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 <[email protected]
<mailto:[email protected]>> 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* <[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
Date: Wed, Jul 18, 2012 at 1:40 PM
Subject: Problems with myDAS parameters
To: "[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>" <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>,
"[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>"
<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>, "[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>" <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>, "Schmidt, Esther"
<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>
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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