From aa0c163235f525eefc4013a75d47d700f380660e Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 7 Nov 2011 11:54:02 +0000
Subject: [PATCH] BaseFeatureAdaptor.pm
---
.../EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 1831 ++++++-----------
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 94 +-
2 files changed, 639 insertions(+), 1286 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index a424187a85..c34fefaa4a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -20,999 +20,399 @@
=head1 NAME
-Bio::EnsEMBL::ArchiveStableIdAdaptor
+Bio::EnsEMBL::DBSQL::BaseAdaptor - Base Adaptor for DBSQL adaptors
=head1 SYNOPSIS
- my $registry = "Bio::EnsEMBL::Registry";
+ # base adaptor provides
- my $archiveStableIdAdaptor =
- $registry->get_adaptor( 'Human', 'Core', 'ArchiveStableId' );
+ # SQL prepare function
+ $adaptor->prepare("sql statement");
- my $stable_id = 'ENSG00000068990';
+ # get of root DBAdaptor object
+ $adaptor->db();
- my $arch_id = $archiveStableIdAdaptor->fetch_by_stable_id($stable_id);
+ # constructor, ok for inheritence
+ $adaptor = Bio::EnsEMBL::DBSQL::SubClassOfBaseAdaptor->new($dbobj)
- print("Latest incarnation of this stable ID:\n");
- printf( " Stable ID: %s.%d\n",
- $arch_id->stable_id(), $arch_id->version() );
- print(" Release: "
- . $arch_id->release() . " ("
- . $arch_id->assembly() . ", "
- . $arch_id->db_name()
- . ")\n" );
+=head1 DESCRIPTION
- print "\nStable ID history:\n\n";
+This is a true base class for Adaptors in the Ensembl DBSQL
+system. Original idea from Arne
- my $history =
- $archiveStableIdAdaptor->fetch_history_tree_by_stable_id(
- $stable_id);
+Adaptors are expected to have the following functions
- foreach my $a ( @{ $history->get_all_ArchiveStableIds } ) {
- printf( " Stable ID: %s.%d\n", $a->stable_id(), $a->version() );
- print(" Release: "
- . $a->release() . " ("
- . $a->assembly() . ", "
- . $a->db_name()
- . ")\n\n" );
- }
+ $obj = $adaptor->fetch_by_dbID($internal_id);
-=head1 DESCRIPTION
+which builds the object from the primary key of the object. This
+function is crucial because it allows adaptors to collaborate relatively
+independently of each other - in other words, we can change the schema
+under one adaptor without too many knock on changes through the other
+adaptors.
-ArchiveStableIdAdaptor does all SQL to create ArchiveStableIds and works
-of
+Most adaptors will also have
- stable_id_event
- mapping_session
- peptite_archive
- gene_archive
+ $dbid = $adaptor->store($obj);
-tables inside the core database.
+which stores the object. Currently the storing of an object also causes
+the objects to set
-This whole module has a status of At Risk as it is under development.
+ $obj->dbID();
-=head1 METHODS
+correctly and attach the adaptor.
- fetch_by_stable_id
- fetch_by_stable_id_version
- fetch_by_stable_id_dbname
- fetch_all_by_archive_id
- fetch_predecessors_by_archive_id
- fetch_successors_by_archive_id
- fetch_history_tree_by_stable_id
- add_all_current_to_history
- list_dbnames
- previous_dbname
- next_dbname
- get_peptide
- get_current_release
- get_current_assembly
-
-=head1 RELATED MODULES
-
- Bio::EnsEMBL::ArchiveStableId
- Bio::EnsEMBL::StableIdEvent
- Bio::EnsEMBL::StableIdHistoryTree
+Other fetch functions go by the convention of
-=head1 METHODS
+ @object_array = @{ $adaptor->fetch_all_by_XXXX($arguments_for_XXXX) };
-=cut
-
-package Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor;
+sometimes it returns an array ref denoted by the 'all' in the name of
+the method, sometimes an individual object. For example
-use strict;
-use warnings;
-no warnings qw(uninitialized);
+ $gene = $gene_adaptor->fetch_by_stable_id($stable_id);
-use Bio::EnsEMBL::DBSQL::BaseAdaptor;
-our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+or
-use Bio::EnsEMBL::ArchiveStableId;
-use Bio::EnsEMBL::StableIdEvent;
-use Bio::EnsEMBL::StableIdHistoryTree;
-use Bio::EnsEMBL::Utils::Exception qw(deprecate warning throw);
+ @fp = @{ $simple_feature_adaptor->fetch_all_by_Slice($slice) };
-use constant MAX_ROWS => 30;
-use constant NUM_HIGH_SCORERS => 20;
+Occassionally adaptors need to provide access to lists of ids. In this
+case the convention is to go list_XXXX, such as
+ @gene_ids = @{ $gene_adaptor->list_geneIds() };
-=head2 fetch_by_stable_id
+(note: this method is poorly named)
- Arg [1] : string $stable_id
- Arg [2] : (optional) string $type
- Example : none
- Description : Retrives an ArchiveStableId that is the latest incarnation of
- given stable_id.
- Returntype : Bio::EnsEMBL::ArchiveStableId or undef if not in database
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+=head1 METHODS
=cut
-sub fetch_by_stable_id {
- my $self = shift;
- my $stable_id = shift;
-
- my $arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $stable_id,
- -adaptor => $self
- );
+package Bio::EnsEMBL::DBSQL::BaseAdaptor;
+require Exporter;
+use vars qw(@ISA @EXPORT);
+use strict;
- @_ ? $arch_id->type(shift) : $self->_resolve_type($arch_id);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use DBI qw(:sql_types);
+use Data::Dumper;
- if ($self->lookup_current($arch_id)) {
+@ISA = qw(Exporter);
+@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
- # stable ID is in current release
- $arch_id->version($arch_id->current_version);
- $arch_id->db_name($self->dbc->dbname);
- $arch_id->release($self->get_current_release);
- $arch_id->assembly($self->get_current_assembly);
-
- } else {
+=head2 new
- # look for latest version of this stable id
- my $extra_sql = defined($arch_id->{'type'}) ?
- " AND sie.type = '@{[lc($arch_id->{'type'})]}'" : '';
+ Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection $dbobj
+ Example : $adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj);
+ Description: Creates a new BaseAdaptor object. The intent is that this
+ constructor would be called by an inherited superclass either
+ automatically or through $self->SUPER::new in an overridden
+ new method.
+ Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Exceptions : none
+ Caller : Bio::EnsEMBL::DBSQL::DBConnection
+ Status : Stable
- my $r = $self->_fetch_archive_id($stable_id, $extra_sql, $extra_sql);
+=cut
- if ($r->{'new_stable_id'} and $r->{'new_stable_id'} eq $stable_id) {
- # latest event is a self event, use new_* data
- $arch_id->version($r->{'new_version'});
- $arch_id->release($r->{'new_release'});
- $arch_id->assembly($r->{'new_assembly'});
- $arch_id->db_name($r->{'new_db_name'});
- } else {
- # latest event is a deletion event (or mapping to other ID; this clause
- # is only used to cope with buggy data where deletion events are
- # missing), use old_* data
- $arch_id->version($r->{'old_version'});
- $arch_id->release($r->{'old_release'});
- $arch_id->assembly($r->{'old_assembly'});
- $arch_id->db_name($r->{'old_db_name'});
- }
+sub new {
+ my ( $class, $dbobj ) = @_;
- $arch_id->type(ucfirst(lc($r->{'type'})));
- }
-
- if (! defined $arch_id->db_name) {
- # couldn't find stable ID in archive or current db
- return undef;
+ my $self = bless {}, $class;
+
+ if ( !defined $dbobj || !ref $dbobj ) {
+ throw("Don't have a db [$dbobj] for new adaptor");
}
- $arch_id->is_latest(1);
+ if ( $dbobj->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
+ $self->db($dbobj);
+ $self->dbc( $dbobj->dbc );
+ $self->species_id( $dbobj->species_id() );
+ $self->is_multispecies( $dbobj->is_multispecies() );
+ } elsif ( ref($dbobj) =~ /DBAdaptor$/ ) {
+ $self->db($dbobj);
+ $self->dbc( $dbobj->dbc );
+ } elsif ( ref($dbobj) =~ /DBConnection$/ ) {
+ $self->dbc($dbobj);
+ } else {
+ throw("Don't have a DBAdaptor [$dbobj] for new adaptor");
+ }
- return $arch_id;
+ return $self;
}
-=head2 fetch_by_stable_id_version
+=head2 prepare
- Arg [1] : string $stable_id
- Arg [2] : int $version
- Example : none
- Description : Retrieve an ArchiveStableId with given version and stable ID.
- Returntype : Bio::EnsEMBL::ArchiveStableId
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+ Arg [1] : string $string
+ a SQL query to be prepared by this adaptors database
+ Example : $sth = $adaptor->prepare("select yadda from blabla")
+ Description: provides a DBI statement handle from the adaptor. A convenience
+ function so you dont have to write $adaptor->db->prepare all the
+ time
+ Returntype : DBI::StatementHandle
+ Exceptions : none
+ Caller : Adaptors inherited from BaseAdaptor
+ Status : Stable
=cut
-sub fetch_by_stable_id_version {
- my $self = shift;
- my $stable_id = shift;
- my $version = shift;
-
- my $arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $stable_id,
- -version => $version,
- -adaptor => $self
- );
-
- @_ ? $arch_id->type(shift) : $self->_resolve_type($arch_id);
-
- if ($self->lookup_current($arch_id) && $arch_id->is_current) {
-
- # this version is the current one
- $arch_id->db_name($self->dbc->dbname);
- $arch_id->release($self->get_current_release);
- $arch_id->assembly($self->get_current_assembly);
-
- } else {
+sub prepare {
+ my ( $self, $string ) = @_;
- # find latest release this stable ID version is found in archive
- my $extra_sql1 = qq(AND sie.old_version = "$version");
- my $extra_sql2 = qq(AND sie.new_version = "$version");
- my $r = $self->_fetch_archive_id($stable_id, $extra_sql1, $extra_sql2);
-
- if ($r->{'new_stable_id'} and $r->{'new_stable_id'} eq $stable_id
- and $r->{'new_version'} == $version) {
- # latest event is a self event, use new_* data
- $arch_id->release($r->{'new_release'});
- $arch_id->assembly($r->{'new_assembly'});
- $arch_id->db_name($r->{'new_db_name'});
- } else {
- # latest event is a deletion event (or mapping to other ID; this clause
- # is only used to cope with buggy data where deletion events are
- # missing), use old_* data
- $arch_id->release($r->{'old_release'});
- $arch_id->assembly($r->{'old_assembly'});
- $arch_id->db_name($r->{'old_db_name'});
- }
+ # Uncomment next line to cancel caching on the SQL side.
+ # Needed for timing comparisons etc.
+ #$string =~ s/SELECT/SELECT SQL_NO_CACHE/i;
- $arch_id->type(ucfirst(lc($r->{'type'})));
- }
-
- if (! defined $arch_id->db_name) {
- # couldn't find stable ID version in archive or current release
- return undef;
- }
-
- return $arch_id;
+ return $self->dbc->prepare($string);
}
-=head2 fetch_by_stable_id_dbname
+=head2 db
- Arg [1] : string $stable_id
- Arg [2] : string $db_name
- Example : none
- Description : Create an ArchiveStableId from given arguments.
- Returntype : Bio::EnsEMBL::ArchiveStableId or undef if not in database
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+ Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj
+ the database this adaptor is using.
+ Example : $db = $adaptor->db();
+ Description: Getter/Setter for the DatabaseConnection that this adaptor is
+ using.
+ Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
+ Exceptions : none
+ Caller : Adaptors inherited from BaseAdaptor
+ Status : Stable
=cut
-sub fetch_by_stable_id_dbname {
- my $self = shift;
- my $stable_id = shift;
- my $db_name = shift;
-
- my $arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $stable_id,
- -db_name => $db_name,
- -adaptor => $self
- );
-
- @_ ? $arch_id->type(shift) : $self->_resolve_type($arch_id);
-
- if ($self->lookup_current($arch_id) and $db_name eq $self->dbc->dbname) {
-
- # this version is the current one
- $arch_id->version($arch_id->current_version);
- $arch_id->release($self->get_current_release);
- $arch_id->assembly($self->get_current_assembly);
-
- } else {
-
- # find version for this dbname in the stable ID archive
- my $extra_sql = defined($arch_id->{'type'}) ?
- " AND sie.type = '@{[lc($arch_id->{'type'})]}'" : '';
- my $extra_sql1 = $extra_sql . qq( AND ms.old_db_name = "$db_name");
- my $extra_sql2 = $extra_sql . qq( AND ms.new_db_name = "$db_name");
- my $r = $self->_fetch_archive_id($stable_id, $extra_sql1, $extra_sql2);
-
- if ($r->{'new_stable_id'} and $r->{'new_stable_id'} eq $stable_id
- and $r->{'new_db_name'} eq $db_name) {
-
- # latest event is a self event, use new_* data
- $arch_id->release($r->{'new_release'});
- $arch_id->assembly($r->{'new_assembly'});
- $arch_id->version($r->{'new_version'});
- } else {
- # latest event is a deletion event (or mapping to other ID; this clause
- # is only used to cope with buggy data where deletion events are
- # missing), use old_* data
- $arch_id->release($r->{'old_release'});
- $arch_id->assembly($r->{'old_assembly'});
- $arch_id->version($r->{'old_version'});
- }
+sub db {
+ my ( $self, $value ) = @_;
- $arch_id->type(ucfirst(lc($r->{'type'})));
- }
-
- if (! defined $arch_id->version ) {
- # couldn't find stable ID version in archive or current release
- return undef;
+ if ( defined($value) ) {
+ $self->{'db'} = $value;
}
- return $arch_id;
+ return $self->{'db'};
}
-#
-# Helper method to do fetch ArchiveStableId from db.
