[GUSDEV] ISF errors when using some files

[<fab...@de...>]

Hello gus-devers and users,

I have the InsertSequenceFeatures plugin loading genbank files in my GUS
installation without problems. Even so, there is some files I tried to lo=
ad
with the same plugin and two specific errors were generated. I'll try to
explain a little about them.

The first case is when I'm loading a genbank file which contains a /db_xr=
ef
parameter and the value is a database that doesn't exist in
Sres.ExternalDatabase. For instance, in tvivax.gb (attached) that paramet=
er is
/db_xref=3D"InterPro:IPR000173". In my case, Interpro isn't in my
Sres.ExternalDatabse table. When I run ISF with this file, the plugin wil=
l try
to load Interpro in Sres.ExternalDatabase and, I think, the
external_database_id
value generated to do the insertion isn't check if already exist. So, the
following error appears:

DBD::Pg::st execute failed: ERROR:  duplicate key violates unique constra=
int
"pk_externaldatabase" at
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GE=
N12>
line 58.

ERROR:

SQL ERROR!! involving

INSERT INTO SRes.ExternalDatabase (  group_write, other_read, group_read,=
 name,
user_read, row_user_id, external_database_id, modification_date, other_wr=
ite,
row_alg_invocation_id, row_project_id, row_group_id, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
 Values: 1, 1, 1, InterPro, 1, 1, 3, 0, 92, 1, 1, 1

As I can see, external_database_id =3D 3. And in my Sres.ExternalDatabase=
 table
has a record with that pk value.

The second fault obtained was it:

ERROR:
In feature map XML file '../../config/genbank2gus.xml' <feature
name=3D"satellite"> does not havea <qualifier> for 'experiment', which is=
 found
in the input at
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line =
88,
<GEN12> line 84.

this happened when I tried to load tvivax1.gb (attached). For some other =
files
plugin worked fine. Maybe you have already known about those plugin behav=
iors.
I'm just reporting my experimentations.=20

Best regards,

Fabr=EDcio.

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