# # Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor # =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =head1 NAME Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor - Simple wrapper class for Funcgen Storable Adaptors =head1 SYNOPSIS $adaptor->store_states($storable); =head1 DESCRIPTION This is a simple wrapper class to hold common methods to all Funcgen StorableAdaptors. Includes status methods. =head1 SEE ALSO Bio::EnsEMBL::DBSQL::BaseAdaptor =cut package Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor; use strict; use warnings; use Bio::EnsEMBL::Utils::Exception qw( throw deprecate ); use Bio::EnsEMBL::Utils::Scalar qw( assert_ref ); use DBI qw(:sql_types); #have to re-import them, as we lose :sql_types $DBI::EXPORT_TAGS in core BaseAdaptor #we could just re-export everything use base qw(Bio::EnsEMBL::DBSQL::BaseAdaptor Exporter); require Exporter; #Still required to use vars @EXPORT use vars qw( @EXPORT ); @EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}}); =head2 new Example : my $adaptor = Description: Returntype : Bio::EnsEMBL::Funcgen::BaseAdaptor Exceptions : None Caller : Bio::EnsEMBL::Funcgen::BaseAdaptor subclass constructor methods Status : At Risk =cut #This is currently adding a requirement for file based adaptor #to have a _true_tables method sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->reset_true_tables; #Set the _tables values #Set the main table attrs to avoid having to #repeatedly handle them in the contrain methods my @tables = $self->_tables; ($self->{_table_name}, $self->{_table_syn}) = @{$tables[0]}; return $self; } =head2 dbfile_data_root Arg[1] : Optional String: Root path of dbfile data directory Example : $rset_adaptor->dbfile_data_root('/data/root/dir/); Description: This allows the root path to be defined. If an adaptor uses files, it will use this to find its data. Returntype : String Exceptions : None Caller : Bio::EnsEMBL::Funcgen::DBAdaptor::ResultSet Status : at risk - move this to SetAdaptor/FileAdaptor? =cut sub dbfile_data_root { my ($self, $root) = @_; if($root){ $root =~ s/\/$//o; # strip off trailing /, as this is present in dbfile_registry.path $self->{dbfile_data_root} = $root; } return $self->{dbfile_data_root} || ''; # Avoids concat warning } =head2 compose_constraint_query Arg [1] : Hash - Params hash containing 'constraints' hash key value pairs Example : my @objs = @{$self->generic_fetch($self->compose_contraint_query($params_hash))}; Description: Given a params Hashref containing a constraints hash e.g. { constraints => { names => [ 'name1', 'name2' ], analyses => [ $analysis_obj1, $analysis_obj2 ], }, optional_contraints => {an_optional_contraint => undef} } This method will iterate through the cosntraints keys calling _constrain_${constraints_key} e.g. _constrain_analyses. SQL is built from all the specified constraint, and tables added for use when a constraint uses dynamic query composition across tables outside the normal specification for this adaptor. Invalid constraints are caught and a helpful list of valid constraints are listed. NOTE: Most constraints operation with OR logic implicitly via an SQL join or IN clause. There is currently one exception to this is the 'states' constraint which uses AND logic, as this provide more appropriate functionality for this constraint. Returntype : Scalar - Constraint SQL string Exceptions : Throws if params hash argument is not valid. Throws if specific constraint name if not valid. Caller : fetch methods Status : At Risk =cut #This approach originated in the need for a fully flexible method call #for the FeatureSetAdaptor to support the Experiment view, but is also #now used to support flexible filtering of pipeline input sets #TODO Add support for final_clause (order/group) and default_where #Currently the API methods only take a constraints hash as an argument #not a full params hash (i.e. constraints, optional_constraints or other config #optional_parameters doesn't actually work that well #as [undef] is not caught as it still has a size of 1 #e.g when passing optional params which are not defined e.g. [$logic_name] sub compose_constraint_query{ my ($self, $params) = @_; if($params && (ref($params) ne 'HASH') ){ throw('You must pass a valid params HASHREF to compose_constraint_query'); } #Get main table syn here and pass, to reduce redundancy in _constrain methods my @constraints; #Currently no redundancy checking between constraints and optional_constraints #Redundant constraints may result in an SQL error if any tables are added #otherwise will either return as normal if the constraint values are the same #else will return nothing due to the mutually exclusive constraint for my $con_type (qw(constraints optional_constraints)){ if( exists ${$params}{$con_type} ){ #Handle/delete logic_names here and return undef if not valid #such that we can return early from caller (as fetch_all_by_Slice_constraint does). foreach my $constraint_key(keys (%{$params->{$con_type}})){ #warn "$con_type $constraint_key = ".