-# Used by fetch_by_stable_id(), fetch_by_stable_id_version() and
-# fetch_by_stable_id_dbname().
-# Returns hashref as returned by DBI::sth::fetchrow_hashref
-#
-sub _fetch_archive_id {
- my $self = shift;
- my $stable_id = shift;
- my $extra_sql1 = shift;
- my $extra_sql2 = shift;
+=head2 dbc
- # using a UNION is much faster in this query than somthing like
- # "... AND (sie.old_stable_id = ? OR sie.new_stable_id = ?)"
- my $sql = qq(
- (SELECT * FROM stable_id_event sie, mapping_session ms
- WHERE sie.mapping_session_id = ms.mapping_session_id
- AND sie.old_stable_id = ?
- $extra_sql1)
- UNION
- (SELECT * FROM stable_id_event sie, mapping_session ms
- WHERE sie.mapping_session_id = ms.mapping_session_id
- AND sie.new_stable_id = ?
- $extra_sql2)
- ORDER BY created DESC
- LIMIT 1
- );
+ Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj
+ the database this adaptor is using.
+ Example : $db = $adaptor->db();
+ Description: Getter/Setter for the DatabaseConnection that this adaptor is
+ using.
+ Returntype : Bio::EnsEMBL::DBSQL::DBConnection
+ Exceptions : none
+ Caller : Adaptors inherited from BaseAdaptor
+ Status : Stable
- my $sth = $self->prepare($sql);
- $sth->execute($stable_id,$stable_id);
- my $r = $sth->fetchrow_hashref;
- $sth->finish;
+=cut
- return $r;
-}
+sub dbc {
+ my ( $self, $value ) = @_;
+ if ( defined($value) ) {
+ $self->{'dbc'} = $value;
+ }
-=head2 fetch_all_by_archive_id
+ return $self->{'dbc'};
+}
- Arg [1] : Bio::EnsEMBL::ArchiveStableId $archive_id
- Arg [2] : String $return_type - type of ArchiveStableId to fetch
- Example : my $arch_id = $arch_adaptor->fetch_by_stable_id('ENSG0001');
- my @archived_transcripts =
- $arch_adaptor->fetch_all_by_archive_id($arch_id, 'Transcript');
- Description : Given a ArchiveStableId it retrieves associated ArchiveStableIds
- of specified type (e.g. retrieve transcripts for genes or vice
- versa).
+=head2 is_multispecies
- See also fetch_associated_archived() for a different approach to
- retrieve this data.
- Returntype : listref Bio::EnsEMBL::ArchiveStableId
- Exceptions : none
- Caller : Bio::EnsEMBL::ArchiveStableId->get_all_gene_archive_ids,
- get_all_transcript_archive_ids, get_all_translation_archive_ids
- Status : At Risk
- : under development
+ Arg [1] : (optional) boolean $arg
+ Example : if ($adaptor->is_multispecies()) { }
+ Description: Getter/Setter for the is_multispecies boolean of
+ to use for this adaptor.
+ Returntype : boolean
+ Exceptions : none
+ Caller : general
+ Status : Stable
=cut
-sub fetch_all_by_archive_id {
- my $self = shift;
- my $archive_id = shift;
- my $return_type = shift;
-
- my @result = ();
- my $lc_self_type = lc($archive_id->type);
- my $lc_return_type = lc($return_type);
+sub is_multispecies {
+ my ( $self, $arg ) = @_;
- my $sql = qq(
- SELECT
- ga.${lc_return_type}_stable_id,
- ga.${lc_return_type}_version,
- m.old_db_name,
- m.old_release,
- m.old_assembly
- FROM gene_archive ga, mapping_session m
- WHERE ga.${lc_self_type}_stable_id = ?
- AND ga.${lc_self_type}_version = ?
- AND ga.mapping_session_id = m.mapping_session_id
- );
-
- my $sth = $self->prepare($sql);
- $sth->bind_param(1, $archive_id->stable_id, SQL_VARCHAR);
- $sth->bind_param(2, $archive_id->version, SQL_SMALLINT);
- $sth->execute;
-
- my ($stable_id, $version, $db_name, $release, $assembly);
- $sth->bind_columns(\$stable_id, \$version, \$db_name, \$release, \$assembly);
-
- while ($sth->fetch) {
- my $new_arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $stable_id,
- -version => $version,
- -db_name => $db_name,
- -release => $release,
- -assembly => $assembly,
- -type => $return_type,
- -adaptor => $self
- );
-
- push( @result, $new_arch_id );
+ if ( defined($arg) ) {
+ $self->{_is_multispecies} = $arg;
}
- $sth->finish();
- return \@result;
+ return $self->{_is_multispecies};
}
+=head2 species_id
-=head2 fetch_associated_archived
-
- Arg[1] : Bio::EnsEMBL::ArchiveStableId $arch_id -
- the ArchiveStableId to fetch associated archived IDs for
- Example : my ($arch_gene, $arch_tr, $arch_tl, $pep_seq) =
- @{ $archive_adaptor->fetch_associated_archived($arch_id) };
- Description : Fetches associated archived stable IDs from the db for a given
- ArchiveStableId (version is taken into account).
- Return type : Listref of
- ArchiveStableId archived gene
- ArchiveStableId archived transcript
- (optional) ArchiveStableId archived translation
- (optional) peptide sequence
- Exceptions : thrown on missing or wrong argument
- thrown if ArchiveStableID has no type
- Caller : Bio::EnsEMBL::ArchiveStableId->get_all_associated_archived()
- Status : At Risk
- : under development
+ Arg [1] : (optional) int $species_id
+ The internal ID of the species in a multi-species database.
+ Example : $db = $adaptor->db();
+ Description: Getter/Setter for the internal ID of the species in a
+ multi-species database. The default species ID is 1.
