[DAS] LDAS/DasClient problems

Mon, 4 Feb 2002 11:26:02 -0500 (EST)

I also recall this in out conversation. We also discussed a "segment
exception" which would be transmitted over SOAP. 

				-B

-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902

On Mon, 4 Feb 2002, Lincoln Stein wrote:

> 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 =
> > >
> > > __________________________________________________
> > > Do You Yahoo!?
> > > Great stuff seeking new owners in Yahoo! Auctions!
> > > http://auctions.yahoo.com
> > > _______________________________________________
> > > 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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