[DAS] LDAS/DasClient problems

[Thomas Down]

Hi...

Well, I think I can see why it's failing in das-client.jar.
It looks like the server is installed correctly, but it's
not quite implementing the DAS protocol the way I'd expect.
If you make a query for a segment which doesn't have any
annotation on, e.g.: 

  http:///zilla.lbl.gov/cgi-bin/das/test/types?segment=chr22

LDAS doesn't return any SEGMENT elements at all (according
to the specification, you'd expect an empty SEGMENT).
This is confusing the request-scheduler in DasClient.
I can put in a temporary fix for this, and I'll try to
get you a new version of DasClient early next week.

[Lincoln: this is basically the scenario I had in mind for
the segmentNotAnnotated response we were discussing in
Tucson.]

I don't know what the Ensembl browser is doing, though.

     Thomas.



On Fri, Feb 01, 2002 at 04:06:57PM -0800, Mr Dmitriy Ryaboy wrote:
> Hi everyone,
> I've been trying to set up a DAS annotation server at
> http://zilla.lbl.gov/cgi-bin/das , but I keep running
> into some problems..  I installed LDAS following
> Lincoln Stein's excellent instructions, and using
> slightly different test data (see below, along with
> the .conf file).  Ldasdump works, http query work.  
> When I try to view the annotation on Ensembl's
> DasClient, however, I get the following error:
> 
> org.biojava.bio.BioError: Assertion failure: types
> fetch hasn't happened yet
> 	at
> org.biojava.bio.program.das.DASFeatureSet.getTypesMap(DASFeatureSet.java:104)
> 
> followed by the stack trace.
> 
> When I try to view it via the ensembl browser using
> the "my data" option, it simply does not show up..
> 
> Any idea what could be happenning? Is it LDAS or
> DasClient acting up?
> 
> 
> Thanks for your help.
> 
> Dmitriy V Ryaboy
> 
> 
> 
> Data file:
> 
> [reference_points]
> 7	Chromosome	163792587
> 
> [annotations]
> Contig	Contig_num	noncoding	Zilla	7	71902664	71904609
> .	.	89.4	1	1949
> Contig	Contig_num	noncoding	Zilla	7	71904635	71906190
> .	.	88.8	1950	3545
> Contig	Contig_num	noncoding	Zilla	7	71906197	71906593
> .	.	91.5	3658	4052
> Contig	Contig_num	noncoding	Zilla	7	71906903	71908121
> .	.	88.4	4057	5209
> Contig	Contig_num	noncoding	Zilla	7	71909258	71910351
> .	.	90.1	5213	6321
> Contig	Contig_num	noncoding	Zilla	7	71911326	71913995
> .	.	88.2	6347	9034
> Contig	Contig_num	noncoding	Zilla	7	71914014	71914195
> .	.	81.7	9557	9757
> Contig	Contig_num	noncoding	Zilla	7	71914208	71914666
> .	.	92.2	10071	10529
> Contig	Contig_num	UTR	Zilla	7	71914667	71916753	.	.
> 90.5	10530	12649
> 
> #followed by more of the same
> 
> 
> 
> .conf file
> 
> [DATA SOURCE]
> description = Test annotations
> adaptor     = dbi::mysqlopt
> mapmaster   =
> http://servlet.sanger.ac.uk:8080/das/ensembl130
> database    = dastest
> fasta_files =
> user        = cgi
> passwd      =
> 
> [CATEGORIES]
> default       = structural
> translation   = stop ATG CDS 5'UTR 3'UTR
> misc_translated
> transcription = exon intron transcript tRNA mRNA ncRNA
> 5'Cap TSS 
> 		PolyA Splice5 Splice3 misc_transcribed
> variation     = insertion deletion substitution
> misc_variation
> structural    = Component clone primer_left
> primer_right oligo assembly_tag misc_structural
> similarity    = similarity NN NP PN PP misc_similarity
> misc_homology noncoding
> repeat        = microsatellite inverted tandom
> transposable_element LINE misc_repeat
> experimental  = knockout expression_tag microarrayed
> RNAi_result RNAi transgenic mutant misc_experimental
> 
> # information necessary for making links from das
> client to web site
> [LINKS]
> #default    =
> http://stein.cshl.org/cgi-bin/test-cgi.pl?name=$name;class=$class;type=$type
> #exon       =
> http://stein.cshl.org/cgi-bin/test-cgi.pl/exon?name=$name;class=$class
> #transcript =
> http://stein.cshl.org/cgi-bin/test-cgi.pl/transcript?name=$name;class=$class
> #insertion  =
> http://stein.cshl.org/cgi-bin/test-cgi.pl/insertion?name=$name;class=$class
> default     = http://zilla.lbl.gov
> exon 	    = http://zilla.lbl.gov
> UTR	    = http://www-gsd.lbl.gov
> noncoding   = http://pga.lbl.gov
> 
> # map annotation types
> [COMPONENTS]
> entry_points = Component:Chromosome Component:Link
> Component:Contig
> has_subparts = Component:Chromosome Component:Link
> has_superparts = Component:Link Component:Contig
> 
> # filters to include and/or exclude certain feature
> types
> [FILTER]
> include = 
> exclude =
> 
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