diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 8350bbfc14080c60ffbc5c6d9bbe671652a99c9a..407dea1c5966336726a62141360a7da6cceed1f0 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -32,13 +32,10 @@ my %dependent_sources;
my %taxonomy2species_id;
my %name2species_id;
-my (
- $host, $port, $dbname,
- $user, $pass, $create,
- $release, $cleanup, $deletedownloaded,
- $skipdownload, $drop_db, $checkdownload,
- $dl_path, $unzip
-);
+my ( $host, $port, $dbname, $user,
+ $pass, $create, $release, $cleanup,
+ $deletedownloaded, $drop_db, $checkdownload, $dl_path,
+ $unzip );
# --------------------------------------------------------------------------------
# Get info about files to be parsed from the database
@@ -46,12 +43,12 @@ my (
sub run {
my $self = shift;
- ( $host, $port, $dbname,
- $user, $pass, my $speciesr,
- my $sourcesr, $skipdownload, $checkdownload,
- $create, $release, $cleanup,
- $drop_db, $deletedownloaded, $dl_path,
- my $notsourcesr, $unzip
+ ( $host, $port, $dbname,
+ $user, $pass, my $speciesr,
+ my $sourcesr, $checkdownload, $create,
+ $release, $cleanup, $drop_db,
+ $deletedownloaded, $dl_path, my $notsourcesr,
+ $unzip
) = @_;
$base_dir = $dl_path if $dl_path;
@@ -248,11 +245,7 @@ sub run {
printf( "Uncompressing '%s' using 'gunzip'\n", $file );
system( "gunzip", "-f", $file );
}
- if ($unzip) {
- $file =~ s/\.(gz|Z)$//; # If skipdownload set this will
- # not have been done yet.
- # If it has, no harm done
- }
+ if ($unzip) { $file =~ s/\.(gz|Z)$// }
# Compare checksums and parse/upload if necessary need to
# check file size as some .SPC files can be of zero length
diff --git a/misc-scripts/xref_mapping/xref_parser.pl b/misc-scripts/xref_mapping/xref_parser.pl
index 73c81785f622de4bac45605270e1a78145fc7d2f..82e49289c69c0f4a29c32ceaec8b6d36d729c1a9 100644
--- a/misc-scripts/xref_mapping/xref_parser.pl
+++ b/misc-scripts/xref_mapping/xref_parser.pl
@@ -3,14 +3,12 @@ use strict;
use Getopt::Long;
use XrefParser::BaseParser;
-my (
- $host, $port, $dbname,
- $user, $pass, @species,
- @sources, $skipdownload, $checkdownload,
- $create, $release, $cleanup,
- $drop_existing_db, $deletedownloaded, $dl_path,
- @notsource, $unzip
-);
+my ( $host, $port, $dbname,
+ $user, $pass, @species,
+ @sources, $checkdownload, $create,
+ $release, $cleanup, $drop_existing_db,
+ $deletedownloaded, $dl_path, @notsource,
+ $unzip );
$unzip = 0; # Do not decompress gzipped files by default
@@ -23,7 +21,6 @@ GetOptions(
'species=s' => \@species,
'source=s' => \@sources,
'download_dir=s' => \$dl_path,
- 'skipdownload' => \$skipdownload, # Skips all downloads
'checkdownload!' => \$checkdownload, # Don't download if exists
'create' => \$create,
'setrelease=s' => \$release,
@@ -34,8 +31,7 @@ GetOptions(
'delete_downloaded' => \$deletedownloaded,
'download_path=s' => \$dl_path,
'unzip' => \$unzip, # Force decompression of files
- 'help' => sub { usage(); exit(0); }
-);
+ 'help' => sub { usage(); exit(0); } );
@species = split(/,/,join(',',@species));
@sources = split(/,/,join(',',@sources));
@@ -50,16 +46,14 @@ if ( !$user || !$host || !$dbname ) {
my $base_parser = XrefParser::BaseParser->new();
$base_parser->run(
- $host, ( defined $port ? $port : '3306' ),
- $dbname, $user,
- $pass, \@species,
- \@sources, $skipdownload,
- $checkdownload, $create,
- $release, $cleanup,
- $drop_existing_db, $deletedownloaded,
- $dl_path, \@notsource,
- $unzip
-);
+ $host, ( defined $port ? $port : '3306' ),
+ $dbname, $user,
+ $pass, \@species,
+ \@sources, $checkdownload,
+ $create, $release,
+ $cleanup, $drop_existing_db,
+ $deletedownloaded, $dl_path,
+ \@notsource, $unzip );
# --------------------------------------------------------------------------------
@@ -67,42 +61,45 @@ sub usage {
print << "EOF";
- xref_parser.pl -user {user} -pass {password} -host {host} -port {port} -dbname {database} -species {species1,species2} -source {source1,source2} -notsource {source1,source2} -skipdownload -create -setrelease
+ xref_parser.pl -user {user} -pass {password} -host {host} \\
+ -port {port} -dbname {database} -species {species1,species2} \\
+ -source {source1,source2} -notsource {source1,source2} \\
+ -create -setrelease
-user User name to access database. Must allow writing.
-
+
-pass Password for user.
-
+
-host Database host.
-
+
-port Database port.
-
+
-dbname Name of xref database to use/create.
-
- -species Which species to import. Multiple -species arguments and/or comma,
- separated lists of species are allowed. Species may be referred to
- by genus/species (e.g. homo_sapiens) or common aliases (e.g. human).
- Specifying an unknown species will cause a list of valid species to
- be printed.
- Not specifying a -species argument will result in all species being
+
+ -species Which species to import. Multiple -species arguments
+ and/or comma, separated lists of species are
+ allowed. Species may be referred to by genus/species
+ (e.g. homo_sapiens) or common aliases (e.g. human).
+ Specifying an unknown species will cause a list
+ of valid species to be printed. Not specifying a
+ -species argument will result in all species being
used.
-
- -source Which sources to import. Multiple -source arguments and/or comma,
- separated lists of sources are allowed.
- Specifying an unknown source will cause a list of valid sources to
- be printed.
- Not specifying a -source argument will result in all species being
+
+ -source Which sources to import. Multiple -source arguments
+ and/or comma, separated lists of sources are
+ allowed. Specifying an unknown source will cause a
+ list of valid sources to be printed. Not specifying
+ a -source argument will result in all species being
used.
-
+
-notsource Which source to skip.
- -create If specified, cause dbname to be deleted and re-created if it
- already exists. User is prompted before database is dropped to
- prevent disasters arising from dropping the wrong database.
-
- -skipdownload Don't download any data, parse existing.
+ -create If specified, cause dbname to be deleted and
+ re-created if it already exists. User is prompted
+ before database is dropped to prevent disasters
+ arising from dropping the wrong database.
- -checkdownload Check if file exists, otherwise downloads the file
+ -checkdownload Check if file exists, otherwise downloads the file.
-deletedownloaded Delete any existing downloaded files first.
@@ -110,11 +107,13 @@ sub usage {
-cleanup Delete the downloaded source files after parsing.
- -drop_db Drop the xref-database without user interaction
+ -drop_db Drop the xref-database without user interaction.
- -download_path Directory into which to download files (default is the current directory)
+ -download_path Directory into which to download files (default is
+ the current directory).
- -unzip Decompress gzipped files (default is to use compressed files)
+ -unzip Decompress gzipped files (default is to use compressed
+ files).
EOF