diff --git a/misc-scripts/sql2html.pl b/misc-scripts/sql2html.pl
deleted file mode 100644
index f29947cbd57f7a1c0409b6e79b491a2d668a4088..0000000000000000000000000000000000000000
--- a/misc-scripts/sql2html.pl
+++ /dev/null
@@ -1,1253 +0,0 @@
-#!/usr/bin/env perl
-# 1st Feb 2011
-# Generate an HTML documentation page from an SQL file.
-#
-# It needs to have a "javascript like" documentation above each table.
-# See the content of the method sql_documentation_format();
-####################################################################################
-
-
-use strict;
-use POSIX;
-use Getopt::Long;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
-
-###############
-### Options ###
-###############
-
-my ($sql_file,$html_file,$db_team,$show_colour,$version,$header_flag,$format_headers,$sort_headers,$sort_tables,$intro_file,$help,$help_format);
-my ($host,$port,$dbname,$user,$pass,$skip_conn,$db_handle);
-
-usage() if (!scalar(@ARGV));
-
-GetOptions(
- 'i=s' => \$sql_file,
- 'o=s' => \$html_file,
- 'd=s' => \$db_team,
- 'c=i' => \$show_colour,
- 'v=i' => \$version,
- 'show_header=i' => \$header_flag,
- 'format_headers=i' => \$format_headers,
- 'sort_headers=i' => \$sort_headers,
- 'sort_tables=i' => \$sort_tables,
- 'host=s' => \$host,
- 'port=i' => \$port,
- 'dbname=s' => \$dbname,
- 'user=s' => \$user,
- 'pass=s' => \$pass,
- 'skip_connection' => \$skip_conn,
- 'intro=s' => \$intro_file,
- 'help!' => \$help,
- 'help_format' => \$help_format,
-);
-
-usage() if ($help);
-sql_documentation_format() if ($help_format);
-
-
-if (!$sql_file) {
- print "> Error! Please give a sql file using the option '-i' \n";
- usage();
-}
-if (!$html_file) {
- print "> Error! Please give an output file using the option '-o'\n";
- usage();
-}
-
-$show_colour = 1 if (!defined($show_colour));
-$header_flag = 1 if (!defined($header_flag));
-$format_headers = 1 if (!defined($format_headers));
-$sort_headers = 1 if (!defined($sort_headers));
-$sort_tables = 1 if (!defined($sort_tables));
-
-$skip_conn = undef if ($skip_conn == 0);
-
-
-# Dababase connection (optional)
-if (defined($host) && !defined($skip_conn)) {
- my $db_adaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- -host => $host,
- -user => $user,
- -pass => $pass,
- -port => $port,
- -dbname => $dbname
- ) or die("DATABASE CONNECTION ERROR: Could not get a database adaptor for $dbname on $host:$port\n");
- $db_handle = $db_adaptor->dbc->db_handle;
-}
-
-
-
-
-################
-### Settings ##
-################
-
-my $default_colour = '#000'; # Black
-my $list_bg = "background-color:#F2F2F2";
-
-my %display_col = ('Show' => 'none', 'Hide' => 'inline');
-my $documentation = {};
-my $tables_names = {'default' => []};
-my @header_names = ('default');
-my @colours = ($default_colour);
-my %legend;
-
-my $in_doc = 0;
-my $in_table = 0;
-my $header = 'default';
-my $table = '';
-my $info = '';
-my $nb_by_col = 15;
-my $count_sql_col = 0;
-my $tag_content = '';
-my $tag = '';
-my $display = 'Show';
-my $parenth_count = 0;
-my $header_colour;
-
-my $SQL_LIMIT = 50;
-my $img_plus = qq{<img src="/i/16/plus-button.png" style="width:12px;height:12px;vertical-align:middle" alt="show"/>};
-my $img_minus = qq{<img src="/i/16/minus-button.png" style="width:12px;height:12px;vertical-align:middle;margin-right:6px" alt="hide"/>};
-my $link_text = 'columns';
-
-
-
-
-##############
-### Header ###
-##############
-
-my $html_header = qq{
-<html>
-<head>
-<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8" />
-<title>$db_team Schema Documentation</title>
-
-<script language="Javascript" type="text/javascript">
- var img_plus = '$img_plus';
- var img_minus = '$img_minus';
- var link_text = 'columns';
- var span_open = ' <span style="vertical-align:middle">';
- var span_close = '</span>';
-
- // Function to show/hide the columns table
- function show_hide (param, type) {
- // Example tables
- if (type === 'example') {
- div = document.getElementById('ex_'+param);
- alink = document.getElementById('e_'+param);
- a_text = 'query results';
- }
- // Schema tables
- else {
- div = document.getElementById('div_'+param);
- alink = document.getElementById('a_'+param);
- a_text = link_text;
- }
-
