[BioMart Users] fail to retrieve sample report ICGC mart

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[BioMart Users] fail to retrieve sample report ICGC mart

Jorge Zamora-2
Hello,

I trying to get a sample report using my local mart under biomart 0.8
rc4 (ICGC),  hoewer  I never get  to retrieve the report back. This how
my url look like:

http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&datasets=sample_no%20data


any idea why I don't get the report back?  (at least an empty one).

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.

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Re: [BioMart Users] fail to retrieve sample report ICGC mart

Syed Haider
Same for this one too, log file please.

thanks
Syed

On 09/02/2011 10:25, Jorge Zamora wrote:

> Hello,
>
> I trying to get a sample report using my local mart under biomart 0.8
> rc4 (ICGC),  hoewer  I never get  to retrieve the report back. This how
> my url look like:
>
> http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&datasets=sample_no%20data
>
>
> any idea why I don't get the report back?  (at least an empty one).
>
> 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
_______________________________________________
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[BioMart Users] FW: fail to retrieve sample report ICGC mart

Junjun Zhang
In reply to this post by Jorge Zamora-2
Forwarding the reply to the biomart list, it may be helpful for other users.


------ Forwarded Message
From: jzhang <[hidden email]>
Date: Wed, 9 Feb 2011 09:14:21 -0500
To: Syed Haider <[hidden email]>
Cc: <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart

This problem was the same as I was trying to explain yesterday. Url to
sample report needs a correct dataset name that is prepared in other view,
hence the sample dataset name is kept in other marts partition table and it
has to be matched properly.

Short solution is to allow users edit this partition column. When 'master'
partition table is in place this problem will be solved at software level,
no user needs to be involved.

Junjun

----- Original Message -----
From: Syed Haider
Sent: Wednesday, February 09, 2011 09:08 AM
To: Junjun Zhang
Cc: '[hidden email]' <[hidden email]>
Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart

Jorge has already shared the logs with me locally


On 09/02/2011 14:01, Junjun Zhang wrote:

> Jorge, please remove password in the log before sending the log
>
> Junjun
>
> ----- Original Message -----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 07:10 AM
> To: Jorge Zamora<[hidden email]>
> Cc: [hidden email]<[hidden email]>
> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>
> Same for this one too, log file please.
>
> thanks
> Syed
>
> On 09/02/2011 10:25, Jorge Zamora wrote:
>> Hello,
>>
>> I trying to get a sample report using my local mart under biomart 0.8
>> rc4 (ICGC),  hoewer  I never get  to retrieve the report back. This how
>> my url look like:
>>
>>
http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&
datasets=sample_no%20data
>>
>>
>> any idea why I don't get the report back?  (at least an empty one).
>>
>> 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

------ End of Forwarded Message

_______________________________________________
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Re: [BioMart Users] FW: fail to retrieve sample report ICGC mart

Jorge Zamora-2
Hi Junjun,

will you show us how to make that fix?

Thanks,
Jorge

Junjun Zhang wrote:

> Forwarding the reply to the biomart list, it may be helpful for other users.
>
>
> ------ Forwarded Message
> From: jzhang <[hidden email]>
> Date: Wed, 9 Feb 2011 09:14:21 -0500
> To: Syed Haider <[hidden email]>
> Cc: <[hidden email]>, Arek Kasprzyk <[hidden email]>
> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>
> This problem was the same as I was trying to explain yesterday. Url to
> sample report needs a correct dataset name that is prepared in other view,
> hence the sample dataset name is kept in other marts partition table and it
> has to be matched properly.
>
> Short solution is to allow users edit this partition column. When 'master'
> partition table is in place this problem will be solved at software level,
> no user needs to be involved.
>
> Junjun
>
> ----- Original Message -----
> From: Syed Haider
> Sent: Wednesday, February 09, 2011 09:08 AM
> To: Junjun Zhang
> Cc: '[hidden email]' <[hidden email]>
> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>
> Jorge has already shared the logs with me locally
>
>
> On 09/02/2011 14:01, Junjun Zhang wrote:
>  
>> Jorge, please remove password in the log before sending the log
>>
>> Junjun
>>
>> ----- Original Message -----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 07:10 AM
>> To: Jorge Zamora<[hidden email]>
>> Cc: [hidden email]<[hidden email]>
>> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>>
>> Same for this one too, log file please.
>>
>> thanks
>> Syed
>>
>> On 09/02/2011 10:25, Jorge Zamora wrote:
>>    
>>> Hello,
>>>
>>> I trying to get a sample report using my local mart under biomart 0.8
>>> rc4 (ICGC),  hoewer  I never get  to retrieve the report back. This how
>>> my url look like:
>>>
>>>
>>>      
> http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&
> datasets=sample_no%20data
>  
>>> any idea why I don't get the report back?  (at least an empty one).
>>>
>>> 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
>>    
>
> ------ End of Forwarded Message
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>  


