[InterMine Dev] one-of constraint not working

Julie Sullivan julie at flymine.org
Wed Nov 21 13:35:40 GMT 2012



1. Do you get this same behaviour on the region search, eg. here:

	http://www.flymine.org/release-34.0/genomicRegionSearch.do

2. Do you get the same behaviour when you use web services?

GET 
http://squirrel.flymine.org/flymine/service/query/results/fasta?query=%3Cquery+name%3D%22%22+model%3D%22genomic%22+view%3D%22Gene.primaryIdentifier%22+sortOrder%3D%22Gene.primaryIdentifier+asc%22%3E%3Cconstraint+path%3D%22Gene%22+op%3D%22LOOKUP%22+value%3D%22eve%22+extraValue%3D%22%22%2F%3E%3C%2Fquery%3E&extension=1

3. Do you get the same behaviour when you click on a FASTA button on a gene 
report page:

http://www.flymine.org/release-34.0/sequenceExporter.do?object=103008969

On 21/11/12 12:32, Dr Intikhab Alam wrote:
>
> Dear Julie,
>
> We are on the master branch. Trying to update this again for some more
> tests.
>
> At present XML, tab,comma separated exporters are all working fine. Only
> Fasta, GFF and BED format not. When we select these formats and download
> the data, they all result in .tsv files with a single column of data.
>
> I kept 0.99 version of the release and populated the same data into
> redseamine, their all fasta,gff and other converters are working fine.
>
>
> Intikhab
>
>
>
>
> On 11/21/12 12:05 PM, "Julie Sullivan"<julie at flymine.org>  wrote:
>
>> No error messages? That's going to make it tricky to debug! Is your mine
>> publicly available? Maybe trying it ourselves would help.
>>
>> The live FlyMine is on old code. Our beta site is on the most recent and
>> it's
>> working fine:
>>
>>     http://beta.flymine.org
>>
>>   1. Are other exports working as expected? (eg. XML, JSON, BED)
>>
>> If they do work correctly, there may be an issue with how your sequence
>> data
>> looks and what the export expects.
>>
>> (Fengyuan, does the export depend on chromosomeLocation being filled in?
>> What
>> about Gene.length?)
>>
>>   2. Does the export fail for all objects you've tested?
>>   3. What does it say when you type `git branch` into your console?
>> Here's mine:
>>
>> ~/git/intermine $ git branch
>> * dev
>>    master
>>
>> You should be on the master branch.
>>
>> On 21/11/12 07:48, Dr Intikhab Alam wrote:
>>> Dear Julie,
>>>
>>> Regarding Fasta and GFF output, we could not locate any errors from the
>>> logs. On flymine website it is working correctly, it could be we are
>>> using
>>> a development or outdated code etc. What release you are using for
>>> flymine?
>>>
>>>
>>> Intikhab
>>>
>>>
>>> On 11/20/12 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>
>>>>> 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
>>>>>> 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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>>>>>
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>>>>>
>>>
>>>
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>
>
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