[DAS] LDAS/DasClient problems

[Lincoln Stein]

Actually the tag will be capitalized as <ERRORSEGMENT> and it will require an 
id attribute equal to the requested reference segment.  The start and stop 
attributes will be present optionally, and only if they were specified in the 
request.

Lincoln

On Saturday 02 February 2002 04:55, Thomas Down wrote:
> 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=$t
> >ype #exon       =
> > http://stein.cshl.org/cgi-bin/test-cgi.pl/exon?name=$name;class=$class
> > #transcript =
> > http://stein.cshl.org/cgi-bin/test-cgi.pl/transcript?name=$name;class=$cl
> >ass #insertion  =
> > http://stein.cshl.org/cgi-bin/test-cgi.pl/insertion?name=$name;class=$cla
> >ss 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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> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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