$params->{$con_type}{$constraint_key}; my $constrain_method = '_constrain_'.$constraint_key; if(! $self->can($constrain_method)){ throw($constraint_key." is not a valid constraint type."); # Valid constraints for ".ref($self)." are:\n\t".join("\n\t", @{$self->list_valid_constraints})); } #Only call constraint method if we have data or it is not optional #The following test allows empty arrayrefs to be passed for optional_cosntraints if((( (ref($params->{$con_type}{$constraint_key}) eq 'ARRAY') && @{$params->{$con_type}{$constraint_key}}) || #arrayref and populated or defined $params->{$con_type}{$constraint_key} ) # otherwise defined (likely scalar or object) || $con_type ne 'optional_constraints'){ #or not optional (implicitly undefined) my ($constraint, $constraint_conf) = $self->$constrain_method($params->{$con_type}{$constraint_key}, $params); push @constraints, $constraint; #Currently only handle tables here but could also #set other dynamic config e.g. final_clause etc. if (exists ${$constraint_conf}{tables}) { $self->_tables($constraint_conf->{tables}); } }#else do nothing } # END OF constraint_keys } } # END OF con_types return join(' AND ', @constraints) || ''; } #=head2 list_valid_constraints # # Example : print "Valid constraints are:\t".join("\t", @{$adaptor->list_valid_constraints}); # Description: This method simply returns a list of valid constraint hash keys for use with # fetch method which support the compose_query_constraint method. # Returntype : Listref of scalar contraint keys # Exceptions : None # Caller : compose_query_constraint # Status : At Risk # #=cut #Grab all the keys from the symbol table and see if they have a coderef assigned #no strict 'refs'; #my @methods = grep { defined &{$_} && ($_ =~ /^_constrain_.*/)} keys %{ref($self).'::'}; #use strict 'refs'; #This doesn't recurse down @ISA and don't seem to have a coderef associated??? #although it is supposed to #sub list_valid_constraints{ # my $self = $_[0]; # #Minor helpful voodoo # return [ map {/_constrain_([a-zA-Z_]+$)/ ? $1 : () } # @{Class::Inspector->methods(ref($self), 'private')} ]; #} #Class::Inspector is not a core perl module =head2 _tables Args : None Example : my @adaptor_tables = @{$adaptor->_tables}; Description: PROTECTED implementation of superclass abstract method. Returns the names and aliases of the tables as defined by the _true_tables method in the subclass and adds tables as required for query composition Returntype : List of listrefs of strings Exceptions : None Caller : Internal Status : At Risk =cut #todo this currently doesn't account for tables being added more than once between constraints #This could be handled quite easily with a hash #but would not solved the problem of duplicating the join clause in the constraint method #would be sensible to be key on alias rather than table name, #to allow multiple joins to the same table sub _tables { my ($self, $new_tables) = @_; if(defined $new_tables){ push @{$_[0]->{_tables}}, @{$new_tables}; } return @{$_[0]->{_tables}}; } sub _true_tables { my $self = shift; return ($self->_tables); } =head2 reset_true_tables Args : None Example : $adaptor->reset_true_tables; Description: Resets the tables attributes to the default or 'true' tables for a given composable adaptor. Returntype : None Exceptions : None Caller : Internal Status : At Risk =cut #change to _reset_true_tables? sub reset_true_tables{ my $self = $_[0]; @{$self->{_tables}} = $self->_true_tables; return; } =head2 _main_table Example : my $syn = $adaptor->_main_table->[1]; Description: Convenience method to retrieve the main table or main table synonym for this adaptor Entirely dependent on ensembl convention of always having main table as first element of tables