[DAS] 1.53E validation errors

Jonathan Warren jw12 at sanger.ac.uk
Wed Sep 1 13:27:31 UTC 2010

Hi Dave

Thanks for the feedback!

I'll look into caching again on the validation - I've previously put  
in all the standard headers etc to prevent caching but maybe I have to  
resort to adding a unique parameter for each response as well to avoid  
caching. I've not really experienced any problems with caching  
recently myself.

With regards to DSN being invalid when stated in the sources document  
I agree it's a bit of a usability issue so I've now changed it so that  
the registry will not complain about this and tolerate it both for  
1.53E and 1.6E specifications. Putting DSN validation is on my todo  
list - but it's very little gain in my opinion as it's simple and not  
got much to validate (as apposed to the sources document) and is also  
completely super-seeded by the sources document. The registry and DAS  
in general is getting more and more dependent on a valid sources  
document (ensembl works much more smoothly with it to name one example  
and in the very near future people can register many sources at once  
using the sources document in the registry and the sources will be  
auto updating to show any changes in the server). So for this reason  
the sources document should be encouraged as much as possible over  
DSN. If others have a strong opinion about DSNs being listed by the  
registry in sources capabilities and validated then let me know and  
I'll bump it up my list of things to do.

On 27 Aug 2010, at 15:54, Andy Jenkinson wrote:

> There is some caching going on in the registry which I've never got  
> to the bottom of (HTTP caching is quite hard to debug!), but it  
> should sort itself out.
> Regarding the dsn thing, I don't think we ever really decided  
> whether it should be a valid capability to report in the sources  
> document, but it isn't in the registry's list and so newer versions  
> of 1.53E proserver don't report it. However, since "das1:sources" - 
> is- reported by servers in 1.6 and the DAS registry itself (because  
> the query_uri has a specific function), my personal view is that we  
> should allow reporting of dsn for 1.53 too. Jon?
> On 27 Aug 2010, at 15:07, Dave Messina wrote:
>> Hi everybody,
>> After receiving an automated notice that my DAS 1.53E servers are  
>> scheduled for deletion, I'm trying to bring them into compliance.  
>> I'm not sure exactly how to fix the validation issues, though, so  
>> I'm here to ask for help.
>> 1. sources
>> When validating my server, the DAS registry reports this error:
>> capability is stated for this server but is not valid or  
>> provided.validating http://das.sbc.su.se:9000//das/sources  
>> RegReportErrorHandler.Error Line Number:4 column number:467  
>> attribute "type" has a bad value. Possible values are:  
>> das1:alignment,das1:component,das1:cors,das1:dna,das1:entry_points,das1:error-segment,das1:feature-by-id,das1:features,das1:interaction,das1:maxbins,das1:sequence,das1:sources,das1:structure,das1:stylesheet,das1:supercomponent,das1:types,das1:unknown-feature,das1:unknown-segment
>> My DAS server does provide a sources response, including  
>> capabilities:
>> 	http://das.sbc.su.se:9000//das/sources
>> But I'm not sure why it's invalid.
>> The capability types my server returns are:
>> das1:dsn
>> das1:features
>> das1:stylesheet
>> das1:dsn isn't in the list possible values; is it no longer valid?
>> Otherwise, I wonder if this is because I'm running an ancient  
>> version of ProServer (v463).
>> 2. stylesheet
>> When validating, the registry reports this error:
>> capability was stated for this server but is either not present or  
>> valid.validating http://das.sbc.su.se:9000//das/hmmtop/stylesheet  
>> RegReportErrorHandler.Error Line Number:9 column number:17 tag name  
>> "FONT" is not allowed. Possible tag names are:  
>> RegReportErrorHandler.Error Line Number:18 column number:17 tag  
>> name "FONT" is not allowed. Possible tag names are:  
>> RegReportErrorHandler.Error Line Number:27 column number:17 tag  
>> name "FONT" is not allowed. Possible tag names are:  
>> <BGCOLOR>,<BUMP>,<HEIGHT>,<LABEL>,<LINEWIDTH> the document is NOT  
>> valid.
>> I've removed that tag from the stylesheet and verified that my  
>> server is no longer presenting it:
>> 	http://das.sbc.su.se:9000/das1/hmmtop/stylesheet
>> However, when I try to revalidate, the registry reports the same  
>> error.
>> Is there perhaps caching going on?
>> Thanks for any suggestions,
>> Dave
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314

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