genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 2)

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Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv24101

Modified Files:
	Configure 
Log Message:
	Added LOCAL_ETC, GENEX_MASON_HANDLER, PRIVATE_PERL_API
	renamed GENEX_MASON_DIR => GENEX_MASON_COMP_ROOT
	brought back the ability to install the Perl API to a private
	   location, but like modifying the default name of the genex
	   installation, it can only be indicated by runing the script as:
	   /usr/bin/perl Configure --PRIVATE_PERL_API
	Changed how GENEX_EXTRALIBS is used, it no longer includes the
	   'use lib' portion, and is instead a list of directory names
	   that must be wrapped like: 'use lib qw(%%GENEX_EXTRALIBS%%') 

Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Configure	9 Apr 2003 21:12:56 -0000	1.16
--- Configure	26 Apr 2003 23:17:27 -0000	1.17
***************
*** 65,68 ****
--- 65,69 ----
  		  get_cache
  		  genex_mkdir
+ 		  $CACHE_FILE_FILE_NAME
  		  $CACHE_FILE_NAME
  		  $CACHE_FILE_PATH
***************
*** 89,93 ****
    $HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
    $GENEX_BIN_DIR $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
!   $LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR
    $MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
    $SYSTMP $SYSTMP_DEF $UPDATE $VNCSERVER
--- 90,94 ----
    $HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
    $GENEX_BIN_DIR $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
!   $LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR $LOCAL_ETC
    $MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
    $SYSTMP $SYSTMP_DEF $UPDATE $VNCSERVER
***************
*** 108,117 ****
    $GENEX_SERVER_INSTALLATION_DATE  $GENEX_SERVER_INSTALLED_BY
    $ISO8601_DATE_FORMAT
!   $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR $GENEX_MASON_DATA_DIR
!   $GENEX_WORKSPACE_DIR   $APACHE_CONF_DIR_DEF
    $GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
    $GENEX_RO_USER   $GENEX_RO_PASSWORD $GENEX_TEST_USER $GENEX_TEST_PASSWORD
    $GENEX_PUBLIC_GROUP $GENEX_SUPERUSER_GROUP $GENEX_VOCAB_DIR
!   $GENEX_MASTER_SEQ
  );
  
--- 109,118 ----
    $GENEX_SERVER_INSTALLATION_DATE  $GENEX_SERVER_INSTALLED_BY
    $ISO8601_DATE_FORMAT
!   $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_COMP_ROOT $GENEX_MASON_DATA_DIR
!   $GENEX_WORKSPACE_DIR   $APACHE_CONF_DIR_DEF $GENEX_MASON_HANDLER
    $GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
    $GENEX_RO_USER   $GENEX_RO_PASSWORD $GENEX_TEST_USER $GENEX_TEST_PASSWORD
    $GENEX_PUBLIC_GROUP $GENEX_SUPERUSER_GROUP $GENEX_VOCAB_DIR
!   $GENEX_MASTER_SEQ $PRIVATE_PERL_API
  );
  
