Allow multiple driver-dependent versions of the same patch; suggest schema...

Allow multiple driver-dependent versions of the same patch; suggest schema patching with db_conn.pl commands.

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -58,33 +58,43 @@ sub new {
         : ($class->SUPER::new(@args) || die "Unable to connect to DBA using parameters (".join(', ', @args).")\n");
 
     unless($no_sql_schema_version_check) {
-        my $code_sql_schema_version = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version();
+
+        my $dbc = $self->dbc();
+        $url ||= $dbc->url();
+
+        my $code_sql_schema_version = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version()
+            || die "DB($url) Could not establish code_sql_schema_version, please check that 'EHIVE_ROOT_DIR' environment variable is set correctly";
 
         my $db_sql_schema_version   = eval { $self->get_MetaAdaptor->fetch_value_by_key( 'hive_sql_schema_version' ); };
         if($@) {
             if($@ =~ /hive_meta.*doesn't exist/) {
 
-                die "\nThe 'hive_meta' table does not seem to exist in the database yet.\nPlease patch the database up to sql_schema_version '$code_sql_schema_version' and try again.\n";
+                die "\nDB($url) The 'hive_meta' table does not seem to exist in the database yet.\nPlease patch the database up to sql_schema_version '$code_sql_schema_version' and try again.\n";
 
             } else {
 
-                die "$@";
+                die "DB($url) $@";
             }
 
         } elsif(!$db_sql_schema_version) {
 
-            die "\nThe 'hive_meta' table does not contain 'hive_sql_schema_version' entry.\nPlease investigate.\n";
+            die "\nDB($url) The 'hive_meta' table does not contain 'hive_sql_schema_version' entry.\nPlease investigate.\n";
 
         } elsif($db_sql_schema_version < $code_sql_schema_version) {
 
-            my @new_patches = @{ Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_sql_schema_patches( $db_sql_schema_version ) };
 
-            die "sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
-               ."Please upgrade the database by applying the following patches:\n\n".join("\n", map { "\t$_" } @new_patches)."\n\nand try again.\n";
+            my $new_patches = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_sql_schema_patches( $db_sql_schema_version, $dbc->driver )
+                || die "DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
+                      ."Unfortunately we cannot patch the database; you may have to create a new database or agree to run older code\n";
+
+            my $patcher_command = "$ENV{'EHIVE_ROOT_DIR'}/scripts/db_conn.pl -url $url";
+
+            die "DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
+               ."Please upgrade the database by applying the following patches:\n\n".join("\n", map { "\t$patcher_command < $_" } @$new_patches)."\n\nand try again.\n";
 
         } elsif($code_sql_schema_version < $db_sql_schema_version) {
 
-            die "sql_schema_version mismatch: the database's version is '$db_sql_schema_version', but your code is still '$code_sql_schema_version'.\n"
+            die "DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version', but your code is still '$code_sql_schema_version'.\n"
                ."Please update the code and try again.\n";
         }
     }

modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm

@@ -23,25 +23,47 @@ package Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
 
 use strict;
 
+sub find_all_sql_schema_patches {
 
-sub get_sql_schema_patches {
-    my $after_version = pop @_ || 0;
+    my %all_patches = ();
 
     if(my $hive_root_dir = $ENV{'EHIVE_ROOT_DIR'} ) {
+        foreach my $patch_path ( split(/\n/, `ls -1 $hive_root_dir/sql/patch_20*.*sql*`) ) {
+            my ($patch_name, $driver) = split(/\./, $patch_path);
+
+            $driver = 'mysql' if ($driver eq 'sql');    # for backwards compatibility
 
-        my @patches = split(/\n/, `ls -1 $hive_root_dir/sql/patch_20*.sql`);
+            $all_patches{$patch_name}{$driver} = $patch_path;
+        }
+    } # otherwise will sliently return an empty hash
+
+    return \%all_patches;
+}
 
-        return [ @patches[$after_version..scalar(@patches)-1] ];
-    } else {
-        warn "WARNING: 'EHIVE_ROOT_DIR' environment variable has not been set, things may start crashing soon\n";
-        return [];
+
+sub get_sql_schema_patches {
+    my ($self, $after_version, $driver) = @_;
+
+    my $all_patches         = $self->find_all_sql_schema_patches();
+    my $code_schema_version = $self->get_code_sql_schema_version();
+
+    my @ordered_patches = ();
+    foreach my $patch_key ( (sort keys %$all_patches)[$after_version..$code_schema_version-1] ) {
+        if(my $patch_path = $all_patches->{$patch_key}{$driver}) {
+            push @ordered_patches, $patch_path;
+        } else {
+            return;
+        }
     }
+
+    return \@ordered_patches;
 }
 
 
 sub get_code_sql_schema_version {
+    my ($self) = @_;
 
-    return scalar( @{ get_sql_schema_patches() } );
+    return scalar( keys %{ $self->find_all_sql_schema_patches() } );   # 0 probably means $ENV{'EHIVE_ROOT_DIR'} not set correctly
 }
 
 1;