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 <[email protected]
<mailto:[email protected]>> 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
<[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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