array. Returntype : Array ref Exceptions : None Caller : General Status : At Risk =cut #set this in new and return attr sub _main_table{ my $self = $_[0]; #Need to do this to put it in list context to avoid just returning the last value my @tables = $self->_tables; return $tables[0]; } #why is this calling SUPER::_tables rather than the _tables method in this module? #This is due to the order of @ISA in the BaseFeatureAdaptor sub _table_syn { return $_[0]->{_table_syn}; } sub _table_name { return $_[0]->{_table_name}; } # =head2 store_states # # Arg [1] : Bio::EnsEMBL::Funcgen::Storable # Arg [2] : Arrayref (optional) - States to store # Example : $rset_adaptor->store_states($result_set); # Description: Stores states in status table. By default will store state # attributes, but will also store optioanlly specified states # Returntype : None # Exceptions : Throws if Storable is not stored # Caller : General # Status : At Risk # # =cut # # sub store_states{ # my $self = shift; # my $storable = shift; # my $states = shift || []; # assert_ref($storable, 'Bio::EnsEMBL::Funcgen::Storable'); # assert_ref($states, 'ARRAY', 'optional states'); # # return unless (defined $states); # # my $all_states = $storable->get_all_states(); # if (defined $all_states) { # push @$states, @$all_states; # } # # foreach my $state(@$states){ # # if (! $self->has_stored_status($state, $storable)){ # $self->store_status($state, $storable) # } # } # # return; # } =head2 fetch_all Arg[1] : Hashref - optional parameters e.g. {constraints => {states => ['DISPLAYABLE']}} or (for backwards compatibility) a status string e.g. 'DISPLAYABLE'. Example : my @dsets = @{$dsa->fetch_all()}; Description: Gets all available objects from the DB modulated by the optional parameters argument. Returntype : Arrayref Exceptions : None Caller : General Status : At Risk =cut sub fetch_all { my ($self, $params) = @_; if($params){ # Still supporting passing a status String arg for now if(ref($params) eq ''){ #This is a scalar status arg $params = {constraints => {states => [$params]}}; } } my $objs = $self->generic_fetch($self->compose_constraint_query($params)); $self->reset_true_tables; return $objs; } # =head2 status_to_constraint # # Arg [1] : string - status e.g. 'DISPLAYABLE' # Arg [2] : string - Constraint # Example : $sql = $self->status_to_constraint($self, $constraint, $status); # Description: Appends the appropriate status constraint dependant on the BaseAdaptor sub class. # Returntype : string - constraint # Exceptions : None # Caller : Bio::EnsEMBL::Funcgen::DBSQL::"BaseAdaptors" # Status : At risk - to be deprecated # # =cut # # #TODO remove this in favour of compose_constraint # # sub status_to_constraint{ # my ($self, $status) = @_; # # #This is now supported in compose_constraint_query # #Which avoid some of the problems below # # my $constraint; # # #This will throw if status not valid, but still may be absent # my $status_id = $self->_get_status_name_id($status); # # # return if (! $status_id); # # my @tables = $self->_tables; # my ($table_name, $syn) = @{$tables[0]}; # # my @status_ids; # # my $sql = "SELECT table_id from status where table_name='$table_name' and status_name_id='$status_id'"; # @status_ids = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)}; # # #This is causing problems as we might get none, which will invalidate the sql # #Hence we return nothing # # $constraint = " $syn.${table_name}_id IN (".join(',', @status_ids).")" if @status_ids; # return $constraint; # } # =head2 _test_funcgen_table # # Arg [1] : Bio::EnsEMBL::"OBJECT" # Example : $status_a->_is_funcgen_object($experimental_chip)}; # Description: Tests if the object is a valid funcgen object with an identifiable table_name # Returntype : string - table_name # Exceptions : Throws if argument if a Bio::EnsEMBL::Funcgen::"OBJECT" not supplied # Throws if not table name identified # Caller : general # Status : At risk # # =cut # # sub _test_funcgen_table{ # my ($self, $obj) = @_; # # #Can we change this to is_stored_and_valid for a Storable? # $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::Storable', $obj); # #Does this test for ad # # my @tables = $obj->adaptor->_tables; # my ($table) = @{$tables[0]}; # # return $table || $self->throw("Cannot identify table name from $obj adaptor"); # } # =head2 fetch_all_states # # Arg [1] : Bio::EnsEMBL::"OBJECT" # Arg [2...] : listref of states # Example : my @ec_states = @{$status_a->fetch_all_states($experimental_chip)}; # Description: Retrieves all states associated with the given "OBJECT" # Returntype : ARRAYREF # Exceptions : None # Caller : general # Status : At risk # # =cut # # sub fetch_all_states{ # my ($self, $obj) = @_; # # my $table = $self->_test_funcgen_table($obj); # my $sql = "SELECT name FROM status_name sn, status s WHERE s.table_name='$table' ". # "AND s.table_id='".