Generic Model Organism Database Project

Update of /cvsroot/gmod/das2/t/conf
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10127

Modified Files:
	apache_test_config.pm extra.conf.in 
Log Message:
Added reload to extra.conf so the 'make test' webserver will automatically reload changed perl modules without restarting... this is really only useful for development work.

Index: extra.conf.in
===================================================================
RCS file: /cvsroot/gmod/das2/t/conf/extra.conf.in,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** extra.conf.in	10 Sep 2004 13:38:33 -0000	1.1.1.1
--- extra.conf.in	27 Sep 2004 07:39:19 -0000	1.2
***************
*** 1,2 ****
--- 1,8 ----
+ PerlModule Apache::Reload
+ PerlInitHandler Apache::Reload
+ PerlPreConnectionHandler Apache::Reload
+ PerlSetVar ReloadAll Off
+ PerlSetVar ReloadModules "ModPerl::* Apache::* Bio::Das2::*"
+ 
  PerlWarn On
  PerlTaintCheck On

Index: apache_test_config.pm
===================================================================
RCS file: /cvsroot/gmod/das2/t/conf/apache_test_config.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** apache_test_config.pm	17 Sep 2004 21:53:59 -0000	1.5
--- apache_test_config.pm	27 Sep 2004 07:39:19 -0000	1.6
***************
*** 1,9 ****
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:751
! # 02: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:769
! # 03: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1530
! # 04: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:437
! # 05: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! # 06: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
  # 07: t/TEST:81
  
--- 1,9 ----
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:875
! # 02: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:893
! # 03: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1710
! # 04: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:500
! # 05: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! # 06: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
  # 07: t/TEST:81
  
***************
*** 13,20 ****
      bless( {
                   'verbose' => undef,
!                  'hostport' => 'localhost.localdomain:8529',
                   'postamble' => [
                                    'TypesConfig "/etc/mime.types"',
!                                   'Include "/nfs/home/aday/cvsroot/gmod-das2/t/conf/extra.conf"',
                                    ''
                                  ],
--- 13,20 ----
      bless( {
                   'verbose' => undef,
!                  'hostport' => 'london:8529',
                   'postamble' => [
                                    'TypesConfig "/etc/mime.types"',
!                                   'Include "/media/home/boconnor/Development/cvsroot/das2/t/conf/extra.conf"',
                                    ''
                                  ],
***************
*** 30,34 ****
                                        'version' => 'Apache/2.0.50',
                                        'rev' => '2',
!                                       'name' => 'localhost.localdomain:8529',
                                        'config' => $VAR1
                                      }, 'Apache::TestServer' ),
--- 30,34 ----
                                        'version' => 'Apache/2.0.50',
                                        'rev' => '2',
!                                       'name' => 'london:8529',
                                        'config' => $VAR1
                                      }, 'Apache::TestServer' ),
***************
*** 38,44 ****
                   'inherit_config' => {
                                         'ServerRoot' => '/etc/httpd',
!                                        'ServerAdmin' => 'root@...',
                                         'TypesConfig' => '/etc/mime.types',
!                                        'DocumentRoot' => '/var/www/html',
                                         'LoadModule' => [
                                                           [
--- 38,44 ----
                   'inherit_config' => {
                                         'ServerRoot' => '/etc/httpd',
!                                        'ServerAdmin' => 'admin@...',
                                         'TypesConfig' => '/etc/mime.types',
!                                        'DocumentRoot' => '/www/turnkey_web/html',
                                         'LoadModule' => [
                                                           [
***************
*** 215,234 ****
                                                           ],
                                                           [
-                                                            'auth_kerb_module',
-                                                            'modules/mod_auth_kerb.so'
-                                                          ],
-                                                          [
-                                                            'mysql_auth_module',
-                                                            'modules/mod_auth_mysql.so'
-                                                          ],
-                                                          [
-                                                            'auth_pgsql_module',
-                                                            'modules/mod_auth_pgsql.so'
-                                                          ],
-                                                          [
-                                                            'jk2_module',
-                                                            'modules/mod_jk2.so'
-                                                          ],
-                                                          [
                                                             'perl_module',
                                                             'modules/mod_perl.so'
--- 215,218 ----
***************
*** 245,256 ****
                                                             'ssl_module',
                                                             'modules/mod_ssl.so'
-                                                          ],
-                                                          [
-                                                            'dav_svn_module',
-                                                            'modules/mod_dav_svn.so'
-                                                          ],
-                                                          [
-                                                            'authz_svn_module',
-                                                            'modules/mod_authz_svn.so'
                                                           ]
                                                         ]
--- 229,232 ----
***************
*** 260,266 ****
                                         sub { "DUMMY" }
                                       ],
-                  'resolved' => {
-                                  'localhost.localdomain' => 'localhost.localdomain'
-                                },
                   'preamble' => [
                                   '<IfModule !mod_access.c>
--- 236,239 ----
***************
*** 436,455 ****
  </IfModule>
  ',
-                                  '<IfModule !mod_auth_kerb.c>
-     LoadModule auth_kerb_module "/etc/httpd/modules/mod_auth_kerb.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_auth_mysql.c>
-     LoadModule mysql_auth_module "/etc/httpd/modules/mod_auth_mysql.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_auth_pgsql.c>
-     LoadModule auth_pgsql_module "/etc/httpd/modules/mod_auth_pgsql.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_jk2.c>
-     LoadModule jk2_module "/etc/httpd/modules/mod_jk2.so"
- </IfModule>
- ',
                                   '<IfModule !mod_perl.c>
      LoadModule perl_module "/etc/httpd/modules/mod_perl.so"
--- 409,412 ----
***************
*** 468,479 ****
  </IfModule>
  ',
-                                  '<IfModule !mod_dav_svn.c>
-     LoadModule dav_svn_module "/etc/httpd/modules/mod_dav_svn.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_authz_svn.c>
-     LoadModule authz_svn_module "/etc/httpd/modules/mod_authz_svn.so"
- </IfModule>
- ',
                                   '<IfModule !mod_mime.c>
      LoadModule mime_module "/usr/lib/httpd/modules/mod_mime.so"
--- 425,428 ----
***************
*** 483,498 ****
                                 ],
                   'vars' => {
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf',
!                              't_dir' => '/nfs/home/aday/cvsroot/gmod-das2/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
                               'thread_module' => 'worker.c',
                               'bindir' => '/usr/bin',
!                              'user' => 'aday',
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/nfs/home/aday/cvsroot/gmod-das2',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
--- 432,448 ----
                                 ],
                   'vars' => {
+                              'defines' => '',
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/media/home/boconnor/Development/cvsroot/das2/t/conf/httpd.conf',
!                              't_dir' => '/media/home/boconnor/Development/cvsroot/das2/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
                               'thread_module' => 'worker.c',
                               'bindir' => '/usr/bin',
!                              'user' => 'boconnor',
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/media/home/boconnor/Development/cvsroot/das2',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
***************
*** 501,523 ****
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf',
!                              'servername' => 'localhost.localdomain',
!                              'inherit_documentroot' => '/var/www/html',
                               'proxy' => 'off',
!                              'serveradmin' => 'root@...',
                               'authname' => 'gold club',
                               'remote_addr' => '127.0.0.1',
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/nfs/home/aday/cvsroot/gmod-das2/t/logs',
!                              'maxclients' => 1,
!                              'group' => 'users',
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/nfs/home/aday/cvsroot/gmod-das2/t/htdocs',
!                              'serverroot' => '/nfs/home/aday/cvsroot/gmod-das2/t',
!                              'sslca' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
--- 451,477 ----
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/media/home/boconnor/Development/cvsroot/das2/t/conf',
!                              'servername' => 'london',
!                              'inherit_documentroot' => '/www/turnkey_web/html',
                               'proxy' => 'off',
!                              'serveradmin' => 'admin@...',
                               'authname' => 'gold club',
                               'remote_addr' => '127.0.0.1',
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
+                              'php_module_name' => 'mod_php4',
+                              'php_module' => 'mod_php4.c',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/media/home/boconnor/Development/cvsroot/das2/t/logs',
!                              'minclients' => 1,
!                              'maxclients' => 2,
!                              'group' => 'boconnor',
!                              'maxclientsthreadedmpm' => 2,
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/media/home/boconnor/Development/cvsroot/das2/t/htdocs',
!                              'serverroot' => '/media/home/boconnor/Development/cvsroot/das2/t',
!                              'sslca' => '/media/home/boconnor/Development/cvsroot/das2/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
***************
*** 527,549 ****
                   'clean' => {
                                'files' => {
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/logs/apache_runtime_status.sem' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/apache_test_config.pm' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf' => 1
                                           }
                              },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
-                                 'mod_auth_mysql.c' => '/etc/httpd/modules/mod_auth_mysql.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
-                                 'mod_auth_kerb.c' => '/etc/httpd/modules/mod_auth_kerb.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
-                                 'mod_authz_svn.c' => '/etc/httpd/modules/mod_authz_svn.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
--- 481,507 ----
                   'clean' => {
                                'files' => {
!                                            '/media/home/boconnor/Development/cvsroot/das2/t/logs/apache_runtime_status.sem' => 1,
!                                            '/media/home/boconnor/Development/cvsroot/das2/t/conf/apache_test_config.pm' => 1,
!                                            '/media/home/boconnor/Development/cvsroot/das2/t/conf/httpd.conf' => 1
                                           }
                              },
+                  'httpd_info' => {
+                                    'BUILT' => 'Jun 29 2004 12:19:05',
+                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
+                                    'VERSION' => 'Apache/2.0.50',
+                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
+                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
+                                  },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
***************
*** 551,555 ****
                                  'mod_auth_digest.c' => '/etc/httpd/modules/mod_auth_digest.so',
                                  'mod_log_config.c' => '/etc/httpd/modules/mod_log_config.so',
-                                 'mod_jk2.c' => '/etc/httpd/modules/mod_jk2.so',
                                  'proxy_connect.c' => '/etc/httpd/modules/mod_proxy_connect.so',
                                  'mod_env.c' => '/etc/httpd/modules/mod_env.so',
--- 509,512 ----
***************
*** 562,566 ****
                                  'mod_dav_fs.c' => '/etc/httpd/modules/mod_dav_fs.so',
                                  'proxy_ftp.c' => '/etc/httpd/modules/mod_proxy_ftp.so',
-                                 'mod_dav_svn.c' => '/etc/httpd/modules/mod_dav_svn.so',
                                  'core.c' => 1,
                                  'http_core.c' => 1,
--- 519,522 ----
***************
*** 579,583 ****
                                  'mod_perl.c' => '/etc/httpd/modules/mod_perl.so',
                                  'mod_expires.c' => '/etc/httpd/modules/mod_expires.so',
-                                 'mod_auth_pgsql.c' => '/etc/httpd/modules/mod_auth_pgsql.so',
                                  'mod_alias.c' => '/etc/httpd/modules/mod_alias.so',
                                  'mod_imap.c' => '/etc/httpd/modules/mod_imap.so',
--- 535,538 ----
***************
*** 591,601 ****
                                  'mod_vhost_alias.c' => '/etc/httpd/modules/mod_vhost_alias.so'
                                },
-                  'httpd_info' => {
-                                    'BUILT' => 'Jun 29 2004 12:19:05',
-                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
-                                    'VERSION' => 'Apache/2.0.50',
-                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
-                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
-                                  },
                   'httpd_defines' => {
                                        'SUEXEC_BIN' => '/usr/sbin/suexec',
--- 546,549 ----

