[DAS] Fwd: Fwd: Problems with myDAS parameters

[Leyla Garcia]

Hi,

It was, as Andy suggested, something related to the URL encoding in MyDAS.

There is already a new version available at 
http://mydas.googlecode.com/svn/snapshot-repository/, 1.6.10-SNAPSHOT 
version. This new version supports URL decoding for the type, category, 
and feature_id parameters in the features command, and for the type 
option in types command.

@Oliver, thanks for bringing this up. If you spot something else, please 
let us know.

Cheers,

Leyla

On 19/07/2012 11:56, Leyla Garcia wrote:
> 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
>>>
>>>
>>>
>>>
>>>
>>>         _______________________________________________
>>>         DAS mailing list
>>>         DAS at lists.open-bio.org <mailto:DAS at lists.open-bio.org>
>>>         http://lists.open-bio.org/mailman/listinfo/das
>>>
>>>
>>
>>
>