preliminary version of an attrib_type upload script

misc-scripts/attribute_types/upload_attributes.pl

@@ -25,13 +25,10 @@ GetOptions( "host=s", \$host,
 
 $file ||= $FindBin::Bin."/attrib_type.txt";
 usage() if(!$host);
-
+usage() if(($release_num && @dbnames) || (!$release_num && !@dbnames));
 
 
 #release num XOR dbname are required
-usage() if(($release_num && @dbnames) || (!$release_num && !@dbnames));
-my $attribs = read_attrib_file( $file );
-
 $port ||= 3306;
 
 my $dsn = "DBI:mysql:host=$host;port=$port";
@@ -55,6 +52,7 @@ print STDERR "The following databases will be external_db updated:\n  ";
 print join("\n  ", @dbnames);
 print "\ncontinue with update (yes/no)>  ";
 
+
 my $input = lc(<STDIN>);
 chomp($input);
 if($input ne 'yes') {
@@ -62,16 +60,123 @@ if($input ne 'yes') {
   exit();
 }
 
+
+my $attribs = read_attrib_file( $file );
+
 # if any attrib_types are loaded that are different from 
 # the file, a consistency problem is reported and the 
 # upload is not done.
+for my $database ( @dbnames ) {
+  if( check_consistency( $attribs, $database, $db )) {
+    # consistent
+    $db->do( "use $database" );
+    $db->do( "delete from attrib_type" );
+    
+    load_attribs( $db, $attribs );
+  } else {
+    print STDERR "Repairing $database, not consistent!\n";
+    repair( $attribs, $database, $db );
+  }
+}
+
+
+# move attrib types wih the same code to the common attrib_type table
+# ones that are not in the table move to an attrib_type_id that is not used
+sub repair {
+  my ( $attribs, $database, $db ) = @_;
+  
+  $db->do( $database );
+
+  my @tables = qw( seq_region_attrib misc_attrib translation_attrib transcript_attrib );
+  my $ref = $db->selectall_arrayref( "show create table attib_type" );
+  my $create_table = $ref->[0]->[0];
+  $db->do( "alter table attrib_type rename old_attrib_type" );
+  $db->do( $create_table );
+
+  load_attribs( $db, $attribs );
+
+  $db->do( "delete old_attrib_type " .
+	   "from old_attrib_type oat, attrib_type at " .
+	   "where oat.attrib_type_id = at.attrib_type_id " .
+	   "and oat.code = at.code" );
+
+  # only the conflicts remain in old attrib type
+  # move non conflicting entries out of the way to upper part of
+  # attrib_type table
+
+  $db->do( "create table tmp_attrib_types ".
+	   "select oat.attrib_type_id, oat.code, oat.name, oat.description " .
+	   "from old_attrib_type oat " .
+	   "left join attrib_type at " .
+	   "on oat.code = at.code " .
+	   "where at.code is null" );
+  $db->do( "insert into attrib_type( code, name, description) ".
+	   "select code, name, description ". 
+	   "from tmp_attrib_types" );
+
+  $ref = $db->selectall_arrayref( "select code from tmp_attrib_type" );
+  $db->do( "drop table tmp_attrib_types" );
+
+  if( ! @$ref ) {
+    # no problem, thats strange
+    print STDERR "Strange condition, $database didnt have conflicts but ".
+	"executed conflict code\n";
+    return;
+  }
+
+  print STDERR "Database $database has following codes different from attrib_type.txt.\n";
+  print STDERR join( ",", map { $_->[0] } @$ref ),"\n";
+    
+  # now do multi table updates on all tables
+  for my $up_table ( @tables ) {
+    $db->do( "update $up_table tb, attrib_type at, old_attrib_type oat ".
+	     "set tb.attrib_type_id = at.attrib_type_id ".
+	     "where tb.attrib_type_id = oat.attrib_type_id ".
+	     "and oat.code = at.code " );
+  }
+}
+
+
+sub load_attribs {
+  my ( $db, $attribs ) = @_;
+    my $sth;
+    $sth = $db->prepare( "insert into attrib_type( attrib_type_id, code, name, description) ".
+			 "values(?,?,?,?)" ); 
+    for my $attrib ( @$attribs ) {
+      $sth->execute( $attrib->{'attrib_type_id'}, $attrib->{'code'},
+		     $attrib->{'name'}, $attrib->{'description'} );
+    }
+}
+  
+
 
 # alternatively consistency can be enforceed to a certain degree 
 sub check_consistency {
   my $attribs = shift;
-  my $database_names = shift;
+  my $database = shift;
   my $db = shift;
 
+  my ( %db_codes, %file_codes );
+  map { $file_codes{$_->{'attrib_type_id'}} = $_->{'code'}} @$attribs;
+  
+  $db->do( "use $database" );
+  my $sth = $db->prepare( "SELECT attrib_type_id, code, name, description ".
+			  "FROM attrib_type" );
+  $sth->execute();
+  while( my $arr = $sth->fetchrow_arrayref() ) {
+    $db_codes{ $arr->[0] } = $arr->[1];
+  }
+
+  # check if any ids in the database colide with the file
+  my $consistent = 1;
+  for my $dbid ( keys %db_codes ) {
+    if(! exists $file_codes{ $dbid } || 
+       $file_codes{$dbid} ne $db_codes{ $dbid } ) {
+      $consistent = 0;
+    }
+  }
+
+  return $consistent;
 }
 
 
@@ -102,4 +207,25 @@ sub read_attrib_file {
   return \@rows;
 }
 
-
+sub usage {
+  GetOptions( "host=s", \$host,
+	    "user=s", \$user,
+	    "pass=s", \$pass,
+	    "port=i", \$port,
+	    "file=s", \$file,
+            "dbnames=s@", \@dbnames,
+	    "release_num=i", \$release_num
+	  );
+  print STDERR <<EOC
+
+Usage perl upload_attributes.pl -host .. -user .. -port .. -pass ..
+      and either -dbnames homo_sap_1 -dbname homo_sap_2 -dbnames .....
+              or -relase_num ..   
+             put -file .. if its not the default 
+                          attrib_type.txt right next to this script
+                     
+
+EOC
+;
+  exit;
+}