+ Returntype : Integer
+ Exceptions : none
+ Caller : Adaptors inherited from BaseAdaptor
+ Status : Stable
=cut
-sub fetch_associated_archived {
- my $self = shift;
- my $arch_id = shift;
-
- throw("Need a Bio::EnsEMBL::ArchiveStableId") unless ($arch_id
- and ref($arch_id) and $arch_id->isa('Bio::EnsEMBL::ArchiveStableId'));
+sub species_id {
+ my ( $self, $value ) = @_;
- my $type = $arch_id->type();
-
- if ( !defined($type) ) {
- throw("Can't deduce ArchiveStableId type.");
+ if ( defined($value) ) {
+ $self->{'species_id'} = $value;
}
- $type = lc($type);
+ return $self->{'species_id'} || 1;
+}
- my $sql = qq(
- SELECT ga.gene_stable_id,
- ga.gene_version,
- ga.transcript_stable_id,
- ga.transcript_version,
- ga.translation_stable_id,
- ga.translation_version,
- pa.peptide_seq,
- ms.old_release,
- ms.old_assembly,
- ms.old_db_name
- FROM (mapping_session ms, gene_archive ga)
- LEFT JOIN peptide_archive pa
- ON ga.peptide_archive_id = pa.peptide_archive_id
- WHERE ga.mapping_session_id = ms.mapping_session_id
- AND ga.${type}_stable_id = ?
- AND ga.${type}_version = ?
- );
- my $sth = $self->prepare($sql);
- $sth->bind_param(1, $arch_id->stable_id, SQL_VARCHAR);
- $sth->bind_param(2, $arch_id->version, SQL_SMALLINT);
- $sth->execute;
+# list primary keys for a particular table
+# args are table name and primary key field
+# if primary key field is not supplied, tablename_id is assumed
+# returns listref of IDs
+sub _list_dbIDs {
+ my ( $self, $table, $pk, $ordered ) = @_;
- my @result = ();
-
- while (my $r = $sth->fetchrow_hashref) {
-
- my @row = ();
-
- # create ArchiveStableIds genes, transcripts and translations
- push @row, Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $r->{'gene_stable_id'},
- -version => $r->{'gene_version'},
- -db_name => $r->{'old_db_name'},
- -release => $r->{'old_release'},
- -assembly => $r->{'old_assembly'},
- -type => 'Gene',
- -adaptor => $self
- );
-
- push @row, Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $r->{'transcript_stable_id'},
- -version => $r->{'transcript_version'},
- -db_name => $r->{'old_db_name'},
- -release => $r->{'old_release'},
- -assembly => $r->{'old_assembly'},
- -type => 'Transcript',
- -adaptor => $self
- );
-
- if ($r->{'translation_stable_id'}) {
- push @row, Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $r->{'translation_stable_id'},
- -version => $r->{'translation_version'},
- -db_name => $r->{'old_db_name'},
- -release => $r->{'old_release'},
- -assembly => $r->{'old_assembly'},
- -type => 'Translation',
- -adaptor => $self
- );
-
- # push peptide sequence onto result list
- push @row, $r->{'peptide_seq'};
- }
-
- push @result, \@row;
- }
+ if ( !defined($pk) ) { $pk = $table . "_id" }
- return \@result;
-}
+ my $sql = sprintf( "SELECT %s FROM %s", $pk, $table );
+ my $join_with_cs = 0;
+ if ( $self->is_multispecies()
+ && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
+ && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
+ {
+ if ( $table =~ /^(\w+)_stable_id$/ ) {
+ # Need to join to the proper base feature table as the stable_id
+ # table do not have seq_region_ids. NOTE: This needs to be removed
+ # if we ever move the stable IDs into the feature tables.
-=head2 fetch_predecessors_by_archive_id
+ my $base_table = $1;
+ my $base_pk = $base_table . "_id";
- Arg [1] : Bio::EnsEMBL::ArchiveStableId
- Example : none
- Description : Retrieve a list of ArchiveStableIds that were mapped to the
- given one. This method goes back only one level, to retrieve
- a full predecessor history use fetch_predecessor_history, or
- ideally fetch_history_tree_by_stable_id for the complete
- history network.
- Returntype : listref Bio::EnsEMBL::ArchiveStableId
- Exceptions : none
- Caller : Bio::EnsEMBL::ArchiveStableId->get_all_predecessors
- Status : At Risk
- : under development
+ $sql .= qq(
+JOIN $base_table USING ($base_pk)
+);
+ }
-=cut
+ $sql .= q(
+JOIN seq_region USING (seq_region_id)
+JOIN coord_system cs USING (coord_system_id)
+WHERE cs.species_id = ?
+);
-sub fetch_predecessors_by_archive_id {
- my $self = shift;
- my $arch_id = shift;
-
- my @result;
-
- if( ! ( defined $arch_id->stable_id() &&
- defined $arch_id->db_name() )) {
- throw( "Need db_name for predecessor retrieval" );
+ $join_with_cs = 1;
}
- my $sql = qq(
- SELECT
- sie.old_stable_id,
- sie.old_version,
- sie.type,
- m.old_db_name,
- m.old_release,
- m.old_assembly
- FROM mapping_session m, stable_id_event sie
- WHERE sie.mapping_session_id = m.mapping_session_id
- AND sie.new_stable_id = ?
- AND m.new_db_name = ?
- );
+ if ( defined($ordered) && $ordered ) {
+ $sql .= " ORDER BY seq_region_id, seq_region_start";
+ }
my $sth = $self->prepare($sql);
- $sth->bind_param(1, $arch_id->stable_id, SQL_VARCHAR);
- $sth->bind_param(2, $arch_id->db_name, SQL_VARCHAR);
- $sth->execute();
-
- my ($old_stable_id, $old_version, $type, $old_db_name, $old_release, $old_assembly);
- $sth->bind_columns(\$old_stable_id, \$old_version, \$type, \$old_db_name, \$old_release, \$old_assembly);
-
- while ($sth->fetch) {
- if (defined $old_stable_id) {
- my $old_arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $old_stable_id,
- -version => $old_version,
- -db_name => $old_db_name,
- -release => $old_release,
- -assembly => $old_assembly,
- -type => $type,
- -adaptor => $self
- );
- push( @result, $old_arch_id );
- }
+
+ if ($join_with_cs) {
+ $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
}
- $sth->finish();
- # if you didn't find any predecessors, there might be a gap in the
- # mapping_session history (i.e. databases in mapping_session don't chain). To
- # bridge the gap, look in the previous mapping_session for identical
- # stable_id.version
- unless (@result) {
-
- $sql = qq(
- SELECT
- sie.new_stable_id,
- sie.new_version,
- sie.type,
- m.new_db_name,
- m.new_release,
- m.new_assembly
- FROM mapping_session m, stable_id_event sie
- WHERE sie.mapping_session_id = m.mapping_session_id
- AND sie.new_stable_id = ?
- AND m.new_db_name = ?