***************
*** 155,158 ****
--- 156,160 ----
     "MPAGE=s"            => \$MPAGE,
     "PATH=s"             => \$PATH,
+    "PRIVATE_PERL_API"   => \$PRIVATE_PERL_API,
     "PREFIX=s"           => \$PREFIX,
     "R=s"                => \$R,
***************
*** 1007,1010 ****
--- 1009,1013 ----
  $VARS{DTD_HTML_DIR} = $DTD_HTML_DIR = "$GENEXML_DIR/genexml-html";
  $VARS{LOCAL_VAR}    = $LOCAL_VAR    = "$LOCAL_ROOT/var";
+ $VARS{LOCAL_ETC}    = $LOCAL_ETC    = "$LOCAL_ROOT/etc";
  $VARS{LOCAL_SHARE}  = $LOCAL_SHARE  = "$LOCAL_ROOT/share";
  $VARS{GENEX_CACHE_DIR}    = $GENEX_CACHE_DIR    = "$LOCAL_ROOT/cache";
***************
*** 1087,1129 ****
  #
  ######################################################################
! # print STDOUT "\n\n  *** Genex.pm Configuration ***\n";
! # unless (defined $PREFIX) {
! #   spacer();
! #   $PREFIX = $DEFAULT_VARS{PREFIX} || "$LOCAL_ROOT/perl5";
! #   my $tmp = prompt(qq[
! # 
! # I plan to install the Genex.pm module under the genex specific library
! # directory \($PREFIX\).
! # 
! # If you want me to install it someplace different, you can specify
! # \$PREFIX here.
! # 
! # To accept to default installation directory, just hit enter
! # >> Genex.pm install prefix?], $PREFIX);
! # 
! #   $tmp =~ s/\s//g;
! #   $PREFIX = check_dir($tmp,$PREFIX,my $no_make=1);
! # }
! # $VARS{PREFIX} = $PREFIX;
! # $VARS{RCLUSTER_PERL_LIB} = $RCLUSTER_PERL_LIB = "$PREFIX/RCluster";
! # print STDERR "\nOK...  PREFIX => $VARS{PREFIX}\n";
! # 
! # #
! # # ExtUtils::MakeMaker is causing me grief. For whatever reason, it seems that
! # #   when perl is built, it allows over-riding of the INSTALLSITELIB variable
! # #   so that it is not based on $PREFIX. This means that I have to set all
! # #   these values by hand to get something like:
! # #
! # #   make install INSTALLSITELIB=/usr/local/lib/genex/lib/perl5/site_lib
! # #                INSTALLMAN1DIR=/usr/local/lib/genex/man/man1
! # #                INSTALLMAN3DIR=/usr/local/lib/genex/man/man3
! # 
! # if ($PREFIX) {
! #   $VARS{GENEX_MAN1}  = $GENEX_MAN1 = "$LOCAL_ROOT/man/man1";
! #   $VARS{GENEX_MAN3}  = $GENEX_MAN3 = "$LOCAL_ROOT/man/man3";
! #   $VARS{GENEX_INSTALLSITE} = $GENEX_INSTALLSITE = $PREFIX;
! #   $INSTALL_PERL_MOD        = "INSTALLSITELIB=$GENEX_INSTALLSITE INSTALLMAN1DIR=$GENEX_MAN1" .
! #                              "INSTALLMAN3DIR=$GENEX_MAN3";
! # }
  
  ######################################################################
--- 1090,1136 ----
  #
  ######################################################################
! if (defined $PRIVATE_PERL_API) {
!   print STDOUT "\n\n  *** Private Perl API Configuration ***\n";
!   spacer();
!   $PREFIX = $DEFAULT_VARS{PREFIX} || "$LOCAL_ROOT/perl5";
!   my $tmp = prompt(qq[
! 
! I plan to install the Genex.pm module under the genex specific library
! directory \($PREFIX\).
! 
! If you want me to install it someplace different, you can specify
! \$PREFIX here.
! 
! To accept to default installation directory, just hit enter
! >> Genex.pm install prefix?], $PREFIX);
! 
!   $tmp =~ s/\s//g;
!   $PREFIX = check_dir($tmp,$PREFIX,my $no_make=1);
! 
!   $VARS{PREFIX} = $PREFIX;
!   $VARS{PRIVATE_PERL_API} = $PRIVATE_PERL_API;
!   $VARS{RCLUSTER_PERL_LIB} = $RCLUSTER_PERL_LIB = "$PREFIX/RCluster";
!   print STDERR "\nOK...  PREFIX => $VARS{PREFIX}\n";
! 
! #
! # ExtUtils::MakeMaker is causing me grief. For whatever reason, it seems that
! #   when perl is built, it allows over-riding of the INSTALLSITELIB variable
! #   so that it is not based on $PREFIX. This means that I have to set all
! #   these values by hand to get something like:
! #
! #   make install INSTALLSITELIB=/usr/local/lib/genex/lib/perl5/site_lib
! #                INSTALLMAN1DIR=/usr/local/lib/genex/man/man1
! #                INSTALLMAN3DIR=/usr/local/lib/genex/man/man3
! 
!   if ($PREFIX) {
!     $VARS{GENEX_MAN1}  = $GENEX_MAN1 = "$LOCAL_ROOT/man/man1";
!     $VARS{GENEX_MAN3}  = $GENEX_MAN3 = "$LOCAL_ROOT/man/man3";
!     $VARS{GENEX_INSTALLSITE} = $GENEX_INSTALLSITE = $PREFIX;
!     $INSTALL_PERL_MOD        = "INSTALLSITELIB=$GENEX_INSTALLSITE "
!                              . "INSTALLMAN1DIR=$GENEX_MAN1 "
!                              . "INSTALLMAN3DIR=$GENEX_MAN3";
!   }
! }
! 
  
