Remove clunky script.

misc-scripts/production_database/scripts/push_analysis_descriptions.pl

-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-
-use DBI qw( :sql_types );
-use Data::Dumper;
-use File::Spec::Functions;
-use Getopt::Long qw( :config no_ignore_case );
-use IO::File;
-use POSIX qw( floor ceil );
-
-$Data::Dumper::Deparse  = 0;
-$Data::Dumper::Indent   = 0;
-$Data::Dumper::Sortkeys = 1;
-$Data::Dumper::Terse    = 1;
-$Data::Dumper::Useqq    = 0;
-
-my $outdir = 'fix-analysis_description';
-
-sub usage {
-  my $padding = ' ' x length($0);
-
-  print <<USAGE_END;
-
-Usage:
-
-  $0 --release NN --master master_server[:port] \\
-  $padding --server server1[:port1] --server server2[:port2] [...] \\
-  $padding --dbuser user --dbpass passwd
-
-or
-  $0 --help
-
-or
-  $0 --about
-
-where
-
-  --release/-r  The current release (required).
-
-  --master/-m   The master server where the production database lives
-                (optional, default is 'ens-staging1').  Specifying the
-                port is optional, the default port is 3306.
-
-  --server/-s   A database server (optional, may occur several times,
-                default is 'ens-staging1' and 'ens-staging2').
-                Specifying the port is optional, the default port is
-                3306.
-
-  --dbuser/-u   The (read-only) user to connect as (optional,
-                default is 'ensro').
-
-  --dbpass/-p   The password to connect with (optional, no default).
-
-  --help/-h     Displays this help text.
-
-  --about/-a    Display a text about this program (what it does etc.).
-
-USAGE_END
-} ## end sub usage
-
-sub about {
-  print <<ABOUT_END;
-TODO: About info.
-ABOUT_END
-}
-
-sub display_banner {
-  my ( $char, $text ) = @_;
-
-  printf( "%s %s %s\n",
-          $char x ( 39 - floor( length($text)/2 ) ),
-          $text, $char x ( 39 - ceil( length($text)/2 ) ) );
-}
-
-my $release;
-my @servers;
-my $master = 'ens-staging1';
-
-my ( $dbuser, $dbpass ) = ( 'ensro', undef );
-
-my $opt_help  = 0;
-my $opt_about = 0;
-
-if ( !GetOptions( 'release|r=i' => \$release,
-                  'master|m=s'  => \$master,
-                  'server|s=s@' => \@servers,
-                  'dbuser|u=s'  => \$dbuser,
-                  'dbpass|p=s'  => \$dbpass,
-                  'help|h!'     => \$opt_help,
-                  'about!'      => \$opt_about )
-     || $opt_help )
-{
-  usage();
-  exit();
-} elsif ($opt_about) {
-  about();
-  exit();
-} elsif ( !defined($release) ) {
-  print("ERROR: Release was not specified! (use -r or --release)\n");
-  usage();
-  exit();
-}
-
-if ( !@servers ) {
-  @servers = ( 'ens-staging1', 'ens-staging2' );
-}
-
-my @dbtypes = ( 'core', 'otherfeatures', 'cdna', 'vega', 'rnaseq' );
-
-my %db_handles;
-
-my %master;
-my %master_r;
-
-{
-  my ( $host, $port ) = ( $master =~ /^([^:]+):?(\d+)?/ );
-
-  if ( !defined($port) ) {
-    $port = 3306;
-  }
-
-  my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
-                     $host, $port, 'ensembl_production' );
-  my $dbh =
-    DBI->connect( $dsn, $dbuser, $dbpass, { 'PrintError' => 1 } );
-
-  my $sth = $dbh->prepare(
-    q(
-SELECT  full_db_name,
-        logic_name,
-        description,
-        display_label,
-        displayable,
-        web_data
-FROM full_analysis_description
-) );
-
-  $sth->execute();
-
-  my ( $full_db_name,  $logic_name,  $description,
-       $display_label, $displayable, $web_data );
-
-  $sth->bind_columns( \( $full_db_name,  $logic_name,  $description,
-                         $display_label, $displayable, $web_data ) );
-
-  while ( $sth->fetch() ) {
-    my $logic_name_lc = lc($logic_name);
-
-    $master{$full_db_name}{$logic_name_lc} = {
-                                      'full_db_name'  => $full_db_name,
-                                      'logic_name'    => $logic_name_lc,
-                                      'description'   => $description,
-                                      'display_label' => $display_label,
-                                      'displayable'   => $displayable,
-                                      'web_data'      => $web_data };
-
-    $master_r{$logic_name_lc}{$full_db_name} =
-      $master{$full_db_name}{$logic_name_lc};
-  }
-
-}
-
-foreach my $server (@servers) {
-  my ( $host, $port ) = ( $server =~ /^([^:]+):?(\d+)?/ );
-
-  if ( !defined($port) ) {
-    $port = 3306;
-  }
-
-  my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d', $host, $port );
-  my $dbh =
-    DBI->connect( $dsn, $dbuser, $dbpass, { 'PrintError' => 1 } );