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32325/lib/Bio/Das2

Added Files:
	Configure.pm 
Log Message:
Created a module for config file reading (Bio::Das2::Configure) which will probably be switch to Package-Tools bundle created by Allen

--- NEW FILE: Configure.pm ---
package Bio::Das2::Configure;

use strict;
require Exporter;
use File::Spec::Functions qw[ catfile catdir ];
use ExtUtils::MakeMaker;


our @ISA = qw(Exporter);
our @EXPORT = qw(read_config);

=head2 read_config()

 Usage   : $args = $object->read_config();
 Returns : hashref of arguments
 Args    : the hashref, build_conf file
 Function: given a hashref and the conf file it fills the 
           hashref with the settings either from the file or 
           by asking the questions contained in the harshref

=cut

sub read_config {
  my ($args, $build_config) = @_;
  my %opts = ();
  if ( -e $build_config && -r _ ) {
    open CONF, "<$build_config" or die "Can't read file '$build_config': $!\n";
    while ( <CONF> ) {
      chomp;
      next if /^\#/;
      if ( /^(.+)=(.+)$/o ) {
        $args->{ $1 }{value} = $2;
      }
    }
    close CONF;
  }

  #
  # Now figure out where the values are coming from -- build.conf, 
  # command-line, or prompt().
  #
  if ( -e $build_config && -r _ ) {
    my $answer = prompt(
      "Previous configuration detected.\nUse values in '$build_config'?", 'Y'
    );
  
    $opts{'RECONFIGURE'} = $answer =~ /^[Yy]/ ? 1 : 0;
  }
  
  if ( !$opts{'RECONFIGURE'} ) {
    #
    # Make sure everything has a value and looks kosher.
    #
    foreach my $key (keys %{$args}) {
      $args->{$key}{value} = prompt( $args->{$key}{prompt}, 
      $args->{$key}{value} || $args->{$key}{default});
    }
  }

  # print out what's in the conf hash
  print "Building with the following options:\n";
  foreach my $key (keys (%{$args})) {
    print "  $key\t=\t$args->{$key}{value}\n";
  }

  # return the $arg ref
  return($args);
}

return(1);

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32325

Modified Files:
	Makefile.PL 
Log Message:
Created a module for config file reading (Bio::Das2::Configure) which will probably be switch to Package-Tools bundle created by Allen

Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Makefile.PL	24 Sep 2004 08:23:19 -0000	1.7
--- Makefile.PL	26 Sep 2004 07:55:09 -0000	1.8
***************
*** 11,14 ****
--- 11,15 ----
  use File::Spec::Functions qw[ catfile catdir ];
  use Data::Dumper;
+ use Bio::Das2::Configure; 
  
  use Symbol;
***************
*** 35,42 ****
  my %args = (
    GBROWSE_LIB => {
!     default => '/path/to/gmod-gbrowse/lib'
    },
    BIOPERL_LIVE => {
!     default => '/path/to/bioperl-live'
    },
  );
--- 36,45 ----
  my %args = (
    GBROWSE_LIB => {
!     default => '/path/to/gmod-gbrowse/lib',
!     prompt  => 'Where is your Gbrowse lib?',
    },
    BIOPERL_LIVE => {
!     default => '/path/to/bioperl-live',
!     prompt  => 'Where is your BioPerl live lib?',
    },
  );
***************
*** 93,158 ****
  
  ######################################################################
- # config file support 
- ######################################################################
- 
- sub read_config {
-   my ($args, $build_config) = @_;
-   my %opts = ();
-   if ( -e $build_config && -r _ ) {
-     open CONF, "<$build_config" or die "Can't read file '$build_config': $!\n";
-     while ( <CONF> ) {
-       chomp;
-       next if /^\#/;
-       if ( /^(.+)=(.+)$/o ) {
-         $args{ $1 }{value} = $2;
-       }
-     }
-     close CONF;
-   }
- 
-   #
-   # Now figure out where the values are coming from -- build.conf, 
-   # command-line, or prompt().
-   #
-   if ( -e $build_config && -r _ ) {
-     my $answer = prompt(
-       "Previous configuration detected.\nUse values in '$build_config'?", 'Y'
-     );
-   
-     $opts{'RECONFIGURE'} = $answer =~ /^[Yy]/ ? 1 : 0;
-   }
-   
-   if ( !$opts{'RECONFIGURE'} ) {
-   #
-   # Make sure everything has a value and looks kosher.
-   #
-   $args{GBROWSE_LIB}{value} = prompt( 'Where is your Gbrowse lib?', 
-     $args{GBROWSE_LIB}{value} || $args{'GBROWSE_LIB'}{'default'}
-   );
- 
-   $args{BIOPERL_LIVE}{value} = prompt( 'Where is your BioPerl live lib?', 
-     $args{BIOPERL_LIVE}{value} || $args{'BIOPERL_LIVE'}{'default'}
-   );
-   }
- 
-   # print out what's in the conf hash
-   print "Building with the following options:\n";
-   foreach my $key (keys (%{$args})) {
-     print "  $key\t=\t$args->{$key}{value}\n";
-   }
- 
-   #
-   # Save build options.
-   #
-   if ( open CONF, ">$build_config" ) {
-   
-     print CONF map { "$_=$args->{ $_ }{value}\n" } keys %{$args};
-     close CONF or die "Can't write file '$build_config': $!\n";
-   }
-   
- 
- } 
- 
- ######################################################################
  # functions to generate log4perl.conf from MANIFEST
  ######################################################################
--- 96,99 ----

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5441

Modified Files:
	Makefile.PL 
Log Message:
Added build.conf support and removed hard coding of libraries in for the startup.pl file generated by Makefile.PL

Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Makefile.PL	21 Sep 2004 07:42:36 -0000	1.6
--- Makefile.PL	24 Sep 2004 08:23:19 -0000	1.7
***************
*** 9,12 ****
--- 9,14 ----
  use Cwd;
  use Term::ANSIColor;
+ use File::Spec::Functions qw[ catfile catdir ];
+ use Data::Dumper;
  
  use Symbol;
***************
*** 28,31 ****
--- 30,47 ----
  my $base = 'lib/';
  
+ my $working_dir  = cwd;
+ my $build_config = catfile $working_dir, 'build.conf';
+ 
+ my %args = (
+   GBROWSE_LIB => {
+     default => '/path/to/gmod-gbrowse/lib'
+   },
+   BIOPERL_LIVE => {
+     default => '/path/to/bioperl-live'
+   },
+ );
+ 
+ read_config(\%args, $build_config);
+ 
  foreach (@scripts){
    Apache::TestMM::generate_script($_);
***************
*** 76,79 ****
--- 92,156 ----
  );
  
+ ######################################################################
+ # config file support 
+ ######################################################################
+ 
+ sub read_config {
+   my ($args, $build_config) = @_;
+   my %opts = ();
+   if ( -e $build_config && -r _ ) {
+     open CONF, "<$build_config" or die "Can't read file '$build_config': $!\n";
+     while ( <CONF> ) {
+       chomp;
+       next if /^\#/;
+       if ( /^(.+)=(.+)$/o ) {
+         $args{ $1 }{value} = $2;
+       }
+     }
+     close CONF;
+   }
+ 
+   #
+   # Now figure out where the values are coming from -- build.conf, 
+   # command-line, or prompt().
+   #
+   if ( -e $build_config && -r _ ) {
+     my $answer = prompt(
+       "Previous configuration detected.\nUse values in '$build_config'?", 'Y'
+     );
+   
+     $opts{'RECONFIGURE'} = $answer =~ /^[Yy]/ ? 1 : 0;
+   }
+   
+   if ( !$opts{'RECONFIGURE'} ) {
+   #
+   # Make sure everything has a value and looks kosher.
+   #
+   $args{GBROWSE_LIB}{value} = prompt( 'Where is your Gbrowse lib?', 
+     $args{GBROWSE_LIB}{value} || $args{'GBROWSE_LIB'}{'default'}
+   );
+ 
+   $args{BIOPERL_LIVE}{value} = prompt( 'Where is your BioPerl live lib?', 
+     $args{BIOPERL_LIVE}{value} || $args{'BIOPERL_LIVE'}{'default'}
+   );
+   }
+ 
+   # print out what's in the conf hash
+   print "Building with the following options:\n";
+   foreach my $key (keys (%{$args})) {
+     print "  $key\t=\t$args->{$key}{value}\n";
+   }
+ 
+   #
+   # Save build options.
+   #
+   if ( open CONF, ">$build_config" ) {
+   
+     print CONF map { "$_=$args->{ $_ }{value}\n" } keys %{$args};
+     close CONF or die "Can't write file '$build_config': $!\n";
+   }
+   
+ 
+ } 
  
