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Commit c4d39b7a authored by Alessandro Vullo's avatar Alessandro Vullo
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[ENSCORESW-411]. Test cases asserting previous version schema plus patches equals current table.sql

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modules/t/schemaPatches.t
+ 195
− 52
View file @ c4d39b7a
use strict;
use warnings;
use Data::Dumper;
use Test::More;
use Bio::EnsEMBL::ApiVersion qw/software_version/;
......@@ -11,36 +12,16 @@ use File::Spec::Functions qw/updir catfile catdir/;
use File::Temp qw/tempfile/;
use FindBin qw/$Bin/;
#Assume if ensembl.org is down then there is no point in continuing with the tests (1 shot)
sub test_ensembl {
my $content = eval { do_GET('http://www.ensembl.org', 1); };
my $success = 1;
if($@) {
note 'ensembl.org is unreachable. Cannot continue with tests';
$success = 0;
}
return $success;
}
sub get_url {
my ($url) = @_;
my $content = eval { do_GET($url, 5, 0.5); };
return $content if defined $content;
diag $@;
fail("We do not have access to HTTP::Tiny or LWP. Cannot continue") if $@;
return;
}
SKIP: {
my $ensembl_ok = test_ensembl();
skip 'Cannot communicate with ensembl.org. We cannot continue with the tests', 1 unless $ensembl_ok;
#Get last DB version and download the last SQL schema
# Get last DB version and download last SQL schema
my $current_release = software_version();
my $last_release = $current_release - 1;
my $cvs_url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/sql/table.sql?root=ensembl&view=co&pathrev=branch-ensembl-${last_release}";
my $table_sql = get_url($cvs_url);
my $last_table_sql = get_table_sql($last_release);
# Get patch location
my $sql_dir = catdir($Bin, updir(), updir(), 'sql');
......@@ -51,50 +32,212 @@ SKIP: {
}
}, $sql_dir);
skip 'Skipping DB patch tests as we cannot find the SQL at URL '.$cvs_url, (scalar(@patches)+1) unless defined $table_sql;
skip "Skipping DB patch tests as we cannot find the SQL for release $last_release", (scalar(@patches)+1)
unless defined $last_table_sql;
my $db = Bio::EnsEMBL::Test::MultiTestDB->new();
my $dba = $db->get_DBAdaptor('core');
my $dbc = $dba->dbc();
my $new_db_name = $db->create_db_name('schemapatchestemp');
# Create last release DB
my $patched_db_name = $db->create_db_name('schemapatchestemp');
note 'Creating database ' . $patched_db_name;
$dba->dbc()->do("create database $patched_db_name");
# Load last release's schema
my ($fh, $sql_schema_file) = tempfile();
print $fh $table_sql;
print $fh $last_table_sql;
close $fh;
my $loaded_schema = load_sql($dbc, $patched_db_name, $sql_schema_file);
#Create DB
skip 'Skipping DB patch tests as we cannot load the last release schema into a database', scalar(@patches)
unless $loaded_schema;
# Create last release DB
my $current_table_sql = get_table_sql($current_release);
skip "Skipping DB patch tests as we cannot find the SQL for release $current_release", (scalar(@patches)+1)
unless defined $current_table_sql;
my $current_db_name = $db->create_db_name('schematemp');
note 'Creating database ' . $current_db_name;
$dba->dbc()->do("create database $current_db_name");
# Load current release's schema
($fh, $sql_schema_file) = tempfile();
print $fh $current_table_sql;
close $fh;
$loaded_schema = load_sql($dbc, $current_db_name, $sql_schema_file);
note 'Creating database '.$new_db_name;
$dba->dbc()->do("create database $new_db_name");
skip 'Skipping DB patch tests as we cannot load current release schema into a database', scalar(@patches)
unless $loaded_schema;
# Now apply all current patches
foreach my $patch (@patches) {
# Get the number of patch entries before applying next patch
my $previous_patches = get_num_patches($dbc, $patched_db_name);
note "Applying patch $patch";
load_sql($dbc, $patched_db_name, $patch);
check_after_patch($dbc, $patched_db_name, $previous_patches);
}
# check the two schemas after applying the patch
compare_after_patches($dbc, $patched_db_name, $current_db_name);
# Load SQL subroutine
my $load_sql = sub {
my ($path) = @_;
my %args = ( host => $dbc->host(), port => $dbc->port(), user => $dbc->username(), password => $dbc->password());
my $cmd_args = join(q{ }, map { "--${_}=$args{$_}" } keys %args);
my $cmd = "mysql $cmd_args $new_db_name < $path 2>&1";
my $output = `$cmd`;
my $ec = ($? >> 8);
if($ec != 0) {
note($output);
return fail("MySQL command failed with error code '$ec'");
}
return pass("MySQL was able to load the file $path core schema");
};
note 'Dropping database ' . $patched_db_name;
$dba->dbc()->do("drop database if exists $patched_db_name");
note 'Dropping database ' . $current_db_name;
$dba->dbc()->do("drop database if exists $current_db_name");
}
done_testing();
# Compare source schema with target after a series of patches
sub compare_after_patches {
my ($dbc, $source_schema, $target_schema) = @_;
# compare source/target schema type/version
$dbc->do("use $target_schema");
my $sql_helper = $dbc->sql_helper;
