From 78b1069f7cb75fed350e05da7f93b21804a2c695 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 12 May 2010 07:31:51 +0000
Subject: [PATCH] many changes but the most important is to only add seq_region
mapping if the seq_region_ids are different
---
misc-scripts/update_mapping_set.pl | 186 +++++++++++++++++------------
1 file changed, 110 insertions(+), 76 deletions(-)
diff --git a/misc-scripts/update_mapping_set.pl b/misc-scripts/update_mapping_set.pl
index ad7bd0927f..4b6eb88f49 100644
--- a/misc-scripts/update_mapping_set.pl
+++ b/misc-scripts/update_mapping_set.pl
@@ -24,12 +24,20 @@ Optional arguments:
--host=host server where the core databases are stored
(default: ens-staging)
+ --oldhost = oldhost server where the old release databases are stored
+
--dbname=dbname if you want a single database to update
the mapping_set information (default: all
databases)
--port=port port (default: 3306)
+ --oldport=port old database server port (default: 5306)
+
+ --olduser=user old database server username
+
+ --oldpass=pass password for old database server
+
--help print help (this message)
=head1 DESCRIPTION
@@ -51,7 +59,7 @@ Update mapping_set information for all databases in ens-staging in
release NN (the usual use case in release process):
$ ./update_mapping_set.pl --user ensadmin \
- --pass password --release NN
+ --pass password --release NN --old_host ensembldb-ensembl.org
Update mapping_set information only for pig database in ens-genomics1:
@@ -88,10 +96,14 @@ use constant NEW_MAPPING => 3;
## Command line options
my $host = 'ens-staging';
+my $oldhost = 'ensembldb.ensembl.org';
my $dbname = undef;
my $user = undef;
my $pass = undef;
my $port = 3306;
+my $oldport = 5306;
+my $olduser = "anonymous";
+my $oldpass = undef;
my $help = undef;
my $release = undef;
@@ -101,7 +113,11 @@ GetOptions('host=s' => \$host,
'pass=s' => \$pass,
'port=s' => \$port,
'release=i' => \$release,
- 'help' => \$help
+ 'oldhost=s' => \$oldhost,
+ 'oldport=s' => \$oldport,
+ 'olduser=s' => \$olduser,
+ 'oldpass=s' => \$oldpass,
+ 'help' => \$help
);
pod2usage(1) if($help);
@@ -111,65 +127,78 @@ throw("--release argument required") if(!defined($release));
my $database = 'information_schema';
my $dbh = DBI->connect("DBI:mysql:database=$database;host=$host;port=$port",$user,$pass);
+my $old_dbh = DBI->connect("DBI:mysql:database=$database;host=$oldhost;port=$oldport",$olduser,$oldpass);
my $status;
my $database_name;
#since there is no database defined, will run it agains all core databases
my $pattern;
if (!defined ($dbname)){
- $pattern = '_core_\$release_';
+ $pattern = "_core_".$release."_";
}
else{
$pattern = $dbname;
}
#fetch all databases matching the pattern
+print STDERR $pattern."\n";
my $sth = $dbh->prepare("SHOW DATABASES WHERE `database` REGEXP \'$pattern\'");
$sth->execute();
my $dbs = $sth->fetchall_arrayref();
my $schema_build;
foreach my $db_name (@{$dbs}){
- print STDERR "Going to update mapping for $db_name->[0]....\n";
- my $mapping_set_id;
- my $current_seq_region = (); # hash containing the relation seq_region_name->seq_region_id for the current database
- my $old_seq_region = (); #hash containing the previous database relation seq_region_name->seq_region_id
- my $sth_seq_mapping = $dbh->prepare("INSERT INTO $db_name->[0].seq_region_mapping VALUES(?,?,?)");
- my $sth_mapping_set = $dbh->prepare("INSERT INTO $db_name->[0].mapping_set VALUES(?,?)");
- $status = &mapping_status($dbh,$db_name->[0],\$mapping_set_id,$release);
- $schema_build = get_schema_and_build($db_name->[0]);
- #add mapping_set information
- $sth_mapping_set->execute($mapping_set_id,$schema_build);
- if ($status == INITIAL_MAPPING){
- #first time run the script, create new entry in mapping_set and copy seq_region entries in seq_region_mapping
- $current_seq_region = &read_seq_region($dbh,$db_name->[0]);
- #copy the seq_region_id in the seq_region_mapping
- foreach my $seq_region_name (keys %{$current_seq_region}){
- #when copying there won't be any ambiguity with coord_systems
- foreach my $region_id (values %{$current_seq_region->{$seq_region_name}}){
- $sth_seq_mapping->execute($region_id,$region_id,$mapping_set_id);
- }
- }
- }
- elsif ($status == SAME_MAPPING){
- #seq_region_mapping has not change, nothing to do for the moment....
