Unverified Commit 49bf55cd authored by sgiorgetti's avatar sgiorgetti Committed by GitHub
Browse files

Revert "add database type gene2phenotype"

parent 3e183b71
Pipeline #192097 failed with stage
in 1 minute and 9 seconds
......@@ -55,7 +55,7 @@ Usage:
--pass / -p\tdatabase user password (optional, no default)
--type / -t restrict to database schema type
(i.e. core, compara, funcgen, gene2phenotype, variation, production or ontology)
(i.e. core, compara, funcgen, variation, production or ontology)
(required if --database is not specified)
--database / -d full name of database, or database name pattern
......@@ -265,7 +265,6 @@ if ( defined($opt_type) &&
$opt_type ne 'core' &&
$opt_type ne 'compara' &&
$opt_type ne 'funcgen' &&
$opt_type ne 'gene2phenotype' &&
$opt_type ne 'variation' &&
$opt_type ne 'production' &&
$opt_type ne 'ontology' )
......@@ -281,13 +280,12 @@ my %patches;
# Get available patches.
foreach my $thing ( [ 'ensembl', 'core', 'table.sql' ],
[ 'ensembl-compara', 'compara', 'table.sql' ],
[ 'ensembl-funcgen', 'funcgen', 'table.sql' ],
[ 'ensembl-gene2phenotype', 'gene2phenotype', 'table.sql' ],
[ 'ensembl-variation', 'variation', 'table.sql' ],
[ 'ensembl-production', 'production', 'table.sql' ],
[ 'ensembl-ontology-schema', 'ontology', 'tables.sql' ] )
foreach my $thing ( [ 'ensembl', 'core', 'table.sql' ],
[ 'ensembl-compara', 'compara', 'table.sql' ],
[ 'ensembl-funcgen', 'funcgen', 'table.sql' ],
[ 'ensembl-variation', 'variation', 'table.sql' ],
[ 'ensembl-production', 'production', 'table.sql' ],
[ 'ensembl-ontology-schema', 'ontology', 'tables.sql' ] )
{
my ($git_repo, $schema_type, $schema_file) = @{$thing};
......@@ -470,7 +468,7 @@ while ( $sth->fetch() ) {
}
if ( !defined($schema_type) ) {
if ( $database =~ /_(core|funcgen|gene2phenotype|variation|compara|production|ontology)_/ ) {
if ( $database =~ /_(core|funcgen|variation|compara|production|ontology)_/ ) {
$schema_type = $1;
if ( defined($opt_type) ) {
if ( $schema_type eq $opt_type ) { $schema_type_ok = 1 }
......@@ -487,7 +485,7 @@ while ( $sth->fetch() ) {
if ($database =~ /compara_([a-z][a-z_]+[a-z])?_\d+_\d+/ or # EG case, e.g. ensembl_compara_fungi_18_71
$database =~ /ensembl[a-z]?_(?:compara|production|ontology)_/ or
$database =~ /_test_db_([a-z_]+)_([a-z])_/ or
$database =~ /([a-z][a-z_]+[a-z])_(?:core|funcgen|gene2phenotype|variation)_/)
$database =~ /([a-z][a-z_]+[a-z])_(?:core|funcgen|variation)_/)
{
$species = $1;
$species = 'multi' unless defined $species;
......
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