  ######################################################################
***************
*** 104,108 ****
    my $call = 'load($_) foreach qw('.join(' ',@modules).');';
  
!   print STARTUP sprintf("use lib qw(%s/lib /nfs/home/aday/cvsroot/gmod-gbrowse/lib /nfs/home/aday/cvsroot/bioperl-live);",$ENV{PWD}), "\n";
  
    print STARTUP <<'_NO_GROK_';
--- 181,185 ----
    my $call = 'load($_) foreach qw('.join(' ',@modules).');';
  
!   print STARTUP sprintf("use lib qw(%s/lib  $args{BIOPERL_LIVE}{value} $args{BIOPERL_LIVE}{value} );",$ENV{PWD}), "\n";
  
    print STARTUP <<'_NO_GROK_';

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12579

Added Files:
	INSTALL 
Log Message:
Some initial install notes

--- NEW FILE: INSTALL ---
don't make install it -- it isn't ready for that.  you should do:

% perl Makefile.PL
% make
% make test

and you'll have a clean httpd running on port 8529.

you need to make sure you have the following rpms installed (and their 
prerequisites, of course):

httpd
httpd-devel
mod_perl

as well as gbrowse and bioperl-live with the default settings.  i can send
you a gbrowse i386 RPM that i made if you like.

you may also need to alter the lib paths in the Makefile.PL subroutine
that generates t/conf/startup.pl... i haven't come up with a way to
autodetect proper lib paths or allow specifying them as a paramter to
Makefile.PL yet.  i'll get on this soon.  it will probably require (for 
developers, who may have libs in alternate locations), running Makefile.PL 
like this:

perl -I/my/dev/libpath1 -I/my/dev/libpath2 Makefile.PL

and then hardcoding the contents of @INC into startup.pl

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22090/lib/Bio/Das2

Modified Files:
	Server.pm 
Log Message:
a bit of cleanup


Index: Server.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Server.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Server.pm	21 Sep 2004 06:36:03 -0000	1.6
--- Server.pm	21 Sep 2004 07:42:36 -0000	1.7
***************
*** 1,10 ****
  package Bio::Das2::Server;
  
  use strict;
  use warnings;
  no warnings 'redefine';
- use Bio::Das2::Base;
- use base qw(Bio::Das2::Base);
  
  use APR::Table;
  use Apache::Const -compile => qw(:common :http);
--- 1,10 ----
  package Bio::Das2::Server;
  
+ #standard libs
  use strict;
  use warnings;
  no warnings 'redefine';
  
+ #apache libs
  use APR::Table;
  use Apache::Const -compile => qw(:common :http);
***************
*** 13,26 ****
  use Apache::Server;
  
! use Bio::Graphics::Browser;
! use Bio::Graphics::Browser::Util;
! use Data::Dumper;
! 
  use Bio::Das2::Constants;
  use Bio::Das2::SourceFactory;
  
! sub setup_arg {
    my $self = shift;
!   my $arg_string = shift || '';
    my %arg = ();
  
--- 13,41 ----
  use Apache::Server;
  
! #libs for this content handler
! use Bio::Das2::Base;
  use Bio::Das2::Constants;
  use Bio::Das2::SourceFactory;
+ use base qw(Bio::Das2::Base);
  
! #other libs
! use Data::Dumper;
! 
! =head2 parse_get_args
! 
!  Title   : parse_get_args
!  Usage   :
!  Function:
!  Example :
!  Returns : 
!  Args    :
! 
! 
! =cut
! 
! sub parse_get_args {
    my $self = shift;
!   my $arg_string = $self->r->args();
! 
    my %arg = ();
  
***************
*** 29,33 ****
  
      #FIXME this does not handle multiple values for a given key
!     $arg{$k} = $v;
    }
  
--- 44,53 ----
  
      #FIXME this does not handle multiple values for a given key
!     if($arg{$k}){
!       $self->log->error("multiple values for GET argument '$k', ignoring all but first.".
!                        "  this needs to be fixed");
!     } else {
!       $arg{$k} = $v;
!     }
    }
  
***************
*** 35,38 ****
--- 55,65 ----
  }
  
+ sub setup_arg {
+   my $self = shift;
+   my $arg_string = shift || '';
+   my %arg = ();
+ 
+ }
+ 
  sub handler {
    my $r = shift;
***************
*** 86,89 ****
--- 113,120 ----
    #P / das2 / <source> / <version> / type    / <record>
  
+ 
+   #FIXME this big if block needs to be restructured and converted to a class-
+   #or at the least subroutine-based dispatching mechanism.
+ 
    my $output = '';
    my $param =

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22090

Modified Files:
	Makefile.PL 
Log Message:
a bit of cleanup


Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Makefile.PL	15 Sep 2004 01:34:51 -0000	1.5
--- Makefile.PL	21 Sep 2004 07:42:36 -0000	1.6
***************
*** 57,61 ****
  	      'PREREQ_PM'    => {
                                   'Apache::Test'      => 1.13,
! 				 'Bio::Perl'         => 1.02,
  				 'Template'          => 2.00,
                                   'Term::ANSIColor'   => 0,
--- 57,61 ----
  	      'PREREQ_PM'    => {
                                   'Apache::Test'      => 1.13,
! 				 'Bio::Perl'         => 1.08,
  				 'Template'          => 2.00,
                                   'Term::ANSIColor'   => 0,

Update of /cvsroot/gmod/das2/t/htdocs/templates
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11659/t/htdocs/templates

Added Files:
	type.tt2 
Log Message:
added template for /type command output.  throw unimplemented error on 
type command (was previously returning DAS2_OK)



--- NEW FILE: type.tt2 ---
what do you want?

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11659/lib/Bio/Das2

Modified Files:
	Server.pm 
Log Message:
added template for /type command output.  throw unimplemented error on 
type command (was previously returning DAS2_OK)



Index: Server.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Server.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Server.pm	21 Sep 2004 06:29:07 -0000	1.5
--- Server.pm	21 Sep 2004 06:36:03 -0000	1.6
***************
*** 179,185 ****
  
          $self->template->process('type.tt2',$param,\$output);
-         $self->r->print($output);
  
!         return $self->success();
  
        } else {
--- 179,187 ----
  
          $self->template->process('type.tt2',$param,\$output);
  
!         #not yet
!         #$self->r->print($output);
!         #return $self->success();
!         return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case O.  FIXME, not implemented');
  
        } else {

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10276/lib/Bio/Das2

Modified Files:
	Constants.pm Server.pm 
Log Message:
added a README, empty, but now if tests fail users at least know where to
look.

modified Bio::Das2::Constants to allow reverse-translation of an error code
to string.  for instance code2string(403) returns 'DAS2_REGION_UNKNOWN'.

started building a URL list from the spec to test commands.  i could use
some help fleshing this out... this is also a convenient way to make sure
we cover all our test cases.



Index: Server.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Server.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Server.pm	17 Sep 2004 21:53:57 -0000	1.4
--- Server.pm	21 Sep 2004 06:29:07 -0000	1.5
***************
*** 3,6 ****
--- 3,7 ----
  use strict;
  use warnings;
+ no warnings 'redefine';
  use Bio::Das2::Base;
  use base qw(Bio::Das2::Base);
***************
*** 172,177 ****
          return $self->success();
  
        } else {
!         return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case D, G, I, L, or O.  FIXME, not implemented');
        }
  
--- 173,188 ----
          return $self->success();
  
+       } elsif($p_command eq 'type'){
+         $self->log->info('case O: /das2/<source>/<version>/type');
+ 
+         $self->log->debug("types: ".$vsource->types());
+ 
+         $self->template->process('type.tt2',$param,\$output);
+         $self->r->print($output);
+ 
+         return $self->success();
+ 
        } else {
!         return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case D, G, I, or L.  FIXME, not implemented');
        }
  

Index: Constants.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Constants.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Constants.pm	17 Sep 2004 21:53:57 -0000	1.2
--- Constants.pm	21 Sep 2004 06:29:07 -0000	1.3
***************
*** 31,34 ****
--- 31,43 ----
  
    push @EXPORT, (keys %constants);
+ 
+   sub code2string {
+     my $code = shift;
+     foreach my $constant (keys %constants){
+       return $constant if $constants{$constant} == $code;
+     }
+     return 'UNKNOWN DAS2 CONSTANT';
+   }
+ 
  }

Update of /cvsroot/gmod/das2/t
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10276/t

Modified Files:
	TEST.PL 
Added Files:
	02.commands.t 
Log Message:
added a README, empty, but now if tests fail users at least know where to
look.

modified Bio::Das2::Constants to allow reverse-translation of an error code
to string.  for instance code2string(403) returns 'DAS2_REGION_UNKNOWN'.

started building a URL list from the spec to test commands.  i could use
some help fleshing this out... this is also a convenient way to make sure
we cover all our test cases.