-
-  $db_handles{$server} = $dbh;
-}
-
-my %sql;
-foreach my $server (@servers) {
-  printf( "###> Looking at '%s'\n", $server );
-  my $dbh = $db_handles{$server};
-
-  my $sth = $dbh->prepare('SHOW DATABASES LIKE ?');
-
-  foreach my $dbtype (@dbtypes) {
-    $sth->bind_param( 1,
-                      sprintf( '%%\\_%s\\_%d\\_%%', $dbtype, $release ),
-                      SQL_VARCHAR );
-
-    $sth->execute();
-
-    my $dbname;
-    $sth->bind_col( 1, \$dbname );
-
-    while ( $sth->fetch() ) {
-      if ( !exists( $master{$dbname} ) ) {
-        printf( "!!> Unknown database '%s'\n", $dbname );
-        next;
-      }
-
-      my $master = $master{$dbname};
-
-      printf( "##> Processing '%s'\n", $dbname );
-
-      my $sth2 = $dbh->prepare(
-                 sprintf(
-                   'SELECT ad.analysis_id, '
-                     . 'a.analysis_id, '
-                     . 'a.logic_name,'
-                     . 'ad.description,'
-                     . 'ad.display_label,'
-                     . 'ad.displayable,'
-                     . 'ad.web_data '
-                     . 'FROM %s a LEFT JOIN %s ad USING (analysis_id)',
-                   $dbh->quote_identifier( undef, $dbname, 'analysis' ),
-                   $dbh->quote_identifier(
-                                  undef, $dbname, 'analysis_description'
-                   ) ) );
-
-      $sth2->execute();
-
-      my %row = ( 'exists'        => undef,
-                  'analysis_id'   => undef,
-                  'logic_name'    => undef,
-                  'description'   => undef,
-                  'display_label' => undef,
-                  'displayable'   => undef,
-                  'web_data'      => undef );
-
-      $sth2->bind_columns(\( $row{'exists'},        $row{'analysis_id'},
-                             $row{'logic_name'},    $row{'description'},
-                             $row{'display_label'}, $row{'displayable'},
-                             $row{'web_data'} ) );
-
-      while ( $sth2->fetch() ) {
-        my $logic_name_lc = lc( $row{'logic_name'} );
-
-        if ( !defined( $row{'exists'} ) ) {
-          # An analysis exists that does not have a corresponding
-          # analysis_description.
-
-          display_banner( '-', $dbname );
-
-          printf( "==> Analysis '%s' "
-                    . "is missing analysis_description entry.\n",
-                  $row{'logic_name'} );
-
-          if ( !exists( $master->{$logic_name_lc} ) ) {
-            if ( exists( $master_r{$logic_name_lc} ) ) {
-              push( @{ $sql{$dbname} },
-                    sprintf( "-- WARNING: missing analysis_desciption "
-                               . "for logic_name '%s'\n\n",
-                             $logic_name_lc ) );
-            } else {
-              push( @{ $sql{$dbname} },
-                    sprintf( "-- WARNING: unknown analysis_desciption "
-                               . "for logic_name '%s'\n\n",
-                             $logic_name_lc ) );
-            }
-          } else {
-
-            push(
-              @{ $sql{$dbname} },
-              sprintf(
-                "-- WARNING: Inserting minimal missing "
-                  . "analysis_description for '%s'\n"
-                  . "-- web_data and displayable fields may be wrong!\n"
-                  . "INSERT INTO %s (\n"
-                  . "\tanalysis_id,\n"
-                  . "\tdescription,\n"
-                  . "\tdisplay_label,\n"
-                  . "\tdisplayable,\n"
-                  . "\tweb_data\n"
-                  . ") VALUES (\n"
-                  . "\t%s,\n"
-                  . "\t%s,\n"
-                  . "\t%s,\n"
-                  . "\t%s,\n"
-                  . "\t%s\n"
-                  . ");\n\n",
-                $logic_name_lc,
-                $dbh->quote_identifier(
-                                  undef, $dbname, 'analysis_description'
-                ),
-                $dbh->quote( $row{'analysis_id'}, SQL_INTEGER ),
-                $dbh->quote( $master->{$logic_name_lc}{'description'},
-                             SQL_VARCHAR ),
-                $dbh->quote( $master->{$logic_name_lc}{'display_label'},
-                             SQL_VARCHAR ),
-                $dbh->quote( $master->{$logic_name_lc}{'displayable'},
-                             SQL_INTEGER ),
-                $dbh->quote( $master->{$logic_name_lc}{'web_data'},
-                             SQL_VARCHAR ) ) );
-
-          } ## end else [ if ( !exists( $master->...))]