- );
-
- $sth = $self->prepare($sql);
-
- my $curr_dbname = $arch_id->db_name;
-
- PREV:
- while (my $prev_dbname = $self->previous_dbname($curr_dbname)) {
-
- $sth->bind_param(1,$arch_id->stable_id, SQL_VARCHAR);
- $sth->bind_param(2,$prev_dbname, SQL_VARCHAR);
- $sth->execute();
-
- $sth->bind_columns(\$old_stable_id, \$old_version, \$type, \$old_db_name, \$old_release, \$old_assembly);
-
- while( $sth->fetch() ) {
- if (defined $old_stable_id) {
- my $old_arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $old_stable_id,
- -version => $old_version,
- -db_name => $old_db_name,
- -release => $old_release,
- -assembly => $old_assembly,
- -type => $type,
- -adaptor => $self
- );
- push( @result, $old_arch_id );
-
- last PREV;
- }
- }
+ eval { $sth->execute() };
+ if ($@) {
+ throw("Detected an error whilst executing SQL '${sql}': $@");
+ }
- $curr_dbname = $prev_dbname;
+ my $id;
+ $sth->bind_col( 1, \$id );
- }
-
- $sth->finish();
+ my @out;
+ while ( $sth->fetch() ) {
+ push( @out, $id );
}
- return \@result;
-}
-
+ return \@out;
+} ## end sub _list_dbIDs
-=head2 fetch_successors_by_archive_id
- Arg [1] : Bio::EnsEMBL::ArchiveStableId
- Example : none
- Description : Retrieve a list of ArchiveStableIds that the given one was
- mapped to. This method goes forward only one level, to retrieve
- a full successor history use fetch_successor_history, or
- ideally fetch_history_tree_by_stable_id for the complete
- history network.
- Returntype : listref Bio::EnsEMBL::ArchiveStableId
- Exceptions : none
- Caller : Bio::EnsEMBL::ArchiveStableId->get_all_successors
- Status : At Risk
- : under development
+# _straight_join
-=cut
+# Arg [1] : (optional) boolean $new_val
+# Example : $self->_straight_join(1);
+# $self->generic_fetch($constraint);
+# $self->_straight_join(0);
+# Description: PROTECTED Getter/Setter that turns on/off the use of
+# a straight join in queries.
+# Returntype : boolean
+# Exceptions : none
+# Caller : general
-sub fetch_successors_by_archive_id {
+sub _straight_join {
my $self = shift;
- my $arch_id = shift;
- my @result;
-
-
- if( ! ( defined $arch_id->stable_id() &&
- defined $arch_id->db_name() )) {
- throw( "Need db_name for successor retrieval" );
- }
-
- my $sql = qq(
- SELECT
- sie.new_stable_id,
- sie.new_version,
- sie.type,
- m.new_db_name,
- m.new_release,
- m.new_assembly
- FROM mapping_session m, stable_id_event sie
- WHERE sie.mapping_session_id = m.mapping_session_id
- AND sie.old_stable_id = ?
- AND m.old_db_name = ?
- );
-
- my $sth = $self->prepare( $sql );
- $sth->bind_param(1,$arch_id->stable_id,SQL_VARCHAR);
- $sth->bind_param(2,$arch_id->db_name,SQL_VARCHAR);
- $sth->execute();
-
- my ($new_stable_id, $new_version, $type, $new_db_name, $new_release, $new_assembly);
- $sth->bind_columns(\$new_stable_id, \$new_version, \$type, \$new_db_name, \$new_release, \$new_assembly);
-
- while( $sth->fetch() ) {
- if( defined $new_stable_id ) {
- my $new_arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $new_stable_id,
- -version => $new_version,
- -db_name => $new_db_name,
- -release => $new_release,
- -assembly => $new_assembly,
- -type => $type,
- -adaptor => $self
- );
-
- push( @result, $new_arch_id );
- }
- }
- $sth->finish();
-
- # if you didn't find any successors, there might be a gap in the
- # mapping_session history (i.e. databases in mapping_session don't chain). To
- # bridge the gap, look in the next mapping_session for identical
- # stable_id.version
- unless (@result) {
-
- $sql = qq(
- SELECT
- sie.old_stable_id,
- sie.old_version,
- sie.type,
- m.old_db_name,
- m.old_release,
- m.old_assembly
- FROM mapping_session m, stable_id_event sie
- WHERE sie.mapping_session_id = m.mapping_session_id
- AND sie.old_stable_id = ?
- AND m.old_db_name = ?
- );
-
- $sth = $self->prepare($sql);
-
- my $curr_dbname = $arch_id->db_name;
-
- NEXTDB:
- while (my $next_dbname = $self->next_dbname($curr_dbname)) {
-
- $sth->bind_param(1, $arch_id->stable_id, SQL_VARCHAR);
- $sth->bind_param(2, $next_dbname, SQL_VARCHAR);
- $sth->execute();
-
- $sth->bind_columns(\$new_stable_id, \$new_version, \$type, \$new_db_name, \$new_release, \$new_assembly);
-
- while( $sth->fetch() ) {
- if (defined $new_stable_id) {
- my $new_arch_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $new_stable_id,
- -version => $new_version,
- -db_name => $new_db_name,
- -release => $new_release,
- -assembly => $new_assembly,
- -type => $type,
- -adaptor => $self
- );
-
- push( @result, $new_arch_id );
-
- last NEXTDB;
- }
- }
-
- $curr_dbname = $next_dbname;
-
- }
-
- $sth->finish();
+ if(@_) {
+ $self->{'_straight_join'} = shift;
}
- return \@result;
+ return $self->{'_straight_join'};
}
+=head2 bind_param_generic_fetch
-=head2 fetch_history_tree_by_stable_id
-
- Arg[1] : String $stable_id - the stable ID to fetch the history tree for
- Arg[2] : (optional) Int $num_high_scorers
- number of mappings per stable ID allowed when filtering
- Arg[3] : (optional) Int $max_rows
- maximum number of stable IDs in history tree (used for
- filtering)
- Example : my $history = $archive_adaptor->fetch_history_tree_by_stable_id(
- 'ENSG00023747897');
- Description : Returns the history tree for a given stable ID. This will
- include a network of all stable IDs it is related to. The
- method will try to return a minimal (sparse) set of nodes
- (ArchiveStableIds) and links (StableIdEvents) by removing any
- redundant entries and consolidating mapping events so that only
- changes are recorded.
- Return type : Bio::EnsEMBL::StableIdHistoryTree
- Exceptions : thrown on missing argument
- Caller : Bio::EnsEMBL::ArchiveStableId::get_history_tree, general
- Status : At Risk
- : under development
+ Arg [1] : (optional) scalar $param
+ This is the parameter to bind
+ Arg [2] : (optional) int $sql_type
+ Type of the parameter (from DBI (:sql_types))
+ Example : $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
+ $adaptor->generic_fetch();
+ Description: When using parameters for the query, will call the bind_param to avoid
+ some security issues. If there are no arguments, will return the bind_parameters
+ ReturnType : listref
+ Exceptions: if called with one argument
=cut
-sub fetch_history_tree_by_stable_id {
- my ($self, $stable_id, $num_high_scorers, $max_rows) = @_;
-
- throw("Expecting a stable ID argument.") unless $stable_id;
-
- $num_high_scorers ||= NUM_HIGH_SCORERS;
- $max_rows ||= MAX_ROWS;
-
- # using a UNION is much faster in this query than somthing like
- # "... AND (sie.old_stable_id = ?) OR (sie.new_stable_id = ?)"
