[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Fri Oct 13 22:08:39 UTC 2006
senger
Fri Oct 13 18:08:39 EDT 2006
Update of /home/repository/moby/moby-live/Java/src/scripts
In directory dev.open-bio.org:/tmp/cvs-serv20067
Modified Files:
config-status.pl generate-datatypes.pl generate-services.pl
install.pl known-registries.pl local-cache.pl
testing-parser.pl testing-service.pl universal-testing.pl
Log Message:
new module names for Perl Moses
moby-live/Java/src/scripts config-status.pl,1.8,1.9 generate-datatypes.pl,1.5,1.6 generate-services.pl,1.6,1.7 install.pl,1.4,1.5 known-registries.pl,1.1,1.2 local-cache.pl,1.4,1.5 testing-parser.pl,1.3,1.4 testing-service.pl,1.6,1.7 universal-testing.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/config-status.pl,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/scripts/config-status.pl 2006/07/26 17:57:56 1.8
+++ /home/repository/moby/moby-live/Java/src/scripts/config-status.pl 2006/10/13 22:08:39 1.9
@@ -29,9 +29,9 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
-use MOBY::Base;
+use MOSES::MOBY::Base;
use strict;
$LOG->level ('INFO') if $opt_v;
@@ -40,20 +40,20 @@
sub say { print @_, "\n"; }
-say "Perl-MoSeS VERSION: $MOBY::Base::VERSION\n";
+say "Perl-MoSeS VERSION: $MOSES::MOBY::Base::VERSION\n";
say 'Configuration';
say '-------------';
-say "Default configuration file: $MOBY::Config::DEFAULT_CONFIG_FILE";
-say "Environment variable $MOBY::Config::ENV_CONFIG_DIR" .
- ( exists $ENV{$MOBY::Config::ENV_CONFIG_DIR} ? ": $ENV{$MOBY::Config::ENV_CONFIG_DIR}" : ' is not set');
+say "Default configuration file: $MOSES::MOBY::Config::DEFAULT_CONFIG_FILE";
+say "Environment variable $MOSES::MOBY::Config::ENV_CONFIG_DIR" .
+ ( exists $ENV{$MOSES::MOBY::Config::ENV_CONFIG_DIR} ? ": $ENV{$MOSES::MOBY::Config::ENV_CONFIG_DIR}" : ' is not set');
say 'Successfully read configuration files:';
-foreach my $file (MOBY::Config->ok_files) {
+foreach my $file (MOSES::MOBY::Config->ok_files) {
say "\t$file";
}
-my %failed = MOBY::Config->failed_files;
+my %failed = MOSES::MOBY::Config->failed_files;
if (keys %failed > 0) {
say 'Failed configuration files:';
foreach my $file (sort keys %failed) {
@@ -63,8 +63,8 @@
}
say 'All configuration parameters:';
-foreach my $name (sort MOBY::Config->param()) {
- say "\t$name => " . MOBY::Config->param ($name);
+foreach my $name (sort MOSES::MOBY::Config->param()) {
+ say "\t$name => " . MOSES::MOBY::Config->param ($name);
}
say 'All imported names (equivalent to parameters above): ';
@@ -85,7 +85,7 @@
say 'Logging';
say '-------';
-my $logger_name = $MOBY::Base::LOGGER_NAME;
+my $logger_name = $MOSES::MOBY::Base::LOGGER_NAME;
my $logger = Log::Log4perl->get_logger ($logger_name);
say "Logger name (use it in the configuration file): $logger_name";
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/generate-datatypes.pl,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/scripts/generate-datatypes.pl 2006/07/08 03:52:17 1.5
+++ /home/repository/moby/moby-live/Java/src/scripts/generate-datatypes.pl 2006/10/13 22:08:39 1.6
@@ -34,19 +34,19 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/generate-datatypes.pl
use strict;
-use MOBY::Base;
-use MOBY::Generators::GenTypes;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Generators::GenTypes;
$LOG->level ('INFO') if $opt_v;
$LOG->level ('DEBUG') if $opt_d;
sub say { print @_, "\n"; }
-my $generator = new MOBY::Generators::GenTypes;
+my $generator = new MOSES::MOBY::Generators::GenTypes;
if (@ARGV) {
say 'Generating ' . (@ARGV+0) . '+ data types.';
if ($opt_s) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/generate-services.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/scripts/generate-services.pl 2006/07/30 12:56:56 1.6
+++ /home/repository/moby/moby-live/Java/src/scripts/generate-services.pl 2006/10/13 22:08:39 1.7
@@ -50,12 +50,12 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/generate-services.pl
