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Re: [GUSDEV] InsertSequenceOntologyOBO error ?
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From: Mark S. H. <mh...@ug...> - 2007-05-05 18:31:27
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That plugin requires the file in OBO format. You can download the latest from the SO Project's repository at http://song.cvs.sourceforge.net/song/ontology/so.obo You can safely ignore the "no 'undoTables()'" message. It just indicates that InsertSequenceOntologyOBO has not implemented some optional record keeping and, as a side effect, is not compatible with the GUS::Community::Plugin::Undo plugin. The "RESULT Inserted n terms into SequenceOntology" message will give an accurate count of what was loaded. On May 5, 2007, at 11:04 AM, davila wrote: > 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=mydb > 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=# \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=# \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 > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
