[InterMine Dev] one-of constraint not working

Fengyuan Hu fh293 at cam.ac.uk
Wed Nov 21 16:06:46 GMT 2012


Hi Intikhab,

Do you have the following settings in MINE/webapp/resources/web-model.xml?

<servlet>
   <servlet-name>gff3-query</servlet-name>
<servlet-class>org.intermine.bio.webservice.GFF3QueryServlet</servlet-class>
   <init-param>
      <param-name>debug</param-name>
      <param-value>true</param-value>
   </init-param>
</servlet>

<servlet-mapping>
   <servlet-name>gff3-query</servlet-name>
<url-pattern>/service/query/results/gff3</url-pattern>
</servlet-mapping>

<servlet>
   <servlet-name>gff3-lists</servlet-name>
<servlet-class>org.intermine.bio.webservice.GFF3ListServlet</servlet-class>
   <init-param>
      <param-name>debug</param-name>
      <param-value>true</param-value>
   </init-param>
</servlet>

<servlet-mapping>
   <servlet-name>gff3-lists</servlet-name>
<url-pattern>/service/list/results/gff3</url-pattern>
</servlet-mapping>

<servlet>
   <servlet-name>fasta-query</servlet-name>
<servlet-class>org.intermine.bio.webservice.FastaQueryServlet</servlet-class>
   <init-param>
      <param-name>debug</param-name>
      <param-value>true</param-value>
   </init-param>
</servlet>

<servlet-mapping>
   <servlet-name>fasta-query</servlet-name>
<url-pattern>/service/query/results/fasta</url-pattern>
</servlet-mapping>

<servlet>
   <servlet-name>bed-query</servlet-name>
<servlet-class>org.intermine.bio.webservice.BEDQueryServlet</servlet-class>
   <init-param>
      <param-name>debug</param-name>
      <param-value>true</param-value>
   </init-param>
</servlet>

<servlet-mapping>
   <servlet-name>bed-query</servlet-name>
<url-pattern>/service/query/results/bed</url-pattern>
</servlet-mapping>

Cheers
Fengyuan

On 21/11/12 13:35, Julie Sullivan wrote:
>
>
> 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
>>>>>>
>>>>>>
>>>>>> This message and its contents including attachments are intended
>>>>>> solely
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>>>>>> have received this message in error, please notify me immediately 
>>>>>> and
>>>>>> delete this message from your computer system. Any unauthorized 
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>>>>>> distribution is prohibited. Please consider the environment before
>>>>>> printing this email.
>>>>>>
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>>>>>>
>>>>
>>>>
>>>> This message and its contents including attachments are intended 
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>>>>
>>
>>
>> This message and its contents including attachments are intended 
>> solely for the original recipient. If you are not the intended 
>> recipient or have received this message in error, please notify me 
>> immediately and delete this message from your computer system. Any 
>> unauthorized use or distribution is prohibited. Please consider the 
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>>
>
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