Index: TEST.PL
===================================================================
RCS file: /cvsroot/gmod/das2/t/TEST.PL,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** TEST.PL	10 Sep 2004 13:38:32 -0000	1.1.1.1
--- TEST.PL	21 Sep 2004 06:29:07 -0000	1.2
***************
*** 40,44 ****
      print <<EOI;
  +-----------------------------------------------------+
! | To report problems please refer to the SUPPORT file |
  +-----------------------------------------------------+
  EOI
--- 40,44 ----
      print <<EOI;
  +-----------------------------------------------------+
! | To report problems please refer to the README file  |
  +-----------------------------------------------------+
  EOI

--- NEW FILE: 02.commands.t ---
use strict;
use warnings FATAL => 'all';

BEGIN {
  use Apache::Test;
  plan tests => 15;
  ok(1);
  use Apache::TestRequest;
  ok(1);
  use Bio::Das2::Constants;
  ok(1);
  use Data::Dumper;
  ok(1);
}


ok(my $config = Apache::Test::config());
ok(my $server = $config->server);
ok($server->ping);

my @urls = qw(
              /das2
              /das2/yeast_chr1
              /das2/yeast_chr1/0.01
              /das2/yeast_chr1/0.01/region
              /das2/yeast_chr1/0.01/feature
              /das2/yeast_chr1/0.01/sequence
              /das2/yeast_chr1/0.01/type
              /das2/yeast_chr1/0.01/attribute
             );

foreach my $url (@urls){
  my $response = GET($url);
  if($response->code == 200){
    ok($url);
  } else {
    print STDERR sprintf(" skipped %-40s response: %s",$url,Bio::Das2::Constants::code2string($response->code)),"\n";
    skip(1);
  }
}

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10276

Added Files:
	README 
Log Message:
added a README, empty, but now if tests fail users at least know where to
look.

modified Bio::Das2::Constants to allow reverse-translation of an error code
to string.  for instance code2string(403) returns 'DAS2_REGION_UNKNOWN'.

started building a URL list from the spec to test commands.  i could use
some help fleshing this out... this is also a convenient way to make sure
we cover all our test cases.



--- NEW FILE: README ---

Update of /cvsroot/gmod/das2/t/conf
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30228/t/conf

Modified Files:
	apache_test_config.pm 
Log Message:
updated handler to attach appropriate X-DAS-* headers to response.

prefixed constants, now DAS2_*



Index: apache_test_config.pm
===================================================================
RCS file: /cvsroot/gmod/das2/t/conf/apache_test_config.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** apache_test_config.pm	15 Sep 2004 01:01:47 -0000	1.4
--- apache_test_config.pm	17 Sep 2004 21:53:59 -0000	1.5
***************
*** 1,10 ****
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:875
! # 02: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:893
! # 03: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1710
! # 04: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:500
! # 05: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! # 06: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! # 07: /usr/local/src/gmod-das2-allenday/t/TEST:81
  
  package apache_test_config;
--- 1,10 ----
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:751
! # 02: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:769
! # 03: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1530
! # 04: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:437
! # 05: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! # 06: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! # 07: t/TEST:81
  
  package apache_test_config;
***************
*** 15,20 ****
                   'hostport' => 'localhost.localdomain:8529',
                   'postamble' => [
!                                   'TypesConfig "/usr/local/src/gmod-das2-allenday/t/conf/mime.types"',
!                                   'Include "/usr/local/src/gmod-das2-allenday/t/conf/extra.conf"',
                                    ''
                                  ],
--- 15,20 ----
                   'hostport' => 'localhost.localdomain:8529',
                   'postamble' => [
!                                   'TypesConfig "/etc/mime.types"',
!                                   'Include "/nfs/home/aday/cvsroot/gmod-das2/t/conf/extra.conf"',
                                    ''
                                  ],
***************
*** 39,43 ****
                                         'ServerRoot' => '/etc/httpd',
                                         'ServerAdmin' => 'root@...',
!                                        'TypesConfig' => '',
                                         'DocumentRoot' => '/var/www/html',
                                         'LoadModule' => [
--- 39,43 ----
                                         'ServerRoot' => '/etc/httpd',
                                         'ServerAdmin' => 'root@...',
!                                        'TypesConfig' => '/etc/mime.types',
                                         'DocumentRoot' => '/var/www/html',
                                         'LoadModule' => [
***************
*** 107,114 ****
                                                           ],
                                                           [
-                                                            'unique_id_module',
-                                                            'modules/mod_unique_id.so'
-                                                          ],
-                                                          [
                                                             'setenvif_module',
                                                             'modules/mod_setenvif.so'
--- 107,110 ----
***************
*** 219,222 ****
--- 215,234 ----
                                                           ],
                                                           [
+                                                            'auth_kerb_module',
+                                                            'modules/mod_auth_kerb.so'
+                                                          ],
+                                                          [
+                                                            'mysql_auth_module',
+                                                            'modules/mod_auth_mysql.so'
+                                                          ],
+                                                          [
+                                                            'auth_pgsql_module',
+                                                            'modules/mod_auth_pgsql.so'
+                                                          ],
+                                                          [
+                                                            'jk2_module',
+                                                            'modules/mod_jk2.so'
+                                                          ],
+                                                          [
                                                             'perl_module',
                                                             'modules/mod_perl.so'
***************
*** 233,236 ****
--- 245,256 ----
                                                             'ssl_module',
                                                             'modules/mod_ssl.so'
+                                                          ],
+                                                          [
+                                                            'dav_svn_module',
+                                                            'modules/mod_dav_svn.so'
+                                                          ],
+                                                          [
+                                                            'authz_svn_module',
+                                                            'modules/mod_authz_svn.so'
                                                           ]
                                                         ]
***************
*** 240,243 ****
--- 260,266 ----
                                         sub { "DUMMY" }
                                       ],
+                  'resolved' => {
+                                  'localhost.localdomain' => 'localhost.localdomain'
+                                },
                   'preamble' => [
                                   '<IfModule !mod_access.c>
***************
*** 305,312 ****
  </IfModule>
  ',
-                                  '<IfModule !mod_unique_id.c>
-     LoadModule unique_id_module "/etc/httpd/modules/mod_unique_id.so"
- </IfModule>
- ',
                                   '<IfModule !mod_setenvif.c>
      LoadModule setenvif_module "/etc/httpd/modules/mod_setenvif.so"
--- 328,331 ----
***************
*** 417,420 ****
--- 436,455 ----
  </IfModule>
  ',
+                                  '<IfModule !mod_auth_kerb.c>
+     LoadModule auth_kerb_module "/etc/httpd/modules/mod_auth_kerb.so"
+ </IfModule>
+ ',
+                                  '<IfModule !mod_auth_mysql.c>
+     LoadModule mysql_auth_module "/etc/httpd/modules/mod_auth_mysql.so"
+ </IfModule>
+ ',
+                                  '<IfModule !mod_auth_pgsql.c>
+     LoadModule auth_pgsql_module "/etc/httpd/modules/mod_auth_pgsql.so"
+ </IfModule>
+ ',
+                                  '<IfModule !mod_jk2.c>
+     LoadModule jk2_module "/etc/httpd/modules/mod_jk2.so"
+ </IfModule>
+ ',
                                   '<IfModule !mod_perl.c>
      LoadModule perl_module "/etc/httpd/modules/mod_perl.so"
***************
*** 433,436 ****
--- 468,479 ----
  </IfModule>
  ',
+                                  '<IfModule !mod_dav_svn.c>
+     LoadModule dav_svn_module "/etc/httpd/modules/mod_dav_svn.so"
+ </IfModule>
+ ',
+                                  '<IfModule !mod_authz_svn.c>
+     LoadModule authz_svn_module "/etc/httpd/modules/mod_authz_svn.so"
+ </IfModule>
+ ',
                                   '<IfModule !mod_mime.c>
      LoadModule mime_module "/usr/lib/httpd/modules/mod_mime.so"
***************
*** 440,448 ****
                                 ],
                   'vars' => {
-                              'defines' => '',
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/usr/local/src/gmod-das2-allenday/t/conf/httpd.conf',
!                              't_dir' => '/usr/local/src/gmod-das2-allenday/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
--- 483,490 ----
                                 ],
                   'vars' => {
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf',
!                              't_dir' => '/nfs/home/aday/cvsroot/gmod-das2/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
***************
*** 452,456 ****
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/usr/local/src/gmod-das2-allenday',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
--- 494,498 ----
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/nfs/home/aday/cvsroot/gmod-das2',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
***************
*** 459,463 ****
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/usr/local/src/gmod-das2-allenday/t/conf',
                               'servername' => 'localhost.localdomain',
                               'inherit_documentroot' => '/var/www/html',
--- 501,505 ----
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf',
                               'servername' => 'localhost.localdomain',
                               'inherit_documentroot' => '/var/www/html',
***************
*** 468,486 ****
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
-                              'php_module_name' => 'mod_php4',
-                              'php_module' => 'mod_php4.c',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/usr/local/src/gmod-das2-allenday/t/logs',
!                              'minclients' => 1,
!                              'maxclients' => 2,
                               'group' => 'users',
-                              'apxs' => '/usr/sbin/apxs',
-                              'maxclientsthreadedmpm' => 2,
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/usr/local/src/gmod-das2-allenday/t/htdocs',
!                              'serverroot' => '/usr/local/src/gmod-das2-allenday/t',
!                              'sslca' => '/usr/local/src/gmod-das2-allenday/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
--- 510,523 ----
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/nfs/home/aday/cvsroot/gmod-das2/t/logs',
!                              'maxclients' => 1,
                               'group' => 'users',
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/nfs/home/aday/cvsroot/gmod-das2/t/htdocs',
!                              'serverroot' => '/nfs/home/aday/cvsroot/gmod-das2/t',
!                              'sslca' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
***************
*** 490,523 ****
                   'clean' => {
                                'files' => {
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/apache_test_config.pm' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/mime.types' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/htdocs/index.html' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/httpd.conf' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/extra.conf' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/logs/apache_runtime_status.sem' => 1
!                                          },
!                               'dirs' => {
!                                           '/usr/local/src/gmod-das2-allenday/t/logs' => 1
!                                         }
                              },
-                  'httpd_info' => {
-                                    'BUILT' => 'Jul  1 2004 08:49:07',
-                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
-                                    'VERSION' => 'Apache/2.0.50',
-                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
-                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
-                                  },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
!                                 'mod_unique_id.c' => '/etc/httpd/modules/mod_unique_id.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
--- 527,549 ----
                   'clean' => {
                                'files' => {
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/logs/apache_runtime_status.sem' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/apache_test_config.pm' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf' => 1
!                                          }
                              },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
+                                 'mod_auth_mysql.c' => '/etc/httpd/modules/mod_auth_mysql.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
+                                 'mod_auth_kerb.c' => '/etc/httpd/modules/mod_auth_kerb.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
!                                 'mod_authz_svn.c' => '/etc/httpd/modules/mod_authz_svn.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
***************
*** 525,528 ****
--- 551,555 ----
                                  'mod_auth_digest.c' => '/etc/httpd/modules/mod_auth_digest.so',
                                  'mod_log_config.c' => '/etc/httpd/modules/mod_log_config.so',
+                                 'mod_jk2.c' => '/etc/httpd/modules/mod_jk2.so',
                                  'proxy_connect.c' => '/etc/httpd/modules/mod_proxy_connect.so',
                                  'mod_env.c' => '/etc/httpd/modules/mod_env.so',
***************
*** 535,538 ****
--- 562,566 ----
                                  'mod_dav_fs.c' => '/etc/httpd/modules/mod_dav_fs.so',
                                  'proxy_ftp.c' => '/etc/httpd/modules/mod_proxy_ftp.so',
+                                 'mod_dav_svn.c' => '/etc/httpd/modules/mod_dav_svn.so',
                                  'core.c' => 1,
                                  'http_core.c' => 1,
***************
*** 551,554 ****
--- 579,583 ----
                                  'mod_perl.c' => '/etc/httpd/modules/mod_perl.so',
                                  'mod_expires.c' => '/etc/httpd/modules/mod_expires.so',
+                                 'mod_auth_pgsql.c' => '/etc/httpd/modules/mod_auth_pgsql.so',
                                  'mod_alias.c' => '/etc/httpd/modules/mod_alias.so',
                                  'mod_imap.c' => '/etc/httpd/modules/mod_imap.so',
***************
*** 562,565 ****
--- 591,601 ----
                                  'mod_vhost_alias.c' => '/etc/httpd/modules/mod_vhost_alias.so'
                                },
+                  'httpd_info' => {
+                                    'BUILT' => 'Jun 29 2004 12:19:05',
+                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
+                                    'VERSION' => 'Apache/2.0.50',
+                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
+                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
+                                  },
                   'httpd_defines' => {
                                        'SUEXEC_BIN' => '/usr/sbin/suexec',

