **CONFIDENTIALITY NOTICE** This email
> communication and any attachments may contain confidential
> and privileged information for the sole use of the
> designated recipient named above. Distribution, reproduction
> or any other use of this transmission by any party other
> than the intended recipient is prohibited. If you are not
> the intended recipient please contact the sender and delete
> all copies.
> >>
> >> _______________________________________________
> >> Users mailing list
> >> [hidden email]
> >> https://lists.biomart.org/mailman/listinfo/users
> > _______________________________________________
> > Users mailing list
> > [hidden email]
> > https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>


     
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC mart, queries never get to finish

Syed Haider
Correct Jorge, you will recoonfigure only your dataset specific
properties again.

Syed

On 11/02/2011 07:28, Jorge Zamora Berna wrote:

> Hi Syed,
>
> Thanks a lot for the patch!
>
> If I understood it right I'll to configure the icgc3.xml from scratch, isn't it?
>
> Jorge
>
>
>
> --- El jue, 10/2/11, Syed Haider<[hidden email]>  escribió:
>
>> De: Syed Haider<[hidden email]>
>> Asunto: Re: [BioMart Users] ICGC mart, queries never get to finish
>> Para: "Jorge Zamora"<[hidden email]>
>> CC: "[hidden email]"<[hidden email]>
>> Fecha: jueves, 10 de febrero, 2011 22:07
>> Hi Jorge,
>>
>> the patch is now available, please svn update your code,
>> followed by ant.
>>
>> You would need to start from icgc3 xml again and add your
>> dataset.
>>
>> Let us know how you get on with this,
>>
>> thanks for your patience,
>> Syed
>>
>> On 09/02/2011 22:59, Syed Haider wrote:
>>> Hi Jorge,
>>>
>>> We have managed to fix this and the patch should
>> become available tomorrow.
>>>
>>> Best,
>>> Syed
>>>
>>> On 09/02/2011 10:46, Jorge Zamora wrote:
>>>> Hello,
>>>>
>>>> I'm experiencing that queries in the Quick
>> Interface work but when I
>>>> query using the other two interfaces the query
>> seems to run forever.
>>>> This happens when in query my local mart but not
>> when I use other ICGC
>>>> marts.
>>>>
>>>> This a example of one of the queries that never
>> finish:
>>>>
>>>>
>>>> <?xml version="1.0"
>> encoding="UTF-8"?><!DOCTYPE Query><Query
>> client=""
>>>> processor="TSV" limit="-1"
>> header="1"><Dataset name="snp_cnioCLL"
>>>> config="snp_3_1_1"><Attribute
>> name="cancertype"/><Attribute
>>>> name="chromosome"/><Attribute
>>>>
>> name="simple_somatic_mutation__dm_mutation_id"/><Attribute
>>>>
>> name="donor_id"/></Dataset></Query>
>>>>
>>>>
>>>> anybody experiencing something similar? I'm using
>> biomart 0.8 rc4
>>>>
>>>> Thanks
>>>> Jorge
>>>>
>>>> **NOTA DE CONFIDENCIALIDAD** Este correo
>> electrónico, y en su caso los ficheros adjuntos, pueden
>> contener información protegida para el uso exclusivo de su
>> destinatario. Se prohíbe la distribución, reproducción o
>> cualquier otro tipo de transmisión por parte de otra
>> persona que no sea el destinatario. Si usted recibe por
>> error este correo, se ruega comunicarlo al remitente y
>> borrar el mensaje recibido.
>>>> **CONFIDENTIALITY NOTICE** This email
>> communication and any attachments may contain confidential
>> and privileged information for the sole use of the
>> designated recipient named above. Distribution, reproduction
>> or any other use of this transmission by any party other
>> than the intended recipient is prohibited. If you are not
>> the intended recipient please contact the sender and delete
>> all copies.
>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users