From 54230ece96ce3cd309616df07e316da3f0e64c40 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Wed, 16 Jun 2010 10:01:40 +0000
Subject: [PATCH] removed the old "did" compatibility mode
---
modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm | 16 ++--------------
modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm | 16 ++--------------
2 files changed, 4 insertions(+), 28 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
index b19ef1439..6a6e9d8f9 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
@@ -21,7 +21,7 @@ This RunnableDB module acts as a wrapper for a (My)SQL command
run against either the current hive database (default) or against one specified by connection parameters.
If you behave you may also use parameter substitution.
-The SQL command(s) can be given using three different syntaxes:
+The SQL command(s) can be given using two different syntaxes:
1) Sql command is stored in the input_id() or parameters() as the value corresponding to the 'sql' key.
THIS IS THE RECOMMENDED WAY as it allows to pass in other parameters and use the parameter substitution mechanism in its full glory.
@@ -30,11 +30,6 @@ The SQL command(s) can be given using three different syntaxes:
(only works with sql commands shorter than 255 bytes).
This is a legacy syntax. Most people tend to use it not realizing there are other possiblities.
-3) A numeric key to the analysis_data table (where the actual sql command is stored)
- is kept in the input_id() or parameters() as the value corresponding to the 'did' key. This allows to overcome the 255 byte limit.
- Well, if you REALLY couldn't fit your sql command into 250~ish bytes, are you sure you can manage big pipelines?
- Just joking :)
-
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
@@ -46,7 +41,6 @@ package Bio::EnsEMBL::Hive::RunnableDB::SqlCmd;
use strict;
use DBI;
-use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
@@ -69,10 +63,6 @@ sub strict_hash_format {
param('sql'): The recommended way of passing in the sql command(s).
- param('did'): Alternative way of passing in a long sql command that is stored in analysis_data table.
- Try to avoid long sql commands at all costs, as it makes debugging a nightmare.
- Keep in mind that parameter substitution mechanism can be used to compose longer strings from shorter ones.
-
param('db_conn'): An optional hash to pass in connection parameters to the database upon which the sql command(s) will have to be run.
param('*'): Any other parameters can be freely used for parameter substitution.
@@ -87,9 +77,7 @@ sub fetch_input {
my $sql = ($self->input_id()!~/^\{.*\}$/)
? $self->input_id() # assume the sql command is given in input_id
: $self->param('sql') # or defined as a hash value (in input_id or parameters)
- or $self->param('did') # or referred to the analysis_data table where longer strings can be stored
- ? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID( $self->param('did') )
- : die "Could not find the command defined in input_id(), param('sql') or param('did')";
+ or die "Could not find the command defined in param('sql') or input_id()";
# Store the sql command array:
#
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
index d77732231..1cbced240 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
@@ -19,7 +19,7 @@ Please refer to Bio::EnsEMBL::Hive::PipeConfig::* pipeline configuration files t
This RunnableDB module acts as a wrapper for shell-level command lines. If you behave you may also use parameter substitution.
-The command can be given using three different syntaxes:
+The command can be given using two different syntaxes:
1) Command line is stored in the input_id() or parameters() as the value corresponding to the 'cmd' key.
THIS IS THE RECOMMENDED WAY as it allows to pass in other parameters and use the parameter substitution mechanism in its full glory.
@@ -28,11 +28,6 @@ The command can be given using three different syntaxes:
(only works with command lines shorter than 255 bytes).
This is a legacy syntax. Most people tend to use it not realizing there are other possiblities.
-3) A numeric key to the analysis_data table (where the actual command line is stored)
- is kept in the input_id() or parameters() as the value corresponding to the 'did' key. This allows to overcome the 255 byte limit.
- Well, if you REALLY couldn't fit your command line into 250~ish bytes, are you sure you can manage big pipelines?
- Just joking :)
-
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
@@ -43,7 +38,6 @@ The command can be given using three different syntaxes:
package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
use strict;
-use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
=head2 strict_hash_format
@@ -64,10 +58,6 @@ sub strict_hash_format {
param('cmd'): The recommended way of passing in the command line.
- param('did'): Alternative way of passing in a long command line that is stored in analysis_data table.
- Try to avoid long command lines at all costs, as it makes debugging a nightmare.
- Keep in mind that parameter substitution mechanism can be used to compose longer strings from shorter ones.
-
param('*'): Any other parameters can be freely used for parameter substitution.
=cut
@@ -80,9 +70,7 @@ sub fetch_input {
my $cmd = ($self->input_id()!~/^\{.*\}$/)
? $self->input_id() # assume the command line is given in input_id
: $self->param('cmd') # or defined as a hash value (in input_id or parameters)
- or $self->param('did') # or referred to the analysis_data table where longer strings can be stored
- ? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID( $self->param('did') )
- : die "Could not find the command defined in input_id(), param('cmd') or param('did')";
+ or die "Could not find the command defined in param('cmd') or input_id()";
# Store the value with parameter substitutions for the actual execution:
#
--
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