Commit 759ab523 authored by cvs2git's avatar cvs2git
Browse files

This commit was manufactured by cvs2svn to create tag 'release-1'.

Sprout from master 1999-11-10 14:29:53 UTC Ewan Birney <birney@sanger.ac.uk> 'added popt..'
Delete:
    Apache/EnsEMBL/Footer.pm
    Apache/EnsEMBL/Header.pm
    Apache/EnsEMBL/NavBar.pm
    Apache/EnsEMBL/NavTrail.pm
    Apache/EnsEMBL/NotFound.pm
    Apache/EnsEMBL/README
    Apache/EnsEMBL/SendDecPage.pm
    Apache/EnsEMBL/ServerError.pm
    Apache/EnsEMBL/contig2gff.pm
    LICENSE
    README
    cgi-bin/clone2embl.pl
    cgi-bin/contig2gff.pl
    cgi-bin/contigview.pl
    corba/artemis/INSTALL
    corba/artemis/README
    corba/artemis/artemis-db-mysql.c
    corba/artemis/artemis-db-mysql.h
    corba/artemis/artemis-exon-impl.c
    corba/artemis/artemis-exon-impl.h
    corba/artemis/artemis-mysql-impl.c
    corba/artemis/artemis-mysql-impl.h
    corba/artemis/artemis-qual-helper.c
    corba/artemis/artemis-qual-helper.h
    corba/artemis/artemis.idl
    corba/artemis/ensembl-artemis-client.c
    corba/artemis/ensembl-artemis-server.c
    corba/artemis/makefile
    corba/artemis/test-art-seq-client.c
    corba/artemis/test-artentry-client.c
    corba/artemis/test-artentry-server.c
    corba/artemis/test-artseq-server.c
    corba/seq/bioseq.idl
    corba/seq/ensembl-seq-server.c
    corba/seq/ensembl-seq-server.h
    docs/README
    docs/map.txt
    minutes/02071999
    minutes/09071999
    minutes/16081999
    minutes/24061999
    modules/Bio/EnsEMBL/AceDB/Clone.pm
    modules/Bio/EnsEMBL/AceDB/Contig.pm
    modules/Bio/EnsEMBL/AceDB/Obj.pm
    modules/Bio/EnsEMBL/Analysis/CdnaResolver.pm
    modules/Bio/EnsEMBL/Analysis/ContigOrder.pm
    modules/Bio/EnsEMBL/Analysis/DNAparse.pm
    modules/Bio/EnsEMBL/Analysis/Exon2Gene.pm
    modules/Bio/EnsEMBL/Analysis/Genscan.pm
    modules/Bio/EnsEMBL/Analysis/LegacyParser.pm
    modules/Bio/EnsEMBL/Analysis/Log.pm
    modules/Bio/EnsEMBL/Analysis/LogMessage.pm
    modules/Bio/EnsEMBL/Analysis/ensConf.pm
    modules/Bio/EnsEMBL/AnnSeq.pm
    modules/Bio/EnsEMBL/DB/CloneI.pm
    modules/Bio/EnsEMBL/DB/ContigI.pm
    modules/Bio/EnsEMBL/DB/ObjI.pm
    modules/Bio/EnsEMBL/DBSQL/Clone.pm
    modules/Bio/EnsEMBL/DBSQL/Contig.pm
    modules/Bio/EnsEMBL/DBSQL/DummyStatement.pm
    modules/Bio/EnsEMBL/DBSQL/Obj.pm
    modules/Bio/EnsEMBL/EMBL_Dump.pm
    modules/Bio/EnsEMBL/Exon.pm
    modules/Bio/EnsEMBL/Gene.pm
    modules/Bio/EnsEMBL/GeneHandler.pm
    modules/Bio/EnsEMBL/PerlDB/Clone.pm
    modules/Bio/EnsEMBL/PerlDB/Contig.pm
    modules/Bio/EnsEMBL/PerlDB/Obj.pm
    modules/Bio/EnsEMBL/TimDB/Clone.pm
    modules/Bio/EnsEMBL/TimDB/Contig.pm
    modules/Bio/EnsEMBL/TimDB/Obj.pm
    modules/Bio/EnsEMBL/Transcript.pm
