Commit b20eb1fd authored by cvs2git's avatar cvs2git
Browse files

This commit was manufactured by cvs2svn to create tag 'temp-before-gene-

comparison-removal'.

Sprout from master 2000-08-25 15:02:17 UTC Ewan Birney <birney@sanger.ac.uk> 'made newgene test pass (error in test)'
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
    cgi-bin/geneview.pl
    cgi-bin/pog.html
    cgi-bin/pog2.html
    cgi-bin/pog3.html
    cgi-bin/pog4.html
    cgi-bin/pog5.html
    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/popt/CHANGES
    corba/popt/COPYING
    corba/popt/Makefile.am
    corba/popt/Makefile.in
    corba/popt/README
    corba/popt/acconfig.h
    corba/popt/aclocal.m4
    corba/popt/autogen.sh
    corba/popt/config.guess
    corba/popt/config.h.in
    corba/popt/config.sub
    corba/popt/configure
    corba/popt/configure.in
    corba/popt/findme.c
    corba/popt/findme.h
    corba/popt/install-sh
    corba/popt/ltconfig
    corba/popt/ltmain.sh
    corba/popt/missing
    corba/popt/mkinstalldirs
    corba/popt/po/Makefile.in.in
    corba/popt/po/POTFILES.in
    corba/popt/po/popt.pot
    corba/popt/po/ro.po
    corba/popt/po/wa.po
    corba/popt/popt.3
    corba/popt/popt.c
    corba/popt/popt.h
    corba/popt/popt.ps
    corba/popt/poptconfig.c
    corba/popt/popthelp.c
    corba/popt/poptint.h
    corba/popt/poptparse.c
    corba/popt/stamp-h.in
    corba/popt/test1.c
    corba/popt/testit.sh
    corba/seq/bioseq.idl
    corba/seq/ensembl-seq-server.c
    corba/seq/ensembl-seq-server.h
    corba/simpleobjectman/makefile
    corba/simpleobjectman/memwatch.c
    corba/simpleobjectman/memwatch.h
    corba/simpleobjectman/simpleobjectmanager.c
    corba/simpleobjectman/simpleobjectmanager.h
    corba/simpleobjectman/test.c
    corba/simpleobjectman/timetolease-private.h
    corba/simpleobjectman/timetolease.c
    corba/simpleobjectman/timetolease.h
    docs/README
    docs/ensembl.txt
    docs/keystone.html
    docs/map.txt
    docs/outline.txt
    docs/test_timdb.pod
    docs/updates.txt
    docs/versioning.txt
    minutes/02071999
    minutes/09071999
    minutes/16081999
    minutes/24061999
    misc-scripts/ePCR_snapshot/snapshot.pl
    misc-scripts/fpc/ALLmap
    misc-scripts/fpc/fpc_parse.pl
    misc-scripts/golden_path/gp_contig_mismatch.pl
    misc-scripts/golden_path/gp_incons_test.pl
    misc-scripts/golden_path/gp_parse.pl
    misc-scripts/new_freeze/deleting.pl
    misc-scripts/new_freeze/loading.pl
    misc-scripts/new_freeze/mixEnsNCBI.pl
    misc-scripts/new_freeze/ncbiSort.pl
    modules/Bio/EnsEMBL/GeneComparison/ExonCompare.pm
    modules/Bio/EnsEMBL/GeneComparison/GeneCompare.pm
    modules/Bio/EnsEMBL/GeneComparison/GeneComparisonStats.pm
    modules/Bio/EnsEMBL/SlimTim/Clone.pm
    modules/Bio/EnsEMBL/SlimTim/Contig.pm
    modules/Bio/EnsEMBL/SlimTim/Obj.pm
    scripts/Analysis/03810.seq
    scripts/Analysis/cdna.msp
    scripts/Analysis/cdna_pep_test
    scripts/Analysis/dJ120G22.03810.gs
    scripts/Analysis/delete_Clone
    scripts/Analysis/featureparser_test2
    scripts/Analysis/featureparser_test3
    scripts/Analysis/find_supporting_evidence
    scripts/Analysis/genomic_cdna_test
    scripts/Analysis/genscan_test
    scripts/Analysis/supporting_evidence_test
    scripts/Analysis/testFeature
    scripts/Analysis/testGFF
    scripts/Analysis/testHMM
    scripts/Analysis/testTimDB
    scripts/Analysis/test_genscan
    scripts/Analysis/testy4
    scripts/README
    scripts/cam2flat.pl
    scripts/cdna2genome.pl
    scripts/cdnapipe.pl
    scripts/clone2contig.pl
    scripts/clone2flat.pl
    scripts/clonestats.pl
    scripts/compare_genes
    scripts/contig2gff.pl
    scripts/dbdiff
    scripts/delete.pl
    scripts/dump072dump08.pl
    scripts/dump_blastdb.pl
    scripts/est_to_transcript.pl
    scripts/fix_alternative.pl
    scripts/gene2flat.pl
    scripts/genscan2sql
    scripts/get_all_clone_id.pl
    scripts/install_ensembl.pl
    scripts/loadstatus.pl
    scripts/make_pfamTop40.pl
    scripts/msp2sql
    scripts/overlap_test
    scripts/pfamTop20.pl
    scripts/process_log
    scripts/repair_fset
    scripts/retransfer_Features
    scripts/set_dbm.pl
    scripts/testDBI
    scripts/test_dbconnection
    scripts/test_genes
    scripts/test_genomehits
    scripts/test_trans_bug.pl
    scripts/test_write_Contig
    scripts/test_write_features
    scripts/testdb
    scripts/trans2xml.pl
    scripts/transfer.pl
    scripts/transfer_Clone
    scripts/update.pl
    scripts/update_list.pl
    scripts/update_list_chunk.pl
    scripts/vc2flat.pl
    scripts/vc_gccontent.scrpt
    scripts/vc_repeatstats.scrpt
    sql/README
    sql/archive.sql
    sql/bugtrack.sql
    sql/contigoverlap.sql
    sql/drop_ensembl
    sql/get_tables
    sql/ghost.sql
    sql/meta.sql
    sql/queries.sql
    sql/table.sql
    systemtests/README
    systemtests/archive.pl
    systemtests/dna_test.pl
    systemtests/every_atleast.pl
    systemtests/exon_duplicates.pl
    systemtests/run_all.pl
    systemtests/stop_codons_test.pl
    systemtests/transcript.pl
    systemtests/transcript_strand.pl
parent 8c29ebfb
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'}),
)
),