[InterMine Dev] one-of constraint not working

Dr Intikhab Alam intikhab.alam at kaust.edu.sa
Wed Nov 21 13:06:55 GMT 2012


Dear Fengyuan,

Yes, we have this in our webconfig-model.xml file and these exporters are
placed just before the reportdisplayers.

What do you think whey we are getting .tsv output when we select fasta,
gff or bed formats. We don¹t see this on flymine website.

IA.



On 11/21/12 3:36 PM, "Fengyuan Hu" <fh293 at cam.ac.uk> wrote:

>Hi Intikhab,
>
>Do you have the following settings in your
>
>MINE/webapp/resources/WEB-INF/webconfig-model.xml
>
><!-- exporters -->
>   <tableExportConfig id="sequence"
>className="org.intermine.bio.web.export.SequenceHttpExporter"/>
>   <tableExportConfig id="gff3"
>className="org.intermine.bio.web.export.GFF3HttpExporter"/>
>   <tableExportConfig id="bed"
>className="org.intermine.bio.web.export.BEDHttpExporter"/>
>
>Cheers
>Fengyuan
>
>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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