Functions
public	table_box ()

public	generate_whole_diagram ()

public	blend_colors ()

public	sub_table_box ()

public	generate_sub_diagram ()

public	clean_name ()

public	rst_title ()

public	block_width ()

public	column_width ()

public	rst_list_table ()

public	rst_list_table_row ()

public	rst_add_indent_to_block ()

public	rst_bullet_list ()

public	display_tables_list ()

public	fill_documentation ()

public	add_description ()

public	add_columns ()

public	add_examples ()

public	add_see ()

public	add_internal_link ()

public	add_column_index ()

public	add_column_type_and_default_value ()

public	parse_column_type ()

public	get_example_table ()

public	remove_char ()

public	slurp_intro ()

public	sql_documentation_format ()

public	usage ()

Function Documentation

◆ add_column_index()

public add_column_index ( )

Undocumented method

Code:

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◆ add_column_type_and_default_value()

public add_column_type_and_default_value ( )

Undocumented method

Code:

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◆ add_columns()

public add_columns ( )

Undocumented method

Code:

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◆ add_description()

public add_description ( )

Undocumented method

Code:

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◆ add_examples()

public add_examples ( )

Undocumented method

Code:

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◆ add_internal_link()

public add_internal_link ( )

Undocumented method

Code:

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◆ add_see()

public add_see ( )

Undocumented method

Code:

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◆ blend_colors()

public blend_colors ( )

Undocumented method

Code:

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◆ block_width()

public block_width ( )

Undocumented method

Code:

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◆ clean_name()

public clean_name ( )

Undocumented method

Code:

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◆ column_width()

public column_width ( )

Undocumented method

Code:

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◆ display_tables_list()

public display_tables_list ( )

Undocumented method

Code:

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◆ fill_documentation()

public fill_documentation ( )

Undocumented method

Code:

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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}},$tag_content);
    }
  }
  # New tag initialised
  if ($t1) {
    $tag = $t1;
    $tag_content = $t2;
  }
  else {
    $tag = $tag_content = '';  
  }
}

◆ generate_sub_diagram()

public generate_sub_diagram ( )

Undocumented method

Code:

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sub generate_sub_diagram {
    my ($cluster, $column_links) = @_;
    my $graph = Bio::EnsEMBL::Hive::Utils::GraphViz->new(
        'label' => "$db_team schema diagram: $cluster tables",
        'fontsize' => 20,
        $column_links
          ? ( 'rankdir' => 'LR', 'concentrate' => 'true', )
          : ( 'splines' => 'ortho', ),
    );
    foreach my $table_name (sort keys %{$documentation->{$cluster}->{tables}}) {
        table_box($graph, $table_name);
    }
    my %clusters_to_draw = ($cluster => 1);
    my %other_table_fields;
    my @drawn_fks;
    foreach my $table_name (sort keys %table_documentation) {
        foreach my $fk (@{$table_documentation{$table_name}->{foreign_keys}}) {
            if ($table_documentation{$table_name}->{category} eq $cluster) {
                $other_table_fields{$fk->[1]}->{$fk->[2]} = 1;
                $clusters_to_draw{ $table_documentation{$fk->[1]}->{category} } = 1;
                push @drawn_fks, [$table_name, @$fk];
            } elsif ($table_documentation{$fk->[1]}->{category} eq $cluster) {
                $other_table_fields{$table_name}->{$fk->[0]} = 1;
                $clusters_to_draw{ $table_documentation{$table_name}->{category} } = 1;
                push @drawn_fks, [$table_name, @$fk];
            }
        }
    }
    foreach my $table_name (sort keys %other_table_fields) {
        sub_table_box($graph, $table_name, $other_table_fields{$table_name} || {}) if $cluster ne $table_documentation{$table_name}->{category};
    }
    foreach my $fk (@drawn_fks) {
        my $table_name = shift @$fk;
        $graph->add_edge($table_name => $fk->[1],
            'style' => 'dashed',
            $column_links ? (
                'from_port' => $fk->[0].':e',
                'to_port' => $fk->[2].':w',
            ) : (),
        );
    }
 
    foreach my $h (sort keys %clusters_to_draw) {
        #next unless $h eq $cluster;
        my $cluster_id = clean_name($h);
        my $c = blend_colors($documentation->{$h}->{colour}, '#FFFFFF', 0.8);
        $graph->cluster_2_attributes()->{$cluster_id} = {
            'cluster_label' => $h,
            ($h eq $cluster) ?
                ( 'style' => 'rounded,filled,noborder', 'fill_colour_pair' => ["#$c"], )
              : ( 'style' => 'filled,noborder', 'fill_colour_pair' => ['white'] ),
        };
        my @cluster_nodes;
        $graph->cluster_2_nodes()->{$cluster_id} = \@cluster_nodes;
        foreach my $t (sort keys %{$documentation->{$h}->{tables}}) {
            push @cluster_nodes, $t if (($h eq $cluster) || $other_table_fields{$t});
        }
    }
    return $graph;
}

◆ generate_whole_diagram()

public generate_whole_diagram ( )

Undocumented method

Code:

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◆ get_example_table()

public get_example_table ( )

Undocumented method

Code:

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◆ parse_column_type()

public parse_column_type ( )

Undocumented method

Code:

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◆ remove_char()

public remove_char ( )

Undocumented method

Code:

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◆ rst_add_indent_to_block()

public rst_add_indent_to_block ( )

Undocumented method

Code:

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◆ rst_bullet_list()

public rst_bullet_list ( )

Undocumented method

Code:

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◆ rst_list_table()

public rst_list_table ( )

Undocumented method

Code:

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◆ rst_list_table_row()

public rst_list_table_row ( )

Undocumented method

Code:

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◆ rst_title()

public rst_title ( )

Undocumented method

Code:

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◆ slurp_intro()

public slurp_intro ( )

Undocumented method

Code:

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◆ sql_documentation_format()

public sql_documentation_format ( )

Undocumented method

Code:

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◆ sub_table_box()

public sub_table_box ( )

Undocumented method

Code:

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◆ table_box()

public table_box ( )

Undocumented method

Code:

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◆ usage()

public usage ( )

Functions

Function Documentation

◆ add_column_index()

◆ add_column_type_and_default_value()

◆ add_columns()

◆ add_description()

◆ add_examples()

◆ add_internal_link()

◆ add_see()

◆ blend_colors()

◆ block_width()

◆ clean_name()

◆ column_width()

◆ display_tables_list()

◆ fill_documentation()

◆ generate_sub_diagram()

◆ generate_whole_diagram()

◆ get_example_table()

◆ parse_column_type()

◆ remove_char()

◆ rst_add_indent_to_block()

◆ rst_bullet_list()

◆ rst_list_table()

◆ rst_list_table_row()

◆ rst_title()

◆ slurp_intro()

◆ sql_documentation_format()

◆ sub_table_box()

◆ table_box()

◆ usage()