- my $sql = qq(
- SELECT sie.old_stable_id, sie.old_version,
- ms.old_db_name, ms.old_release, ms.old_assembly,
- sie.new_stable_id, sie.new_version,
- ms.new_db_name, ms.new_release, ms.new_assembly,
- sie.type, sie.score
- FROM stable_id_event sie, mapping_session ms
- WHERE sie.mapping_session_id = ms.mapping_session_id
- AND sie.old_stable_id = ?
- UNION
- SELECT sie.old_stable_id, sie.old_version,
- ms.old_db_name, ms.old_release, ms.old_assembly,
- sie.new_stable_id, sie.new_version,
- ms.new_db_name, ms.new_release, ms.new_assembly,
- sie.type, sie.score
- FROM stable_id_event sie, mapping_session ms
- WHERE sie.mapping_session_id = ms.mapping_session_id
- AND sie.new_stable_id = ?
- );
-
- my $sth = $self->prepare($sql);
-
- my $history = Bio::EnsEMBL::StableIdHistoryTree->new(
- -CURRENT_DBNAME => $self->dbc->dbname,
- -CURRENT_RELEASE => $self->get_current_release,
- -CURRENT_ASSEMBLY => $self->get_current_assembly,
- );
-
- # remember stable IDs you need to do and those that are done. Initialise the
- # former hash with the focus stable ID
- my %do = ($stable_id => 1);
- my %done;
-
- # while we got someting to do
- while (my ($id) = keys(%do)) {
-
- # if we already have more than MAX_ROWS stable IDs in this tree, we can't
- # build the full tree. Return undef.
- if (scalar(keys(%done)) > $max_rows) {
- # warning("Too many related stable IDs (".scalar(keys(%done)).") to draw a history tree.");
- $history->is_incomplete(1);
- $sth->finish;
- last;
- }
-
- # mark this stable ID as done
- delete $do{$id};
- $done{$id} = 1;
-
- # fetch all stable IDs related to this one from the database
- $sth->bind_param(1, $id, SQL_VARCHAR);
- $sth->bind_param(2, $id, SQL_VARCHAR);
- $sth->execute;
-
- my @events;
-
- while (my $r = $sth->fetchrow_hashref) {
-
- #
- # create old and new ArchiveStableIds and a StableIdEvent to link them
- # add all of these to the history tree
- #
- my ($old_id, $new_id);
-
- if ($r->{'old_stable_id'}) {
- $old_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $r->{'old_stable_id'},
- -version => $r->{'old_version'},
- -db_name => $r->{'old_db_name'},
- -release => $r->{'old_release'},
- -assembly => $r->{'old_assembly'},
- -type => $r->{'type'},
- -adaptor => $self
- );
- }
-
- if ($r->{'new_stable_id'}) {
- $new_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $r->{'new_stable_id'},
- -version => $r->{'new_version'},
- -db_name => $r->{'new_db_name'},
- -release => $r->{'new_release'},
- -assembly => $r->{'new_assembly'},
- -type => $r->{'type'},
- -adaptor => $self
- );
- }
-
- my $event = Bio::EnsEMBL::StableIdEvent->new(
- -old_id => $old_id,
- -new_id => $new_id,
- -score => $r->{'score'}
- );
-
- push @events, $event;
+sub bind_param_generic_fetch{
+ my $self = shift;
+ my $param = shift;
+ my $sql_type = shift;
+ if (defined $param && !defined $sql_type){
+ throw("Need to specify sql_type for parameter $param\n");
}
-
- # filter out low-scoring events; the number of highest scoring events
- # returned is defined by NUM_HIGH_SCORERS
- my @others;
-
- foreach my $event (@events) {
-
- my $old_id = $event->old_ArchiveStableId;
- my $new_id = $event->new_ArchiveStableId;
-
- # creation, deletion and mapping-to-self events are added to the history
- # tree directly
- if (!$old_id || !$new_id || ($old_id->stable_id eq $new_id->stable_id)) {
- $history->add_StableIdEvents($event);
- } else {
- push @others, $event;
- }
-
+ elsif (defined $param && defined $sql_type){
+ #check when there is a SQL_INTEGER type that the parameter is really a number
+ if ($sql_type eq SQL_INTEGER){
+ throw "Trying to assign a non numerical parameter to an integer value in the database" if ($param !~ /^\d+$/);
+ }
+ #both paramters have been entered, push it to the bind_param array
+ push @{$self->{'_bind_param_generic_fetch'}},[$param,$sql_type];
}
-
- #if (scalar(@others) > $num_high_scorers) {
- # warn "Filtering ".(scalar(@others) - $num_high_scorers).
- # " low-scoring events.\n";
- #}
-
- my $k = 0;
- foreach my $event (sort { $b->score <=> $a->score } @others) {
- $history->add_StableIdEvents($event);
-
- # mark stable IDs as todo if appropriate
- $do{$event->old_ArchiveStableId->stable_id} = 1
- unless $done{$event->old_ArchiveStableId->stable_id};
- $do{$event->new_ArchiveStableId->stable_id} = 1
- unless $done{$event->new_ArchiveStableId->stable_id};
-
- last if (++$k == $num_high_scorers);
+ elsif (!defined $param && !defined $sql_type){
+ #when there are no arguments, return the array
+ return $self->{'_bind_param_generic_fetch'};
}
-
- }
-
- $sth->finish;
-
- # try to consolidate the tree (remove redundant nodes, bridge gaps)
- $history->consolidate_tree;
-
- # now add ArchiveStableIds for current Ids not found in the archive
- $self->add_all_current_to_history($history);
-
- # calculate grid coordinates for the sorted tree; this will also try to
- # untangle the tree
- $history->calculate_coords;
-
- return $history;
+
}
-=head2 add_all_current_to_history
- Arg[1] : Bio::EnsEMBL::StableIdHistoryTree $history -
- the StableIdHistoryTree object to add the current IDs to
- Description : This method adds the current versions of all stable IDs found
- in a StableIdHistoryTree object to the tree, by creating
- appropriate Events for the stable IDs found in the *_stable_id
- tables. This is a helper method for
- fetch_history_tree_by_stable_id(), see there for more
- documentation.
- Return type : none (passed-in object is manipulated)
- Exceptions : thrown on missing or wrong argument
- Caller : internal
- Status : At Risk
- : under development
+=head2 generic_fetch
-=cut
+ Arg [1] : (optional) string $constraint
+ An SQL query constraint (i.e. part of the WHERE clause)
+ Arg [2] : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
+ A mapper object used to remap features
+ as they are retrieved from the database
+ Arg [3] : (optional) Bio::EnsEMBL::Slice $slice
+ A slice that features should be remapped to
+ Example : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
+ Description: Performs a database fetch and returns feature objects in
+ contig coordinates.
+ Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
+ Exceptions : none
+ Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
+ Status : Stable
-sub add_all_current_to_history {
- my $self = shift;
- my $history = shift;
+=cut
- unless ($history and $history->isa('Bio::EnsEMBL::StableIdHistoryTree')) {
- throw("Need a Bio::EnsEMBL::StableIdHistoryTree.");
- }
+sub generic_fetch {
+ my ($self, $constraint, $mapper, $slice) = @_;
+<<<<<<< ArchiveStableIdAdaptor.pm
+ my @tabs = $self->_tables();
+=======
my @ids = @{ $history->get_unique_stable_ids };
my $id_string = join("', '", @ids);
@@ -1027,420 +427,359 @@ sub add_all_current_to_history {
);
my $sth = $self->prepare($sql);
$sth->execute;
-
- while (my ($stable_id, $version) = $sth->fetchrow_array) {
-
- my $new_id = Bio::EnsEMBL::ArchiveStableId->new(
- -stable_id => $stable_id,
- -version => $version,
- -current_version => $version,
- -db_name => $self->dbc->dbname,
- -release => $self->get_current_release,
- -assembly => $self->get_current_assembly,
- -type => $type,
- -adaptor => $self
- );
-
- my $event = $history->get_latest_StableIdEvent($new_id);
- next unless ($event);
-
- if ($event->old_ArchiveStableId and
- $event->old_ArchiveStableId->stable_id eq $stable_id) {
-
- # latest event was a self event
- # update it with current stable ID and add to tree
- $event->new_ArchiveStableId($new_id);
-
- } else {
-
- # latest event was a non-self event
- # create a new event where the old_id is the new_id from latest
- my $new_event = Bio::EnsEMBL::StableIdEvent->new(
- -old_id => $event->new_ArchiveStableId,
- -new_id => $new_id,
- -score => $event->score,
- );
- $history->add_StableIdEvents($new_event);
+>>>>>>> 1.40
+
+ my $extra_default_where;
+
+ # Hack for feature types that needs to be restricted to species_id (in
+ # coord_system).
+ if ( $self->is_multispecies()
+ && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
+ && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
+ {
+ # We do a check to see if there is already seq_region
+ # and coord_system defined to ensure we get the right
+ # alias. We then do the extra query irrespectively of
+ # what has already been specified by the user.
+ my %thash = map { $_->[0] => $_->[1] } @tabs;
+
+ my $sr_alias =
+ ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
+ my $cs_alias =
+ ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );
+
+ if ( !exists( $thash{seq_region} ) ) {
+ push( @tabs, [ 'seq_region', $sr_alias ] );
+ }
+ if ( !exists( $thash{coord_system} ) ) {
+ push( @tabs, [ 'coord_system', $cs_alias ] );
}
-
- }
-
- # refresh node cache
- $history->flush_ArchiveStableIds;
- $history->add_ArchiveStableIds_for_events;
-}
-
-
-=head2 fetch_successor_history
-
- Arg [1] : Bio::EnsEMBL::ArchiveStableId $arch_id
- Example : none
- Description : Gives back a list of archive stable ids which are successors in
- the stable_id_event tree of the given stable_id. Might well be
- empty.
-
- This method isn't deprecated, but in most cases you will rather
- want to use fetch_history_tree_by_stable_id().
- Returntype : listref Bio::EnsEMBL::ArchiveStableId
- Since every ArchiveStableId knows about it's successors, this is
- a linked tree.
- Exceptions : none
- Caller : webcode for archive
- Status : At Risk
- : under development
-
-=cut
-
-sub fetch_successor_history {
- my $self = shift;
- my $arch_id = shift;
- my $current_db_name = $self->list_dbnames->[0];
- my $dbname = $arch_id->db_name;
+ $extra_default_where = sprintf(
+ '%s.seq_region_id = %s.seq_region_id '
+ . 'AND %s.coord_system_id = %s.coord_system_id '
+ . 'AND %s.species_id = ?',
+ $tabs[0]->[1], $sr_alias, $sr_alias,
+ $cs_alias, $cs_alias );
- if ($dbname eq $current_db_name) {
- return [$arch_id];
- }
+ $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
+ } ## end if ( $self->is_multispecies...)
- my $old = [];
- my @result = ();
-
- push @$old, $arch_id;
+ my $columns = join(', ', $self->_columns());
- while ($dbname ne $current_db_name) {
- my $new = [];
- while (my $asi = (shift @$old)) {
- push @$new, @{ $asi->get_all_successors };
- }
+ my $db = $self->db();
- if (@$new) {
- $dbname = $new->[0]->db_name;
- } else {
- last;
+ #
+ # Construct a left join statement if one was defined, and remove the
+ # left-joined table from the table list
+ #
+ my @left_join_list = $self->_left_join();
+ my $left_join_prefix = '';
+ my $left_join = '';
+ my @tables;
+ if(@left_join_list) {
+ my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
+ while(my $t = shift @tabs) {
+ my $t_alias = $t->[0] . " " . $t->[1];
+ if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
+ my $condition = $left_join_hash{ $t->[0] };
+ $condition ||= $left_join_hash{$t_alias};
+ my $syn = $t->[1];
+ $left_join .=
+ "\n LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
+ $left_join_prefix .= '(';
+ } else {
+ push @tables, $t;
+ }
}
-
- # filter duplicates
- my %unique = map { join(":", $_->stable_id, $_->version, $_->release) =>
- $_ } @$new;
- @$new = values %unique;
-
- @$old = @$new;
- push @result, @$new;
+ } else {
+ @tables = @tabs;
}
- return \@result;
-}
-
-
-=head2 fetch_predecessor_history
-
- Arg [1] : Bio::EnsEMBL::ArchiveStableId $arch_id
- Example : none
- Description : Gives back a list of archive stable ids which are predecessors
- in the stable_id_event tree of the given stable_id. Might well
- be empty.
-
- This method isn't deprecated, but in most cases you will rather
- want to use fetch_history_tree_by_stable_id().
- Returntype : listref Bio::EnsEMBL::ArchiveStableId
- Since every ArchiveStableId knows about it's successors, this is
- a linked tree.
