Hi, Sorry for the slow response on this one - the help is much appreciated. :)
Here's the output from the logs for the three separate queries. It all looks
sensible to me...
Cheers,
Daz
----
KOMP-CSD Only:
2011/02/02 09:07:21 martservice:1016:WARN> RECEIVED QUERY:<?xml version="1.0"
encoding="UTF-8"?>
<!DOCTYPE Query>
<Query formatter="TSV" header="0" virtualSchemaName="default" count=""
uniqueRows="1" datasetConfigVersion="0.6">
<Dataset name="idcc_targ_rep" interface="default">
<Filter value="KOMP-CSD" name="pipeline"/>
<Attribute name="escell_clone"/>
</Dataset>
</Query>
2011/02/02 09:07:21 BioMart.QueryRunner:163:WARN> ATTRIBUTE: idcc_targ_rep
escell_clone main
2011/02/02 09:07:21 BioMart.QueryRunner:174:WARN> FILTER TABLE: idcc_targ_rep
pipeline main
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 200
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 200,200
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 400,400
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 800,800
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 1600,1600
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 3200,3200
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 6400,6400
2011/02/02 09:07:21 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 12800,12800
2011/02/02 09:07:22 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 25600,25600
2011/02/02 09:07:23 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'KOMP-CSD') LIMIT 51200,50000
----
EUCOMM Only:
2011/02/02 09:07:29 martservice:1016:WARN> RECEIVED QUERY:<?xml version="1.0"
encoding="UTF-8"?>
<!DOCTYPE Query>
<Query formatter="TSV" header="0" virtualSchemaName="default" count=""
uniqueRows="1" datasetConfigVersion="0.6">
<Dataset name="idcc_targ_rep" interface="default">
<Filter value="EUCOMM" name="pipeline"/>
<Attribute name="escell_clone"/>
</Dataset>
</Query>
2011/02/02 09:07:29 BioMart.QueryRunner:163:WARN> ATTRIBUTE: idcc_targ_rep
escell_clone main
2011/02/02 09:07:29 BioMart.QueryRunner:174:WARN> FILTER TABLE: idcc_targ_rep
pipeline main
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 200
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 200,200
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 400,400
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 800,800
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 1600,1600
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 3200,3200
2011/02/02 09:07:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 6400,6400
2011/02/02 09:07:30 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 12800,12800
2011/02/02 09:07:30 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 25600,25600
2011/02/02 09:07:31 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 51200,50000
2011/02/02 09:07:33 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 101200,50000
2011/02/02 09:07:34 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline = 'EUCOMM') LIMIT 117710,50000
----
Both projects together:
2011/02/02 08:59:14 martservice:1016:WARN> RECEIVED QUERY:<?xml version="1.0"
encoding="UTF-8"?>
<!DOCTYPE Query>
<Query formatter="TSV" header="0" virtualSchemaName="default" count=""
uniqueRows="1" datasetConfigVersion="0.6">
<Dataset name="idcc_targ_rep" interface="default">
<Filter value="KOMP-CSD,EUCOMM" name="pipeline"/>
<Attribute name="escell_clone"/>
</Dataset>
</Query>
2011/02/02 08:59:14 BioMart.QueryRunner:163:WARN> ATTRIBUTE: idcc_targ_rep
escell_clone main
2011/02/02 08:59:14 BioMart.QueryRunner:174:WARN> FILTER TABLE: idcc_targ_rep
pipeline main
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 200
2011/02/02 08:59:14 BioMart.Configuration.URLLocation:100:WARN> RESPONSE: 0.6
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 200,200
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 400,400
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 800,800
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 1600,1600
2011/02/02 08:59:14 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 3200,3200
2011/02/02 08:59:15 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 6400,6400
2011/02/02 08:59:15 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 12800,12800
2011/02/02 08:59:16 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 25600,25600
2011/02/02 08:59:17 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 51200,50000
2011/02/02 08:59:20 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 101200,50000
2011/02/02 08:59:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 151200,50000
2011/02/02 08:59:27 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 201200,50000
2011/02/02 08:59:29 BioMart.Dataset.TableSet:736:INFO> QUERY SQL: SELECT
main.escell_clone FROM ikmc_mart_alt.idcc_targ_rep__idcc_targ_rep__main main
WHERE (main.pipeline IN('KOMP-CSD','EUCOMM')) LIMIT 218452,50000
-----
On 2 Feb 2011, at 00:23, Syed Haider wrote:
> Hi Daz,
>
> Please turn on the logging in log file:
>
> conf/log4perl.conf
>
> by setting:
>
> log4perl.logger = DEBUG,Screen
>
> Please check if the SQL compilation is as per your expectation. That will
> give us more pointers as in how to debug it further.
>
> Best,
> Syed
>
> On 31/01/2011 11:19, Darren Oakley wrote:
>> Hi All,
>>
>> Hope you can help me with this one...
>>
>> I have a filter on one of our marts
>> (www.knockoutmouse.org<http://www.knockoutmouse.org/>, idcc_targ_rep
>> dataset) configured as a multi-select like so:
>>
>> ---
>> <FilterCollection displayName="Pipeline" internalName="pipeline">
>> <FilterDescription displayName="Pipeline" displayType="list"
>> field="pipeline" internalName="pipeline" key="id_1022_key"
>> legal_qualifiers="=" multipleValues="1" qualifier="=" style="menu"
>> tableConstraint="main" type="list">
>> <Option displayName="KOMP-CSD" internalName="KOMP-CSD"
>> isSelectable="true" value="KOMP-CSD"/>
>> <Option displayName="KOMP-Regeneron" internalName="KOMP-Regeneron"
>> isSelectable="true" value="KOMP-Regeneron"/>
>> <Option displayName="EUCOMM" internalName="EUCOMM"
>> isSelectable="true" value="EUCOMM"/>
>> <Option displayName="NorCOMM" internalName="NorCOMM"
>> isSelectable="true" value="NorCOMM"/>
>> <Option displayName="mirKO" internalName="mirKO" isSelectable="true"
>> value="mirKO"/>
>> </FilterDescription>
>> </FilterCollection>
>> ---
>>
>> But, it's producing unexpected results when you query for either of the
>> pipelines separately, or together...
>>
>> i.e. the following xml:
>>
>> ---
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName = "default" formatter = "CSV" header = "0"
>> uniqueRows = "1" count = "" datasetConfigVersion = "0.6">
>>
>> <Dataset name = "idcc_targ_rep" interface = "default">
>> <Filter name = "pipeline" value = "KOMP-CSD,EUCOMM"/>
>> <Attribute name = "escell_clone" />
>> </Dataset>
>> </Query>
>> ---
>>
>> retrieves 129816 rows of data, but when you do the different pipelines
>> separately, they do not add up to this number...
>>
>> KOMP-CSD on its own is 59440
>> EUCOMM on its own is 76076
>>
>> So, combined they give 135516 rows of results - 5700 more than the first
>> query!
>>
>> The attribute i'm selecting ('escell_clone') is unique for every row in the
>> database, so it's not that i'm getting duplicates for the separate queries.
>>
>> Any ideas as to why i'm getting this shortfall in the first query? Is there
>> something wrong with the way I set up the filter?
>>
>> Any help is much appreciated. :)
>>
>> Thanks,
>>
>> Daz
>>
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