    modules/Bio/EnsEMBL/Translation.pm
    modules/Bio/SeqFeature2GFF.pm
    modules/Bio/Tracking/README
    modules/EnsEMBL/README
    modules/Makefile.PL
    modules/README
    modules/ensembl.lisp
    modules/t/AnalysisLog.t
    modules/t/DB.t
    modules/t/EmblDump.t
    modules/t/Gene.t
    modules/t/Genscan.t
    modules/t/PerlDB.t
    modules/t/README
    modules/t/cdnaresolver.t
    modules/t/emblloader.t
    modules/t/human.genomic
    scripts/README
    scripts/cdna2genome.pl
    scripts/cdnapipe.pl
    scripts/clone2contig.pl
    scripts/clone2embl.pl
    scripts/contig2gff.pl
    scripts/delete.pl
    scripts/gene2flat.pl
    scripts/genscan2sql
    scripts/get_all_clone_id.pl
    scripts/install_ensembl.pl
    scripts/loadstatus.pl
    scripts/msp2sql
    scripts/testDBI
    scripts/test_write_Contig
    scripts/test_write_features
    scripts/testdb
    scripts/transfer.pl
    sql/README
    sql/queries.sql
    sql/table.sql
parent 1e0c90c2
package Apache::EnsEMBL::Footer;
use strict;
use vars qw/@ISA @EXPORT @EXPORT_OK/;
#############################################################
# Construct the standard EnsEMBL page header
#############################################################
sub make_ensembl_footer {
my ($req_ref, $footer_ref) = @_;
my $modtime = localtime (time - $$req_ref->mtime);
$$footer_ref=<<EOS;
<P>
<TABLE WIDTH="100%" BORDER="0">
<TR>
<TD CLASS="trailbar">
&nbsp;
</TD>
</TR>
</TABLE>
<HR>
<!P>
<TABLE BORDER="0" WIDTH="100%">
<TR>
<TD CLASS="lfooter"><I>
last modified : $modtime </I>
</TD>
<TD CLASS="rfooter" ALIGN="RIGHT">
<I><A HREF=mailto:webmaster\@sanger.ac.uk>webmaster\@sanger.ac.uk</A></I>
</TD>
</TR>
</TABLE>
</BODY>
</HTML>
EOS
return;
} # end of sub"
######################### This is the list of exported subroutines #######################
@EXPORT = qw(make_ensembl_footer);
##########################################################################
1;
__END__
#
# EnsEMBL module for Apache::EnsEMBL::Footer
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs after the code
=head1 NAME
Apache::EnsEMBL::Footer - Apache Mod_perl module to generate a standard EnsEMBL
HTML page footer
=head1 SYNOPSIS
=head2 General
This mod_perl module is used to take a standard EnsEMBL
HTML page footer
=head1 RELATED MODULES
See also: Apache::EnsEMBL::SendPage, Apache::EnsEMBL::Header
=head1 FEED_BACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
EnsEMBL modules. Send your comments and suggestions to one of the
EnsEMBL mailing lists. Your participation is much appreciated.
http://ensembl.ebi.ac.uk/? - About the mailing lists
=head2 Reporting Bugs
Report bugs to the EnsEMBL bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
?@ensembl.ebi.ac.uk
http://ensembl.ebi.ac.uk/?
