From 99a68e976a880479d63b4bf9dc1a0789ad1f7ba7 Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Mon, 15 Apr 2013 12:49:30 +0000
Subject: [PATCH] Added a new option "-v" which will replace the string
"####DB_VERSION####" by the value of the parameter "-v", in the introduction
text.
---
misc-scripts/sql2html.pl | 58 ++++++++++++++++++++++------------------
1 file changed, 32 insertions(+), 26 deletions(-)
diff --git a/misc-scripts/sql2html.pl b/misc-scripts/sql2html.pl
index 4c6a3c3d97..71f71e6628 100644
--- a/misc-scripts/sql2html.pl
+++ b/misc-scripts/sql2html.pl
@@ -17,7 +17,7 @@ use Bio::EnsEMBL::DBSQL::DBAdaptor;
### Options ###
###############
-my ($sql_file,$html_file,$db_team,$show_colour,$header_flag,$format_headers,$sort_headers,$sort_tables,$intro_file,$help,$help_format);
+my ($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));
@@ -27,6 +27,7 @@ GetOptions(
'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,
@@ -322,10 +323,10 @@ while (<SQLFILE>) {
#---------#
# INDEXES #
#---------#
-
- # Skip the FOREIGN KEY
- next if ($doc =~ /^\s*foreign\s+key/i);
-
+
+ # Skip the FOREIGN KEY
+ next if ($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;
@@ -334,7 +335,7 @@ while (<SQLFILE>) {
add_column_index("$1$2",$4,$3);
next;
}
- elsif ($doc =~ /^\s*(unique)\s+(\S*)\s*\((.+)\)/i) { # Unique
+ elsif ($doc =~ /^\s*(unique)\s+(\S*)\s*\((.+)\)/i) { # Unique
add_column_index("$1",$3,$2);
next;
}
@@ -349,7 +350,7 @@ while (<SQLFILE>) {
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;
@@ -773,10 +774,10 @@ sub add_table_name {
# 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);
-
+
+ # 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};
}
@@ -784,20 +785,20 @@ sub add_description {
# Method generating the HTML code to display additional information contained in the tags @info
sub add_info {
my $infos = shift;
- my $data = 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));
-
+ $content = add_internal_link($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;
}
@@ -820,8 +821,8 @@ sub add_columns {
my $desc = $col->{desc};
my $index = $col->{index};
- # links
- $desc = add_internal_link($desc,$data);
+ # 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; }
@@ -867,9 +868,9 @@ sub add_examples {
}
}
$html .= qq{</p>};
-
- # Search if there are some @link tags in the example description.
- $html = add_internal_link($html,$data);
+
+ # 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)) {
@@ -908,8 +909,8 @@ sub add_see {
# 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;
+ my $desc = shift;
+ my $data = shift;
while ($desc =~ /\@link\s?(\w+)/) {
my $link = $1;
if ((!grep {$link eq $_} @{$data->{see}}) and defined($link)) {
@@ -995,7 +996,7 @@ sub get_example_table {
my $table = shift;
my $nb = shift;
my $html;
-
+
$sql =~ /select\s+(.+)\s+from/i;
my $cols = $1;
my @tcols;
@@ -1085,6 +1086,7 @@ sub length_names {
return ";width:200px" if ($max<=25);
}
+# Insert the introduction text of the web page
sub slurp_intro {
my ($intro_file) = @_;
if (!defined $intro_file) {
@@ -1095,6 +1097,9 @@ sub slurp_intro {
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;
}
@@ -1105,11 +1110,11 @@ sub slurp_intro {
sub sql_documentation_format {
print q{
-
+
#--------------------------#
-# Example of documentation #
+# Example of documentation #
#--------------------------#
-
+
/**
@table variation
@@ -1203,6 +1208,7 @@ sub usage {
-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.
--
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