Update of /cvsroot/gmod/das2/t/htdocs/templates
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30228/t/htdocs/templates

Modified Files:
	das.tt2 
Log Message:
updated handler to attach appropriate X-DAS-* headers to response.

prefixed constants, now DAS2_*



Index: das.tt2
===================================================================
RCS file: /cvsroot/gmod/das2/t/htdocs/templates/das.tt2,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** das.tt2	15 Sep 2004 01:38:32 -0000	1.2
--- das.tt2	17 Sep 2004 21:53:59 -0000	1.3
***************
*** 12,16 ****
    [%- END %]
    </SOURCE>
! [%- END %]
  </SOURCES>
  [% ELSIF format == 'compact' %]
--- 12,16 ----
    [%- END %]
    </SOURCE>
! [% END -%]
  </SOURCES>
  [% ELSIF format == 'compact' %]

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30228/lib/Bio/Das2

Modified Files:
	Constants.pm Server.pm 
Log Message:
updated handler to attach appropriate X-DAS-* headers to response.

prefixed constants, now DAS2_*



Index: Server.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Server.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Server.pm	11 Sep 2004 02:04:22 -0000	1.3
--- Server.pm	17 Sep 2004 21:53:57 -0000	1.4
***************
*** 6,9 ****
--- 6,10 ----
  use base qw(Bio::Das2::Base);
  
+ use APR::Table;
  use Apache::Const -compile => qw(:common :http);
  use Apache::RequestIO;
***************
*** 35,38 ****
--- 36,41 ----
  sub handler {
    my $r = shift;
+   $r->err_headers_out->add('X-DAS-Version','DAS/2.0');
+ 
    my $self = __PACKAGE__->new(r => $r);
  
***************
*** 93,98 ****
  
      if($arg{format} ne 'das2xml' and $arg{format} ne 'compact'){
!       $self->log->error("bad format: '$arg{format}'");
!       return BAD_DATA_FORMAT;
      }
  
--- 96,100 ----
  
      if($arg{format} ne 'das2xml' and $arg{format} ne 'compact'){
!       return $self->error(DAS2_BAD_DATA_FORMAT,"bad format: '$arg{format}'");
      }
  
***************
*** 100,104 ****
      $self->template->process('das.tt2',$param,\$output);
      $self->r->print($output);
!     return OK;
  
    }
--- 102,106 ----
      $self->template->process('das.tt2',$param,\$output);
      $self->r->print($output);
!     return $self->success();
  
    }
***************
*** 107,112 ****
      $self->log->info('case B: /das2/<source>');
      if($arg{format} ne 'das2xml' and $arg{format} ne 'compact'){
!       $self->log->error("bad format: '$arg{format}'");
!       return BAD_DATA_FORMAT;
      }
  
--- 109,113 ----
      $self->log->info('case B: /das2/<source>');
      if($arg{format} ne 'das2xml' and $arg{format} ne 'compact'){
!       return $self->error(DAS2_BAD_DATA_FORMAT,"bad format: '$arg{format}'")
      }
  
***************
*** 116,120 ****
      $self->r->print($output);
  
!     return OK;
    }
  
--- 117,121 ----
      $self->r->print($output);
  
!     return $self->success();
    }
  
***************
*** 133,138 ****
  
      if(!$vsource){
!       $self->log->info('bad source, could not be located');
!       return BAD_DATA_SOURCE;
      }
  
--- 134,138 ----
  
      if(!$vsource){
!       return $self->error(DAS2_BAD_DATA_SOURCE,'bad source, could not be located');
      }
  
***************
*** 146,156 ****
      if(defined($p_selection)){
  
!       $self->log->error('case F, K, or N.  FIXME, not implemented');
!       return UNIMPLEMENTED_FEATURE;
  
      } elsif(defined($p_record)) {
  
!       $self->log->error('case E, H, J, M, or P.  FIXME, not implemented');
!       return UNIMPLEMENTED_FEATURE;
  
      } elsif($p_command){
--- 146,154 ----
      if(defined($p_selection)){
  
!       return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case F, K, or N.  FIXME, not implemented');
  
      } elsif(defined($p_record)) {
  
!       return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case E, H, J, M, or P.  FIXME, not implemented');
  
      } elsif($p_command){
***************
*** 164,168 ****
  
          if(!@regions){
!           return REGION_UNKNOWN;
          }
  
--- 162,166 ----
  
          if(!@regions){
!           return $self->error(DAS2_REGION_UNKNOWN,'');
          }
  
***************
*** 172,180 ****
          $self->r->print($output);
  
!         return OK;
  
        } else {
!         $self->log->error('case D, G, I, L, or O.  FIXME, not implemented');
!         return UNIMPLEMENTED_FEATURE;
        }
  
--- 170,177 ----
          $self->r->print($output);
  
!         return $self->success();
  
        } else {
!         return $self->error(DAS2_UNIMPLEMENTED_FEATURE,'case D, G, I, L, or O.  FIXME, not implemented');
        }
  
***************
*** 184,189 ****
  
        if($arg{format} ne 'das2xml'){
!         $self->log->error("bad format: '$arg{format}'");
!         return BAD_DATA_FORMAT;
        } else {
  
--- 181,185 ----
  
        if($arg{format} ne 'das2xml'){
!         return $self->error(DAS2_BAD_DATA_FORMAT,"bad format: '$arg{format}'");
        } else {
  
***************
*** 194,206 ****
          $self->r->print($output);
  
!         return OK;
        }
      }
    } else {
  
!     $self->log->error('unknown exception');
!     return SERVER_ERROR;
  
!   }
  }
  
--- 190,242 ----
          $self->r->print($output);
  
!         return $self->success();
        }
      }
    } else {
+     return $self->error(DAS2_SERVER_ERROR,'unknown exception');
+   }
+ }
  
! #FIXME should this be in Bio::Das2::Base?
  
