[DAS] Fwd: Fwd: Problems with myDAS parameters
Leyla Garcia
ljgarcia at ebi.ac.uk
Thu Jul 19 10:56:56 UTC 2012
Ok, I understand now, I did not know that was the original query, I will
look into it but I cannot commit to a date yet. I will keep you post.
This could be an issue as well in some other datasources.
Cheers,
Leyla
On 19/07/2012 11:40, Thomas Down wrote:
> I think Oliver's original query was:
>
> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732;type=RNAi%20reagent;type=RNAi%20phenotype
>
> (i.e. two type filters, not one -- which, as per DAS spec should be
> treated as a logical OR). I would expect this query to return four
> features, but it isn't returning anything.
>
> Thomas.
>
> On Thu, Jul 19, 2012 at 11:35 AM, Leyla Garcia <ljgarcia at ebi.ac.uk
> <mailto:ljgarcia at ebi.ac.uk>> wrote:
>
> Hi all,
>
> I do not see any problem in the request or response handled by
> MyDas, nor in Dalliance as far as I can tell. MyDas is giving
> different results from those in Dalliance because no type filter
> has been added.
>
> If I request
> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732
> <http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732;type=RNAi%20phenotype>
> I get 4 features, regardless of the type.
>
> However, if I request
> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732;type=RNAi%20phenotype
> Then I get no features, same as Oliver says it happens in
> Dalliance, because the same type filter is being used and none of
> the features has "RNAi phenotype" type. By the way, the %20 was
> automatically added by the browser, originally I used a regular space.
>
> Oliver, does it solve your question? In both cases you are getting
> the same set of results, am I right?
>
> Leyla
>
>
> On 19/07/2012 11:23, Thomas Down wrote:
>> I've already been in contact with Oliver about this. It's
>> possible to supress Dalliance's tendency to generate type filters
>> by setting a default style in the stylesheet (if there's no
>> default style, Dalliance will use type filters to ensure that it
>> only fetches the features that it's actually going to render).
>>
>> However, as far as I can tell there's nothing wrong with the
>> query that's being issued in this case, so I'm wondering if there
>> might be a MyDAS-side issue which means no features are being
>> returned. My best guess is that the spaces in the type names
>> (which Dalliance is -- correctly as far as I can tell --
>> URL-encoding as "%20") are causing a problem somewhere, but I'm
>> not familiar enough with MyDAS to know how plausible this is.
>>
>> Thomas.
>>
>> On Thu, Jul 19, 2012 at 11:10 AM, Leyla Garcia
>> <ljgarcia at ebi.ac.uk <mailto:ljgarcia at ebi.ac.uk>> wrote:
>>
>> Hi all,
>>
>> I got this email from a MyDas user but his questions are
>> related to Dalliance and my experience there is limited.
>> Maybe someone else in the list could suggest something about
>> the problems he is facing?
>>
>> Cheers,
>>
>> ---------- Forwarded message ----------
>> From: *Pelz, Oliver* <o.pelz at dkfz-heidelberg.de
>> <mailto:o.pelz at dkfz-heidelberg.de>
>> <mailto:o.pelz at dkfz-heidelberg.de
>> <mailto:o.pelz at dkfz-heidelberg.de>>>
>> Date: Wed, Jul 18, 2012 at 1:40 PM
>> Subject: Problems with myDAS parameters
>> To: "philip.j.r.jones at gmail.com
>> <mailto:philip.j.r.jones at gmail.com>
>> <mailto:philip.j.r.jones at gmail.com
>> <mailto:philip.j.r.jones at gmail.com>>"
>> <philip.j.r.jones at gmail.com
>> <mailto:philip.j.r.jones at gmail.com>
>> <mailto:philip.j.r.jones at gmail.com
>> <mailto:philip.j.r.jones at gmail.com>>>,
>> "gustavoadolfo.salazar at gmail.com
>> <mailto:gustavoadolfo.salazar at gmail.com>
>> <mailto:gustavoadolfo.salazar at gmail.com
>> <mailto:gustavoadolfo.salazar at gmail.com>>"
>> <gustavoadolfo.salazar at gmail.com
>> <mailto:gustavoadolfo.salazar at gmail.com>
>> <mailto:gustavoadolfo.salazar at gmail.com
>> <mailto:gustavoadolfo.salazar at gmail.com>>>,
>> "leylajael at gmail.com <mailto:leylajael at gmail.com>
>> <mailto:leylajael at gmail.com <mailto:leylajael at gmail.com>>"
>> <leylajael at gmail.com <mailto:leylajael at gmail.com>
>> <mailto:leylajael at gmail.com <mailto:leylajael at gmail.com>>>,
>> "Schmidt, Esther" <e.schmidt at dkfz-heidelberg.de
>> <mailto:e.schmidt at dkfz-heidelberg.de>
>> <mailto:e.schmidt at dkfz-heidelberg.de
>> <mailto:e.schmidt at dkfz-heidelberg.de>>>
>>
>>
>> Dear you,
>>
>> First I want to say that I asked this questions in biodas
>> mailing list but did not get any reply so I am writing you.
>>
>> I am just setting up a simple DAS source using the MyDAS java
>> implementation but have problems with the type parameter.
>>
>> If I use a simple request:
>> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732
>> It works fine.
>>
>> The Dalliance GenomeBrowser 0.7.0pre4 adds the types parmaeter :
>>
>> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732;type=RNAi%20reagent;type=RNAi%20phenotype;
>>
>> This will filter out all results returning zero results.
>>
>> I have debugged my mydas code and the method
>>
>> public DasAnnotatedSegment getFeatures(String segmentId, int
>> start, int stop, Integer maxbins) in my
>> RangeHandlingAnnotationDataSource implementation returns the
>> results correctly.
>>
>> Somehow after this step the filtering out occurs which I
>> cannot influence.
>>
>> Is there a way to adjust this in my MyDAS java code or can I
>> disable type parameters in Dalliance?
>>
>> Thank you for your help
>> Oliver
>>
>>
>>
>>
>>
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>
>
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