[BioMart Users] soak test log interpretation. ICGC mart (biomart 0.8 rc4)

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[BioMart Users] soak test log interpretation. ICGC mart (biomart 0.8 rc4)

Jorge Zamora-2
Hello,

I'm going through the log obtained after running the  soak test.  This
is an chuck of text of what I see and some questions about it.

NO VALID ATTRIBUTES
    hsapiens_gene_ensembl_cnioCLL
        A: cancertype NOT TESTED (PSEUDO)
        A: assemblyversion NOT TESTED (PSEUDO)
        A: ensembl_gene_id NOT TESTED (PSEUDO)

What does mean 'NO VALID ATTRIBUTES'? Does it mean in this case that
'cancertype', 'assemblyversion', 'ensembl_gene_id' are not working
properly? I just ask this because it also says they are NOT  TESTED and
I wouldn't consider an attribute as not valid if it's not tested before.

Also I understand that 'A:' stands for 'Attribute', however I don't see
any 'F:' in the log reporting about Filters. Is this expected?

Finally, PSEUDO, is a PseudoAttribute and attribute hardcoded in the
configuration and therefore not testable?


Thanks,
Jorge



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Re: [BioMart Users] soak test log interpretation. ICGC mart (biomart 0.8 rc4)

Syed Haider
Jorge, a pseudo attribute is an attribute whereby the value is not
retrieved from underlying Source, it just has a hardcoded value in
configuration and is used for adding CONSTANT type values.


Syed


On 23/02/2011 15:30, Jorge Zamora wrote:

> Hello,
>
> I'm going through the log obtained after running the  soak test.  This
> is an chuck of text of what I see and some questions about it.
>
> NO VALID ATTRIBUTES
>      hsapiens_gene_ensembl_cnioCLL
>          A: cancertype NOT TESTED (PSEUDO)
>          A: assemblyversion NOT TESTED (PSEUDO)
>          A: ensembl_gene_id NOT TESTED (PSEUDO)
>
> What does mean 'NO VALID ATTRIBUTES'? Does it mean in this case that
> 'cancertype', 'assemblyversion', 'ensembl_gene_id' are not working
> properly? I just ask this because it also says they are NOT  TESTED and
> I wouldn't consider an attribute as not valid if it's not tested before.
>
> Also I understand that 'A:' stands for 'Attribute', however I don't see
> any 'F:' in the log reporting about Filters. Is this expected?
>
> Finally, PSEUDO, is a PseudoAttribute and attribute hardcoded in the
> configuration and therefore not testable?
>
>
> 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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Re: [BioMart Users] soak test log interpretation. ICGC mart (biomart 0.8 rc4)

Jorge Zamora-2
Hello Syed,

Then, what should I expect if a Filter/Attribute is not working?

Thanks,
Jorge

Syed Haider wrote:

> Jorge, a pseudo attribute is an attribute whereby the value is not
> retrieved from underlying Source, it just has a hardcoded value in
> configuration and is used for adding CONSTANT type values.
>
>
> Syed
>
>
> On 23/02/2011 15:30, Jorge Zamora wrote:
>> Hello,
>>
>> I'm going through the log obtained after running the  soak test.  This
>> is an chuck of text of what I see and some questions about it.
>>
>> NO VALID ATTRIBUTES
>>      hsapiens_gene_ensembl_cnioCLL
>>          A: cancertype NOT TESTED (PSEUDO)
>>          A: assemblyversion NOT TESTED (PSEUDO)
>>          A: ensembl_gene_id NOT TESTED (PSEUDO)
>>
>> What does mean 'NO VALID ATTRIBUTES'? Does it mean in this case that
>> 'cancertype', 'assemblyversion', 'ensembl_gene_id' are not working
>> properly? I just ask this because it also says they are NOT  TESTED and
>> I wouldn't consider an attribute as not valid if it's not tested before.
>>
>> Also I understand that 'A:' stands for 'Attribute', however I don't see
>> any 'F:' in the log reporting about Filters. Is this expected?
>>
>> Finally, PSEUDO, is a PseudoAttribute and attribute hardcoded in the
>> configuration and therefore not testable?
>>
>>
>> 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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Re: [BioMart Users] soak test log interpretation. ICGC mart (biomart 0.8 rc4)

Jonathan Guberman
If a Filter or Attribute is not working, it will print FAILED as well as the martservice URL that it tested that created the failure state. These URLs will also be reprinted to STDOUT at the end of the test run, along with the mart name, config name, and dataset name.