! =head2 error
! 
!  Title   : error
!  Usage   : $self->error(DAS2_CODE,$message);
!  Function: writes an error to the log, sets the X-DAS-Status header
!            to DAS2_CODE (See Bio::Das2::Constants), and returns
!            DAS2_CODE.
!  Example :
!  Returns : A Bio::Das2::Constant value
!  Args    : A Bio::Das2::Constant, and an error message.
! 
! 
! =cut
! 
! sub error {
!   my($self,$code,$message) = @_;
!   $self->log->error($message);
!   $self->r->err_headers_out->add('X-DAS-Status',$code);
!   return $code;
! }
! 
! =head2 success
! 
!  Title   : success
!  Usage   : $self->success();
!  Function: sets the X-DAS-Status header and returns DAS2_OK.  The
!            intent is that the handler return this to Apache.
!  Example :
!  Returns : DAS2_OK
!  Args    : 
! 
! 
! =cut
! 
! sub success {
!   my $self = shift;
!   $self->log->info('successful.  exiting handler');
!   $self->r->headers_out->add('X-DAS-Status',200);
!   return DAS2_OK;
  }
  

Index: Constants.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Constants.pm,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** Constants.pm	10 Sep 2004 13:38:33 -0000	1.1.1.1
--- Constants.pm	17 Sep 2004 21:53:57 -0000	1.2
***************
*** 12,25 ****
  
    my %constants = (
!                    OK                      => Apache::OK,
!                    BAD_NAMESPACE           => Apache::HTTP_BAD_REQUEST,
!                    BAD_DATA_SOURCE         => Apache::HTTP_UNAUTHORIZED,
!                    BAD_DATA_FORMAT         => Apache::HTTP_PAYMENT_REQUIRED,
!                    REGION_UNKNOWN          => Apache::HTTP_FORBIDDEN,
!                    RESERVED                => Apache::HTTP_NOT_FOUND,
!                    REGION_COORDINATE_ERROR => Apache::HTTP_METHOD_NOT_ALLOWED,
!                    LOCK_TIMED_OUT          => Apache::HTTP_NOT_ACCEPTABLE,
!                    SERVER_ERROR            => Apache::HTTP_INTERNAL_SERVER_ERROR,
!                    UNIMPLEMENTED_FEATURE   => Apache::HTTP_NOT_IMPLEMENTED,
                    );
  
--- 12,25 ----
  
    my %constants = (
!                    DAS2_OK                      => Apache::OK,
!                    DAS2_BAD_NAMESPACE           => Apache::HTTP_BAD_REQUEST,
!                    DAS2_BAD_DATA_SOURCE         => Apache::HTTP_UNAUTHORIZED,
!                    DAS2_BAD_DATA_FORMAT         => Apache::HTTP_PAYMENT_REQUIRED,
!                    DAS2_REGION_UNKNOWN          => Apache::HTTP_FORBIDDEN,
!                    DAS2_RESERVED                => Apache::HTTP_NOT_FOUND,
!                    DAS2_REGION_COORDINATE_ERROR => Apache::HTTP_METHOD_NOT_ALLOWED,
!                    DAS2_LOCK_TIMED_OUT          => Apache::HTTP_NOT_ACCEPTABLE,
!                    DAS2_SERVER_ERROR            => Apache::HTTP_INTERNAL_SERVER_ERROR,
!                    DAS2_UNIMPLEMENTED_FEATURE   => Apache::HTTP_NOT_IMPLEMENTED,
                    );

Update of /cvsroot/gmod/das2/t/htdocs/templates
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15330/t/htdocs/templates

Modified Files:
	das.tt2 source.tt2 
Log Message:
method name changes propagated to templates (source -> versionedsource)


Index: source.tt2
===================================================================
RCS file: /cvsroot/gmod/das2/t/htdocs/templates/source.tt2,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** source.tt2	10 Sep 2004 13:38:33 -0000	1.1.1.1
--- source.tt2	15 Sep 2004 01:38:32 -0000	1.2
***************
*** 4,8 ****
  <!DOCTYPE DAS2DSNDETAILS SYSTEM "http://www.biodas.org/dtd/das2dsndetails.dtd">
  <SOURCE xmlns="http://www.biodas.org/ns/das/2.00" xmlns:xlink="http://www.w3.org/1999/xlink" xml:base="[% server_hostname %]" id="[% source.id %]" description="[% source.description %]">
!   [%- FOREACH version = source.get_versions %]
    <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]" created="FIXME, a timestamp" modified="FIXME, a timestamp">
      <CAPABILITIES>
--- 4,8 ----
  <!DOCTYPE DAS2DSNDETAILS SYSTEM "http://www.biodas.org/dtd/das2dsndetails.dtd">
  <SOURCE xmlns="http://www.biodas.org/ns/das/2.00" xmlns:xlink="http://www.w3.org/1999/xlink" xml:base="[% server_hostname %]" id="[% source.id %]" description="[% source.description %]">
!   [%- FOREACH version = source.get_versionedsources %]
    <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]" created="FIXME, a timestamp" modified="FIXME, a timestamp">
      <CAPABILITIES>
***************
*** 49,53 ****
        xml:base="[% server_hostname %]">
    <SOURCE id="[% source.id %]" description="[% source.description %]" taxon="http://www.ncbi.nlm.nih.gov/taxon-browser?id=[% source.organism %]">
!     [% FOREACH version = source.get_versions -%]
      <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]" />
      [%- END %]
--- 49,53 ----
        xml:base="[% server_hostname %]">
    <SOURCE id="[% source.id %]" description="[% source.description %]" taxon="http://www.ncbi.nlm.nih.gov/taxon-browser?id=[% source.organism %]">
!     [% FOREACH version = source.get_versionedsources -%]
      <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]" />
      [%- END %]
***************
*** 56,60 ****
  
    [% ELSIF format == 'compact' %]
!     [% FOREACH version = source.get_versions %]
  [% source.id %]    [% version.id %]   [% source.organism %]   [% source.description %] [% version.description %]
      [% END %]
--- 56,60 ----
  
    [% ELSIF format == 'compact' %]
!     [% FOREACH version = source.get_versionedsources %]
  [% source.id %]    [% version.id %]   [% source.organism %]   [% source.description %] [% version.description %]
      [% END %]

Index: das.tt2
===================================================================
RCS file: /cvsroot/gmod/das2/t/htdocs/templates/das.tt2,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** das.tt2	10 Sep 2004 13:38:33 -0000	1.1.1.1
--- das.tt2	15 Sep 2004 01:38:32 -0000	1.2
***************
*** 8,12 ****
  [% FOREACH source = sources -%]
    <SOURCE id="[% source.id %]" description="[% source.description %]" taxon="[% source.organism %]">
!   [% FOREACH version = source.get_versions -%]
      <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]"/>
    [%- END %]
--- 8,12 ----
  [% FOREACH source = sources -%]
    <SOURCE id="[% source.id %]" description="[% source.description %]" taxon="[% source.organism %]">
!   [% FOREACH version = source.get_versionedsources -%]
      <VERSION id="[% source.id %]/[% version.id %]" description="[% version.description %]"/>
    [%- END %]
***************
*** 16,20 ****
  [% ELSIF format == 'compact' %]
  [% FOREACH source = sources -%]
! [% FOREACH version = source.get_versions -%]
  [% source.id %]    [% version.id %]   [% source.organism %]   [% source.description %] [% version.description %]
  [%- END %]
--- 16,20 ----
  [% ELSIF format == 'compact' %]
  [% FOREACH source = sources -%]
! [% FOREACH version = source.get_versionedsources -%]
  [% source.id %]    [% version.id %]   [% source.organism %]   [% source.description %] [% version.description %]
  [%- END %]

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14686

Modified Files:
	Makefile.PL 
Log Message:
removed hardcoded paths, leveraged %ENV.

added debugging to base class.


Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Makefile.PL	15 Sep 2004 01:02:47 -0000	1.4
--- Makefile.PL	15 Sep 2004 01:34:51 -0000	1.5
***************
*** 104,111 ****
    my $call = 'load($_) foreach qw('.join(' ',@modules).');';
  
    print STARTUP <<'_NO_GROK_';
  use strict;
  use Term::ANSIColor;
- use lib qw(/nfs/home/aday/cvsroot/gmod-das2/lib /nfs/home/aday/cvsroot/gmod-gbrowse/lib /nfs/home/aday/cvsroot/bioperl-live);
  
  my $statusformat = "%-60s[%s]\n";
--- 104,112 ----
    my $call = 'load($_) foreach qw('.join(' ',@modules).');';
  
+   print STARTUP sprintf("use lib qw(%s/lib /nfs/home/aday/cvsroot/gmod-gbrowse/lib /nfs/home/aday/cvsroot/bioperl-live);",$ENV{PWD}), "\n";
+ 
    print STARTUP <<'_NO_GROK_';
  use strict;
  use Term::ANSIColor;
  
  my $statusformat = "%-60s[%s]\n";

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14686/lib/Bio/Das2

Modified Files:
	Base.pm Source.pm 
Log Message:
removed hardcoded paths, leveraged %ENV.

added debugging to base class.


Index: Base.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Base.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Base.pm	15 Sep 2004 01:02:47 -0000	1.2
--- Base.pm	15 Sep 2004 01:34:52 -0000	1.3
***************
*** 149,152 ****
--- 149,155 ----
  
    if(!$self->{'log'}){
+     #must warn here b/c logger is not set up yet.
+     warn "setting up logger for $self";
+ 
      my $log4perl_path = $self->r->dir_config('das2_log4perl');
      Log::Log4perl->init($log4perl_path);

Index: Source.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Source.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Source.pm	11 Sep 2004 01:12:34 -0000	1.2
--- Source.pm	15 Sep 2004 01:34:52 -0000	1.3
***************
*** 136,140 ****
  =cut
  
! sub organism{
      my $self = shift;
  
--- 136,140 ----
  =cut
  
! sub organism {
      my $self = shift;
  
***************
*** 155,159 ****
  =cut
  
! sub get_versionedsources{
      my $self = shift;
  
--- 155,159 ----
  =cut
  
! sub get_versionedsources {
      my $self = shift;
  
***************
*** 174,182 ****
  =cut
  
! sub add_versionedsource{
      my $self = shift;
  
      $self->{'_versionedsources'} = [] unless exists($self->{'_versionedsources'});
!     push(@{$self->{'_versionedsources'}}, @_);
  }
  
--- 174,187 ----
  =cut
  
! sub add_versionedsource {
      my $self = shift;
+     my @vals = @_;
  
      $self->{'_versionedsources'} = [] unless exists($self->{'_versionedsources'});
! 
!     foreach my $val (@vals){
!       $self->log->debug("adding VersionedSource $val to $self");
!       push(@{$self->{'_versionedsources'}}, $val);
!     }
  }