my ($target_schema_type, $target_schema_version) =
($sql_helper->execute_single_result(-SQL => "select meta_value from meta where meta_key='schema_type'"),
$sql_helper->execute_single_result(-SQL => "select meta_value from meta where meta_key='schema_version'"));
$dbc->do("use $source_schema");
my ($source_schema_type, $source_schema_version) =
($sql_helper->execute_single_result(-SQL => "select meta_value from meta where meta_key='schema_type'"),
$sql_helper->execute_single_result(-SQL => "select meta_value from meta where meta_key='schema_version'"));
is($source_schema_type, $target_schema_type, "Schema type after patches");
is($source_schema_version, $target_schema_version, "Schema version after patches");
#Load last release's schema
my $loaded_schema = $load_sql->($sql_schema_file);
# Check if the patch meta value does not contain line breaks
my $patch_meta_values_with_newlines =
$sql_helper->execute_simple(-SQL => "select meta_value from meta where meta_key='patch' and meta_value like '%\n%'");
is(scalar @{$patch_meta_values_with_newlines}, 0, "No line breaks in patch meta values");
# check the two schemas contain the same tables
my $source_tables = get_table_names($dbc, $source_schema);
my $target_tables = get_table_names($dbc, $target_schema);
my $diff = (union_intersection_difference($source_tables, $target_tables))[2];
is(scalar @{$diff}, 0, "Same table set");
skip 'Skipping DB patch tests as we cannot load the last release schema into a database', scalar(@patches) unless $loaded_schema;
# check each table has the same definition in both schemas
map { is(get_create_table($dbc, $source_schema, $_),
get_create_table($dbc, $target_schema, $_),
"Table $_ definition")}
@{$source_tables};
}
# Get the name of all tables of a certain schema
sub get_table_names {
my ($dbc, $schema_name) = @_;
$dbc->do("use $schema_name");
return
$dbc->sql_helper->execute_simple(-SQL => 'show tables');
}
# Get the create table SQL statement
sub get_create_table {
my ($dbc, $schema_name, $table_name) = @_;
$dbc->do("use $schema_name");
my $sql_helper = $dbc->sql_helper;
my $create_table = $sql_helper->execute(
-SQL => "show create table $table_name",
-CALLBACK => sub {
return (shift @_)->[1];
}
)->[0];
#Now apply all current patches
foreach my $patch (@patches) {
note "Applying patch $patch";
$load_sql->($patch);
# stripping AUTOINCREMENT=? definitions in the way since
# they are allowed to be different
$create_table =~ s/AUTO_INCREMENT=\d+?//;
return $create_table;
}
# Check source schema after applying one patch
sub check_after_patch {
my ($dbc, $source_schema, $num_previous_patches) = @_;
# see if after patch we gain a meta key corresponding to the applied patch
my $num_current_patches = get_num_patches($dbc, $source_schema);
is($num_current_patches, $num_previous_patches + 1, "Source schema gains patch meta key after patch");
}
# Get the number of patches applied
sub get_num_patches {
my ($dbc, $schema) = @_;
$dbc->do("use $schema");
my $sql_helper = $dbc->sql_helper;
return
$sql_helper->execute_single_result(-SQL => "select count(*) from meta where meta_key='patch' and species_id is NULL");
}
# Load SQL subroutine
sub load_sql {
my ($dbc, $dbname, $path) = @_;
my %args = ( host => $dbc->host(), port => $dbc->port(), user => $dbc->username(), password => $dbc->password());
my $cmd_args = join(q{ }, map { "--${_}=$args{$_}" } keys %args);
my $cmd = "mysql $cmd_args $dbname < $path 2>&1";
my $output = `$cmd`;
my $ec = ($? >> 8);
if($ec != 0) {
note($output);
return fail("MySQL command failed with error code '$ec'");
}
return pass("MySQL was able to load the file $path core schema");
}
# Get table.sql for a given Ensembl release
sub get_table_sql {
my $release = shift;
$release = $release == software_version()?'HEAD':"branch-ensembl-${release}";
note 'Dropping database '.$new_db_name;
$dba->dbc()->do("drop database if exists $new_db_name");
my $cvs_url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/sql/table.sql?root=ensembl&view=co&pathrev=${release}";
return get_url($cvs_url);
}
done_testing();
\ No newline at end of file
# Assume if ensembl.org is down then there is no point in continuing with the tests (1 shot)
sub test_ensembl {
my $content = eval { do_GET('http://www.ensembl.org', 1); };
my $success = 1;
if($@) {
note 'ensembl.org is unreachable. Cannot continue with tests';
$success = 0;
}
return $success;
}
sub get_url {
my ($url) = @_;
my $content = eval { do_GET($url, 5, 0.5); };
return $content if defined $content;
diag $@;
fail("We do not have access to HTTP::Tiny or LWP. Cannot continue") if $@;
return;
}
# Computing Union, Intersection, or Difference of Unique Lists
sub union_intersection_difference {
my ($a, $b) = @_;
my (@union, @isect, @diff);
my %count = ();
foreach my $e (@$a, @$b) { $count{$e}++ }
foreach my $e (keys %count) {
push(@union, $e);
if ($count{$e} == 2) {
push @isect, $e;
} else {
push @diff, $e;
}
}
return (\@union, \@isect, \@diff);
}
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