use strict;
-use MOBY::Base;
-use MOBY::Generators::GenServices;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Generators::GenServices;
$LOG->level ('INFO') if $opt_v;
$LOG->level ('DEBUG') if $opt_d;
@@ -63,7 +63,7 @@
sub say { print @_, "\n"; }
-my $generator = new MOBY::Generators::GenServices;
+my $generator = new MOSES::MOBY::Generators::GenServices;
if ($opt_a) {
say 'Generating all services.';
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/install.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/scripts/install.pl 2006/07/30 12:56:56 1.4
+++ /home/repository/moby/moby-live/Java/src/scripts/install.pl 2006/10/13 22:08:39 1.5
@@ -72,13 +72,13 @@
}
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/install.pl
use File::Spec;
use IO::Prompt;
-use MOBY::Base;
-use MOBY::Cache::Central;
-use MOBY::Cache::Registries;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Cache::Central;
+use MOSES::MOBY::Cache::Registries;
use English qw( -no_match_vars ) ;
use strict;
@@ -104,8 +104,8 @@
# what registry to use
sub prompt_for_registry {
- my $cache = new MOBY::Cache::Central;
- my @regs = MOBY::Cache::Registries->list;
+ my $cache = new MOSES::MOBY::Cache::Central;
+ my @regs = MOSES::MOBY::Cache::Registries->list;
my $registry = prompt ("What registry to use? [default] ",
-m => [@regs]);
$registry ||= 'default';
@@ -214,7 +214,7 @@
if ('y' eq prompt ('Should I try to fill or update the local cache [y]? ', -ynd=>'y')) {
$registry = prompt_for_registry;
my $details =
- MOBY::Cache::Registries->get ($registry);
+ MOSES::MOBY::Cache::Registries->get ($registry);
if ($details) {
my $endpoint = $details->{endpoint};
my $uri = $details->{namespace};
@@ -239,8 +239,8 @@
# configuration file (will be found and used, or created)
my $config_file = File::Spec->catfile
- ($ENV{$MOBY::Config::ENV_CONFIG_DIR} || $pmoses_home,
- $MOBY::Config::DEFAULT_CONFIG_FILE);
+ ($ENV{$MOSES::MOBY::Config::ENV_CONFIG_DIR} || $pmoses_home,
+ $MOSES::MOBY::Config::DEFAULT_CONFIG_FILE);
if (-e $config_file and ! $opt_F) {
say "Configuration file $config_file exists.";
say "It will be used and not overwritten unless you start 'install.pl -F'.\n";
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/known-registries.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/scripts/known-registries.pl 2006/07/27 17:16:07 1.1
+++ /home/repository/moby/moby-live/Java/src/scripts/known-registries.pl 2006/10/13 22:08:39 1.2
@@ -7,16 +7,16 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/install.pl
-use MOBY::Cache::Registries;
+use MOSES::MOBY::Cache::Registries;
use Data::Dumper;
use strict;
sub say { print @_, "\n"; }
-say join (", ", MOBY::Cache::Registries->list);
-say (Data::Dumper->Dump ( [ MOBY::Cache::Registries->all ], ['Registries']));
+say join (", ", MOSES::MOBY::Cache::Registries->list);
+say (Data::Dumper->Dump ( [ MOSES::MOBY::Cache::Registries->all ], ['Registries']));
__END__
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/local-cache.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/scripts/local-cache.pl 2006/07/27 17:16:07 1.4
+++ /home/repository/moby/moby-live/Java/src/scripts/local-cache.pl 2006/10/13 22:08:39 1.5
@@ -58,28 +58,28 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/config-status.pl
use strict;
-use MOBY::Base;
-use MOBY::Cache::Central;
-use MOBY::Cache::Registries;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Cache::Central;
+use MOSES::MOBY::Cache::Registries;
$LOG->level ('INFO') if $opt_v;
$LOG->level ('DEBUG') if $opt_d;
sub say { print @_, "\n"; }
-my $cache = new MOBY::Cache::Central;
+my $cache = new MOSES::MOBY::Cache::Central;
# --- get info
if ($opt_i) {
say 'Currently used registry: ' . $cache->registry;
- say "(it can be changed in $MOBY::Config::DEFAULT_CONFIG_FILE)\n";
+ say "(it can be changed in $MOSES::MOBY::Config::DEFAULT_CONFIG_FILE)\n";
my $details =
