group_on = display_name causes exception in Bio::DB::Das::Chado::Segment

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group_on = display_name causes exception in Bio::DB::Das::Chado::Segment

Michael Dondrup-3
Hi,

I have imported cDNA alignments from GMAP into CHADO and display them as a GBrowse segments track, using Bio::DB::Das::Chado adaptor.
This works including balloon hover and links, as long as I do not enable
group_on = display_name. If I do, I get the Exception 1) pasted in below for hovering over feature "CL1320Contig1".  For another feature with the name
"zslaa0_015078.cl1.scf" I see exception 2). Though the segments are displayed correctly.

Could this be an indication of missing quoting  in the backend?


Best
Michael


1)

[Wed May 21 14:40:05 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr: i-bin/gbrowse2/gbrowse:35, referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1
[Wed May 21 14:40:05 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr: -----------------------------------------------------------, referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1
[Wed May 21 14:40:57 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr: DBD::Pg::st execute failed: ERROR:  column "cl1320contig1" does not exist, referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1
[Wed May 21 14:40:57 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr: LINE 4: where f.feature_id = CL1320Contig1 and fl.rank=0 , referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1
[Wed May 21 14:40:57 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr:                              ^ at /home/licebase/perl5/lib/perl5/Bio/DB/Das/Chado/Segment.pm line 1154., referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1

2)

[Wed May 21 14:58:56 2014] [warn] [client 129.177.118.245] mod_fcgid: stderr: DBD::Pg::st execute failed: ERROR:  schema "zslaa0_015078" does not exist at /home/licebase/perl5/lib/perl5/Bio/DB/Das/Chado/Segment.pm line 1154., referer: https://licebase.org/fgb2/gbrowse/lsalmonis/?name=LSalAtl2s1


Config stanzas:

[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn  'dbi:Pg:dbname=licebase;host=spinner'
                -user 'XYZ'
                -pass 'XYZ'
#                -srcfeatureslice 1
        -inferCDS 1
search options = all

[annotations:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn  'dbi:Pg:dbname=licebase;host=spinner'
                -user
                -pass
                -srcfeatureslice 1
        -inferCDS 1
search options = all




[CLs]
feature       = cDNA_match
glyph         = segments
height        = 20
bgcolor       = orange
group_on = display_name
category      = Genes
key           = Consensus clusters
balloon hover = sub {tooltip(shift)}
citation     = This track shows GMAP alignments of consensus clusters (CL) of the FN ESTs.
link = /fgb2/gbrowse_details/lsalmonis/?ref=$ref;start=$start;end=$end;name=$name;class=$class;feature_id=$id;db_id=annotations%3Adatabase
link_target = _blank





Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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