scripts/misc/generate-pg-audit-ddl

#!/usr/bin/env perl

use strict;
use warnings FATAL => 'all';

use DBI;
use Getopt::Long;
use Const::Fast;
use Term::ReadPassword;
use Template;
use Getopt::Long;

const my %IGNORE_TABLE => (
    cached_reports              => 1,
    crispr_off_targets          => 1,
    summaries                   => 1,
    fixture_md5                 => 1,
    crispr_off_target_summaries => 1,
    design_attempts             => 1,
    crisprs                     => 1,
    project_alleles             => 1,
);

const my $MAIN_SCHEMA  => 'public';
const my $AUDIT_SCHEMA => 'audit';

const my $CREATE_AUDIT_TABLE_TT => <<'EOT';
CREATE TABLE [% audit_schema %].[% table_name %] (
audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
audit_user TEXT NOT NULL,
audit_stamp TIMESTAMP NOT NULL,
audit_txid INTEGER NOT NULL,
[% column_spec.join(",\n") %]
);
EOT

const my $CREATE_AUDIT_FUNCTION_TT => <<'EOT';
CREATE OR REPLACE FUNCTION [% main_schema %].process_[% table_name %]_audit()
RETURNS TRIGGER AS $[% table_name %]_audit$
    BEGIN
        IF (TG_OP = 'DELETE') THEN
           INSERT INTO [% audit_schema %].[% table_name %] SELECT 'D', user, now(), txid_current(), OLD.*;
        ELSIF (TG_OP = 'UPDATE') THEN
           INSERT INTO [% audit_schema %].[% table_name %] SELECT 'U', user, now(), txid_current(), NEW.*;
        ELSIF (TG_OP = 'INSERT') THEN
           INSERT INTO [% audit_schema %].[% table_name %] SELECT 'I', user, now(), txid_current(), NEW.*;
        END IF;
        RETURN NULL;
    END;
$[% table_name %]_audit$ LANGUAGE plpgsql;
EOT

const my $CREATE_AUDIT_TRIGGER_TT => <<'EOT';
CREATE TRIGGER [% table_name %]_audit
AFTER INSERT OR UPDATE OR DELETE ON [% main_schema %].[% table_name %]
    FOR EACH ROW EXECUTE PROCEDURE [% main_schema %].process_[% table_name %]_audit();
EOT

const my $DROP_AUDIT_TABLE_COLUMN_TT => <<'EOT';
ALTER TABLE [% audit_schema %].[% table_name %] DROP COLUMN [% column_name %];
EOT

const my $ADD_AUDIT_TABLE_COLUMN_TT => <<'EOT';
ALTER TABLE [% audit_schema %].[% table_name %] ADD COLUMN [% column_name %] [% column_type %];
EOT

const my $DROP_AUDIT_TABLE_TT => <<'EOT';
DROP TABLE [% audit_schema %].[% table_name %];
EOT

const my %IS_AUDIT_COL => map { $_ => 1 } qw( audit_op audit_user audit_stamp audit_txid );

const my %NEEDS_SIZE => map { $_ => 1 } qw( char character varchar );

{

    my $pg_host   = $ENV{PGHOST};
    my $pg_port   = $ENV{PGPORT};
    my $pg_dbname = $ENV{PGDATABASE};
    my $pg_user   = 'lims2';

    GetOptions(
        'host=s'   => \$pg_host,
        'port=s'   => \$pg_port,
        'dbname=s' => \$pg_dbname,
        'user=s'   => \$pg_user
    ) or die "Usage: $0 [OPTIONS]\n";

    my $pg_password;
    while ( not defined $pg_password ) {
        $pg_password = read_password("Enter PostgreSQL password for $pg_user: ");
    }

    my $dsn = 'dbi:Pg:dbname=' . $pg_dbname;

    if ( defined $pg_host ) {
        $dsn .= ";host=" . $pg_host;
    }

    if ( defined $pg_port ) {
        $dsn .= ";port=" . $pg_port;
    }

    my $dbh = DBI->connect( $dsn, $pg_user, $pg_password, { AutoCommit => 1, RaiseError => 1, PrintError => 0 } )
        or die "Failed to connect to $dsn: $DBI::errstr\n";

    const my %VARS => (
        main_schema  => $MAIN_SCHEMA,
        audit_schema => $AUDIT_SCHEMA,
    );

    my $tt = Template->new;

    my $main_tables  = get_tables( $dbh, $MAIN_SCHEMA );
    my $audit_tables = get_tables( $dbh, $AUDIT_SCHEMA );

    while ( my ( $table_name, $main_table ) = each %{$main_tables} ) {
        next if exists $IGNORE_TABLE{$table_name};
        my $audit_table = $audit_tables->{$table_name};
        if ($audit_table) {
            diff_tables( $table_name, $main_table, $audit_table, $tt, \%VARS );
        }
        else {
            initialize_auditing( $table_name, $main_table, $tt, \%VARS );
        }
    }

