[DAS2] Trellis/Ivy: DAS1 --> DAS2 transformational proxy

Tue Oct 28 18:58:54 UTC 2008

Yes, I was actually thinking of the HapMap DAS/2 server as one potential
project.  I'd definitely be interested in helping!

In the Trellis source code there's a Trellis DAS/2 data model API in package
genomancer.trellis.das2.model.  These Java interfaces are based on a UML
model -- I'll try to post the UML later today.  Plugins for particular data
backends need to implement the
genomancer.trellis.das2.server.TrellisSourcesPluginI interface, which in
turn relies on the plugin having implementations of the DAS/2 data model.
Trellis is a Java servlet, and you configure Trellis to use a plugin by
setting the TrellisDas2Servlet "sources_plugin_class" init-param, either
programatically or via configuration in the web application deployment
descriptor.

Currently there are two Trellis-based servers in the genomancer source code,
a DAS2-->DAS2 proxy (genomancer.vine.das2.proxy.JettyDas2ProxyServer) and a
DAS1-->DAS2 proxy (genomancer.ivy.das2.proxy.JettyDas1ProxyServer).  Both of
these use Jetty for the HTTP server and servlet container, and have the
plugin hardcoded as well as a hardcoded localhost address and port.  I plan
to have more general examples using Tomcat and standard web app deployment
descriptors by the end of the week.

For my implementations of the Trellis DAS/2 data model, many of the classes
are really data structs with little or no behavior, and just setter/getter
methods.  If you don't want to reimplement the whole data model for these
data-struct classes you should be able to reuse the implementations in the
Vine DAS2 proxy plugin (genomancer.vine.das2.client.modelimpl).  It's the
higher-level parts of the model (particularly the Das2***CapabilityI
interfaces) that will likely need custom implementations for each plugin.

      Gregg

On Tue, Oct 28, 2008 at 11:18 AM, Brian Gilman <
gilmanb at pantherinformatics.com> wrote:

> Greg,
>
>        Can I use the DAS2 server framework to write the Haploview service?
>
> -B
> --
> Brian Gilman
> President Panther Informatics Inc.
> E-Mail: gilmanb at pantherinformatics.com
>        gilmanb at jforge.net
> AIM: gilmanb1
>
> <a href="www.scilink.com/people/gilmanb"><img src="
> http://www.scilink.com/images/buttons/scilink_viewmy_black.png"/></a>
>
>
> On Oct 28, 2008, at 2:02 PM, Gregg Helt wrote:
>
>  I'm pleased to announce I've got a DAS1 to DAS2 transformational proxy
>> working.  I'm calling it Trellis/Ivy.  Trellis is the overall DAS2 server
>> framework, and Ivy is the DAS1 proxy plugin.  The source code is available
>> via SVN at http://code.google.com/p/genomancer/ .  This should definitely
>> be
>> considered a beta release, there are plenty of features that aren't yet
>> implemented and I'm sure still some bugs in what is implemented.
>>
>> I'm hoping a stable version of this can eventually be set up close to or
>> integrated with the DAS1 registry.  For current testing I've deployed an
>> instance of Trellis/Ivy at genomancer.org in the Amazon EC2 cloud.  It's
>> hardwired to proxy for the Sanger DAS1
>> registry<http://www.dasregistry.org/das1/sources>.
>>
>> Some example DAS2 queries and the DAS1 queries they proxy for:
>>
>> All DAS1 registry sources:
>> http://www.dasregistry.org/das1/sources
>> All DAS1 registry sources --> DAS1+2 sources
>> http://www.genomancer.org/das2/das1_proxy/sources
>>
>> DAS1 filtered sources
>> http://www.dasregistry.org/das1/sources?type=Chromosome&capability=types
>> DAS1 filtered sources --> DAS1+2 filtered sources
>>
>> http://www.genomancer.org/das2/das1_proxy/sources?type=Chromosome&capability=types
>>
>> Ensembl DAS1 entry points
>> http://www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points
>> Ensembl DAS1 entry points --> DAS2 segments
>>
>> http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points
>>
>> Uniprot DAS1 types
>> http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types
>> Uniprot DAS1 types --> DAS2 types:
>>
>> http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types
>>
>> Uniprot DAS1 features (from UniProt DAS home page example)
>> http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502
>> UniProt DAS1 features --> DAS2 features
>>
>> http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502
>>
>> Ensembl DAS1 features (from Ensembl DAS home page example)
>>
>> http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13:31787617,31871806
>> Ensembl DAS1 features --> DAS2 features
>>
>> http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13;overlaps=31787616:31871806
>>
>> UCSC-Gencode segment/overlap/type-filtered, URL-encoded, DAS2 feature
>> request (copied from IGB testing):
>>
>> http://www.genomancer.org/das2/das1_proxy/hgwdev-gencode.cse.ucsc.edu/cgi-bin/das/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2F21;overlaps=26014828%3A26071595;type=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2FknownGene
>>
>>
>> Basic DAS1.53 query --> DAS2.0 conversions not yet implemented:
>>   DAS1 sequence --> DAS2 segments
>>   DAS1 dsn --> DAS2 sources
>>   DAS1 stylesheet --> DAS2 stylesheet
>> I'll post a summary of plans for these queries and other features soon,
>> but
>> I wanted to at least send out this announcement so people who are
>> interested
>> can check out the examples.  Please let me know what you think.
>>
>>   Gregg
>> _______________________________________________
>> DAS2 mailing list
>> DAS2 at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das2
>>
>>
>