**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.

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Re: [BioMart Users] FW: fail to retrieve sample report ICGC mart

Junjun Zhang
Re: [BioMart Users] FW:  fail to retrieve sample report ICGC mart Hi Jorge,

For the views (eg, Simple mutation, Copy number variation etc) where there is a link to the sample report, such as the one you are having problem, there is a pseudo attribute named ‘dataset’, it should be under a hidden container named ‘helper_attributes’ (as shown in the attached screenshot). After you localized it, select it, then double-click ‘(p0c16)’ (close to the bottom of the screenshot). This will bring up a window where you can put in the value of dataset. First find the entry of your own dataset (snp_cnioCLL?), then in the third column you can type in ‘cinoCLL’. This is assuming your datasets are named as *_cnioCLL, for examples, snp_cnioCLL, sample_cnioCLL, cnv_cnioCLL etc.

Let me know if this works.

Best,
Junjun




On 11-02-09 11:33 AM, "Jorge Zamora" <jazamora@...> wrote:

Hi Junjun,

will you show us how to make that fix?

Thanks,
Jorge

Junjun Zhang wrote:
> Forwarding the reply to the biomart list, it may be helpful for other users.
>
>
> ------ Forwarded Message
> From: jzhang <junjun.zhang@...>
> Date: Wed, 9 Feb 2011 09:14:21 -0500
> To: Syed Haider <syed.haider@...>
> Cc: <jazamora@...>, Arek Kasprzyk <Arek.Kasprzyk@...>
> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>
> This problem was the same as I was trying to explain yesterday. Url to
> sample report needs a correct dataset name that is prepared in other view,
> hence the sample dataset name is kept in other marts partition table and it
> has to be matched properly.
>
> Short solution is to allow users edit this partition column. When 'master'
> partition table is in place this problem will be solved at software level,
> no user needs to be involved.
>
> Junjun
>
> ----- Original Message -----
> From: Syed Haider
> Sent: Wednesday, February 09, 2011 09:08 AM
> To: Junjun Zhang
> Cc: 'jazamora@...' <jazamora@...>
> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>
> Jorge has already shared the logs with me locally
>
>
> On 09/02/2011 14:01, Junjun Zhang wrote:
>  
>> Jorge, please remove password in the log before sending the log
>>
>> Junjun
>>
>> ----- Original Message -----
>> From: Syed Haider [[hidden email]]
>> Sent: Wednesday, February 09, 2011 07:10 AM
>> To: Jorge Zamora<jazamora@...>
>> Cc: users@...<users@biomart.org>
>> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>>
>> Same for this one too, log file please.
>>
>> thanks
>> Syed
>>
>> On 09/02/2011 10:25, Jorge Zamora wrote:
>>    
>>> Hello,
>>>
>>> I trying to get a sample report using my local mart under biomart 0.8
>>> rc4 (ICGC),  hoewer  I never get  to retrieve the report back. This how
>>> my url look like:
>>>
>>>
>>>      
> http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&
> datasets=sample_no%20data
>  
>>> any idea why I don't get the report back?  (at least an empty one).
>>>
>>> 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
>>> Users@...
>>> https://lists.biomart.org/mailman/listinfo/users
>>>      
>> _______________________________________________
>> Users mailing list
>> Users@...
>> https://lists.biomart.org/mailman/listinfo/users
>>    
>
> ------ End of Forwarded Message
>
> _______________________________________________
> Users mailing list
> Users@...
> https://lists.biomart.org/mailman/listinfo/users
>  


**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.



_______________________________________________
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datasetPseudoAttr.png (60K) Download Attachment
editTheValueOfDatasetPseudo.png (79K) Download Attachment
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Re: [BioMart Users] FW: fail to retrieve sample report ICGC mart

Jorge Zamora-2
Hi Junjun,

It worked fine!