On 2011-02-23, at 10:38 AM, Jorge Zamora wrote:

> Hello Syed,
>
> Then, what should I expect if a Filter/Attribute is not working?
>
> Thanks,
> Jorge
>
> Syed Haider wrote:
>> Jorge, a pseudo attribute is an attribute whereby the value is not
>> retrieved from underlying Source, it just has a hardcoded value in
>> configuration and is used for adding CONSTANT type values.
>>
>>
>> Syed
>>
>>
>> On 23/02/2011 15:30, Jorge Zamora wrote:
>>> Hello,
>>>
>>> I'm going through the log obtained after running the  soak test.  This
>>> is an chuck of text of what I see and some questions about it.
>>>
>>> NO VALID ATTRIBUTES
>>>     hsapiens_gene_ensembl_cnioCLL
>>>         A: cancertype NOT TESTED (PSEUDO)
>>>         A: assemblyversion NOT TESTED (PSEUDO)
>>>         A: ensembl_gene_id NOT TESTED (PSEUDO)
>>>
>>> What does mean 'NO VALID ATTRIBUTES'? Does it mean in this case that
>>> 'cancertype', 'assemblyversion', 'ensembl_gene_id' are not working
>>> properly? I just ask this because it also says they are NOT  TESTED and
>>> I wouldn't consider an attribute as not valid if it's not tested before.
>>>
>>> Also I understand that 'A:' stands for 'Attribute', however I don't see
>>> any 'F:' in the log reporting about Filters. Is this expected?
>>>
>>> Finally, PSEUDO, is a PseudoAttribute and attribute hardcoded in the
>>> configuration and therefore not testable?
>>>
>>>
>>> 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
>
>
> **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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Re: [BioMart Users] soak test log interpretation. ICGC mart(biomart 0.8 rc4)

Jorge Zamora-2
Thanks Jonathan!

Jorge

Jonathan Guberman wrote:

> If a Filter or Attribute is not working, it will print FAILED as well as the martservice URL that it tested that created the failure state. These URLs will also be reprinted to STDOUT at the end of the test run, along with the mart name, config name, and dataset name.
>
> On 2011-02-23, at 10:38 AM, Jorge Zamora wrote:
>
>  
>> Hello Syed,
>>
>> Then, what should I expect if a Filter/Attribute is not working?
>>
>> Thanks,
>> Jorge
>>
>> Syed Haider wrote:
>>    
>>> Jorge, a pseudo attribute is an attribute whereby the value is not
>>> retrieved from underlying Source, it just has a hardcoded value in
>>> configuration and is used for adding CONSTANT type values.
>>>
>>>
>>> Syed
>>>
>>>
>>> On 23/02/2011 15:30, Jorge Zamora wrote:
>>>      
>>>> Hello,
>>>>
>>>> I'm going through the log obtained after running the  soak test.  This
>>>> is an chuck of text of what I see and some questions about it.
>>>>
>>>> NO VALID ATTRIBUTES
>>>>     hsapiens_gene_ensembl_cnioCLL
>>>>         A: cancertype NOT TESTED (PSEUDO)
>>>>         A: assemblyversion NOT TESTED (PSEUDO)
>>>>         A: ensembl_gene_id NOT TESTED (PSEUDO)
>>>>
>>>> What does mean 'NO VALID ATTRIBUTES'? Does it mean in this case that
>>>> 'cancertype', 'assemblyversion', 'ensembl_gene_id' are not working
>>>> properly? I just ask this because it also says they are NOT  TESTED and
>>>> I wouldn't consider an attribute as not valid if it's not tested before.
>>>>
>>>> Also I understand that 'A:' stands for 'Attribute', however I don't see
>>>> any 'F:' in the log reporting about Filters. Is this expected?
>>>>
>>>> Finally, PSEUDO, is a PseudoAttribute and attribute hardcoded in the
>>>> configuration and therefore not testable?
>>>>
>>>>
>>>> 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
>>>>        
>> **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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