[DAS] Fwd: Fwd: Problems with myDAS parameters
Andy Jenkinson
andy.jenkinson at ebi.ac.uk
Thu Jul 19 11:00:53 UTC 2012
But the features -do- have the type being filtered:
http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732
produces some features, including those with the "RNAi reagent" type
http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanReagentDatasource/features?segment=6:133119869,133155732;type=RNAi%20reagent
produces zero features
So it's a bug in the MyDas type filtering. Probably to due with the space encoding (MyDas should expect spaces to be encoded and decode them, because they are not valid URL characters). Just as it should encode non-XML characters in the response (such as angle brackets inside element cdata).
On 19 Jul 2012, at 11:35, Leyla Garcia 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
>>
>>
>>
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org <mailto:DAS at lists.open-bio.org>
>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
More information about the DAS
mailing list