From ca7cf4ed7c88469d330f3e80956f31f32dc10430 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 18 Jun 2010 12:38:22 +0000
Subject: [PATCH] allow for negative matches
---
.../EnsEMBL/Hive/PipeConfig/TableDumperZipper_conf.pm | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/TableDumperZipper_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/TableDumperZipper_conf.pm
index c4dd7bdb9..d463af556 100644
--- a/modules/Bio/EnsEMBL/Hive/PipeConfig/TableDumperZipper_conf.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipeConfig/TableDumperZipper_conf.pm
@@ -58,7 +58,7 @@ sub default_options {
'pipeline_name' => 'zip_tables', # name used by the beekeeper to prefix job names on the farm
'pipeline_db' => { # connection parameters
- -host => 'compara3',
+ -host => 'compara2',
-port => 3306,
-user => 'ensadmin',
-pass => $self->o('password'), # a rule where a previously undefined parameter is used (which makes either of them obligatory)
@@ -66,7 +66,7 @@ sub default_options {
},
'source_db' => {
- -host => 'compara3',
+ -host => 'compara2',
-port => 3306,
-user => 'ensadmin',
-pass => $self->o('password'),
@@ -75,6 +75,7 @@ sub default_options {
'with_schema' => 1, # include table creation statement before inserting the data
'only_tables' => '%', # use 'protein_tree%' or 'analysis%' to only dump those tables
+ 'invert_selection' => 0, # use 'NOT LIKE' instead of 'LIKE'
'target_dir' => $ENV{'HOME'}.'/'.$self->o('source_dbname'), # where we want the compressed files to appear
'dumping_capacity' => 10, # how many tables can be dumped in parallel
};
@@ -115,7 +116,9 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
-parameters => {
'db_conn' => $self->o('source_db'),
- 'inputquery' => 'SHOW TABLES LIKE "'.$self->o('only_tables').'"',
+# 'inputquery' => 'SHOW TABLES LIKE "'.$self->o('only_tables').'"', # to support negative patterns in MySQL 5.1 we need a trick
+ 'inputquery' => 'SELECT table_name FROM information_schema.tables WHERE table_schema = "'.$self->o('source_dbname').'" AND table_name '
+ .($self->o('invert_selection')?'NOT LIKE':'LIKE').' "'.$self->o('only_tables').'"',
},
-input_ids => [
{ 'input_id' => { 'table_name' => '#_range_start#' }, },
--
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