[DAS] LDAS/DasClient problems

[Lincoln Stein]

Thomas,

I'm fixing this now.  When we talked last week, I recall you wanted an 
<ErrorSegment> segment when a segment wasn't found, and an empty <Segment> 
section when the segment was unannotated.  Please confirm that I am 
remembering right.

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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