- if (div.style.display=='inline') {
- div.style.display='none';
- alink.innerHTML=img_plus+span_open+'Show '+a_text+span_close;
- }
- else {
- if (div.style.display=='none') {
- div.style.display='inline';
- alink.innerHTML=img_minus+span_open+'Hide '+a_text+span_close;
- }
- }
- }
-
- // Function to show/hide all the tables
- function show_hide_all () {
- expand_flag = document.getElementById('expand');
- divs = document.getElementsByTagName('div');
- for(var i=0; i < divs.length; i++){
- param = divs[i].id.substring(4);
- div = document.getElementById('div_'+param);
- alink = document.getElementById('a_'+param);
-
- if (div && alink) {
- if (expand_flag.value=='0') {
- div.style.display='inline';
- alink.innerHTML=img_minus+span_open+'Hide '+link_text+span_close;
- }
- else {
- div.style.display='none';
- alink.innerHTML=img_plus+span_open+'Show '+link_text+span_close;
- }
- }
- }
- if (expand_flag.value=='0') {
- expand_flag.value='1';
- }
- else {
- expand_flag.value='0';
- }
- }
-</script>
-
-</head>
-<body>
-};
-
-
-##############
-### Footer ##
-##############
-
-my $html_footer = qq{
-</body>
-</html>};
-
-
-
-
-#############
-## Parser ##
-#############
-
-# Create a complex hash "%$documentation" to store all the documentation content
-
-open SQLFILE, "< $sql_file" or die "Can't open $sql_file : $!";
-while (<SQLFILE>) {
- chomp $_;
- next if ($_ eq '');
- next if ($_ =~ /^\s*(DROP|PARTITION)/i);
- next if ($_ =~ /^\s*(#|--)/); # Escape characters
-
- # Verifications
- if ($_ =~ /^\/\*\*/) { $in_doc=1; next; } # start of a table documentation
- if ($_ =~ /^\s*create\s+table\s+(if\s+not\s+exists\s+)?`?(\w+)`?/i) { # start to parse the content of the table
- if ($table eq $2) {
- $in_table=1;
- $parenth_count++;
- }
- else {
- print STDERR "The documentation of the table $2 has not be found!\n";
- }
- next;
- }
- next if ($in_doc==0 and $in_table==0);
-
- my $doc = remove_char($_);
-
- #================================================#
- # Parsing the documentation part of the SQL file #
- #================================================#
- if ($in_doc==1) {
- # Header name
- if ($doc =~ /^\@header\s*(.+)$/i and $header_flag == 1) {
- $header = $1;
- push (@header_names,$header);
- $tables_names->{$header} = [];
- next;
- }
- # Table name
- elsif ($doc =~ /^\@table\s*(\w+)/i) {
- $table = $1;
- push(@{$tables_names->{$header}},$table);
- $documentation->{$header}{'tables'}{$table} = { 'desc' => '', 'colour' => '', 'column' => [], 'example' => [], 'see' => [], 'info' => [] };
- $tag = $tag_content = '';
- }
- # Description (used for both set, table and info tags)
- elsif ($doc =~ /^\@(desc)\s*(.+)$/i) {
- fill_documentation ($1,$2);
- }
- # Colour of the table header (used for both set, table) (optional)
- elsif ($doc =~ /^\@(colour)\s*(.+)$/i and $show_colour) {
- fill_documentation ($1,$2);
- }
- # Column
- elsif ($doc =~ /^\@(column)\s*(.+)$/i) {
- fill_documentation ($1,$2);
- }
- # Example
- elsif ($doc =~ /^\@(example)\s*(.+)$/i) {
- fill_documentation ($1,$2);
- }
- # See other tables
- elsif ($doc =~ /^\@(see)\s*(\w+)\s*$/i) {
- fill_documentation ($1,$2);
- }
- # Addtional information block
- elsif ($doc =~ /^\@(info)\s*(.+)$/i) {
- fill_documentation ();
- $info = $2;
- next;
- }
- # End of documentation
- elsif ($doc =~ /^\*\//) { # End of the documentation block
- fill_documentation (); # Add the last tag content to the documentation hash
- $in_doc=0;
- next;
- }
- # Add legend colour description
- elsif ($doc =~ /^\@(legend)\s*(#\S+)\s+(.+)$/i) {
- $legend{$2} = $3;
- }
- elsif ($doc =~ /^\s*(.+)$/) { # If a tag content is split in several lines
- $tag_content .= " $1";
- }
- }
-
- #=====================================================#
- # Parsing of the SQL table to fetch the columns types #
- #=====================================================#
- elsif ($in_table==1) {
-
- # END OF TABLE DEFINITION
- # Can't do this easily with a simply regex as there are varying valid formats
- # The end of the table definition is actually defined by 2nd enclosing bracket
-
- # Regex counting VOODOO!
- # This basically puts the regex in a list context
- # before inc/dec'ing with it in a scalar context.