-
- }
- elsif ($status == NEW_MAPPING){
- #there has been a seq_region change between releases, add a new mapping_set and the relation old_seq_region_id->new_seq_region_id
- my $previous_dbname = &get_previous_dbname($dbh,$db_name->[0],$release);
- $current_seq_region = &read_seq_region($dbh,$db_name->[0]);
- $old_seq_region = &read_seq_region($dbh,$previous_dbname);
- #update the seq_region_mapping table with the old->new seq_region_id relation
- foreach my $seq_region_name (keys %{$old_seq_region}){
- next if (!defined $current_seq_region->{$seq_region_name}); #the seq_region might have disappeared
- foreach my $coord_system_id (keys %{$old_seq_region->{$seq_region_name}}){
- next if (!defined $current_seq_region->{$seq_region_name}->{$coord_system_id}); #the coord_system might have been removed in current database
- $sth_seq_mapping->execute($old_seq_region->{$seq_region_name}->{$coord_system_id},$current_seq_region->{$seq_region_name}->{$coord_system_id},$mapping_set_id);
- }
- }
- }
- else{
- throw("Mapping status not recognized by script: $status \n\n");
- }
+ print STDERR "Going to update mapping for $db_name->[0]....\n";
+ my $mapping_set_id;
+ my $current_seq_region = (); # hash containing the relation seq_region_name->seq_region_id for the current database
+ my $old_seq_region = (); #hash containing the previous database relation seq_region_name->seq_region_id
+ my $sth_seq_mapping = $dbh->prepare("INSERT INTO $db_name->[0].seq_region_mapping VALUES(?,?,?)");
+ my $sth_mapping_set = $dbh->prepare("INSERT INTO $db_name->[0].mapping_set VALUES(?,?)");
+ $status = &mapping_status($dbh,$old_dbh, $db_name->[0],\$mapping_set_id,$release);
+ $schema_build = get_schema_and_build($db_name->[0]);
+
+ #add mapping_set information
+ if ($status == INITIAL_MAPPING){
+ $sth_mapping_set->execute($mapping_set_id,$schema_build);
+ #first time run the script, create new entry in mapping_set and copy seq_region entries in seq_region_mapping
+
+ ############
+ #Actually NO only store the differences so for the initial one it is NONE.
+ ############
+
+ # $current_seq_region = &read_seq_region($dbh,$db_name->[0]);
+ # #copy the seq_region_id in the seq_region_mapping
+ # foreach my $seq_region_name (keys %{$current_seq_region}){
+ # #when copying there won't be any ambiguity with coord_systems
+ # foreach my $region_id (values %{$current_seq_region->{$seq_region_name}}){
+ # $sth_seq_mapping->execute($region_id,$region_id,$mapping_set_id);
+ # }
+ # }
+ }
+ elsif ($status == SAME_MAPPING){
+ #seq_region_mapping has not change, nothing to do for the moment....