=head1 AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
=cut
package Apache::EnsEMBL::Header;
# need to be able to change TITLE and header gif
use strict;
#use Apache::Constants qw(:response :methods :http);
use vars qw/@ISA @EXPORT @EXPORT_OK/;
#############################################################
# Construct the standard EnsEMBL page header
#############################################################
sub make_ensembl_header {
my ($req_ref, $header_ref) = @_;
$$header_ref=<<EOS;
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<HTML>
<HEAD>
<TITLE>EnsEMBL Genome Views Server</TITLE>
<LINK REL="stylesheet" HREF="/EnsEMBL.css">
</HEAD>
<BODY TEXT="#000000" BGCOLOR="#FFFFFF">
<TABLE WIDTH="100%" BORDER="0">
<TR>
<TD>
<A HREF="http://ensembl.ebi.ac.uk/">
<IMG SRC="/icons/humembl.gif" ALIGN="CENTER" BORDER="0">
</A>
</TD>
</TR>
</TABLE>
<!P>
EOS
return;
} # end of sub"
######################### This is the list of exported subroutines #######################
@EXPORT = qw(make_ensembl_header);
##########################################################################
1;
__END__
#
# EnsEMBL module for Apache::EnsEMBL::Header
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs after the code
=head1 NAME
Apache::EnsEMBL::Header - Apache Mod_perl module to generate a standard EnsEMBL
HTML page header
=head1 SYNOPSIS
=head2 General
This mod_perl module is used to generate a standard EnsEMBL
HTML page header
=head1 RELATED MODULES
See also: Apache::EnsEMBL::SendPage, Apache::EnsEMBL::Footer
=head1 FEED_BACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
EnsEMBL modules. Send your comments and suggestions to one of the
EnsEMBL mailing lists. Your participation is much appreciated.
http://ensembl.ebi.ac.uk/? - About the mailing lists
=head2 Reporting Bugs
Report bugs to the EnsEMBL bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
?@ensembl.ebi.ac.uk
http://ensembl.ebi.ac.uk/?
=head1 AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
=cut
package Apache::EnsEMBL::NavBar;
use strict;
use vars qw/@ISA @EXPORT @EXPORT_OK/;
#############################################################
# Make menu HTML
#############################################################
sub make_menu {
my ($req_ref, $file) = @_;
my %menu =();
my @menu_order;
my $html;
my $oldRS = $/;
$/ = "";
open (MENU, $file) or $$req_ref->log->error("Can't open nav menu conf file [$file]: $!");
my @menus = <MENU>;
foreach my $m (@menus){
chomp ($m);
next if (/^#/);
my @this_menu = reverse(split (/\n/,$m));
my $header = pop(@this_menu);
my ($h,$u) = split (/;/,$header);
$html .=<<EOH;
<TR>
<TD>&nbsp;</TD>
<TD CLASS="navbarhead"><A HREF="$u">$h</A></TD>
<TD>&nbsp;</TD>
</TR>
EOH
foreach my $item (reverse(@this_menu)){
my ($h,$u) = split (/;/,$item);
$html .=<<EOI;
<TR>
<TD>&nbsp;</TD>
<TD CLASS="navbar"><A HREF="$u">$h</A>&nbsp;&nbsp;&nbsp;</TD>
<TD>&nbsp;</TD>
</TR>
EOI
} # end of foreach my $item
$html .=<<EOH;
<TR>
<TD COLSPAN="3"><IMG HEIGHT="10" WIDTH="1" SRC="/icons/nothing.gif" ALT=""></TD>
</TR>
EOH
} # end of foreach my $m
$/ = $oldRS;
close (MENU) or $$req_ref->log->error("Can't close nav menu conf file [$file]: $!");
return ($html)
} # end of sub