- $parenth_count +=()= $doc =~ /\(/gi;
- $parenth_count -=()= $doc =~ /\)/gi;
-
-
- if ($parenth_count == 0) { # End of the sql table definition
- if (scalar @{$documentation->{$header}{'tables'}{$table}{column}} > $count_sql_col) {
- print STDERR "Description of a non existant column in the table $table!\n";
- }
-
- $in_table=0;
- $count_sql_col = 0;
- $table='';
- $parenth_count = 0;
- }
- else {
-
- #---------#
- # INDEXES #
- #---------#
-
- # Skip the FOREIGN KEY
- next if ($doc =~ /^\s*foreign\s+key/i);
-
- if ($doc =~ /^\s*(primary\s+key)\s*\w*\s*\((.+)\)/i or $doc =~ /^\s*(unique)\s*\((.+)\)/i){ # Primary or unique;
- add_column_index($1,$2);
- next;
- }
- elsif ($doc =~ /^\s*(unique\s+)?(key|index)\s+([^\s\(]+)\s*\((.+)\)/i) { # Keys and indexes
- add_column_index("$1$2",$4,$3);
- next;
- }
- elsif ($doc =~ /^\s*(unique)\s+(\S*)\s*\((.+)\)/i) { # Unique
- add_column_index("$1",$3,$2);
- next;
- }
- elsif ($doc =~ /^\s*(key)\s+\((.+)\)/i) { # Keys
- add_column_index("$1",$2);
- next;
- }
-
- #----------------------------------#
- # COLUMNS & TYPES & DEFAULT VALUES #
- #----------------------------------#
- my $col_name = '';
- my $col_type = '';
- my $col_def = '';
-
- # All the type is contained in the same line (type followed by parenthesis)
- if ($doc =~ /^\W*(\w+)\W+(\w+\s?\(.*\))/ ){
- $col_name = $1;
- $col_type = $2;
- if ($doc =~ /default\s+([^,\s]+)\s*.*(,|#).*/i) { $col_def = $1; } # Default value
- add_column_type_and_default_value($col_name,$col_type,$col_def);
- }
-
- # The type is written in several lines
- elsif ($doc =~ /^\W*(\w+)\W+(enum|set)(\s?\(.*)/i){ # The content is split in several lines
- $col_name= $1;
- $col_type="$2$3<br />";
- my $end_type = 0;
- while ($end_type != 1){
- my $line = <SQLFILE>;
- chomp $line;
- $line = remove_char($line);
-
- # Regex counting VOODOO again
- $parenth_count +=()= $line =~ /\(/gi;
- $parenth_count -=()= $line =~ /\)/gi;
-
- if ($line =~ /\)/) { # Close parenthesis
- $end_type=1;
- $line =~ /^\s*(.+)\)/;
- $col_type .= "$1)";
- }
- else { # Add the content of the line
- $line =~ /^\s*(.+)/;
- $col_type .= $1.'<br />';
- }
- if ($line =~ /default\s+([^,\s]+)\s*.*(,|#).*/i) { $col_def = $1; } # Default value
- }
- add_column_type_and_default_value($col_name,$col_type,$col_def);
- }
-
- # All the type is contained in the same line (type without parenthesis)
- elsif ($doc =~ /^\s*\W*(\w+)\W+(\w+)/ ){
- $col_name = $1;
- $col_type = $2;
- if ($doc =~ /default\s*([^,\s]+)\s*.*(,|#).*/i) { $col_def = $1;} # Default value
- add_column_type_and_default_value($col_name,$col_type,$col_def);
- }
- }
- }
-}
-close(SQLFILE);
-
-
-
-
-###########
-## Core ##
-###########
-
-my $html_content;
-
-# Sort the headers names by alphabetic order
-if ($sort_headers == 1) {
- @header_names = sort(@header_names);
-}
-# Sort the tables names by alphabetic order
-if ($sort_tables == 1) {
- while ( my($header_name,$tables) = each (%{$tables_names})) {
- @{$tables} = sort(@{$tables});
- }
-}
-
-# Legend link
-if ($show_colour and scalar @colours > 1 and $header_flag != 1) {
- $html_content .= qq{A colour legend is available at the <a href="#legend">bottom of the page</a>.\n<br /><br />};
-}
-
-#=============================================#
-# List of tables by header (i.e. like a menu) #
-#=============================================#
-$html_content .= display_tables_list();
-my $table_count = 1;
-my $col_count = 1;
-
-#========================================#
-# Display the detailled tables by header #
-#========================================#
-foreach my $header_name (@header_names) {
- my $tables = $tables_names->{$header_name};
- my $hcolour = $documentation->{$header_name}{'colour'};
-
- #----------------#
- # Header display #
- #----------------#
- if ($header_flag == 1 and $header_name ne 'default') {
- $html_content .= qq{\n<br /><br />
-<div style="$list_bg;padding:5px;margin:5px 0px;border-top:2px solid $hcolour">
- <h2 style="display:inline;color:#000">$header_name</h2>
-</div>\n};
- my $header_desc = $documentation->{$header_name}{'desc'};
- $html_content .= qq{<p style="width:800px">$header_desc</p>} if (defined($header_desc));
- }
-
- #------------------------#
- # Additional information #
- #------------------------#
- if ($header_name eq 'default' and defined($documentation->{$header_name}{'info'})) {
- $html_content .= qq{<h2>Additional information about the schema</h2>\n};
- }
- $html_content .= add_info($documentation->{$header_name}{'info'});
-
- #----------------#
- # Tables display #
- #----------------#
- foreach my $t_name (@{$tables}) {
- my $data = $documentation->{$header_name}{'tables'}{$t_name};
- my $colour = ($header_flag && $hcolour) ? $hcolour : $data->{colour};
-
- $html_content .= add_table_name($t_name,$colour);
- $html_content .= add_description($data);
- $html_content .= add_info($data->{info},$data);
- $html_content .= add_columns($t_name,$data);
- $html_content .= add_examples($t_name,$data);
- $html_content .= add_see($data->{see});
- }
-}
-$html_content .= add_legend();
-
-
-
-
-######################
-## HTML/output file ##
-######################
-open HTML, "> $html_file" or die "Can't open $html_file : $!";
-print HTML $html_header."\n";
-print HTML slurp_intro($intro_file)."\n";
-print HTML $html_content."\n";
-print HTML $html_footer."\n";
-close(HTML);
-
-
-
-
-###############
-## Methods ##
-###############
-
-# List the table names.