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9269

Modified Files:
	MANIFEST 
Log Message:
removed startup.pl from manifest


Index: MANIFEST
===================================================================
RCS file: /cvsroot/gmod/das2/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** MANIFEST	11 Sep 2004 01:14:34 -0000	1.2
--- MANIFEST	15 Sep 2004 01:03:15 -0000	1.3
***************
*** 16,20 ****
  t/conf/apache_test_config.pm
  t/conf/extra.conf.in
- t/conf/startup.pl
  t/htdocs/index.html
  t/htdocs/templates/das.tt2
--- 16,19 ----

Update of /cvsroot/gmod/das2/t/conf
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8991

Modified Files:
	apache_test_config.pm 
Removed Files:
	startup.pl 
Log Message:
auto generate this file at Makefile.PL time due to flock problems at
server start


--- startup.pl DELETED ---

Index: apache_test_config.pm
===================================================================
RCS file: /cvsroot/gmod/das2/t/conf/apache_test_config.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** apache_test_config.pm	11 Sep 2004 01:13:42 -0000	1.3
--- apache_test_config.pm	15 Sep 2004 01:01:47 -0000	1.4
***************
*** 1,10 ****
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:751
! # 02: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:769
! # 03: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1530
! # 04: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:437
! # 05: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! # 06: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! # 07: t/TEST:81
  
  package apache_test_config;
--- 1,10 ----
  # WARNING: this file is generated, do not edit
! # 01: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:875
! # 02: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:893
! # 03: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1710
! # 04: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:500
! # 05: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! # 06: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! # 07: /usr/local/src/gmod-das2-allenday/t/TEST:81
  
  package apache_test_config;
***************
*** 15,20 ****
                   'hostport' => 'localhost.localdomain:8529',
                   'postamble' => [
!                                   'TypesConfig "/etc/mime.types"',
!                                   'Include "/nfs/home/aday/cvsroot/gmod-das2/t/conf/extra.conf"',
                                    ''
                                  ],
--- 15,20 ----
                   'hostport' => 'localhost.localdomain:8529',
                   'postamble' => [
!                                   'TypesConfig "/usr/local/src/gmod-das2-allenday/t/conf/mime.types"',
!                                   'Include "/usr/local/src/gmod-das2-allenday/t/conf/extra.conf"',
                                    ''
                                  ],
***************
*** 39,43 ****
                                         'ServerRoot' => '/etc/httpd',
                                         'ServerAdmin' => 'root@...',
!                                        'TypesConfig' => '/etc/mime.types',
                                         'DocumentRoot' => '/var/www/html',
                                         'LoadModule' => [
--- 39,43 ----
                                         'ServerRoot' => '/etc/httpd',
                                         'ServerAdmin' => 'root@...',
!                                        'TypesConfig' => '',
                                         'DocumentRoot' => '/var/www/html',
                                         'LoadModule' => [
***************
*** 107,110 ****
--- 107,114 ----
                                                           ],
                                                           [
+                                                            'unique_id_module',
+                                                            'modules/mod_unique_id.so'
+                                                          ],
+                                                          [
                                                             'setenvif_module',
                                                             'modules/mod_setenvif.so'
***************
*** 215,234 ****
                                                           ],
                                                           [
-                                                            'auth_kerb_module',
-                                                            'modules/mod_auth_kerb.so'
-                                                          ],
-                                                          [
-                                                            'mysql_auth_module',
-                                                            'modules/mod_auth_mysql.so'
-                                                          ],
-                                                          [
-                                                            'auth_pgsql_module',
-                                                            'modules/mod_auth_pgsql.so'
-                                                          ],
-                                                          [
-                                                            'jk2_module',
-                                                            'modules/mod_jk2.so'
-                                                          ],
-                                                          [
                                                             'perl_module',
                                                             'modules/mod_perl.so'
--- 219,222 ----
***************
*** 245,256 ****
                                                             'ssl_module',
                                                             'modules/mod_ssl.so'
-                                                          ],
-                                                          [
-                                                            'dav_svn_module',
-                                                            'modules/mod_dav_svn.so'
-                                                          ],
-                                                          [
-                                                            'authz_svn_module',
-                                                            'modules/mod_authz_svn.so'
                                                           ]
                                                         ]
--- 233,236 ----
***************
*** 260,266 ****
                                         sub { "DUMMY" }
                                       ],
-                  'resolved' => {
-                                  'localhost.localdomain' => 'localhost.localdomain'
-                                },
                   'preamble' => [
                                   '<IfModule !mod_access.c>
--- 240,243 ----
***************
*** 328,331 ****
--- 305,312 ----
  </IfModule>
  ',
+                                  '<IfModule !mod_unique_id.c>
+     LoadModule unique_id_module "/etc/httpd/modules/mod_unique_id.so"
+ </IfModule>
+ ',
                                   '<IfModule !mod_setenvif.c>
      LoadModule setenvif_module "/etc/httpd/modules/mod_setenvif.so"
***************
*** 436,455 ****
  </IfModule>
  ',
-                                  '<IfModule !mod_auth_kerb.c>
-     LoadModule auth_kerb_module "/etc/httpd/modules/mod_auth_kerb.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_auth_mysql.c>
-     LoadModule mysql_auth_module "/etc/httpd/modules/mod_auth_mysql.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_auth_pgsql.c>
-     LoadModule auth_pgsql_module "/etc/httpd/modules/mod_auth_pgsql.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_jk2.c>
-     LoadModule jk2_module "/etc/httpd/modules/mod_jk2.so"
- </IfModule>
- ',
                                   '<IfModule !mod_perl.c>
      LoadModule perl_module "/etc/httpd/modules/mod_perl.so"
--- 417,420 ----
***************
*** 468,479 ****
  </IfModule>
  ',
-                                  '<IfModule !mod_dav_svn.c>
-     LoadModule dav_svn_module "/etc/httpd/modules/mod_dav_svn.so"
- </IfModule>
- ',
-                                  '<IfModule !mod_authz_svn.c>
-     LoadModule authz_svn_module "/etc/httpd/modules/mod_authz_svn.so"
- </IfModule>
- ',
                                   '<IfModule !mod_mime.c>
      LoadModule mime_module "/usr/lib/httpd/modules/mod_mime.so"
--- 433,436 ----
***************
*** 483,490 ****
                                 ],
                   'vars' => {
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf',
!                              't_dir' => '/nfs/home/aday/cvsroot/gmod-das2/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
--- 440,448 ----
                                 ],
                   'vars' => {
+                              'defines' => '',
                               'cgi_module_name' => 'mod_cgi',
                               'conf_dir' => '/etc/httpd/conf',
!                              't_conf_file' => '/usr/local/src/gmod-das2-allenday/t/conf/httpd.conf',
!                              't_dir' => '/usr/local/src/gmod-das2-allenday/t',
                               'cgi_module' => 'mod_cgi.c',
                               'target' => 'httpd',
***************
*** 494,498 ****
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/nfs/home/aday/cvsroot/gmod-das2',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
--- 452,456 ----
                               'access_module_name' => 'mod_access',
                               'auth_module_name' => 'mod_auth',
!                              'top_dir' => '/usr/local/src/gmod-das2-allenday',
                               'httpd_conf' => '/etc/httpd/conf/httpd.conf',
                               'httpd' => '/usr/sbin/httpd',
***************
*** 501,505 ****
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf',
                               'servername' => 'localhost.localdomain',
                               'inherit_documentroot' => '/var/www/html',
--- 459,463 ----
                               'port' => 8529,
                               'sbindir' => '/usr/sbin',
!                              't_conf' => '/usr/local/src/gmod-das2-allenday/t/conf',
                               'servername' => 'localhost.localdomain',
                               'inherit_documentroot' => '/var/www/html',
***************
*** 510,523 ****
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/nfs/home/aday/cvsroot/gmod-das2/t/logs',
!                              'maxclients' => 1,
                               'group' => 'users',
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/nfs/home/aday/cvsroot/gmod-das2/t/htdocs',
!                              'serverroot' => '/nfs/home/aday/cvsroot/gmod-das2/t',
!                              'sslca' => '/nfs/home/aday/cvsroot/gmod-das2/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
--- 468,486 ----
                               'perlpod' => '/usr/lib/perl5/5.8.3/pod',
                               'sslcaorg' => 'asf',
+                              'php_module_name' => 'mod_php4',
+                              'php_module' => 'mod_php4.c',
                               'ssl_module' => 'mod_ssl.c',
                               'auth_module' => 'mod_auth.c',
                               'access_module' => 'mod_access.c',
!                              't_logs' => '/usr/local/src/gmod-das2-allenday/t/logs',
!                              'minclients' => 1,
!                              'maxclients' => 2,
                               'group' => 'users',
+                              'apxs' => '/usr/sbin/apxs',
+                              'maxclientsthreadedmpm' => 2,
                               'thread_module_name' => 'worker',
!                              'documentroot' => '/usr/local/src/gmod-das2-allenday/t/htdocs',
!                              'serverroot' => '/usr/local/src/gmod-das2-allenday/t',
!                              'sslca' => '/usr/local/src/gmod-das2-allenday/t/conf/ssl/ca',
                               'perl' => '/usr/bin/perl',
                               'src_dir' => undef,
***************
*** 527,551 ****
                   'clean' => {
                                'files' => {
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/logs/apache_runtime_status.sem' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/extra.conf' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/apache_test_config.pm' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/conf/httpd.conf' => 1,
!                                            '/nfs/home/aday/cvsroot/gmod-das2/t/htdocs/index.html' => 1
!                                          }
                              },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
-                                 'mod_auth_mysql.c' => '/etc/httpd/modules/mod_auth_mysql.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
-                                 'mod_auth_kerb.c' => '/etc/httpd/modules/mod_auth_kerb.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
!                                 'mod_authz_svn.c' => '/etc/httpd/modules/mod_authz_svn.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
--- 490,523 ----
                   'clean' => {
                                'files' => {
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/apache_test_config.pm' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/mime.types' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/htdocs/index.html' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/httpd.conf' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/conf/extra.conf' => 1,
!                                            '/usr/local/src/gmod-das2-allenday/t/logs/apache_runtime_status.sem' => 1
!                                          },
!                               'dirs' => {
!                                           '/usr/local/src/gmod-das2-allenday/t/logs' => 1
!                                         }
                              },
+                  'httpd_info' => {
+                                    'BUILT' => 'Jul  1 2004 08:49:07',
+                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
+                                    'VERSION' => 'Apache/2.0.50',
+                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
+                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
+                                  },
                   'modules' => {
                                  'mod_include.c' => '/etc/httpd/modules/mod_include.so',
                                  'mod_headers.c' => '/etc/httpd/modules/mod_headers.so',
                                  'mod_cache.c' => '/etc/httpd/modules/mod_cache.so',
                                  'mod_negotiation.c' => '/etc/httpd/modules/mod_negotiation.so',
                                  'mod_speling.c' => '/etc/httpd/modules/mod_speling.so',
                                  'mod_usertrack.c' => '/etc/httpd/modules/mod_usertrack.so',
                                  'mod_cern_meta.c' => '/etc/httpd/modules/mod_cern_meta.so',
                                  'mod_setenvif.c' => '/etc/httpd/modules/mod_setenvif.so',
                                  'mod_suexec.c' => '/etc/httpd/modules/mod_suexec.so',
                                  'mod_python.c' => '/etc/httpd/modules/mod_python.so',
!                                 'mod_unique_id.c' => '/etc/httpd/modules/mod_unique_id.so',
                                  'mod_auth_ldap.c' => '/etc/httpd/modules/mod_auth_ldap.so',
                                  'mod_status.c' => '/etc/httpd/modules/mod_status.so',
***************
*** 553,557 ****
                                  'mod_auth_digest.c' => '/etc/httpd/modules/mod_auth_digest.so',
                                  'mod_log_config.c' => '/etc/httpd/modules/mod_log_config.so',
-                                 'mod_jk2.c' => '/etc/httpd/modules/mod_jk2.so',
                                  'proxy_connect.c' => '/etc/httpd/modules/mod_proxy_connect.so',
                                  'mod_env.c' => '/etc/httpd/modules/mod_env.so',
--- 525,528 ----
***************
*** 564,568 ****
                                  'mod_dav_fs.c' => '/etc/httpd/modules/mod_dav_fs.so',
                                  'proxy_ftp.c' => '/etc/httpd/modules/mod_proxy_ftp.so',
-                                 'mod_dav_svn.c' => '/etc/httpd/modules/mod_dav_svn.so',
                                  'core.c' => 1,
                                  'http_core.c' => 1,
--- 535,538 ----
***************
*** 581,585 ****
                                  'mod_perl.c' => '/etc/httpd/modules/mod_perl.so',
                                  'mod_expires.c' => '/etc/httpd/modules/mod_expires.so',
-                                 'mod_auth_pgsql.c' => '/etc/httpd/modules/mod_auth_pgsql.so',
                                  'mod_alias.c' => '/etc/httpd/modules/mod_alias.so',
                                  'mod_imap.c' => '/etc/httpd/modules/mod_imap.so',
--- 551,554 ----
***************
*** 593,603 ****
                                  'mod_vhost_alias.c' => '/etc/httpd/modules/mod_vhost_alias.so'
                                },
-                  'httpd_info' => {
-                                    'BUILT' => 'Jun 29 2004 12:19:05',
-                                    'MODULE_MAGIC_NUMBER_MINOR' => '8',
-                                    'VERSION' => 'Apache/2.0.50',
-                                    'MODULE_MAGIC_NUMBER' => '20020903:8',
-                                    'MODULE_MAGIC_NUMBER_MAJOR' => '20020903'
-                                  },
                   'httpd_defines' => {
                                        'SUEXEC_BIN' => '/usr/sbin/suexec',
--- 562,565 ----