  ######################################################################
***************
*** 1137,1141 ****
  } else {
    spacer();
!   $VARS{GENEX_EXTRALIBS} = $GENEX_EXTRALIBS = '';
  
    print STDOUT <<"EXTRALIBS";
--- 1144,1148 ----
  } else {
    spacer();
!   $VARS{GENEX_EXTRALIBS} = $GENEX_EXTRALIBS = [];
  
    print STDOUT <<"EXTRALIBS";
***************
*** 1146,1149 ****
--- 1153,1157 ----
  cancel the configuration now (^C), set PERL5LIB properly and restart
  the configuration.
+ 
  EXTRALIBS
  
***************
*** 1154,1158 ****
    #   to use the value.
    #
!   if (exists $DEFAULT_VARS{GENEX_EXTRALIBS}) {
      print STDOUT <<"EXTRALIBS";
  The previous value you used for this was
--- 1162,1168 ----
    #   to use the value.
    #
!   if (exists $DEFAULT_VARS{GENEX_EXTRALIBS} and $DEFAULT_VARS{GENEX_EXTRALIBS}
!       and $DEFAULT_VARS{GENEX_EXTRALIBS} !~ /use lib/) {
! 
      print STDOUT <<"EXTRALIBS";
  The previous value you used for this was
***************
*** 1166,1170 ****
      $tmp =~ s/\s//g;		# kill whitespace
      unless ($tmp =~ /n/i) {
!       $VARS{GENEX_EXTRALIBS} = $DEFAULT_VARS{GENEX_EXTRALIBS};
      }
    }
--- 1176,1180 ----
      $tmp =~ s/\s//g;		# kill whitespace
      unless ($tmp =~ /n/i) {
!       push(@{$VARS{GENEX_EXTRALIBS}},split(/\s+/,$DEFAULT_VARS{GENEX_EXTRALIBS}));
      }
    }
***************
*** 1188,1192 ****
        unless ($tmp =~ m/^n$/i) {
  	print STDOUT "  Adding ";
! 	$VARS{GENEX_EXTRALIBS}   .= "use lib q[$lib];\n";
        } else {
  	print STDOUT "OK - Skipping this one:  ";
--- 1198,1202 ----
        unless ($tmp =~ m/^n$/i) {
  	print STDOUT "  Adding ";
! 	push(@{$VARS{GENEX_EXTRALIBS}},$lib);
        } else {
  	print STDOUT "OK - Skipping this one:  ";
***************
*** 1196,1216 ****
    }
  
! #   print STDOUT <<"EOM";
! # 
! # You have instructed me to install Genex.pm in the following directory:
! # 
! #    $PREFIX
! # 
! # If you have not already added this directory to the list of extra libraries
! # you should do so now.
! # EOM
! # 
! #   print STDOUT " Add $PREFIX ? [y] ";
! #   $tmp = <STDIN>;
! #   $tmp =~ s/\s//g;		# kill whitespace
! #   unless ($tmp =~ /n/i) {
! #     $VARS{GENEX_EXTRALIBS} .= "use lib q[$PREFIX];\n";
! #   }
! #  $GENEX_EXTRALIBS = $VARS{GENEX_EXTRALIBS};
  }
  print STDERR "\nOK... GENEX_EXTRALIBS = $VARS{GENEX_EXTRALIBS}";
--- 1206,1217 ----
    }
  