+
+ }
+ elsif ($status == NEW_MAPPING){
+ $sth_mapping_set->execute($mapping_set_id,$schema_build);
+ #there has been a seq_region change between releases, add a new mapping_set and the relation old_seq_region_id->new_seq_region_id
+ my $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
+ $current_seq_region = &read_seq_region($dbh,$db_name->[0]);
+ $old_seq_region = &read_seq_region($old_dbh,$previous_dbname);
+ #update the seq_region_mapping table with the old->new seq_region_id relation
+ my $count = 0;
+ foreach my $seq_region_name (keys %{$old_seq_region}){
+ next if (!defined $current_seq_region->{$seq_region_name}); #the seq_region might have disappeared
+ foreach my $coord_system_id (keys %{$old_seq_region->{$seq_region_name}}){
+ next if (!defined $current_seq_region->{$seq_region_name}->{$coord_system_id}); #the coord_system might have been removed in current database
+ next if ($old_seq_region->{$seq_region_name}->{$coord_system_id} == $current_seq_region->{$seq_region_name}->{$coord_system_id}); # if no change no need to write out
+ $sth_seq_mapping->execute($old_seq_region->{$seq_region_name}->{$coord_system_id},$current_seq_region->{$seq_region_name}->{$coord_system_id},$mapping_set_id);
+ $count++;
+ }
+ }
+ print STDERR "Added $count seq_region_mapping entry\n\n";
+ }
+ else{
+ throw("Mapping status not recognized by script: $status \n\n");
+ }
}
#will for a given database, will return the seq_region_name->seq_region_id relation
@@ -194,43 +223,48 @@ sub read_seq_region{
#method to check the status of the current core database: INITIAL_MAPPING, SAME_MAPPING and NEW_MAPPING are the possible states
sub mapping_status{
- my $dbh = shift;
- my $dbname = shift;
- my $mapping_set_id_ref = shift;
- my $release = shift;
-
- my $sth_max_mapping = $dbh->prepare("select max(mapping_set_id) from $dbname.mapping_set");
- $sth_max_mapping->execute();
- ( $$mapping_set_id_ref ) = $sth_max_mapping->fetchrow_array();
- if (! $$mapping_set_id_ref){
- #the table is empty, first mapping
- $$mapping_set_id_ref = 1;
- return INITIAL_MAPPING;
- }
- else{
- #there is information, find out if it is the same mapping as previous release
- my $previous_dbname = &get_previous_dbname($dbh,$dbname,$release);
- throw("No previous database present for $dbname\n") if (!defined $previous_dbname);
- my $cur_seq_region_size = &get_seq_region_size($dbh,$dbname);
- my $previous_seq_region_size = &get_seq_region_size($dbh,$previous_dbname);
- if ($cur_seq_region_size == $previous_seq_region_size){
- #if both tables have same size, SAME_MAPPING
- return SAME_MAPPING;
- }
- else{
- #if tables have different size, NEW_MAPPING
- $$mapping_set_id_ref++;
- return NEW_MAPPING;
- }
- }
+ my $dbh = shift;
+ my $old_dbh = shift;
+ my $dbname = shift;
+ my $mapping_set_id_ref = shift;
+ my $release = shift;
+
+ # my $sth_max_mapping = $dbh->prepare("select max(mapping_set_id) from $dbname.mapping_set");
+ # $sth_max_mapping->execute();
+ # ( $$mapping_set_id_ref ) = $sth_max_mapping->fetchrow_array();
+ # if (! $$mapping_set_id_ref){
+ # #the table is empty, first mapping
+ # $$mapping_set_id_ref = 1;
+ # return INITIAL_MAPPING;
+ # }
+ # else{
+ #there is information, find out if it is the same mapping as previous release
+
+ my $previous_dbname = &get_previous_dbname($old_dbh,$dbname,$release);
+ if(!defined($previous_dbname)){
+ print "No previous database present for $dbname so cannot do diff so will initialise with this as the first version of the database\n";
+ $$mapping_set_id_ref = 1;
+ return INITIAL_MAPPING;
+ }
+ my $cur_seq_region_size = &get_seq_region_size($dbh,$dbname);
+ my $previous_seq_region_size = &get_seq_region_size($old_dbh,$previous_dbname);
+ if ($cur_seq_region_size == $previous_seq_region_size){
+ #if both tables have same size, SAME_MAPPING
+ return SAME_MAPPING;
+ }
+ else{
+ #if tables have different size, NEW_MAPPING
+ $$mapping_set_id_ref++;
+ return NEW_MAPPING;
+ }
+ #}
}
-
#for a given database, returns the size of the seq_region_table
sub get_seq_region_size{
my $dbh = shift;
my $dbname = shift;
- my $sth_status = $dbh->prepare("show table status from $dbname like 'seq_region'");
+ my $sth_status = $dbh->prepare("show table status from $dbname like 'seq_region'") ;
$sth_status->execute();
my @table_status = $sth_status->fetchrow_array();
return $table_status[6]; #return the size of the table
--
GitLab