-
-          next;
-        } ## end if ( !defined( $row{'exists'...}))
-
-        if ( exists( $master->{$logic_name_lc} )
-             && $row{'logic_name'} ne
-             $master->{$logic_name_lc}{'logic_name'} )
-        {
-          # Wrong capitalization in analysis.logic_name.
-
-          display_banner( '-', $dbname );
-
-          printf(
-               "==> The logic name '%s' should be all in lower case.\n",
-               $row{'logic_name'} );
-
-          push( @{ $sql{$dbname} },
-                sprintf( "-- Updating (lower-casing) logic_name '%s'\n"
-                           . "UPDATE %s\n"
-                           . "SET logic_name = %s\n"
-                           . "WHERE logic_name = %s;\n\n",
-                         $row{'logic_name'},
-                         $dbh->quote_identifier(
-                                              undef, $dbname, 'analysis'
-                         ),
-                         $dbh->quote( $logic_name_lc,     SQL_VARCHAR ),
-                         $dbh->quote( $row{'logic_name'}, SQL_VARCHAR )
-                ) );
-        } ## end if ( exists( $master->...))
-
-        if ( !exists( $master->{$logic_name_lc} ) ) {
-          # Missing in master.
-
-          display_banner( '-', $dbname );
-
-          print("==> Analysis description MISSING IN MASTER:\n");
-
-          printf( "==> logic_name = '%s'\n"
-                    . "==> description = '%s'\n"
-                    . "==> display_label = '%s'\n"
-                    . "==> displayable = '%s'\n"
-                    . "==> web_data = '%s'\n",
-                  $row{'logic_name'}    || 'NULL',
-                  $row{'description'}   || 'NULL',
-                  $row{'display_label'} || 'NULL',
-                  $row{'displayable'}   || 'NULL',
-                  $row{'web_data'}      || 'NULL' );
-
-          push( @{ $sql{$dbname} },
-                sprintf(
-                    "#!! WARNING: THE FOLLOWING IS ONLY A GUIDELINE\n"),
-                sprintf(
-                    "#!! -- MASTER: Inserting logic_name '%s' "
-                      . "into analysis_description\n"
-                      . "#!! INSERT INTO %s (\n"
-                      . "#!! \tlogic_name, description, display_label\n"
-                      . "#!! ) VALUES (\n"
-                      . "#!! \t%s,\n"
-                      . "#!! \t%s,\n"
-                      . "#!! \t%s\n"
-                      . "#!! );\n",
-                    $logic_name_lc,
-                    $dbh->quote_identifier( undef, 'ensembl_production',
-                                            'analysis_description' ),
-                    $dbh->quote( $logic_name_lc,        SQL_VARCHAR ),
-                    $dbh->quote( $row{'description'},   SQL_VARCHAR ),
-                    $dbh->quote( $row{'display_label'}, SQL_VARCHAR ) ),
-                sprintf( "#!! -- MASTER: Inserting above logic_name "
-                           . "into web_data\n"
-                           . "#!! INSERT INTO %s (\n"
-                           . "#!!\tdata\n"
-                           . "#!! ) VALUES (\n"
-                           . "#!!\t%s\n"
-                           . "#!! );\n",
-                         $dbh->quote_identifier(
-                                 undef, 'ensembl_production', 'web_data'
-                         ),
-                         $dbh->quote( (
-                                    defined( $row{'web_data'} )
-                                    ? Dumper( eval( $row{'web_data'} ) )
-                                    : undef ),
-                                  SQL_VARCHAR ) ),
-                sprintf(
-                  "#!! NOW CONNECT THESE IN analysis_web_data! :-)\n\n")
-          );
-
-          $master->{$logic_name_lc} = {
-                               'logic_name'    => $logic_name_lc,
-                               'description'   => $row{'description'},
-                               'display_label' => $row{'display_label'},
-                               'displayable'   => $row{'displayable'},
-                               'web_data'      => $row{'web_data'} };
-
-        } else {
-          # Compare all fields.