-# Group them if the header option "-format_headers" is selected.
-# By default there is one group, named "default" and it contains all the tables.
-sub display_tables_list {
-
- my $html;
-
- $header_flag = 0 if (scalar @header_names == 1);
-
- if ($header_flag == 1) {
- $html .= qq{\n<h3 id="top">List of the tables:</h3>\n};
- $html .= qq{<div>\n} if ($format_headers == 1);
- }
- else {
- my $list_width;
- if (scalar @header_names == 1) {
- my $list_count = scalar @{$tables_names->{'default'}};
- my $list_nb_col = ceil($list_count/$nb_by_col);
- $list_width = length_names($tables_names->{'default'},$list_nb_col);
- }
- $html .= qq{
-<div>
- <div id="top" style="$list_bg;border-radius:5px;margin-bottom:20px;float:left;$list_width">
- <div style="padding:5px;background-color:#336;border-top-left-radius:5px;border-top-right-radius:5px">
- <img src="/i/16/rev/info.png" style="vertical-align:top" />
- <h3 style="display:inline;color:#FFF">List of the tables:</h3>
- </div>};
- }
-
- my $has_header = 0;
- my $nb_col_line = 0;
-
- foreach my $header_name (@header_names) {
-
- my $tables = $tables_names->{$header_name};
- my $count = scalar @{$tables};
- next if ($count == 0);
-
- # Number of columns needed to display the tables of the group
- my $nb_col = ceil($count/$nb_by_col);
- my $nbc = $nb_col;
- my $table_count = 0;
- my $col_count = 1;
-
- if ($nb_col>3) {
- while ($nb_col>3) {
- $nb_by_col += 5;
- $nb_col = ceil($count/$nb_by_col);
- }
- $nb_col = 3;
- }
-
-
- # Header #
- if ($header_flag == 1) {
- if ($header_name ne 'default') {
- if ($nb_col_line+$nbc > 4 and $format_headers == 1) {
- $html .= qq{ <div style="clear:both" />\n</div>\n\n<div>};
- $nb_col_line = 0;
- }
-
- $html .= display_header($header_name,$nbc);
- $nb_col_line += $nbc;
- $has_header = 1;
- }
-
- # List of tables #
- $html .= qq{\n <div style="float:left">} if ($count > $nb_by_col);
- $html .= qq{\n <ul style="padding:0px 4px 0px 22px;margin-bottom:2px">\n};
- my $t_count = 0;
- foreach my $t_name (@{$tables}) {
- my $t_colour;
- if ($has_header == 0 && $show_colour) {
- $t_colour = $documentation->{$header_name}{'tables'}{$t_name}{'colour'};
- }
- $html .= add_table_name_to_list($t_name,$t_colour);
- $t_count++;
- if ($t_count>=$nb_by_col) {
- $html .= qq{\n </ul>\n </div>};
- $html .= qq{\n <div style="float:left">};
- $html .= qq{\n <ul style="padding:0px 4px 0px 22px;margin-bottom:2px">\n};
- $t_count = 0;
- }
- }
- $html .= qq{\n </ul>};
- $html .= qq{\n </div>} if ($count > $nb_by_col);
- $html .= qq{\n </div>\n} if ($format_headers == 1);
- }
- else {
- $html .= qq{\n <table style="padding:0px 2px"><tr><td>\n <ul style="padding-left:20px">\n};
-
- # List of tables #
- foreach my $t_name (@{$tables}) {
- if ($table_count == $nb_by_col and $col_count<$nb_col and $nb_col>1){
- $html .= qq{ </ul>\n </td><td>\n <ul style="padding-left:20px">\n};
- $table_count = 0;
- }
- my $t_colour;
- if ($has_header == 0 && $show_colour) {
- $t_colour = $documentation->{$header_name}{'tables'}{$t_name}{'colour'};
- }
- $html .= add_table_name_to_list($t_name,$t_colour);
- $table_count ++;
- }
- $html .= qq{ </ul>\n </td></tr></table>\n};
- }
- }
-
- my $input_margin;
- if ($header_flag == 1 and $format_headers == 1){
- $html .= qq{\n <div style="clear:both" />\n</div>};
- } else {
- $input_margin = qq{ style="margin-left:10px;margin-bottom:5px"};
- }
- $html .= qq{
- <input type="button" onclick="show_hide_all()" class="fbutton" value="Show/hide all"$input_margin/>
- <input type="hidden" id="expand" value="0" />
- };
-
- $html .= qq{\n </div>\n <div style="clear:both" />\n</div>} if ($header_flag!=1 and $format_headers == 1);
-
- return $html;
-}
-
-
-# If the option "-show_header" is selected, the tables will be displayed by group ("Header") in the HTML page.
-# This method generates the HTML code to display the group names & descriptions.