    for my $table_name ( keys %{$audit_tables} ) {
        unless ( $main_tables->{$table_name} ) {
            $tt->process( \$DROP_AUDIT_TABLE_TT, { %VARS, table_name => $table_name } );
        }
    }
}

sub diff_tables {
    my ( $table_name, $col_spec, $audit_col_spec, $tt, $VARS ) = @_;

    my %vars = ( %{$VARS}, table_name => $table_name );

    my %cols       = map { @{$_} } @{$col_spec};
    my %audit_cols = map { @{$_} } @{$audit_col_spec};

    for my $cs ( @{$col_spec} ) {
        my ( $column_name, $column_type ) = @{$cs};
        my $audit_column_type = $audit_cols{$column_name};
        if ($audit_column_type) {
            if ( $audit_column_type ne $column_type ) {
                warn "Table $table_name column $column_name type mismatch ($column_type vs $audit_column_type)\n";
            }
        }
        else {
            $tt->process( \$ADD_AUDIT_TABLE_COLUMN_TT,
                { %vars, column_name => $column_name, column_type => $column_type } );
        }
    }

    for my $audit_column_name ( keys %audit_cols ) {
        unless ( $cols{$audit_column_name} or exists $IS_AUDIT_COL{$audit_column_name} ) {
            $tt->process( \$DROP_AUDIT_TABLE_COLUMN_TT, { %vars, column_name => $audit_column_name } );
        }
    }

    return;
}

sub initialize_auditing {
    my ( $table_name, $col_spec, $tt, $VARS ) = @_;

    my %vars = (
        %{$VARS},
        table_name  => $table_name,
        column_spec => [ map { join q{ }, @{$_} } @{$col_spec} ]
    );

    $tt->process( \$CREATE_AUDIT_TABLE_TT,    \%vars );
    $tt->process( \$CREATE_AUDIT_FUNCTION_TT, \%vars );
    $tt->process( \$CREATE_AUDIT_TRIGGER_TT,  \%vars );

    return;
}

sub get_tables {
    my ( $dbh, $schema_name ) = @_;

    my $sth = $dbh->table_info( undef, $schema_name, undef, 'TABLE' );

    my %tables;

    while ( my $r = $sth->fetchrow_hashref ) {
        $tables{ $r->{TABLE_NAME} } = get_column_info( $dbh, $schema_name, $r->{TABLE_NAME} );
    }

    return \%tables;
}

sub get_column_info {
    my ( $dbh, $schema_name, $table_name ) = @_;

    my @column_info;

    my $sth = $dbh->column_info( undef, $schema_name, $table_name, undef );
    while ( my $r = $sth->fetchrow_hashref ) {
        my $type = $r->{TYPE_NAME};
        if ( exists $NEEDS_SIZE{$type} ) {
            # HACK for bpchar type columns in qc_template_well_genotyping_primers and
            # qc_template_well_crispr_primers tables ( qc_run_id column )
            my $col_size = $r->{COLUMN_SIZE} ? $r->{COLUMN_SIZE} : '36';
            $type = $type . '(' . $col_size . ')';
        }
        push @column_info, [ $r->{COLUMN_NAME}, $type ];
    }

    return \@column_info;
}

__END__

=pod

=head1 NAME

generate-pg-audit-ddl

=head1 SYNOPSIS

  generate-pg-audit-ddl --host pgsrv5 --port 5437 --dbname lims2_devel --user lims2

=head1 DESCRIPTION

This script interrogates the database specified by the C<--dbname>
command-line option and compares the I<public> schema with the
I<audit> schema. It emits SQL to create a table in the I<audit> schema
shadowing each table in the B<public> schema, a function to insert a
row in the corresponding I<audit> table for each C<INSERT>, C<UPDATE>
or C<DELETE> in the I<public> schema, and a trigger that calls this
function.

=head1 LIMITATIONS

This script assumes that the I<audit> schema already exists. It
attempts to create SQL that will transition the current state of the
I<audit> schema to the desired state (shadowing the current state of
the I<public> schema). Note, however, that it cannot accurately detect
column and table renames.

If you have renamed a column or table in the main schema, this script
will emit C<DROP> and C<CREATE> statements that will B<delete data
from your audit schema>. Please review the generated SQL carefully in
case this is not what you intended.

=head1 SEE ALSO

The I<audit> tables, functions, and triggers are derived from an
example described here:
L<http://www.postgresql.org/docs/9.0/static/plpgsql-trigger.html>

=head1 AUTHOR

Ray Miller E<lt>rm7@sanger.ac.ukE<gt>

=cut