Update of /cvsroot/gmod/das2/lib/Bio/Das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9125/lib/Bio/Das2

Modified Files:
	Base.pm 
Log Message:
autogenerate startup.pl now.  this may have consequences for 'make install'


Index: Base.pm
===================================================================
RCS file: /cvsroot/gmod/das2/lib/Bio/Das2/Base.pm,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** Base.pm	10 Sep 2004 13:38:33 -0000	1.1.1.1
--- Base.pm	15 Sep 2004 01:02:47 -0000	1.2
***************
*** 68,72 ****
  use strict;
  
! use Carp qw(longmess);
  use Apache::RequestUtil;
  
--- 68,72 ----
  use strict;
  
! use Carp qw(cluck);
  use Apache::RequestUtil;

Update of /cvsroot/gmod/das2/t/htdocs
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9125/t/htdocs

Modified Files:
	index.html 
Log Message:
autogenerate startup.pl now.  this may have consequences for 'make install'


Index: index.html
===================================================================
RCS file: /cvsroot/gmod/das2/t/htdocs/index.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** index.html	11 Sep 2004 01:13:42 -0000	1.3
--- index.html	15 Sep 2004 01:02:47 -0000	1.4
***************
*** 1,11 ****
  <!-- WARNING: this file is generated, do not edit
! 01: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:751
! 02: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:769
! 03: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1061
! 04: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1264
! 05: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:436
! 06: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! 07: /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:621
! 08: t/TEST:81
   -->
  welcome to localhost.localdomain:8529
--- 1,11 ----
  <!-- WARNING: this file is generated, do not edit
! 01: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:875
! 02: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:893
! 03: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1194
! 04: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestConfig.pm:1427
! 05: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:499
! 06: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! 07: /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Apache/TestRun.pm:714
! 08: /usr/local/src/gmod-das2-allenday/t/TEST:81
   -->
  welcome to localhost.localdomain:8529

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9125

Modified Files:
	Makefile.PL 
Log Message:
autogenerate startup.pl now.  this may have consequences for 'make install'


Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile.PL	15 Sep 2004 00:35:51 -0000	1.3
--- Makefile.PL	15 Sep 2004 01:02:47 -0000	1.4
***************
*** 19,22 ****
--- 19,26 ----
  my $VERSION = 2.001;
  
+ my $statusformat = "%-60s[%s]\n";
+ my $fail         = colored('FAILED','red');
+ my $pass         = colored('  OK  ','green');
+ 
  use constant TOP_LEVEL => !exists $ENV{MOD_PERL_2_BUILD};
  
***************
*** 40,43 ****
--- 44,55 ----
  close(LOG4PERL);
  
+ print STDERR colored("generating t/conf/startup.pl\n", 'cyan');
+ open(STARTUP,">t/conf/startup.pl");
+ startup_pl(process_manifest());
+ close(STARTUP);
+ 
+ print STDERR colored("eval()ing modules from MANIFEST\n", 'cyan');
+ testload($_) foreach process_manifest();
+ 
  WriteMakefile(
  	      'NAME'	     => 'Distributed_Annotation_System_v2',
***************
*** 88,91 ****
--- 100,130 ----
  }
  
+ sub startup_pl {
+   my @modules = @_;
+   my $call = 'load($_) foreach qw('.join(' ',@modules).');';
+ 
+   print STARTUP <<'_NO_GROK_';
+ use strict;
+ use Term::ANSIColor;
+ use lib qw(/nfs/home/aday/cvsroot/gmod-das2/lib /nfs/home/aday/cvsroot/gmod-gbrowse/lib /nfs/home/aday/cvsroot/bioperl-live);
+ 
+ my $statusformat = "%-60s[%s]\n";
+ my $fail         = colored('FAILED','red');
+ my $pass         = colored('  OK  ','green');
+ 
+ sub load {
+   my $pack = shift;
+   eval "use $pack";
+   if($@){ print "\n$@\n" }
+   print STDERR sprintf($statusformat,"    use $pack", ($@ ? $fail : $pass));
+ }
+ 
+ _NO_GROK_
+ 
+   print STARTUP $call, "\n";
+   print STARTUP "1;\n";
+ 
+ }
+ 
  sub logstub {
    my $pack = shift;
***************
*** 114,117 ****
--- 153,163 ----
  }
  
+ sub testload {
+   my $pack = shift;
+   eval "use $pack";
+   if($@){ print "\n$@\n" }
+   print STDERR sprintf($statusformat,"use $pack", ($@ ? $fail : $pass));
+ }
+ 
  ######################################################################
  # the following is ripped off verbatim from Apache::Test's Makefile.PL

Update of /cvsroot/gmod/das2
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4688

Modified Files:
	Makefile.PL 
Log Message:
updated prereqs


Index: Makefile.PL
===================================================================
RCS file: /cvsroot/gmod/das2/Makefile.PL,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile.PL	11 Sep 2004 01:12:34 -0000	1.2
--- Makefile.PL	15 Sep 2004 00:35:51 -0000	1.3
***************
*** 44,52 ****
  	      'VERSION'      => $VERSION,
  	      'PREREQ_PM'    => {
  				 'Bio::Perl'         => 1.02,
! 				 'Template'          => 2.0,
                                   'Term::ANSIColor'   => 0,
                                   'Text::Wrap'        => 0,
! 				 'Log::Log4perl'     => 0, 
  				}, # e.g., Module::Name => 1.1
  	      PL_FILES       => {
--- 44,53 ----
  	      'VERSION'      => $VERSION,
  	      'PREREQ_PM'    => {
+                                  'Apache::Test'      => 1.13,
  				 'Bio::Perl'         => 1.02,
! 				 'Template'          => 2.00,
                                   'Term::ANSIColor'   => 0,
                                   'Text::Wrap'        => 0,
! 				 'Log::Log4perl'     => 0,
  				}, # e.g., Module::Name => 1.1
  	      PL_FILES       => {