Thanks a lot,
Jorge

Junjun Zhang wrote:

> Hi Jorge,
>
> For the views (eg, Simple mutation, Copy number variation etc) where
> there is a link to the sample report, such as the one you are having
> problem, there is a pseudo attribute named ‘dataset’, it should be
> under a hidden container named ‘helper_attributes’ (as shown in the
> attached screenshot). After you localized it, select it, then
> double-click ‘(p0c16)’ (close to the bottom of the screenshot). This
> will bring up a window where you can put in the value of dataset.
> First find the entry of your own dataset (snp_cnioCLL?), then in the
> third column you can type in ‘cinoCLL’. This is assuming your datasets
> are named as *_cnioCLL, for examples, snp_cnioCLL, sample_cnioCLL,
> cnv_cnioCLL etc.
>
> Let me know if this works.
>
> Best,
> Junjun
>
>
>
>
> On 11-02-09 11:33 AM, "Jorge Zamora" <[hidden email]> wrote:
>
>     Hi Junjun,
>
>     will you show us how to make that fix?
>
>     Thanks,
>     Jorge
>
>     Junjun Zhang wrote:
>     > Forwarding the reply to the biomart list, it may be helpful for
>     other users.
>     >
>     >
>     > ------ Forwarded Message
>     > From: jzhang <[hidden email]>
>     > Date: Wed, 9 Feb 2011 09:14:21 -0500
>     > To: Syed Haider <[hidden email]>
>     > Cc: <[hidden email]>, Arek Kasprzyk <[hidden email]>
>     > Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>     >
>     > This problem was the same as I was trying to explain yesterday.
>     Url to
>     > sample report needs a correct dataset name that is prepared in
>     other view,
>     > hence the sample dataset name is kept in other marts partition
>     table and it
>     > has to be matched properly.
>     >
>     > Short solution is to allow users edit this partition column. When
>     'master'
>     > partition table is in place this problem will be solved at
>     software level,
>     > no user needs to be involved.
>     >
>     > Junjun
>     >
>     > ----- Original Message -----
>     > From: Syed Haider
>     > Sent: Wednesday, February 09, 2011 09:08 AM
>     > To: Junjun Zhang
>     > Cc: '[hidden email] <%[hidden email]>' <[hidden email]>
>     > Subject: Re: [BioMart Users] fail to retrieve sample report ICGC mart
>     >
>     > Jorge has already shared the logs with me locally
>     >
>     >
>     > On 09/02/2011 14:01, Junjun Zhang wrote:
>     >
>     >> Jorge, please remove password in the log before sending the log
>     >>
>     >> Junjun
>     >>
>     >> ----- Original Message -----
>     >> From: Syed Haider [mailto:[hidden email]]
>     >> Sent: Wednesday, February 09, 2011 07:10 AM
>     >> To: Jorge Zamora<[hidden email]>
>     >> Cc: [hidden email]<users <[hidden email]%3Cusers>@biomart.org>
>     >> Subject: Re: [BioMart Users] fail to retrieve sample report ICGC
>     mart
>     >>
>     >> Same for this one too, log file please.
>     >>
>     >> thanks
>     >> Syed
>     >>
>     >> On 09/02/2011 10:25, Jorge Zamora wrote:
>     >>
>     >>> Hello,
>     >>>
>     >>> I trying to get a sample report using my local mart under
>     biomart 0.8
>     >>> rc4 (ICGC), hoewer I never get to retrieve the report back.
>     This how
>     >>> my url look like:
>     >>>
>     >>>
>     >>>
>     > http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&
>     <http://localhost:9000/martreport/?report=sample_report&mart=sample_2&donor_id=3&>
>     > datasets=sample_no%20data
>     >
>     >>> any idea why I don't get the report back? (at least an empty one).
>     >>>
>     >>> 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
>     >>
>     >
>     > ------ End of Forwarded Message
>     >
>     > _______________________________________________
>     > Users mailing list
>     > [hidden email]
>     > https://lists.biomart.org/mailman/listinfo/users
>     >
>
>
>     **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.
>
>


**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