[GUSDEV] InsertSequenceOntologyOBO error ?

[davila <da...@io...>]

Hi folks,

With GUS 3.5 got from SVN, tryig to use the =
GUS::Supported::Plugin::InsertSequenceOntologyOBO plugin I got no rows =
inserted, see the log:

GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile =
so.definition --soCvsVersion '1.42' --soVersion
'1.419' --user user --group group --commit >so1.log

Sat May  5 11:41:22 2007        DSN     dbi:Pg:dbname=3Dmydb
Sat May  5 11:41:22 2007        PLUGIN
GUS::Supported::Plugin::InsertSequenceOntologyOBO
Sat May  5 11:41:22 2007        ARG     algoinvo        1
Sat May  5 11:41:22 2007        ARG     comment
Sat May  5 11:41:22 2007        ARG     commit  1
Sat May  5 11:41:22 2007        ARG     debug   0
Sat May  5 11:41:22 2007        ARG     group   dba
Sat May  5 11:41:22 2007        ARG     gusconfigfile =
$GUS_HOME/gus.config
Sat May  5 11:41:22 2007        ARG     help
Sat May  5 11:41:22 2007        ARG     helpHTML
Sat May  5 11:41:22 2007        ARG     inputFile so.definition
Sat May  5 11:41:22 2007        ARG     project
Sat May  5 11:41:22 2007        ARG     soCvsVersion    1.42
Sat May  5 11:41:22 2007        ARG     soVersion       1.419
Sat May  5 11:41:22 2007        ARG     sqlVerbose      0
Sat May  5 11:41:22 2007        ARG     user    dba
Sat May  5 11:41:22 2007        ARG     verbose 0
Sat May  5 11:41:22 2007        ARG     veryVerbose     0
Sat May  5 11:41:22 2007        AlgInvocationId 14
Sat May  5 11:41:22 2007        COMMIT  commit on
Sat May  5 11:41:22 2007        TIME    < 1 sec  (0:00:00)
Sat May  5 11:41:22 2007        RESULT  Inserted 0 terms into
SequenceOntology
Sat May  5 11:41:22 2007        Rows Written    N/A (plugin has no
'undoTables()' method)
Sat May  5 11:41:22 2007        AlgInvocationId 14
Sat May  5 11:41:22 2007        COMMIT  commit on


What exactly means this warining "Rows Written    N/A (plugin has no =
'undoTables()' method)" ?

and where one can find and download the most updated "so.definitions" =
file ?


My sres.gorelationship and sres.sequenceontology are like this:


mydb=3D# \d sres.gorelationship
                    Table "sres.gorelationship"
         Column          |            Type             | Modifiers
-------------------------+-----------------------------+-----------
 go_relationship_id      | numeric(10,0)               | not null
 parent_term_id          | numeric(10,0)               | not null
 child_term_id           | numeric(10,0)               | not null
 go_relationship_type_id | numeric(10,0)               | not null
 modification_date       | timestamp without time zone | not null
 user_read               | numeric(1,0)                | not null
 user_write              | numeric(1,0)                | not null
 group_read              | numeric(1,0)                | not null
 group_write             | numeric(1,0)                | not null
 other_read              | numeric(1,0)                | not null
 other_write             | numeric(1,0)                | not null
 row_user_id             | numeric(12,0)               | not null
 row_group_id            | numeric(4,0)                | not null
 row_project_id          | numeric(4,0)                | not null
 row_alg_invocation_id   | numeric(12,0)               | not null
Indexes:
    "gorelationship_pk" PRIMARY KEY, btree (go_relationship_id)
    "gorelationship_ind01" btree (parent_term_id, child_term_id)
    "gorelationship_ind02" btree (child_term_id, parent_term_id)
    "gorelationship_ind03" btree (go_relationship_type_id)


mydb=3D# \d sres.sequenceontology
                  Table "sres.sequenceontology"
        Column         |            Type             | Modifiers
-----------------------+-----------------------------+-----------
 sequence_ontology_id  | numeric(10,0)               | not null
 so_id                 | character varying(12)       | not null
 ontology_name         | character varying(30)       | not null
 so_version            | character varying(255)      | not null
 so_cvs_version        | character varying(10)       | not null
 term_name             | character varying(255)      | not null
 definition            | character varying(2000)     | not null
 modification_date     | timestamp without time zone | not null
 user_read             | numeric(1,0)                | not null
 user_write            | numeric(1,0)                | not null
 group_read            | numeric(1,0)                | not null
 group_write           | numeric(1,0)                | not null
 other_read            | numeric(1,0)                | not null
 other_write           | numeric(1,0)                | not null
 row_user_id           | numeric(12,0)               | not null
 row_group_id          | numeric(4,0)                | not null
 row_project_id        | numeric(4,0)                | not null
 row_alg_invocation_id | numeric(12,0)               | not null
Indexes:
    "pk_sequenceontology" PRIMARY KEY, btree (sequence_ontology_id)

Thanks, Alberto