$obj->dbID()."' and s.status_name_id=sn.status_name_id"; # # # print "\n\n---------------------------------------\n\n"; # # print "Sql to fetch the states:\n"; # # print "\n\n$sql\n\n"; # # print "\n\n---------------------------------------\n\n"; # # my @states = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)}; # # return \@states; # } # =head2 has_stored_status # # Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE # Arg [2] : Bio::EnsEMBL::Storable # Example : if($status_a->has_stored_status('IMPORTED', $array){ ... skip import ... }; # Description: Tests wether a given object has a given state # Returntype : BOOLEAN # Exceptions : None # Caller : Bio::EnsEMBL::Funcgen::BaseAdaptor # Status : At risk # # =cut # # #Only used for set_status, merge with set_status? # # sub has_stored_status{ # my ($self, $state, $obj) = @_; # # my (@row); # my $status_id = $self->_get_status_name_id($state); # # if ($status_id){ # # my $table = $self->_test_funcgen_table($obj); # # if($status_id){ # my $sql = "SELECT status_name_id FROM status WHERE table_name=\"$table\"". # " AND table_id=\"".$obj->dbID()."\" AND status_name_id=\"$status_id\""; # # #could just return the call directly? # @row = $self->db->dbc->db_handle->selectrow_array($sql); # } # } # # return (@row) ? 1 : 0; # } # =head2 store_status # # Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE # Arg [2] : Bio::EnsEMBL::"OBJECT" # Example : $status_a->store_status('IMPORTED', $array_chip); # Description: Sets a state for a given object # Returntype : None # Exceptions : None # Caller : general # Status : At risk - Move to Status.pm? # # =cut # # sub store_status{ # my $self = shift; # my $state = shift; # my $obj = shift; # my $table = $self->_test_funcgen_table($obj); # # if(! $self->has_stored_status($state, $obj)){ # my $status_id = $self->_get_status_name_id($state); # # if(! $status_id){ # throw("$state is not a valid status_name for $obj:\t".$obj->dbID); # } # # my $sql = "INSERT into status(table_id, table_name, status_name_id) VALUES('". # $obj->dbID()."', '$table', '$status_id')"; # # if(! eval { $self->db->dbc->do($sql); 1}){ # throw("Failed to store apparently unstored $state status for $obj (dbID=". # $obj->dbID."\nPotential race condition with parallel process\n$@"); # } # # #Setting it in the obj if it is not already present. # $obj->add_status($state) if ! $obj->has_status($state, $obj); # } # # return; # } # =head2 revoke_status # # Arg [1] : String - status name e.g. 'IMPORTED' # Arg [2] : Bio::EnsEMBL::Funcgen::Storable # Arg [3] : Boolean - Validate status name flag. Will throw if not valid. # Example : $rset_adaptor->revoke_status('DAS DISPLAYABLE', $result_set); # Description: Revokes the given state of Storable in status table. # Returntype : Boolean - Success or Failure # Exceptions : Warns if storable does not have state # Throws is status name is not defined # Throws if status record delete fails # Caller : General # Status : Stable # # =cut # # #Where is the return value use(d|ful) # # sub revoke_status{ # my $self = shift; # my $state = shift or throw('Must provide a status name'); # my $storable = shift; # my $validate_status = shift; # my $table_name = $self->_test_funcgen_table($storable); # my $status_id = $self->_get_status_name_id($state, $validate_status); # my $revoked = 0; # # if ($status_id){ # # if(! $self->has_stored_status($state, $storable)){ # warn $storable.' '.$storable->dbID()." does not have status $state to revoke\n"; # } # else{ # #do sanity checks on table to ensure that IMPORTED does not get revoke before data deleted? # #how would we test this easily? # my $sql = "delete from status where table_name='${table_name}'". # " and status_name_id=${status_id} and table_id=".$storable->dbID(); # if(! eval { $self->db->dbc->do($sql); 1}){ # throw("Failed to delete $state status from DB for $storable (dbID=". # $storable->dbID.")