#############################################################
# Construct the nav menu
#############################################################
sub make_nav_menu {
my ($req_ref, $navmenu_ref) = @_;
my $default_filename = '/def_nav.conf';
my $local_filename = 'nav.conf';
my $menufile;
my %nav = ();
my $uri = $$req_ref->filename;
$uri =~ s/\w+\.*\w+$//;
if (-e "$uri$local_filename"){
$menufile = "$uri$local_filename";
$$navmenu_ref = &make_menu($req_ref, $menufile);
}
else{
$menufile = $$req_ref->document_root.$default_filename;
$$navmenu_ref = &make_menu($req_ref, $menufile);
}
} # end of sub
#############################################################
# Construct the nav bar top
#############################################################
sub make_nav_start {
my ($req_ref, $start_ref, $menu_ref) = @_;
$$start_ref=<<EOS;
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0">
<TR>
<TD VALIGN="TOP" ROWSPAN=2 BGCOLOR="#EFEFFF">
<!-- table cell for left navbar -->
<!-- navbar items begin here -->
<TABLE WIDTH="90" BORDER="0" CELLPADDING="0" CELLSPACING="3">
$$menu_ref
</TABLE>
<!-- navbar items end here -->
<!-- end of table cell for left navbar -->
</TD>
<TD ROWSPAN="2" WIDTH="30">&nbsp;</TD>
<!-- margin between navbar and main-page -->
<TD WIDTH="80%"><IMG WIDTH="1" HEIGHT="10" SRC="/icons/nothing.gif" ALT=""></TD>
<!-- cell just above main page to keep distance from top header -->
<TD ROWSPAN="2" WIDTH="5%">&nbsp;</TD>
<!-- right margin -->
</TR>
<TR>
<TD ALIGN="LEFT" VALIGN="TOP">
<!-- table cell for main page -->
<!-- ---------------page content starts here--------------- -->
EOS
} # end of sub"
#############################################################
# Construct the nav bar top
#############################################################
sub make_nav_end {
my ($req_ref, $end_ref) = @_;
$$end_ref=<<EOS;
<!-- ---------------page content ends here--------------- -->
<!-- end of table cell for main page -->
</TD>
</TR>
</TABLE>
<!-- close table for page content -->
EOS
}# end of sub"
#############################################################
######################### This is the list of exported subroutines #######################
@EXPORT = qw(make_menu make_nav_menu make_nav_start make_nav_end);
##########################################################################
1;
__END__
#
# EnsEMBL module for Apache::EnsEMBL::NavBar
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs after the code
=head1 NAME
Apache::EnsEMBL::NavBar - Apache Mod_perl module to generate an EnsEMBL
HTML navigation sidebar
=head1 SYNOPSIS
=head2 General
This mod_perl module is used to generate a standard EnsEMBL
HTML navigation sidebar
=head1 RELATED MODULES
See also: Apache::EnsEMBL::SendPage, Apache::EnsEMBL::Footer, Apache::EnsEMBL::Header
=head1 FEED_BACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
EnsEMBL modules. Send your comments and suggestions to one of the
EnsEMBL mailing lists. Your participation is much appreciated.
http://ensembl.ebi.ac.uk/? - About the mailing lists
=head2 Reporting Bugs
Report bugs to the EnsEMBL bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
?@ensembl.ebi.ac.uk
http://ensembl.ebi.ac.uk/?
