[InterMine Dev] one-of constraint not working

Allan Kamau kamauallan at gmail.com
Tue Nov 20 14:03:50 GMT 2012


Dear Julie,


As mentioned in the last email that we observe no results being returned
when we select multiple items from e.g. the summary table of an annotation
column, TargetOrganism in my case. Error logs show no errors.

A test shows that intermine trims the trailing white spaces in the values
while constructing postgres queries, but this only happens when multiple
items are selected for filtering from the summary popup of a column. This
in turn show no results.

Here is an example:

When we look at a list of genes with TargetOrganism column shown, we click
on the summary icon and select two organisms (you see in the statement
below). Clicking on the filter button gives the following error:

NO RESULTS This query returned 0 results.

While performing the above operation, we enable extended logging from
postgres and observed the postgres queries being executed. We tested those
queries ourselves and it seems like when we introduce a trailing space in
the name of the organism, it works otherwise not.

The following intermine issued query does not work:

SELECT COUNT(*) FROM (SELECT a1_.id AS a1_id, a1_.primaryIdentifier AS
orderbyfield1, a1_.symbol AS orderbyfield2, a1_.name AS orderbyfield3,
a1_.length AS orderbyfield4, a1_.TargetOrganism AS orderbyfield5 FROM Gene
AS a1_, osbag_int AS indirect0 WHERE a1_.id = indirect0.value AND
indirect0.bagid = 52000000 AND a1_.TargetOrganism IN ('Candidatus
Pelagibacter ubique HTCC1062', 'Nitrosopumilus maritimus SCM1') ORDER BY
a1_.primaryIdentifier, a1_.symbol, a1_.name, a1_.length,
a1_.TargetOrganism, a1_.id) as fake_table



but this one works (when we added trailing spaces to the TargetOrganism:


SELECT COUNT(*) FROM (SELECT a1_.id AS a1_id, a1_.primaryIdentifier AS
orderbyfield1, a1_.symbol AS orderbyfield2, a1_.name AS orderbyfield3,
a1_.length AS orderbyfield4, a1_.TargetOrganism AS orderbyfield5 FROM Gene
AS a1_, osbag_int AS indirect0 WHERE a1_.id = indirect0.value AND
indirect0.bagid = 52000000 AND a1_.TargetOrganism IN ('Candidatus
Pelagibacter ubique HTCC1062', 'Nitrosopumilus maritimus SCM1') ORDER BY
a1_.primaryIdentifier, a1_.symbol, a1_.name, a1_.length,
a1_.TargetOrganism, a1_.id) as fake_table




Can you check this on your end?


Many thanks,

Intikhab




On Tue, Nov 20, 2012 at 12:25 PM, Julie Sullivan <julie at flymine.org> wrote:

>
>
> On 20/11/12 08:00, Dr Intikhab Alam wrote:
>
>> Dear Dev at intermine,
>>
>> In this new release of intermine, when we click on e.g. An annotation
>> column summary graph it correctly shows the list of items and also gives
>> an option to filter the data by selecting an item in the summary popup
>> window. If we select more then one item in the summary popup list, it
>> fails to show any results.
>>
>
> Hi Intikhab,
>
> Sorry you are having problems! Can you tell me which JavaScript errors are
> appearing? You can view these in your browser's Error Console or you can
> install FireBug (what we use).
>
> We're not able to replicate this error and we can't see your webapp, so
> you'll have to walk us through what's happening!
>
>
>  Any help in this? Please also help us fixed the fasta and gff3 exporters.
>>
>
> Again, we can't replicate this error, so can you tell us what errors are
> in your log files?
>
> These files would be located where you started Tomcat:
>
>         $TOMCAT/*mine.log
>         $TOMCAT/logs/catalina.out
>         $TOMCAT/logs/localhost$DATE.**out
>
> These errors should tell us what's going wrong. Let us know what you find!
>
>
>  Many Thanks,
>>
>> Intikhab
>>
>>
>>
>>
>>
>>
>> On 11/19/12 7:18 PM, "Dr Intikhab Alam"<intikhab.alam at kaust.edu.**sa<intikhab.alam at kaust.edu.sa>>
>>  wrote:
>>
>>  Dear Dev at Intermine,
>>>
>>> We are running the latest release from flymine, 1.1. We reported
>>> previously that one-of constraint is not working. Julie update us that it
>>> has now been fixed. But it is still not working. Even at flymine website
>>> this shows now results e.g. the following query:
>>>
>>> <query name="" model="genomic" view="SequenceFeature.symbol
>>> SequenceFeature.name
>>> SequenceFeature.**primaryIdentifier
>>> SequenceFeature.**sequenceOntologyTerm.name<http://SequenceFeature.sequenceOntologyTerm.name>
>>> SequenceFeature.locations.**locatedOn.primaryIdentifier
>>> SequenceFeature.locations.**start SequenceFeature.locations.end
>>> SequenceFeature.locations.**strand SequenceFeature.organism.**shortName"
>>> longDescription="Return genome features that
>>> match a specified string. (ID, symbol, name, synonym) for the specified
>>> species." sortOrder="SequenceFeature.**symbol asc"
>>> constraintLogic="A and B"><constraint
>>> path="SequenceFeature.**organism.shortName" code="B" op="ONE
>>> OF"><value>H.
>>> sapiens</value><value>M. musculus</value></constraint><**constraint
>>> path="SequenceFeature" code="A" op="LOOKUP"
>>> value="Fgf4"/></query>
>>>
>>>
>>>
>>> Similarly there is no update on how to get the Fasta and GFF3 export
>>> working.
>>>
>>> Any help here, please.
>>>
>>> Intikhab
>>>
>>
>>
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