\n$@"); # } # # my @tmp_states; # # for my $stored_state(@{$storable->{states}}){ # # if($stored_state ne $state){ # push @tmp_states, $stored_state; # } # } # # $storable->{states} = \@tmp_states; # $revoked = 1; # } # } # #else{ Don't throw as the state of the object is as expected, but # #this may be a mis-spelled status, and the real status may persist # #So handle in the caller # # return $revoked; # } # =head2 revoke_states # # Arg [1] : Bio::EnsEMBL::Funcgen::Storable # Arg [2] : Arrayref (optional) - States to revoke # Arg [3] : Boolean (optional) - Validate status exists # Example : $rset_adaptor->revoke_status($result_set); # Description: Deletes all or specified status records from the Storable. # Returntype : Bio::EnsEMBL::Funcgen::Storable # Exceptions : None # Caller : General + Helper rollback methods # Status : At Risk # # =cut # # sub revoke_states{ # my $self = shift; # my $storable = shift; # my $states = shift || []; # my $validate = shift; # assert_ref($states, 'ARRAY', 'optional states'); # # if(! @$states){ # my $table_name = $self->_test_funcgen_table($storable); # undef $storable->{states}; # my $sql = "delete from status where table_name='${table_name}'". # " and table_id=".$storable->dbID(); # # if(! eval {$self->db->dbc->do($sql); 1}){ # throw('Failed to revoke states('.join(' ', @{$storable->get_all_states}). # ") for $storable (dbID=".$storable->dbID."\n$@"); # } # } # else{ # # foreach my $state(@$states){ # $self->revoke_status($state, $storable, $validate); # #Cannot return revoked boolean here. Bu this only return false if # #it didn't already have the status # } # } # # return $storable; # } # =head2 set_imported_states_by_Set # # Arg [1] : Bio::EnsEMBL::Funcgen::Set e.g. a FeatureSet or ResultSet # Example : $self->set_imported_states_by_Set($set); # Description: Sets default states for imported Feature|ResultSets # Returntype : None # Exceptions : None # Caller : Import parsers and RunnableDBs # Status : At risk - move to BaseImporter # # =cut # # #Move a wrapper to Storable, which handles the obj attributes # #which then call this method to remove the status entries? # # #This needs to be used by RunnableDBs too! # #All state stuff is handled by BaseAdaptor? # #Can we put this in the SetAdaptor? # # #CoordSystem specific status may go, if we are removing multi CoordSys support # # sub set_imported_states_by_Set{ # my $self = shift; # my $set = shift; # $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::Set', $set); # return $self->store_states($set, $self->_imported_states); # } # # sub revoke_imported_states_by_Set{ # my $self = shift; # my $set = shift; # $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::Set', $set); # return $self->revoke_states($set, $self->_imported_states); # } # # # # # sub _imported_states{ # my $self = shift; # #Get default chromosome version for this dnadb # # if(! defined $self->{imported_states}){ # $self->{imported_states} = ['IMPORTED', # 'IMPORTED_'. # $self->db->dnadb->get_CoordSystemAdaptor->fetch_by_name('chromosome')->version]; # } # # return $self->{imported_states}; # } # # =head2 status_filter # # Arg [1] : String - status e.g. IMPORTED, DISPLAYABLE # Arg [2] : String - table name e.g. experimental_chip # Arg [3] : List - table dbIDs # Exmaple : my @displayable_ec_ids = @{$ec_adaptor->status_filter('DISPLAYABLE', # 'experimental_chip', # (map $_->dbID, @echips))}; # Description: Quick method for filtering dbIDs based on their table and and status # Returntype : ARRAYREF # Exceptions : Warns if state already set # Throws is status name is not already stored. # Caller : general # Status : At risk - Move to Status? # # =cut # # sub status_filter{ # my ($self, $status, $table_name, @table_ids) = @_; # # my @status_ids; # my $status_id = $self->_get_status_name_id($status); # # if($status_id){ # # if(! ($table_name && @table_ids)){ # throw("Must provide a table_name and table_ids to filter non-displayable ids"); # } # # my $sql = "SELECT table_id from status where table_name='$table_name' and ". # "table_id in (".join(", ", @table_ids).") and status.status_name_id". # "='$status_id'"; # @status_ids = map $_ = "@$_", # @{$self->db->dbc->db_handle->selectall_arrayref($sql)}; # } # # return \@status_ids; # } # =head2 _get_status_name_id # # Arg [1] : String - status_name e.g. IMPORTED, DISPLAYABLE # Arg [2] : Boolean - optional flag to throw