From 5935d5913cd63591ee4c86c942b745b9cb9b2a65 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 2 May 2012 13:09:24 +0000
Subject: [PATCH] Release not version.
---
modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm | 4 ++--
.../Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm | 6 +++---
modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm | 18 +++++++++---------
modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm | 2 +-
.../Pipeline/FASTA/ReuseSpeciesFactory.pm | 8 ++++----
.../EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm | 2 +-
.../EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm | 10 +++++-----
7 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm
index c423e11564..9fa9176b53 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm
@@ -95,8 +95,8 @@ sub old_path {
my ($self, $species) = @_;
my $base = $self->param('ftp_dir');
my $prod = $self->production_name($species);
- my $version = $self->param('previous_version');
- my $dir = File::Spec->catdir($base, "release-$version", 'fasta', $prod, 'dna');
+ my $release = $self->param('previous_release');
+ my $dir = File::Spec->catdir($base, "release-$release", 'fasta', $prod, 'dna');
}
# Closes file handle, and deletes the file stub if it contains no data
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
index a1b475c188..b23fecfd82 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
@@ -34,7 +34,7 @@ Allowed parameters are:
=over 8
-=item version - Needed to build the target path
+=item release - Needed to build the target path
=item species - Required to indicate which species we are working with
@@ -69,7 +69,7 @@ sub param_defaults {
sub fetch_input {
my ($self) = @_;
- foreach my $key (qw/data_type species version base_path/) {
+ foreach my $key (qw/data_type species release base_path/) {
$self->throw("Cannot find the required parameter $key") unless $self->param($key);
}
return;
@@ -135,7 +135,7 @@ sub target_file {
my @name_bits;
push @name_bits, $self->web_name();
push @name_bits, $self->assembly();
- push @name_bits, $self->param('version');
+ push @name_bits, $self->param('release');
push @name_bits, $self->param('data_type');
push @name_bits, 'toplevel';
push @name_bits, 'fa', 'gz';
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm
index 8cf05e3b05..e4f5346a1e 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm
@@ -25,19 +25,19 @@ Bio::EnsEMBL::Pipeline::FASTA::CopyDNA
=head1 DESCRIPTION
Performs a find in the DNA dumps directory, for the given species, in the
-previous version FTP dump directory. Any files matching the normal gzipped
+previous release FTP dump directory. Any files matching the normal gzipped
fasta extension will be copied over to this release's directory.
-Previous version is defined as V<version-1>; override this class if your
-definition of the previous version is different.
+Previous release is defined as V<release-1>; override this class if your
+definition of the previous release is different.
Allowed parameters are:
=over 8
-=item version - Needed to build the target path
+=item release - Needed to build the target path
-=item previous_version - Needed to build the source path
+=item previous_release - Needed to build the source path
=item ftp_dir - Current location of the FTP directory for the previous
release. Should be the root i.e. the level I<release-XX> is in
@@ -63,7 +63,7 @@ use File::Spec;
sub fetch_input {
my ($self) = @_;
- my @required = qw/version ftp_dir species/;
+ my @required = qw/release ftp_dir species/;
foreach my $key (@required) {
$self->throw("Need to define a $key parameter") unless $self->param($key);
}
@@ -86,10 +86,10 @@ sub run {
sub new_filename {
my ($self, $old_filename) = @_;
my ($old_volume, $old_dir, $old_file) = File::Spec->splitpath($old_filename);
- my $old_version = $self->param('previous_version');
- my $version = $self->param('version');
+ my $old_release = $self->param('previous_release');
+ my $release = $self->param('release');
my $new_file = $old_file;
- $new_file =~ s/\.$old_version\./.$version./;
+ $new_file =~ s/\.$old_release\./.$release./;
my $new_path = $self->new_path();
return File::Spec->catfile($new_path, $new_file);
}
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
index 6c02d6fc0c..e088aeca30 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
@@ -421,7 +421,7 @@ sub _generate_file_name {
my @name_bits;
push @name_bits, $self->web_name();
push @name_bits, $self->assembly();
- push @name_bits, $self->param('version');
+ push @name_bits, $self->param('release');
push @name_bits, lc($data_type);
push @name_bits, $level if $level;
push @name_bits, $section if $section;
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm
index 6c071e3395..203ff1d86d 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm
@@ -32,7 +32,7 @@ Allowed parameters are:
=over 8
-=item version - Needed to query production with
+=item release - Needed to query production with
=item ftp_dir - If not specified then we cannot reuse
@@ -77,7 +77,7 @@ sub param_defaults {
sub fetch_input {
my ($self) = @_;
$self->SUPER::fetch_input();
- $self->throw("Need to define a version parameter") unless $self->param('version');
+ $self->throw("Need to define a release parameter") unless $self->param('release');
#Calculate quick lookup
my %force_species_lookup;
@@ -129,8 +129,8 @@ and production_name = ?
SQL
my $production_name = $dba->get_MetaContainer()->get_production_name();
$dba->dbc()->disconnect_if_idle();
- my $version = $self->param('version');
- my $params = [ $version, 'Y', 'Y', 'Genebuild', 'handed_over', $production_name ];
+ my $release = $self->param('release');
+ my $params = [ $release, 'Y', 'Y', 'Genebuild', 'handed_over', $production_name ];
my $prod_dba = $self->get_production_DBAdaptor();
my $result = $prod_dba->dbc()->sql_helper()->execute_single_result(-SQL => $sql, -PARAMS => $params);
$prod_dba->dbc()->disconnect_if_idle();
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm
index 0434372eb8..bee7dc623b 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm
@@ -27,7 +27,7 @@ Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer
Creates WUBlast indexes of the given GZipped file. The resulting index
is created under the parameter location I<base_path> in blast and then in a
directory defined by the type of dump. The type of dump also changes the file
-name generated. Genomic dumps have their release version replaced with the
+name generated. Genomic dumps have their release number replaced with the
last repeat masked date.
Allowed parameters are:
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm
index 7b4acd5bf8..5597fcd021 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm
@@ -30,9 +30,9 @@ sub default_options {
force_species => [],
- version => software_version(),
+ release => software_version(),
- previous_version => (software_version() - 1),
+ previous_release => (software_version() - 1),
### SCP code
@@ -45,7 +45,7 @@ sub default_options {
### Defaults
- pipeline_name => 'fasta_dump_'.$self->o('version'),
+ pipeline_name => 'fasta_dump_'.$self->o('release'),
wublast_exe => 'xdformat',
blat_exe => 'faToTwoBit',
@@ -261,8 +261,8 @@ sub pipeline_wide_parameters {
%{ $self->SUPER::pipeline_wide_parameters() }, # inherit other stuff from the base class
base_path => $self->o('base_path'),
db_types => $self->o('db_types'),
- version => $self->o('version'),
- previous_version => $self->o('previous_version'),
+ release => $self->o('release'),
+ previous_release => $self->o('previous_release'),
};
}
--
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