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Commit 33171ae1 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Remove the '-skipdownload' switch. 

Also keep help text below 80 chars/line.
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misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+ 11
− 18
View file @ 33171ae1
......@@ -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
......
misc-scripts/xref_mapping/xref_parser.pl
+ 48
− 49
View file @ 33171ae1
......@@ -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
......
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