error if status_name is not # present in the DB. # Example : my $status_id = $self->_get_status_name_id('IMPORTED'); # Description: Retrieves the dbID of a given status_name record # Returntype : Int # Exceptions : Throws if status name argument not defined or if throw flag is # set and status_name is not in the DB. # Caller : Bio::EnsEMBL::Funcgen::BaseAdaptor # Status : At risk - Move to Status? # # =cut # # sub _get_status_name_id{ # my ($self, $status, $throw) = @_; # # if(! defined $status){ # throw('You must provide a status_name string argument'); # } # # my $sql = "SELECT status_name_id from status_name where name='$status'"; # my ($status_id) = $self->db->dbc->db_handle->selectrow_array($sql); # # if (! $status_id){ # if($throw){ # throw("Status name $status is not valid. ". # 'Maybe you need to add it to the status_name table?'); # } # else{ # warn("Status name $status is not valid. ". # 'Maybe you need to add it to the status_name table?'); # } # } # # return $status_id; # } # # =head2 fetch_all_by_external_name # # Arg [1] : String $external_name # An external identifier of the feature to be obtained # Arg [2] : (optional) String $external_db_name # The name of the external database from which the # identifier originates. # Example : my @features = # @{ $adaptor->fetch_all_by_external_name( 'NP_065811.1') }; # Description: Retrieves all features which are associated with # an external identifier such as an Ensembl Gene or Transcript # stable ID etc. Usually there will only be a single # feature returned in the list reference, but not # always. Features are returned in their native # coordinate system, i.e. the coordinate system in which # they are stored in the database. If they are required # in another coordinate system the Feature::transfer or # Feature::transform method can be used to convert them. # If no features with the external identifier are found, # a reference to an empty list is returned. # Returntype : arrayref of Bio::EnsEMBL::Funcgen::Storable objects # Maybe any Feature, FeatureType, Probe or ProbeSet # Exceptions : Warns if method not available for given object adaptor # Caller : general # Status : at risk # # =cut # # sub fetch_all_by_external_name { # my ( $self, $external_name, $external_db_name ) = @_; # # my $entryAdaptor = $self->db->get_DBEntryAdaptor; # my (@ids, $type, $type_name); # # if(ref($self) =~ /.+::(.+)Adaptor$/o){ # $type = $1; # } # else{ # throw("Failed to identify data class name from adaptor namespace:\t".ref($self)); # } # # return $self->fetch_all_by_dbID_list( # [ $entryAdaptor->_type_by_external_id( $external_name, $type, undef, $external_db_name) ]); # } # # # =head2 fetch_all_by_external_names # # Arg [1] : ARRAYREF of strings. External identifiers of the features to be obtained # Arg [2] : (optional) String $external_db_name # The name of the external database from which the # identifier originates. # Example : my @features = # @{ $adaptor->fetch_all_by_external_names(['ENST00003548913', ...])}; # Description: Retrieves all features which are associated with # the external identifiers such as a Ensembl gene or transcript # stable IDs, etc. Features are returned in their native # coordinate system, i.e. the coordinate system in which # they are stored in the database. If they are required # in another coordinate system the Feature::transfer or # Feature::transform method can be used to convert them. # If no features with the external identifier are found, # a reference to an empty list is returned. # Returntype : arrayref of Bio::EnsEMBL::Funcgen::Storable objects # Maybe any Feature, FeatureType, Probe or ProbeSet # Exceptions : Warns if xref method not available for given object adaptor # Caller : general # Status : at risk # # =cut # # sub fetch_all_by_external_names{ # my ( $self, $external_names, $external_db_name ) = @_; # # my $entryAdaptor = $self->db->get_DBEntryAdaptor(); # my ($type, $type_name); # ($type = ref($self)) =~ s/.*:://; # $type =~ s/Adaptor$//; # ($type_name = $type) =~ s/Feature$/_feature/; # my $xref_method = 'list_'.lc($type_name).'