-
-          my @differs;
-
-          foreach my $field (
-                     qw(description display_label displayable web_data))
-          {
-
-            if ( $field eq 'web_data' ) {
-              if ( (
-                     !defined( $row{$field} )
-                   && defined( $master->{$logic_name_lc}{$field} ) )
-                 || ( defined( $row{$field} )
-                      && !defined( $master->{$logic_name_lc}{$field} ) )
-                 || ( defined( $row{$field} )
-                   && defined( $master->{$logic_name_lc}{$field} )
-                   && Dumper( eval( $row{$field} ) ) ne
-                   Dumper( eval( $master->{$logic_name_lc}{$field} ) ) )
-                )
-              {
-                # Some field differs.
-                push( @differs, $field );
-              }
-            } else {
-              if ( (
-                    !defined( $row{$field} )
-                  && defined( $master->{$logic_name_lc}{$field} ) )
-                || ( defined( $row{$field} )
-                     && !defined( $master->{$logic_name_lc}{$field} ) )
-                || ( defined( $row{$field} )
-                  && defined( $master->{$logic_name_lc}{$field} )
-                  && $row{$field} ne $master->{$logic_name_lc}{$field} )
-                )
-              {
-                # Some field differs.
-                push( @differs, $field );
-              }
-            }
-          } ## end foreach my $field (...)
-
-          if ( scalar(@differs) > 0 ) {
-            my $csth =
-              $dbh->column_info( undef, $dbname, 'analysis_description',
-                                 '%' );
-            my $colinfo = $csth->fetchall_hashref( ['COLUMN_NAME'] );
-
-            display_banner( '-', $dbname );
-
-            $Data::Dumper::Terse  = 0;
-            $Data::Dumper::Indent = 1;
-            $Data::Dumper::Useqq  = 1;
-            printf( "==> Analysis description differs "
-                      . "for logic_name '%s'\n",
-                    $row{'logic_name'} );
-            printf( "==> in the following fields: %s\n",
-                    join( ', ', @differs ) );
-            printf( "==> In table:\n%s\n", Dumper( \%row ) );
-            printf( "==> In master:\n%s\n",
-                    Dumper( $master->{$logic_name_lc} ) );
-            $Data::Dumper::Terse  = 1;
-            $Data::Dumper::Indent = 0;
-            $Data::Dumper::Useqq  = 0;
-
-            push(
-              @{ $sql{$dbname} },
-              sprintf(
-                "-- Updating %s for logic_name '%s'\n"
-                  . "UPDATE %s ad,\n"
-                  . "       %s a\n"
-                  . "SET %s\n"
-                  . "WHERE a.logic_name = %s\n"
-                  . "AND ad.analysis_id = a.analysis_id;\n",
-                join( ', ', @differs ),
-                $logic_name_lc,
-                $dbh->quote_identifier(
-                                  undef, $dbname, 'analysis_description'
-                ),
-                $dbh->quote_identifier( undef, $dbname, 'analysis' ),
-                join(
-                  ",\n",
-                  map {
-                    sprintf( "ad.%s = %s",
-                             $_,
-                             $dbh->quote( $master->{$logic_name_lc}{$_},
-                                          $colinfo->{$_}{'DATA_TYPE'} )
-                      )
-                    } @differs ),
-                $dbh->quote( $logic_name_lc, SQL_VARCHAR ) ),
-              sprintf(
-                "-- previous value(s) were:\n%s\n",
-                join(
-                  "\n",
-                  map {
-                    sprintf( "-- %s = '%s'", $_, $row{$_} )
-                    } @differs ) ),
-              "\n" );
-
-          } ## end if ( scalar(@differs) ...)
-        } ## end else [ if ( !exists( $master->...))]
-
-      } ## end while ( $sth2->fetch() )
-
-    } ## end while ( $sth->fetch() )
-  } ## end foreach my $dbtype (@dbtypes)
-} ## end foreach my $server (@servers)
-
-if ( scalar( keys(%sql) ) > 0 ) {
-  if ( !-d $outdir ) {
-    mkdir($outdir);
-  }
-
-  foreach my $db_name ( keys(%sql) ) {
-    my $filename =
-      catfile( $outdir, sprintf( 'fix-%s.sql', $db_name ) );
-
-    printf( "==> Writing SQL to '%s'\n", $filename );
-    my $out = IO::File->new( $filename, 'w' );
-    $out->print( @{ $sql{$db_name} } );
-    $out->close();
-  }
-} else {
-  print("Nothing to do, all seems ok\n");
-}
-
-END {
-  foreach my $dbh ( values(%db_handles) ) {
-    $dbh->disconnect();
-  }
-}