-sub display_header {
- my $header_name = shift;
- my $nb_col = shift;
-
- my $html;
-
- if ($format_headers == 1) {
- my $width = length_names($tables_names->{$header_name},$nb_col);
-
- $html .= qq{\n <div style="$list_bg;border-radius:5px;margin-bottom:15px;float:left;margin-right:20px$width">
- <div style="padding:2px 5px;background-color:#336;border-top-left-radius:5px;border-top-right-radius:5px">};
-
- my $text_colour = '#FFF';
-
- if ($show_colour && $header_colour) {
- my $hcolour = $documentation->{$header_name}{colour};
- $hcolour = $default_colour if (!defined($hcolour));
-
- $html .= qq{
- <div style="background-color:$hcolour;border:1px solid #FFF;padding:0px 8px;display:inline;vertical-align:middle"></div>
- <h2 style="margin-left:8px;display:inline;color:$text_colour;vertical-align:middle">$header_name</h2>\n};
- }
- else {
- $html .= qq{<h2 style="display:inline;color:$text_colour">$header_name</h2>\n};
- }
- $html .= qq{ </div>};
- }
- else {
- $html .= qq{ <h2 >$header_name</h2>};
- }
- return $html;
-}
-
-
-# Method to pick up the documentation information contained in the SQL file.
-# If the line starts by a @<tag>, the previous tag content is added to the documentation hash.
-# This method allows to describe the content of a tag in several lines.
-sub fill_documentation {
- my $t1 = shift;
- my $t2 = shift;
-
- if ($tag ne '') {
- # Description tag (info, table or header)
- if ($tag eq 'desc') {
- # Additional description
- if ($info ne '') {
- $tag_content = $info.'@info@'.$tag_content;
- # Table: additional information
- if ($table ne '') {
- push(@{$documentation->{$header}{'tables'}{$table}{'info'}},$tag_content);
- }
- # Header: additional information
- else {
- if (!$documentation->{$header}{'info'}) {
- $documentation->{$header}{'info'} = [];
- }
- push(@{$documentation->{$header}{'info'}},$tag_content);
- }
- $info = '';
- }
- # Header description
- elsif(!$documentation->{$header}{'tables'}) {
- $documentation->{$header}{'desc'} = $tag_content;
- }
- # Table description
- else {
- $documentation->{$header}{'tables'}{$table}{$tag} = $tag_content;
- }
- }
- elsif ($tag eq 'colour') {
- if(!$documentation->{$header}{'tables'}) {
- $documentation->{$header}{'colour'} = $tag_content;
- $header_colour = 1;
- }
- elsif ($table ne '') {
- $documentation->{$header}{'tables'}{$table}{$tag} = $tag_content;
- if (! grep {$tag_content eq $_} @colours) {
- push (@colours,$tag_content);
- }
- }
- }
- elsif ($tag eq 'column') {
- $tag_content =~ /(\w+)[\s\t]+(.*)/;
-
- my $column = { 'name' => $1,
- 'type' => '',
- 'default' => '',
- 'index' => '',
- 'desc' => $2
- };
- if ($2 eq '') {
- print STDERR "COLUMN: The description content of the column '$1' is missing in the table $table!\n";
- }
- push(@{$documentation->{$header}{'tables'}{$table}{$tag}},$column);
- }
- else{
- push(@{$documentation->{$header}{'tables'}{$table}{$tag}},$tag_content);
- }
- }
- # New tag initialized
- if ($t1) {
- $tag = $t1;
- $tag_content = $t2;
- }
- else {
- $tag = $tag_content = '';
- }
-}
-
-
-# Method generating the HTML code to display the table name into the top menu.
-sub add_table_name_to_list {
- my $t_name = shift;
- my $t_colour = shift;
- my $c = $t_colour;
- if (defined($t_colour)) {
- $t_colour = ($t_colour ne '') ? qq{;background-color:$t_colour} : '';
- $t_colour = qq{<div style="padding:0px;margin-left:0px$t_colour;display:inline"> </div> };
- }
- my $html = qq{ <li>$t_colour<a href="#$t_name"><b>$t_name</b></a></li>\n};
- return $html;
-}
-
-
-# Method generating the HTML code to display the title/header of the table description block
-sub add_table_name {
- my $t_name = shift;
- my $colour = shift || '#000';
-
- my $c_box = '';
- if ($show_colour) {
- $c_box = qq{ <div style="float:left;padding:0px;height:20px;width:10px;background-color:$colour;margin-right:10px"></div>};
- }
-
- my $html = qq{
- <div id="$t_name" style="width:820px;height:20px;border: 2px groove #CCC;background-color:#FAFAFF;padding:2px;margin-top:35px;margin-bottom:2px">
- $c_box
- <div style="float:left;text-align:left;font-size:11pt;font-weight:bold">$t_name</div>
- <div style="float:right;text-align:right;padding-right:1px">
- <a id="a_$t_name" style="cursor:pointer;text-decoration:none" onclick="show_hide('$t_name')">
- $img_plus
- <span style="vertical-align:middle">Show $link_text</span>
- </a>
- <b> | </b> <a href="#top">[Back to top]</a>
- </div>
- </div>\n};
-
- return $html;
-}
-
-
-# Method generating the HTML code to display the description content
-sub add_description {
- my $data = shift;
-
- # Search if there are some @link tags in the description text.