_ids_by_extids'; # # # if(! $entryAdaptor->can($xref_method)){ # warn "Does not yet accomodate $type external names"; # return []; # } # # #Would be better if _list_ method returned and arrayref # my @ids = $entryAdaptor->$xref_method($external_names, $external_db_name); # # return $self->fetch_all_by_dbID_list(\@ids); # } # # =head2 fetch_all_by_linked_Transcript # # Arg [1] : Bio::EnsEMBL::Transcript # Example : my @psets = # @{ $probe_set_adaptor->fetch_all_by_linked_Transcript($tx_obj); # Description: Retrieves all features which are associated with # the given Ensembl Transcript. # Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Storable objects # Maybe any Feature, FeatureType, Probe or ProbeSet # Exceptions : Throws if arguments not valid # Caller : general # Status : at risk # # =cut # # sub fetch_all_by_linked_Transcript{ # my $self = shift; # my $tx = shift; # assert_ref($tx, 'Bio::EnsEMBL::Transcript'); # # if(! $tx->dbID ){ # throw('You must provide a stored Bio::EnsEMBL:Transcript object'); # } # # return $self->fetch_all_by_external_name($tx->stable_id, $self->db->species.'_core_Transcript') # } # # =head2 fetch_all_by_linked_transcript_Gene # # Arg [1] : Bio::EnsEMBL::Gene # Example : my @psets = # @{ $probe_set_adaptor->fetch_all_by_linked_transcript_Gene($gene_obj); # Description: Retrieves all features which are indirectly associated with # the given Ensembl Gene, through it's Transcripts. # Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Storable objects # Maybe any Feature, FeatureType, Probe or ProbeSet # Exceptions : Throws if arguments not valid # Caller : general # Status : at risk # # =cut # # sub fetch_all_by_linked_transcript_Gene{ # my $self = shift; # my $gene = shift; # assert_ref($gene, 'Bio::EnsEMBL::Gene'); # # if(! $gene->dbID ){ # throw('You must provide a stored Bio::EnsEMBL::Gene object'); # } # # #No need to pass params here as we know the gene ID is an int from the db # my $tx_sids = $gene->adaptor->db->dbc->sql_helper->execute_simple('select t.stable_id from transcript t where t.gene_id='.$gene->dbID); # return $self->fetch_all_by_external_names($tx_sids, $self->db->species.'_core_Transcript'); # } # =head2 store_associated_feature_types # # Arg [1] : Bio::EnsEMBL::Funcgen::Storable # Example : $ext_feat_adaptor->store_associated_feature_type($ext_feat); # Description : Store FeatureTypes assoicated with a given Storable # Returntype : None # Exceptions : Throws if FeatureTypes are not valid or stored # Caller : Adaptors # Status : At risk # # =cut # # #This currently does not validation # #of existing types # #we may want to rollback the associated ftypes from a specific analysis # #is rollback function safe here # #do we want to split this into update/add and store methods? # # # sub store_associated_feature_types { # my ($self, $storable, $rollback) = @_; # # #Direct access to avoid lazy loading with an unstored SetFeature # my $assoc_ftypes = $storable->{'associated_feature_types'}; # # #Could be undef or empty # return if ! defined $assoc_ftypes || scalar(@$assoc_ftypes) == 0; # # my $table_name = $storable->adaptor->_main_table->[0]; # my $dbid = $storable->dbID; # my $sql; # # if($rollback){ # $sql = 'DELETE from associated_feature_type where '. # "table_name='$table_name' and table_id=$dbid"; # $self->db->dbc->db_handle->do($sql); # } # # $sql = 'INSERT into associated_feature_type(table_id, table_name, feature_type_id) values (?,?,?)'; # # foreach my $ftype(@$assoc_ftypes){ # # #We have already tested the class but not whether it is stored # $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureType', $ftype); # # my $sth = $self->prepare($sql); # $sth->bind_param(1, $dbid, SQL_INTEGER); # $sth->bind_param(2, $table_name, SQL_VARCHAR); # $sth->bind_param(3, $ftype->dbID, SQL_INTEGER); # $sth->execute(); # } # # return; # } # # =head2 fetch_all_by_associated_FeatureType # # Arg [1] : Bio::EnsEMBL::Funcgen::FeatureType # Example : my $assoc_ftypes = $ft_adaptor->fetch_all_by_associated_FeatureType($ftype); # Description: Fetches all objects which have associated FeatureType. # Note this is not the main FeatureType for this object. # Likely only relevant for FeatureTypeAdaptor and ExternalFeatureAdaptor. # Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Storable objects # Exceptions : Throws if FeatureType not valid or stored # Caller : General # Status : At risk # # =cut # # #todo add _constrain_associated_FeatureType method # # sub fetch_all_by_associated_FeatureType{ # my ($self, $ftype) = @_; # # $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureType', $ftype); # my ($table_name, $table_syn) = @{$self->_main_table}; # # $self->_tables([['associated_feature_type', 'aft']]); # my $constraint = "aft.feature_type_id=? AND aft.table_name='${table_name}' ". # "AND aft.table_id=${table_syn}.