[biomart-users] pointed marts does not allow "<,>,<=,>=" filters

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[biomart-users] pointed marts does not allow "<,>,<=,>=" filters

vladie7
Dear Admins,

Upon using BioMart I have encountered an issue where BioMarts greater/smaller than filters does not work when a pointed mart is used ( an seperated table in a MySQL database).
Instead BioMart uses equals, even when the qualifier is set to <= or >=. This does not occur in filters enforced on the "main" mart.
Is there a way to solve this issue without creating a materialized view of the combined tables ?

Thanks in Advance,
Volodimir

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Re: [biomart-users] pointed marts does not allow "<,>,<=,>=" filters

Arek Kasprzyk
Hi Volodimir,

just a quick question ... Did you verify the  issue by checking the actual SQL that is compiled in the logs?

a.

On 15 February 2016 at 15:43, Volodimir Olexiouk <[hidden email]> wrote:
Dear Admins,

Upon using BioMart I have encountered an issue where BioMarts greater/smaller than filters does not work when a pointed mart is used ( an seperated table in a MySQL database).
Instead BioMart uses equals, even when the qualifier is set to <= or >=. This does not occur in filters enforced on the "main" mart.
Is there a way to solve this issue without creating a materialized view of the combined tables ?

Thanks in Advance,
Volodimir

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Re: [biomart-users] pointed marts does not allow "<,>,<=,>=" filters

vladie7
Dear Kasprzyk,

Update on the issue:

It seems I managed to pinpoint the issue and found a temporary solution:

When martconfigurator stores filters in the XML file of pointed marts, it correctly specifies the qualifier at this level:

<filter rdf="" required="false" pointerinsource="" function="" name="ReSpin__psms_101" displayname="min number of PSMs" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="mouse" config="mouse_config" pointer="true" pointeddataset="(p0c18)" pointedfilter="ReSpin__psms_101" pointedmart="ReSpin" pointedconfig="ReSpin" hide="false" type="text" attribute="ReSpin__psms_101" spliton="" operation="or" datafile="" filterlist="" qualifier="&gt;=" refcontainer="" inusers="" dependson="" />

However there is another XML filter tag associated with pointed marts filter where the qualifier is neglected :
 <filter rdf="class:PRIDE_Respin;attribute:ReSpin__psms_101;rdf:PlainLiteral" required="" pointerinsource="" function="" name="ReSpin__psms_101" displayname="Psms 101" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="ReSpin" config="PRIDE_Respin" pointer="false" hide="false" type="" attribute="ReSpin__psms_101" spliton="" operation="" datafile="" filterlist="" qualifier="" refcontainer="" inusers="" dependson="" />

Manually adjusting the qualifier value solves the issue:

 <filter rdf="class:PRIDE_Respin;attribute:ReSpin__psms_101;rdf:PlainLiteral" required="" pointerinsource="" function="" name="ReSpin__psms_101" displayname="Psms 101" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="ReSpin" config="PRIDE_Respin" pointer="false" hide="false" type="" attribute="ReSpin__psms_101" spliton="" operation="" datafile="" filterlist="" qualifier="&gt;=" refcontainer="" inusers="" dependson="" />

Is it possible to update the source code to solve this issue ?

Thanks in advance
Volodimir Olexiouk


On 02/19/2016 10:56 AM, Arek Kasprzyk wrote:
Hi Volodimir,

just a quick question ... Did you verify the  issue by checking the actual SQL that is compiled in the logs?

a.

On 15 February 2016 at 15:43, Volodimir Olexiouk <[hidden email]> wrote:
Dear Admins,

Upon using BioMart I have encountered an issue where BioMarts greater/smaller than filters does not work when a pointed mart is used ( an seperated table in a MySQL database).
Instead BioMart uses equals, even when the qualifier is set to <= or >=. This does not occur in filters enforced on the "main" mart.
Is there a way to solve this issue without creating a materialized view of the combined tables ?

Thanks in Advance,
Volodimir
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Re: [biomart-users] pointed marts does not allow "<,>,<=,>=" filters

Arek Kasprzyk
Hi Volodimir,

Great work. thank you for the patch.

a.

On 19 February 2016 at 13:20, Volodimir Olexiouk <[hidden email]> wrote:
Dear Kasprzyk,

Update on the issue:

It seems I managed to pinpoint the issue and found a temporary solution:

When martconfigurator stores filters in the XML file of pointed marts, it correctly specifies the qualifier at this level:

<filter rdf="" required="false" pointerinsource="" function="" name="ReSpin__psms_101" displayname="min number of PSMs" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="mouse" config="mouse_config" pointer="true" pointeddataset="(p0c18)" pointedfilter="ReSpin__psms_101" pointedmart="ReSpin" pointedconfig="ReSpin" hide="false" type="text" attribute="ReSpin__psms_101" spliton="" operation="or" datafile="" filterlist="" qualifier="&gt;=" refcontainer="" inusers="" dependson="" />

However there is another XML filter tag associated with pointed marts filter where the qualifier is neglected :
 <filter rdf="class:PRIDE_Respin;attribute:ReSpin__psms_101;rdf:PlainLiteral" required="" pointerinsource="" function="" name="ReSpin__psms_101" displayname="Psms 101" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="ReSpin" config="PRIDE_Respin" pointer="false" hide="false" type="" attribute="ReSpin__psms_101" spliton="" operation="" datafile="" filterlist="" qualifier="" refcontainer="" inusers="" dependson="" />

Manually adjusting the qualifier value solves the issue:

 <filter rdf="class:PRIDE_Respin;attribute:ReSpin__psms_101;rdf:PlainLiteral" required="" pointerinsource="" function="" name="ReSpin__psms_101" displayname="Psms 101" internalname="ReSpin__psms_101" description="ReSpin__psms_101" mart="ReSpin" config="PRIDE_Respin" pointer="false" hide="false" type="" attribute="ReSpin__psms_101" spliton="" operation="" datafile="" filterlist="" qualifier="&gt;=" refcontainer="" inusers="" dependson="" />

Is it possible to update the source code to solve this issue ?

Thanks in advance
Volodimir Olexiouk



On 02/19/2016 10:56 AM, Arek Kasprzyk wrote:
Hi Volodimir,

just a quick question ... Did you verify the  issue by checking the actual SQL that is compiled in the logs?

a.

On 15 February 2016 at 15:43, Volodimir Olexiouk <[hidden email]> wrote:
Dear Admins,

Upon using BioMart I have encountered an issue where BioMarts greater/smaller than filters does not work when a pointed mart is used ( an seperated table in a MySQL database).
Instead BioMart uses equals, even when the qualifier is set to <= or >=. This does not occur in filters enforced on the "main" mart.
Is there a way to solve this issue without creating a materialized view of the combined tables ?

Thanks in Advance,
Volodimir
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