=head1 AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
=cut
package Apache::EnsEMBL::NavTrail;
use strict;
use vars qw/@ISA @EXPORT @EXPORT_OK/;
#############################################################
# Construct the navigation trail
#############################################################
sub make_nav_trail {
my ($req_ref, $trail_ref) = @_;
my %map = ();
my %trail =();
my $uri = $$req_ref->uri;
my @dirs = split (/\//,$uri);
my $mapfile = $$req_ref->document_root."/urlmappings.txt";
pop(@dirs); # remove the html filename at the end of the URL
shift(@dirs); # remove the root dir
unless (open (MAP, "$mapfile")) {
$$req_ref->log->error("Cannot open URL map file: $!");
return;
}
my @lines = <MAP>;
foreach my $l (@lines){
chomp ($l);
my ($url, $label) = split (/ /,$l, 2);
$url =~ s/^\///; # remove the leading slash from URL mapping
$map{$url} = $label;
}
my $path_tmp ="";
$$trail_ref = "<B CLASS=\"trailbar\">You are here:</B> <A HREF=\"/\">Home</A>";
for (my $i=0;$i<(scalar(@dirs));$i++){
$path_tmp .= "$dirs[$i]/";
if ($i < $#dirs){
if ($map{$path_tmp}){
$$trail_ref .= " -> <A HREF=\"/$path_tmp\">$map{$path_tmp}</A>";
}
else{
$$trail_ref .= " -> <A HREF=\"/$path_tmp\">$dirs[$i]</A>";
}
}
else{
if ($map{$path_tmp}){
$$trail_ref .= " -> $map{$path_tmp}";
}
else{
$$trail_ref .= " -> $dirs[$i]";
}
}
}
$$trail_ref=<<EOS;
<TABLE WIDTH="100%" BORDER="0">
<TR>
<TD CLASS="trailbar">
$$trail_ref
</TD>
</TR>
</TABLE>
<P>
EOS
} # end of sub"
######################### This is the list of exported subroutines #######################
@EXPORT = qw(make_nav_trail);
##########################################################################
1;
__END__
#
# EnsEMBL module for Apache::EnsEMBL::NavTrail
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs after the code
=head1 NAME
Apache::EnsEMBL::NavTrail - Apache Mod_perl module to generate
a navigation trail for an EnsEMBL HTML page
=head1 SYNOPSIS
=head2 General
This mod_perl module is used to take a standard EnsEMBL
HTML page footer
=head1 RELATED MODULES
See also: Apache::EnsEMBL::SendPage, Apache::EnsEMBL::Header, Apache::EnsEMBL::Footer,
Apache::EnsEMBL::NavBar
=head1 FEED_BACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
EnsEMBL modules. Send your comments and suggestions to one of the
EnsEMBL mailing lists. Your participation is much appreciated.
http://ensembl.ebi.ac.uk/? - About the mailing lists
=head2 Reporting Bugs
Report bugs to the EnsEMBL bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
?@ensembl.ebi.ac.uk
http://ensembl.ebi.ac.uk/?
=head1 AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
=cut
package Apache::EnsEMBL::NotFound;
use strict;
use Apache::Constants qw(:response :methods :http);
use Apache::File ();
use Apache::Log ();
use CGI qw(:html);
use Apache::EnsEMBL::Header;
use Apache::EnsEMBL::Footer;
sub handler {
my $r = shift;
my $error = $ENV{'REDIRECT_ERROR_NOTES'};
unless ($error){
$error = 'unknown (no specific information available)';
}
$error =~ s/\/mysql\/ensembl\/www\/apache_1.3.6\/htdocs//i;
$r->content_type('text/html');
$r->send_http_header;
return OK if $r->header_only;
my $original_request = $r->prev;
my $original_uri = $original_request ? $original_request->uri : '';
my $admin = $r->server->server_admin;
my $header = "";
&Apache::EnsEMBL::Header::make_ensembl_header(\$r, \$header);
$r->print($header);
$r->print (
start_html( -title => 'Server Error',
-bgcolor => 'white',
-style => {-src => '/EnsEMBL.css'}
),
h1('EnsEMBL Server: Page Not Found'),
p("Sorry, the page you requested was not found on this server.
Please check that you have typed in the correct URL or else use the site search
facility to try and locate information you require.
If you think an error has occurred please send email to the server administrator
using the link below."),
p(b("The error was:")),
p(
blockquote({-class=> "error"},
strong($error),
)
),
p(b("URL:")),
p(
blockquote({-class=> "error"},
strong($ENV{'REDIRECT_URL'}),
)
),
p(b("HTTP Status Code:")),
p(
blockquote({-class=> "error"},
strong($ENV{'REDIRECT_STATUS'}),
)
),
p(b("Request Method:")),
p(