- my $desc = add_internal_link($data->{desc},$data);
-
- return qq{ <p style="padding:5px 0px;margin-bottom:0px;width:800px">$desc</p>\n};
-}
-
-
-# Method generating the HTML code to display additional information contained in the tags @info
-sub add_info {
- my $infos = shift;
- my $data = shift;
- my $html = '';
-
- foreach my $inf (@{$infos}) {
- my ($title,$content) = split('@info@', $inf);
- $content = add_internal_link($content,$data) if (defined($data));
-
- $html .= qq{
- <table>
- <tr class="bg3"><th>$title</th></tr>
- <tr class="bg1"><td>$content</td></tr>
- </table>\n};
- }
-
- return $html;
-}
-
-
-# Method generating the HTML code of the table listing the columns of the given SQL table.
-sub add_columns {
- my $table = shift;
- my $data = shift;
- my $cols = $data->{column};
- my $display_style = $display_col{$display};
-
- my $html = qq{\n <div id="div_$table" style="display:$display_style">
- <table style="border:1px solid #667aa6;padding:0px;min-width:1000px;max-width:1200px">
- <tr class="center" style="color:#FFFFFF;background-color:#667aa6"><th style="color:#FFF;padding:2px">Column</th><th style="color:#FFF;padding:2px">Type</th><th style="color:#FFF;padding:2px;min-width:80px">Default value</th><th style="color:#FFF;padding:2px;min-width:500px">Description</th><th style="color:#FFF;padding:2px;min-width:100px">Index</th></tr>\n};
- my $bg = 1;
-
- foreach my $col (@$cols) {
- my $name = $col->{name};
- my $type = $col->{type};
- my $default = $col->{default};
- my $desc = $col->{desc};
- my $index = $col->{index};
-
- # links
- $desc = add_internal_link($desc,$data);
-
- $html .= qq{ <tr class="bg$bg"><td><b>$name</b></td><td>$type</td><td>$default</td><td>$desc</td><td>$index</td></tr>\n};
- if ($bg==1) { $bg=2; }
- else { $bg=1; }
- }
- $html .= qq { </table>\n </div>\n};
-
- return $html;
-}
-
-
-# Method generating the HTML code to display the content of the tags @example (description + SQL query + Table of SQL query results)
-sub add_examples {
- my $table = shift;
- my $data = shift;
- my $examples = $data->{example};
- my $html;
-
- my $nb = (scalar(@$examples) > 1) ? 1 : '';
-
- foreach my $ex (@$examples) {
- my @lines = split("\n",$ex);
- my $nb_display = ($nb ne '') ? " $nb" : $nb;
- $html .= qq{<div style="margin: 10px 5px"><p style="font-weight:bold">Example$nb_display:</p>};
- my $has_desc = 0;
- my $sql;
-
- # Parse the example lines
- foreach my $line (@lines) {
- chomp($line);
-
- # Pick up the SQl query if it exists
- if ($line =~ /(.*)\s*\@sql\s*(.+)/) {
- $html .= ($has_desc == 1) ? $1 : qq{<p style="padding-left:10px">$1};
- $sql = $2;
- } elsif (!defined($sql)){
- $html .= qq{<p style="padding-left:10px">} if ($has_desc == 0);
- $html .= $line;
- $has_desc = 1;
- }
- else {
- $sql .= $line;
- }
- }
- $html .= qq{</p>};
-
- # Search if there are some @link tags in the example description.
- $html = add_internal_link($html,$data);
-
- # Add a table of examples
- if (defined($sql)) {
- my $show_hide = '';
- my $sql_table = '';
- if (!defined($skip_conn) && defined($host)) {
- $show_hide .= qq{<a id="e_$table$nb" style="cursor:pointer;text-decoration:none" onclick="show_hide('$table$nb','example')">$img_plus<span style="vertical-align:middle"> Show query results</span></a>};
- $sql_table = get_example_table($sql,$table,$nb);
- }
- if (defined($sql)) {
- foreach my $word (qw(SELECT DISTINCT CONCAT FROM LEFT JOIN USING WHERE LIMIT DESC ORDER GROUP)) {
- $sql =~ s/$word /$word /i;
- }
- }
- $html .= qq{<pre style="display:inline;border:1px solid #555;padding:2px;margin-right:15px;margin-left:10px">$sql</pre> $show_hide\n$sql_table};
- }
- $html .= qq{</div>};
- $nb ++;
- }
-
- return $html;
-}
-
-
-# Method generating the HTML code to display the content of the tags @see
-sub add_see {
- my $sees = shift;
- my $html = '';
-
- if (scalar @$sees) {
- $html .= qq{ <p style="margin-top:10px"><b>See also:</b></p>\n <ul>\n};
- foreach my $see (@$sees) {
- $html .= qq{ <li><a href="#$see">$see</a></li>\n};
- }
- $html .= qq{ </ul>\n\n};
- }
-
- return $html;
-}
-
-
-# Method searching the tag @link into the string given as argument and replace it by an internal HTML link
-sub add_internal_link {
- my $desc = shift;
- my $data = shift;
- while ($desc =~ /\@link\s?(\w+)/) {
- my $link = $1;
- if ((!grep {$link eq $_} @{$data->{see}}) and defined($link)) {
- push @{$data->{see}}, $link;
- }
- my $table_to_link = qq{<a href="#$link">$link</a>};
- $desc =~ s/\@link\s?\w+/$table_to_link/;
- }
- return $desc;
-}
-
-
-# Method parsing the index information from the SQL table description in order to display it in the
-# HTML table listing the columns of the corresponding SQL table.