!   # if we've been given an installation prefix, $PREFIX, check to see
!   # if we've already got it in our list, if not add it
!   push(@{$VARS{GENEX_EXTRALIBS}},$PREFIX)
!     unless grep {$_ eq $PREFIX} @{$VARS{GENEX_EXTRALIBS}};
! 
!   # take the array ref of library paths and conver it to a string
!   $VARS{GENEX_EXTRALIBS} = join(' ',@{$VARS{GENEX_EXTRALIBS}});
!   $GENEX_EXTRALIBS = $VARS{GENEX_EXTRALIBS};
  }
  print STDERR "\nOK... GENEX_EXTRALIBS = $VARS{GENEX_EXTRALIBS}";
***************
*** 1246,1259 ****
  #
  ######################################################################
! $VARS{GENEX_MASON_DIR} = $GENEX_MASON_DIR = "$GENEX_HTMLDIR/mason";
! $VARS{GENEX_WORKSPACE_DIR} = $GENEX_WORKSPACE_DIR = "$GENEX_MASON_DIR/workspace";
  $VARS{GENEX_MASON_URL} = $GENEX_MASON_URL = "$GENEX_HTML_URL/mason";
  $VARS{GENEX_WORKSPACE_URL} = $GENEX_WORKSPACE_URL = "$GENEX_MASON_URL/workspace";
  $VARS{GENEX_SESSION_PATH} = $GENEX_SESSION_PATH = "/$GENEX_DIR";
  $VARS{GENEX_MASON_DATA_DIR} = $GENEX_MASON_DATA_DIR = "$LOCAL_ROOT/mason";
  unless (defined $MASON_COMP_DATA_ROOT) {
     # we set up the CompRoot regardless
    $VARS{MASON_COMP_DATA_ROOT} = <<EOT;
! PerlAddVar MasonCompRoot $GENEX_MASON_DIR
  PerlSetVar MasonDataDir  $GENEX_MASON_DATA_DIR
  EOT
--- 1247,1262 ----
  #
  ######################################################################
! $VARS{GENEX_MASON_COMP_ROOT} = $GENEX_MASON_COMP_ROOT = "$GENEX_HTMLDIR/mason";
! $VARS{GENEX_WORKSPACE_DIR} = $GENEX_WORKSPACE_DIR = "$GENEX_MASON_COMP_ROOT/workspace";
  $VARS{GENEX_MASON_URL} = $GENEX_MASON_URL = "$GENEX_HTML_URL/mason";
  $VARS{GENEX_WORKSPACE_URL} = $GENEX_WORKSPACE_URL = "$GENEX_MASON_URL/workspace";
  $VARS{GENEX_SESSION_PATH} = $GENEX_SESSION_PATH = "/$GENEX_DIR";
  $VARS{GENEX_MASON_DATA_DIR} = $GENEX_MASON_DATA_DIR = "$LOCAL_ROOT/mason";
+ $VARS{GENEX_MASON_HANDLER} = $GENEX_MASON_HANDLER = "Bio::Genex::ApacheHandler::$GENEX_DIR";
+ 
  unless (defined $MASON_COMP_DATA_ROOT) {
     # we set up the CompRoot regardless
    $VARS{MASON_COMP_DATA_ROOT} = <<EOT;
! PerlAddVar MasonCompRoot $GENEX_MASON_COMP_ROOT
  PerlSetVar MasonDataDir  $GENEX_MASON_DATA_DIR
  EOT
***************
*** 1696,1703 ****
  # that when build the Perl API the cache file will be installed along
  # with the rest of the API
! my $DIR = 'Genex/Config';
  #genex_mkdir($DIR);
! genex_system("cp $CACHE_FILE_NAME $DIR/$CACHE_FILE_NAME");
! 
  print STDOUT <<"EOM";
  
--- 1699,1706 ----
  # that when build the Perl API the cache file will be installed along
  # with the rest of the API
! my $DIR = 'Genex/Genex';
  #genex_mkdir($DIR);
! genex_system("cp $CACHE_FILE_NAME $DIR/$CACHE_FILE_FILE_NAME");
! print STDERR "\n\n\tCopying config file to $DIR\n\n\n";
  print STDOUT <<"EOM";

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 2)

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