Difference between revisions of "DAS1.6"

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(Distributed Annotation System (DAS) 1.6)
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'''Note: this is NOT the official version of the [http://biodas.org/documents/spec.html DAS specification].'''
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=Distributed Annotation System (DAS) 1.6=
  
=Distributed Annotation System (DAS) 1.6=
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[http://www.biodas.org/documents/spec-1.6.html DAS 1.6] is, as of 19th October 2010, the latest official version of the DAS specification.
  
This is a working document and a proposal for a reworked DAS specification which hopes to:
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It is the first official version published in several years, and aims to:
* clarify the existing DAS spec
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* clarify ambiguities in the previous DAS specification
 
* better reflect how DAS is being used in the community today
 
* better reflect how DAS is being used in the community today
 
* better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
 
* better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
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* migrate from the use of DTDs for describing the XML formats to RelaxNG
 
* migrate from the use of DTDs for describing the XML formats to RelaxNG
  
Note: the DAS specification is a technical document but with some effort should hopefully be readable and understandable by people without a deep understanding of broader technical issues and other system architectures. That is, it makes only basic assumptions.
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The DAS specification is a technical document but with some effort should hopefully be readable and understandable by people without a deep understanding of broader technical issues and other system architectures. That is, it makes only basic assumptions.
  
The specification has been written as a number of drafts:
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The specification was developed via progression through a number of drafts:
 
* [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2]
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* [http://www.ebi.ac.uk/~aj/1.6_draft6/documents/spec.html Draft 6]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft6/documents/spec.html Draft 6]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft7/documents/spec.html Draft 7]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft7/documents/spec.html Draft 7]
Last modified: 22nd September 2010
 
  
=(DAS) 1.6 Development and Tutorials=
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==Links==
==Dazzle Example Adaptor for 1.6 spec source compliant with the registry ==
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[[DAS 1.6 in Dazzle]]
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=DAS 1.6 Development and Tutorials=
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==Dazzle Example Adaptor==
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Below is an example adaptor plugin for the Dazzle DAS server. It follows the 1.6 spec and is compliant with the [[DasRegistry|DAS Registry]].
  
 
Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle
 
Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle

Revision as of 08:57, 19 October 2010

Distributed Annotation System (DAS) 1.6

DAS 1.6 is, as of 19th October 2010, the latest official version of the DAS specification.

It is the first official version published in several years, and aims to:

  • clarify ambiguities in the previous DAS specification
  • better reflect how DAS is being used in the community today
  • better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
  • ratify commands from the 1.53E spec
  • introduce some ideas inspired by DAS/2
  • formally introduce the DAS registry
  • migrate from the use of DTDs for describing the XML formats to RelaxNG

The DAS specification is a technical document but with some effort should hopefully be readable and understandable by people without a deep understanding of broader technical issues and other system architectures. That is, it makes only basic assumptions.

The specification was developed via progression through a number of drafts:

Links

DAS 1.6 in Dazzle

DAS 1.6 Development and Tutorials

Dazzle Example Adaptor

Below is an example adaptor plugin for the Dazzle DAS server. It follows the 1.6 spec and is compliant with the DAS Registry.

Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle See class org.biojava.servlets.dazzle.datasource.SimpleFile16ExampleSource for a datasource that conforms to the new 1.6 Spec.

<datasource id="test16genes" jclass="org.biojava.servlets.dazzle.datasource">
     <string name="name" value="16 File Test" />
     <string name="description" value="Data source for testing 1.6 heirachy structure" />
     <string name="version" value="1.0" /> 
     
     <string name="fileName" value="test16genes.txt" />

     <string name="stylesheet" value="test16.style" />
   </datasource>

Note: Older style adapters/datasources can be used in the new 16Dazzle and will be converted to the new 1.6 specification (you may need to add a allTypes method). However you will miss out on some of the advantages of the new spec if you update your source by this method rather than extending one of the new 16 classes.

The new Dazzle implements the single Data Source sources.xml request: blah/das/myDataSourceName. The current implementation relies on on a valid sources.xml document being available and then parses the appropriate section from this document in response to a request.

The das registry also now responds to these requests e.g. http://www.dasregistry.org/das/DS_109