- MOBY::Cache::Registries->get ($cache->registry) ||
- MOBY::Cache::Registries->get ('default');
+ MOSES::MOBY::Cache::Registries->get ($cache->registry) ||
+ MOSES::MOBY::Cache::Registries->get ('default');
foreach my $key (sort keys %{ $details }) {
printf " %-12s: %-s\n", $key, $details->{$key};
}
@@ -89,9 +89,9 @@
printf
"%-13s %+13s %+13s %+10s\n",
'Registry', 'Data types', 'Authorities', 'Services';
- foreach my $reg (MOBY::Cache::Registries->list) {
+ foreach my $reg (MOSES::MOBY::Cache::Registries->list) {
next unless $cache->cache_exists ($reg);
- my $new_cache = new MOBY::Cache::Central ( registry => $reg );
+ my $new_cache = new MOSES::MOBY::Cache::Central ( registry => $reg );
my $datatypes_count = $new_cache->get_datatype_names;
my %authorities = $new_cache->get_service_names;
my $services_count = 0;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/testing-parser.pl,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/scripts/testing-parser.pl 2006/07/08 13:52:12 1.3
+++ /home/repository/moby/moby-live/Java/src/scripts/testing-parser.pl 2006/10/13 22:08:39 1.4
@@ -42,12 +42,12 @@
# -----------------------------------------------------------
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/testing-parser.pl
use strict;
-use MOBY::Base;
-use MOBY::Parser;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Parser;
$LOG->level ('INFO') if $opt_v;
$LOG->level ('DEBUG') if $opt_d;
@@ -57,7 +57,7 @@
my ($input_name, $known_type) = split (/\s*:\s*/, $opt_b, 2);
push (@parser_args, ( lowestKnownDataTypes => { $input_name => $known_type }));
}
-my $parser = new MOBY::Parser (@parser_args);
+my $parser = new MOSES::MOBY::Parser (@parser_args);
my $package = $parser->parse ( method => 'file', data => $ARGV[0] );
print $package unless $opt_n;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/testing-service.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/scripts/testing-service.pl 2006/07/31 15:23:57 1.6
+++ /home/repository/moby/moby-live/Java/src/scripts/testing-service.pl 2006/10/13 22:08:39 1.7
@@ -62,7 +62,7 @@
require lib ; lib->import ("$FindBin::Bin/../Perl/services");
require lib ; lib->import ("$FindBin::Bin/../Perl/generated");
unshift (@INC, $opt_l) if $opt_l;
- eval "use MOBY::Base; 1;";
+ eval "use MOSES::MOBY::Base; 1;";
$LOG->level ('INFO') if $opt_v;
$LOG->level ('DEBUG') if $opt_d;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/universal-testing.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/scripts/universal-testing.pl 2006/07/26 17:57:56 1.2
+++ /home/repository/moby/moby-live/Java/src/scripts/universal-testing.pl 2006/10/13 22:08:39 1.3
@@ -36,13 +36,13 @@
use Carp;
use FindBin qw( $Bin );
-use lib "$Bin/../Perl"; # assuming: Perl/MOBY/...
+use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/universal-testing.pl
use strict;
-use MOBY::Base;
-use MOBY::Cache::Central;
-use MOBY::Generators::GenServices;
+use MOSES::MOBY::Base;
+use MOSES::MOBY::Cache::Central;
+use MOSES::MOBY::Generators::GenServices;
use File::Spec;
$LOG->level ('INFO') if $opt_v;
@@ -50,7 +50,7 @@
sub say { print @_, "\n"; }
-my $cache = new MOBY::Cache::Central;
+my $cache = new MOSES::MOBY::Cache::Central;
my $tmpdir = File::Spec->tmpdir();
# create an empty XML input
@@ -69,10 +69,10 @@
# service generator
my $outdir = File::Spec->catfile ($tmpdir, 'generated-services');
-MOBY::Config->param ('generators.impl.outdir', $outdir);
-MOBY::Config->param ('generators.impl.package.prefix', 'Testing');
+MOSES::MOBY::Config->param ('generators.impl.outdir', $outdir);
+MOSES::MOBY::Config->param ('generators.impl.package.prefix', 'Testing');
unshift (@INC, $MOBYCFG::GENERATORS_IMPL_OUTDIR);
-my $generator = new MOBY::Generators::GenServices;
+my $generator = new MOSES::MOBY::Generators::GenServices;
# outputs
my $outputs = File::Spec->catfile ($tmpdir, 'generated-outputs');
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