From 8d6aca933489a984f33db69e107f0909013d2e05 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Mon, 26 Apr 2010 22:05:23 +0000
Subject: [PATCH] an example of using SqlCmd
---
docs/test_SqlCmd.conf | 73 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 73 insertions(+)
create mode 100755 docs/test_SqlCmd.conf
diff --git a/docs/test_SqlCmd.conf b/docs/test_SqlCmd.conf
new file mode 100755
index 000000000..581603346
--- /dev/null
+++ b/docs/test_SqlCmd.conf
@@ -0,0 +1,73 @@
+# mini-pipeline for testing meta-parameter evaluation and SqlCmd in "external_db" mode
+
+my $cvs_root_dir = $ENV{'HOME'}.'/work';
+
+ # family database connection parameters (our main database):
+my $pipeline_db = {
+ -host => 'compara3',
+ -port => 3306,
+ -user => 'ensadmin',
+ -pass => 'ensembl',
+ -dbname => "lg4_test_sqlcmd",
+};
+
+my $slave_db = {
+ -host => 'compara3',
+ -port => 3306,
+ -user => 'ensadmin',
+ -pass => 'ensembl',
+ -dbname => "lg4_test_sqlcmd_slave",
+};
+
+return {
+ # pass connection parameters into the pipeline initialization script to create adaptors:
+ -pipeline_db => $pipeline_db,
+
+ # shell commands that create and pre-fill the pipeline database:
+ -pipeline_create_commands => [
+ 'mysql '.dbconn_2_mysql($pipeline_db, 0)." -e 'CREATE DATABASE $pipeline_db->{-dbname}'",
+
+ 'mysql '.dbconn_2_mysql($pipeline_db, 1)." <$cvs_root_dir/ensembl-hive/sql/tables.sql",
+ 'mysql '.dbconn_2_mysql($pipeline_db, 1)." <$cvs_root_dir/ensembl-hive/sql/procedures.sql",
+
+ 'mysql '.dbconn_2_mysql($pipeline_db, 0)." -e 'CREATE DATABASE $slave_db->{-dbname}'",
+ ],
+
+ -pipeline_wide_parameters => { # these parameter values are visible to all analyses, can be overridden by parameters{} and input_id{}
+
+ 'db_conn' => $slave_db, # testing the stringification of a structure here
+ },
+
+ -resource_classes => {
+ 0 => { -desc => 'default, 8h', 'LSF' => '' },
+ 1 => { -desc => 'urgent', 'LSF' => '-q yesterday' },
+ },
+
+ -pipeline_analyses => [
+ { -logic_name => 'create_table',
+ -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd',
+ -parameters => { },
+ -hive_capacity => 20, # to enable parallel branches
+ -input_ids => [
+ { 'sql' => 'CREATE TABLE distance (place_from char(40) NOT NULL, place_to char(40) NOT NULL, miles float, PRIMARY KEY (place_from, place_to))', },
+ ],
+ -rc_id => 1,
+ },
+
+ { -logic_name => 'fill_in_table',
+ -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd',
+ -parameters => {
+ 'sql' => [ "INSERT INTO distance (place_from, place_to, miles) VALUES ('#from#', '#to#', #miles#)",
+ "INSERT INTO distance (place_from, place_to, miles) VALUES ('#to#', '#from#', #miles#)", ],
+ },
+ -hive_capacity => 20, # to enable parallel branches
+ -input_ids => [
+ { 'from' => 'Cambridge', 'to' => 'Ely', 'miles' => 18.3 },
+ { 'from' => 'London', 'to' => 'Cambridge', 'miles' => 60 },
+ ],
+ -wait_for => 'create_table',
+ -rc_id => 1,
+ },
+ ],
+};
+
--
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