-sub add_column_index {
- my $idx_type = shift;
- my $idx_col = shift;
- my $idx_name = shift;
-
- my $index = $idx_type;
- if (!defined($idx_name)) {
- $idx_name = $idx_col;
- }
- if ($idx_type !~ /primary/i) {
- $index .= ": $idx_name";
- }
- my @idx_cols = split(',',$idx_col); # The index can involve several columns
-
- my %is_found = ();
- foreach my $i_col (@idx_cols) {
- $i_col =~ s/\s//g; # Remove white spaces
- # In case of index using a number characters for a column
- if ($i_col =~ /(.+)\(\d+\)/) {
- $i_col = $1;
- }
- $is_found{$i_col} = 0;
- foreach my $col (@{$documentation->{$header}{tables}{$table}{column}}) {
- if ($col->{name} eq $i_col) {
- if ($col->{index} ne '') {
- $col->{index} .= '<br />';
- }
- $col->{index} .= lc($index);
- $is_found{$i_col} = 1;
- last;
- }
- }
- }
- # Description missing
- while (my ($k,$v) = each(%is_found)) {
- if ($v==0) {
- print STDERR "INDEX: The description of the column '$k' is missing in the table $table!\n";
- }
- }
-}
-
-
-# Method parsing the column type and default value from the SQL table description, in order to display them in the
-# HTML table listing the columns of the corresponding SQL table.
-sub add_column_type_and_default_value {
- my $c_name = shift;
- my $c_type = shift;
- my $c_default = shift;
- $count_sql_col ++;
-
- my $is_found = 0;
- foreach my $col (@{$documentation->{$header}{'tables'}{$table}{column}}) {
- if ($col->{name} eq $c_name) {
- $col->{type} = $c_type;
- $col->{default} = $c_default if ($c_default ne '');
- $is_found = 1;
- last;
- }
- }
- # Description missing
- if ($is_found==0) {
- print STDERR "COLUMN: The description of the column '$c_name' is missing in the table $table!\n";
- }
-}
-
-
-# Method to query the database with the SQL query example, get the result and display it
-# in an HTML table.
-sub get_example_table {
- my $sql = shift;
- my $table = shift;
- my $nb = shift;
- my $html;
-
- $sql =~ /select\s+(.+)\s+from/i;
- my $cols = $1;
- my @tcols;
-
- foreach my $col (split(',',$cols)) {
-
- # Columns selection like the expressions "table.*" or "*"
- my $table_name;
- $table_name = $table if ($cols eq '*');
- $table_name = $1 if ($col =~ /(\S+)\.\*/ and !defined($table_name));
- if (defined($table_name)) {
- my $table_cols = $db_handle->selectall_arrayref(qq{SHOW COLUMNS FROM $table_name});
- foreach my $col (@$table_cols) {
- push(@tcols,$col->[0]);
- }
- next;
- }
-
- # Check for alias
- $col = $1 if ($col =~ /\s+as\s+(\S+)$/i);
-
- $col =~ s/ //g;
- push(@tcols,$col);
- }
-
- my $results = $db_handle->selectall_arrayref($sql);
- if (scalar(@$results)) {
- $html .= qq{
- <div id="ex_$table$nb" style="display:none;">
- <table class="ss" style="width:50%;margin-top:20px;margin-left:10px;border-spacing:2px">\n <tr><th>};
- $html .= join("</th><th>",@tcols);
- $html .= qq{</th></tr>};
-
- my $bg = '';
-
- my $count = 0;
- foreach my $result (@$results) {
- last if ($count >= $SQL_LIMIT);
- $html .= qq{ <tr$bg><td>};
- $html .= join("</td><td>", @$result);
- $html .= qq{</td></tr>};
-
- $bg = ($bg eq '') ? ' class="bg2"' : '';
- $count ++;
- }
- $html .= qq{ </table>\n </div>};
- } else {
- my $msg = qq{ERROR: the SQL query displayed above returned no results!};
- $html .= qq{<div style="padding:5px;margin:10px;width:500px;font-weight:bold;border:2px solid red;color:red">$msg</div>};
- print STDERR qq{SQL: $sql\n$msg\n};
- }
-
- return $html;
-}
-
-
-# Method generating a "Colour legend" paragraph, based on the header colours.
-sub add_legend {
- my $html = '';
- my $default = 'Other tables';
-
- return $html if (scalar @colours == 1 or $header_colour);
-
- $html .= qq{<br />\n<hr />\n<h3 id="legend">Colour legend</h3>\n<table>};
-
- foreach my $c (@colours) {
- my $desc = '';
- if ($c eq $default_colour && !$legend{$default_colour}) {
- $desc = $default;
- }
- else {
- $desc = $legend{$c};
- }
- $html .= qq{ <tr><td style="width:25px;height:15px;background-color:$c"></td><td>$desc</td></tr>\n};
- }
- $html .= qq{</table>};
-
- return $html;
-}
-
-
-# Removed the character(s) ` from the read line.