${table_name}_id"; # # $self->bind_param_generic_fetch($ftype->dbID, SQL_INTEGER); # my $objs = $self->generic_fetch($constraint); # $self->reset_true_tables; # # return $objs; # } # # =head2 _list_dbIDs # # Example : my @table_ids = @{$adaptor->_list_dbIDs()}; # Description: Wrapper for parent method, dynamically passes correct table name to query. # Gets an array of internal IDs for all objects in the main table of this class. # Returntype : List of Ints # Exceptions : None # Caller : General # Status : Stable # # =cut # # sub _list_dbIDs{ # my $self = shift; # return $self->SUPER::_list_dbIDs($self->_table_name); # } # # =head2 build_feature_class_name Arg[1] : String - feature_class e.g. annotated, dna_methylation, regulatory etc. Example : my $fclass_name = $adaptor->build_feature_class_name; Description: Builds the full feature class name for a given feature class. Returntype : String Exceptions : None Caller : FeatureSet::get_FeatureAdaptor and Set::feature_class_name, webcode fails without this Status : Stable =cut sub build_feature_class_name{ my ($self, $fclass) = @_; if(! defined $fclass){ throw('You must pass a feature class argument to build the feature class name'); } my @words = split('_', $fclass); foreach my $word(@words){ $word = ucfirst($word); $word = 'DNA' if $word eq 'Dna'; } return join('', (@words, 'Feature') ); } # # sub stable_id_prefix{ # my $self = shift; # # if (! defined $self->{'stable_id_prefix'}) { # ($self->{'stable_id_prefix'}) = @{$self->db->dnadb->get_MetaContainer->list_value_by_key # ( # 'species.stable_id_prefix' # )}; # # #Only add R if it is defined # $self->{'stable_id_prefix'} .= 'R' if $self->{'stable_id_prefix'}; # } # # return $self->{'stable_id_prefix'} # } # ### GENERIC CONSTRAINT METHODS ### # Used by compose_constraint_query =head2 _constraint_states Arg[1] : Arrayref - Status name strings. Arg[2] : Hashref - Constraint parameters e.g. {string_param_exists => 1} # This validates the status name exists Example : my ($constraint, $constraint_conf) = $self->$constrain_method($params->{constraints}{$constraint_key}, $params); Description: Builds the constraint sql for resitricting to Storables with all the status names specified (AND logic). Returntype : List constaining a constraint sql string, and a hashref of constraint config. Exceptions : Throws if args are not valid. Caller : BaseAdaptor::compose_constraint_query Status : At risk =cut #This uses AND logic, rather than the OR logic of the other constrain methods #todo allow OR logic via a different method? #todo move string_params_exists to caller or just use directly? #and never assume if exists is true? sub _constrain_states { my ($self, $states, $params) = @_; return ("1=1", {}); # if(! (defined $states && # (ref($states) eq 'ARRAY') && # (scalar(@$states) > 0) )){ # throw('Must pass an Arrayref of states (strings) to contrain by'); # } # # if(defined $params && # (ref($params) ne 'HASH') ){ # throw('Params argument must be a Hashref'); # } # # # my @tables = $self->_tables; # my ($table_name, $syn) = @{$self->_main_table}; # my ($status_table, $sn_ids_clause); # # # my @sn_ids = sort {$a<=>$b} # (map $self->_get_status_name_id($_, $params->{string_param_exists}) || # 'NULL', @$states); # #|| NULL here accounts for absent status_names # #i.e. $sn_ids_clause will never be true # # if(scalar(@$states) != 1){ # #add in table_name to make it faster # #can't put in table_id as this would be a join between select and subselect # $status_table = '(SELECT table_id, table_name, group_concat(status_name_id) ids '. # 'FROM status WHERE table_name="'.$table_name.'" and ('. # join(' OR ', (map "status_name_id=$_", @sn_ids)). # ') group by table_id order by status_name_id)'; # # #This enforces AND logic, whilst allowing for records with a superset of states # $sn_ids_clause = ' s.ids like "%'.join('%,', @sn_ids).'%"'; # } # else{ # $status_table = 'status'; # $sn_ids_clause = 's.status_name_id='.$sn_ids[0]; # } # # # my $constraint_conf = { tables => [[$status_table, 's']]}; #,['status_name', 'sn']), # # my $constraint = " $syn.${table_name}_id=s.table_id AND ". # "s.table_name='$table_name' AND ".$sn_ids_clause; # # return ($constraint, $constraint_conf); } 1;