[DAS] MyDAS / DASRegistry and valid XML

[jwarren]

Hi Oliver

I've fixed the source in the trunk so it will always return xml…if you would like to update the server core code it should work.

For help and support with the DAS Registry email dasregistry at sanger.ac.uk which is on the home page or das-core at sanger.ac.uk, or write to this list like you have done (I'd advise writing to das-core and this list).

Let me know if any more problems.

Cheers

Jonathan.


On 31 Aug 2012, at 14:56, jwarren wrote:

> Hi
> 
> I think json may well be the problem. To fix this i.e. get rid of the json responses is easy I think, Looking at the mydas server core code the DasCommandManager has a load of if else statements as below for the different commands… remove these and the json code shouldn't be called ever….and problem solved. I can do this - but I no longer work on DAS and will have to pull back the projects etc. So if someone who has these builds working wants to remove the if else clauses it would be good and fixed. I've tried pulling the core from svn and loading it into netbeans but there seems to be something wrong with the pom as I get an unload able error for the server_core project?
> 
> 
> if (accepts != null && accepts.contains("json")) {
> 
> blah
> }else{
> 
> On 31 Aug 2012, at 13:27, Leyla Garcia wrote:
> 
>> Hi Oliver,
>> 
>> It seems that when no header is specified, MyDas indeed is responding with JSON by default, not sure if that is the case. The current JSON response in MyDAS does not correspond to the spec so it will be totally removed, we are working on it.
>> 
>> What response do you get when you manually try your URL's, JSON or XML? If it is XML, then the problem could be something in the Registry Validator.
>> 
>> We, in UniProt, had an issue with the Registry validator some months ago. I would suggest to also the help desk for the DAS Registry. Unfortunately, I do not know the URL, maybe someone else in the list? I tried the "Help" link in the Registry but it takes me to a complete different place.
>> 
>> Cheers,
>> 
>> Leyla
>> 
>> On 31/08/2012 12:48, Pelz, Oliver wrote:
>>> Dear Group,
>>> 
>>> I am currently trying to register my MyDAS sources with DASRegistry.
>>> 
>>> Since I had some problems with Dalliance, Leyla Garcia fixed some
>>> parameter filtering and URL encodings
>>> (http://www.mail-archive.com/das@lists.open-bio.org/msg00598.html) and
>>> made a new "Mydas 1.6.10-SNAPSHOT" which fixed my problems and which I am
>>> currently using .
>>> 
>>> 
>>> I used the validator on the site:
>>> http://www.dasregistry.org/validateServer.jsp because my sources had some
>>> errors when I tried to register them.
>>> If I try to validate my source:
>>> 
>>> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanPhenotypeDatasource
>>> 
>>> With the settings:
>>> 
>>> capabilities:  sources,stylesheet,features,types,entry-points  (I multi
>>> selected it, but you can test single ones as well)
>>> 
>>> And the segment id : 6:133119869,133155732
>>> 
>>> I get errors of that kind:
>>> 
>>> "RegReportErrorHandler.Fatal Line Number:1 column number:1 Content is not
>>> allowed in prolog. the document is NOT valid."
>>> 
>>> A quick google for "Content is not allowed in prolog." shows me that there
>>> mustn't be content before the <xml> tag when parsing xml.
>>> 
>>> If I look into my Chrome's network activities, I see that the XML response
>>> is valid for a DAS request to e.g.
>>> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanPhenotypeDatasource/e
>>> ntry_points
>>> 
>>> 
>>> But maybe the DASRegistry interprets the URL encoding as JSON ? If I do a :
>>> curl -O
>>> http://genomernai.de/DASGenomeRNAi/das/GenomeRNAiHumanPhenotypeDatasource/e
>>> ntry_points
>>> 
>>> I get a JSON response so maybe Mydas sends JSON and DASRegistry expects
>>> valid XML?
>>> 
>>> Thanks in advance for your help
>>> 
>>> Oliver
>>> 
>> 
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