-sub remove_char {
- my $text = shift;
- $text =~ s/`//g;
- return $text;
-}
-
-
-# Count largest length in the table names
-sub length_names {
- my $list = shift;
- my $nb_col = shift;
-
- my $max = 0;
- foreach my $name (@$list) {
- my $length = length($name);
- $max = $length if ($length>$max);
- }
- return '' if ($nb_col>1 || $max>25);
- return ";width:200px" if ($max<=25);
-}
-
-# Insert the introduction text of the web page
-sub slurp_intro {
- my ($intro_file) = @_;
- if (!defined $intro_file) {
- return qq{<h1>Ensembl $db_team Schema Documentation</h1>\n<h2>Introduction</h2>\n<p><i>please, insert your introduction here</i><p><br />};
- }
-
- local $/=undef;
- open my $fh, "< $intro_file" or die "Can't open $intro_file: $!";
- my $intro_html = <$fh>;
- close $fh;
-
- $intro_html =~ s/####DB_VERSION####/$version/g if (defined($version));
-
- return $intro_html;
-}
-
-
-##################
-## Help methods ##
-##################
-
-sub sql_documentation_format {
- print q{
-
-#--------------------------#
-# Example of documentation #
-#--------------------------#
-
-/**
-@table variation
-
-@desc This is the schema's generic representation of a variation.
-
-@colour #FF0000
-
-@column variation_id Primary key, internal identifier.
-@column source_id Foreign key references to the \@link source table.
-@column name Name of the variation. e.g. "rs1333049".
-@column validation_status Variant discovery method and validation from dbSNP.
-@column ancestral_allele Taken from dbSNP to show ancestral allele for the variation.
-@column flipped This is set to 1 if the variant is flipped.
-@column class_so_id Class of the variation, based on the Sequence Ontology.
-
-@example Example of SQL query for to retrieve data from this table:
- @sql SELECT * FROM variation WHERE source_id=1 LIMIT 10;
-
-@see variation_synonym
-@see flanking_sequence
-@see failed_variation
-@see variation_feature
-@see variation_group_variation
-@see allele
-@see allele_group_allele
-@see individual_genotype_multiple_bp
-*/
-
-
-create table variation (
- variation_id int(10) unsigned not null auto_increment, # PK
- source_id int(10) unsigned not null,
- name varchar(255),
- validation_status SET('cluster','freq','submitter','doublehit','hapmap','1000Genome','failed','precious'),
- ancestral_allele text,
- flipped tinyint(1) unsigned NULL DEFAULT NULL,
- class_so_id ENUM('SO:0001483','SO:1000002','SO:0000667') DEFAULT 'SO:0001059', # default to sequence_alteration
-
- primary key( variation_id ),
- unique ( name ),
- key source_idx (source_id)
-);
-
-/**
-@legend #FF0000 Table storing variation data
-*/
-
-
-#========================================================================================================================#
-
-
-#------------------#
-# Tags description #
-#------------------#
-
- /** and */ : begin and end of the document block
- @header : tag to create a group of tables
- @table : name of the sql table
- @desc : description of the role/content of the table, set or info tags
- @colour : tag to colour the header of the table (e.g. if the tables are coloured in the graphic SQL schema and you want to reproduce it in the HTML version)
- @column : column_name [tab(s)] Column description. Note: 1 ligne = 1 column
- @see : tables names linked to the described table
- @link : Internal link to an other table description. The format is ... @link table_name ...
- @info : tag to describe additional information about a table or a set of tables
- @legend : tag to fill the colour legend table at the end of the HTML page
- @example : tag to add some examples, like examples of SQL queries
- @sql : tag inside the @example tag, used to delimit a SQL query
-
-};
- exit(0);
-}
-
-
-sub usage {
-
- print q{
- Usage: perl sql2html.pl [OPTION]
-
- Convert the SQL documentation into an HTML document.
-
- Options:
-
- -help Print this message
- -help_format Print the description of the documentation format in the SQL files
-
- An input file must be specified. This file must be a SQL file, with the "Java-doc like documentation".
- For more information, please visit the following page:
- http://www.ebi.ac.uk/seqdb/confluence/display/EV/SQL+documentation
-
- -i A SQL file name (Required)
- -o An HTML output file name (Required)
- -d The name of the database (e.g Core, Variation, Functional Genomics, ...)
- -c A flag to display the colours associated with the tables (1) or not (0). By default, the value is set to 1.
- -v Version of the schema. Replace the string ####DB_VERSION#### by the value of the parameter "-v", in the introduction text. (Optional)
- -intro A html/text file to include in the Introduction section (Optional. If not provided a default text will be inserted)
- -show_header A flag to display headers for a group of tables (1) or not (0). By default, the value is set to 1.
- -format_headers A flag to display formatted headers for a group of tables (1) or not (0) in the top menu list. By default, the value is set to 1.
- -sort_headers A flag to sort (1) or not (0) the headers by alphabetic order. By default, the value is set to 1.
- -sort_tables A flag to sort (1) or not (0) the tables by alphabetic order. By default, the value is set to 1.
-
- Other optional options - if you want to add some SQL query results as examples
-
- -host Host name of the MySQL server
- -port Port of the MySQL server
- -dbname Database name
- -user MySQL user name
- -pass MySQL password (not always required)
- -skip_connection Avoid to run the MySQL queries contained in the "@example" tags.
-
- } . "\n";
- exit(0);
-}