- Exceptions : none
- Caller : webcode for archive
- Status : At Risk
- : under development
-
-=cut
-
-sub fetch_predecessor_history {
- my $self = shift;
- my $arch_id = shift;
-
- my $oldest_db_name = $self->list_dbnames->[-1];
- my $dbname = $arch_id->db_name;
+ my $straight_join = '';
- if ($dbname eq $oldest_db_name) {
- return [$arch_id];
+ if($self->_straight_join()) {
+ $straight_join = "STRAIGHT_JOIN";
}
- my $old = [];
- my @result = ();
+ #construct a nice table string like 'table1 t1, table2 t2'
+ my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
- push @$old, $arch_id;
+ my $sql =
+ "SELECT $straight_join $columns\n"
+ . "FROM $left_join_prefix ($tablenames) $left_join";
- while ($dbname ne $oldest_db_name) {
- my $new = [];
- while (my $asi = (shift @$old)) {
- push @$new, @{ $asi->get_all_predecessors };
- }
+ my $default_where = $self->_default_where_clause();
+ my $final_clause = $self->_final_clause;
- if( @$new ) {
- $dbname = $new->[0]->db_name;
+ if ($extra_default_where) {
+ if ($default_where) {
+ $default_where .= "\n AND $extra_default_where";
} else {
- last;
+ $default_where = $extra_default_where;
}
-
- # filter duplicates
- my %unique = map { join(":", $_->stable_id, $_->version, $_->release) =>
- $_ } @$new;
- @$new = values %unique;
-
- @$old = @$new;
- push @result, @$new;
}
- return \@result;
-}
-
-
-=head2 list_dbnames
+ #append a where clause if it was defined
+ if ($constraint) {
+ $sql .= "\n WHERE $constraint ";
+ if ($default_where) {
+ $sql .= " AND\n $default_where ";
+ }
+ } elsif ($default_where) {
+ $sql .= "\n WHERE $default_where ";
+ }
- Args : none
- Example : none
- Description : A list of available database names from the latest (current) to
- the oldest (ordered).
- Returntype : listref of strings
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+ #append additional clauses which may have been defined
+ $sql .= "\n$final_clause";
-=cut
-sub list_dbnames {
- my $self = shift;
+ # FOR DEBUG:
+ #printf(STDERR "SQL:\n%s\n", $sql);
- if( ! defined $self->{'dbnames'} ) {
-
- my $sql = qq(
- SELECT old_db_name, new_db_name
- FROM mapping_session
- ORDER BY created DESC
- );
- my $sth = $self->prepare( $sql );
- $sth->execute();
- my ( $old_db_name, $new_db_name );
-
- my @dbnames = ();
- my %seen;
-
- $sth->bind_columns( \$old_db_name, \$new_db_name );
-
- while( $sth->fetch() ) {
- # this code now can deal with non-chaining mapping sessions
- push(@{ $self->{'dbnames'} }, $new_db_name) unless ($seen{$new_db_name});
- $seen{$new_db_name} = 1;
-
- push(@{ $self->{'dbnames'} }, $old_db_name) unless ($seen{$old_db_name});
- $seen{$old_db_name} = 1;
- }
-
- $sth->finish();
-
+
+ my $sth = $db->dbc->prepare($sql);
+ my $bind_parameters = $self->bind_param_generic_fetch();
+ if (defined $bind_parameters){
+ #if we have bind the parameters, call the DBI to bind them
+ my $i = 1;
+ foreach my $param (@{$bind_parameters}){
+ $sth->bind_param($i,$param->[0],$param->[1]);
+ $i++;
+ }
+ #after binding parameters, undef for future queries
+ $self->{'_bind_param_generic_fetch'} = ();
+ }
+ eval { $sth->execute() };
+ if ($@) {
+ throw("Detected an error whilst executing SQL '${sql}': $@");
}
- return $self->{'dbnames'};
+ my $res = $self->_objs_from_sth($sth, $mapper, $slice);
+ $sth->finish();
+ return $res;
}
-=head2 previous_dbname
-
- Arg[1] : String $dbname - focus db name
- Example : my $prev_db = $self->previous_dbname($curr_db);
- Description : Returns the name of the next oldest database which has mapping
- session information.
- Return type : String (or undef if not available)
- Exceptions : none
- Caller : general
- Status : At Risk
+=head2 fetch_by_dbID
+
+ Arg [1] : int $id
+ The unique database identifier for the feature to be obtained
+ Example : $feat = $adaptor->fetch_by_dbID(1234));
+ $feat = $feat->transform('contig');
+ Description: Returns the feature created from the database defined by the
+ the id $id. The feature will be returned in its native
+ coordinate system. That is, the coordinate system in which it
+ is stored in the database. In order to convert it to a
+ particular coordinate system use the transfer() or transform()
+ method. If the feature is not found in the database then
+ undef is returned instead
+ Returntype : Bio::EnsEMBL::Feature or undef
+ Exceptions : thrown if $id arg is not provided
+ does not exist
+ Caller : general
+ Status : Stable
=cut
-sub previous_dbname {
- my $self = shift;
- my $dbname = shift;
-
- my $curr_idx = $self->_dbname_index($dbname);
- my @dbnames = @{ $self->list_dbnames };
-
- if ($curr_idx == @dbnames) {
- # this is the oldest dbname, so no previous one available
- return undef;
- } else {
- return $dbnames[$curr_idx+1];
- }
-}
-
-
-=head2 next_dbname
+sub fetch_by_dbID{
+ my ($self,$id) = @_;
- Arg[1] : String $dbname - focus db name
- Example : my $prev_db = $self->next_dbname($curr_db);
- Description : Returns the name of the next newest database which has mapping
- session information.
- Return type : String (or undef if not available)
- Exceptions : none
- Caller : general
- Status : At Risk
+ throw("id argument is required") if(!defined $id);
-=cut
+ #construct a constraint like 't1.table1_id = 123'
+ my @tabs = $self->_tables;
+ my ($name, $syn) = @{$tabs[0]};
+ $self->bind_param_generic_fetch($id,SQL_INTEGER);
+ my $constraint = "${syn}.${name}_id = ?";
-sub next_dbname {
- my $self = shift;
- my $dbname = shift;
+ #Should only be one
+ my ($feat) = @{$self->generic_fetch($constraint)};
- my $curr_idx = $self->_dbname_index($dbname);
- my @dbnames = @{ $self->list_dbnames };
+ return undef if(!$feat);
- if ($curr_idx == 0) {
- # this is the latest dbname, so no next one available
- return undef;
- } else {
- return $dbnames[$curr_idx-1];
- }
+ return $feat;
}
-#
-# helper method to return the array index of a database in the ordered list of
-# available databases (as returned by list_dbnames()
-#
-sub _dbname_index {
- my $self = shift;
- my $dbname = shift;
+=head2 fetch_all_by_dbID_list
+
+ Arg [1] : listref of integers $id_list
+ The unique database identifiers for the features to
+ be obtained.
+ Arg [2] : optional - Bio::EnsEMBL::Slice to map features onto.
+ Example : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
+ Description: Returns the features created from the database
+ defined by the the IDs in contained in the provided
+ ID list $id_list. The features will be returned
+ in their native coordinate system. That is, the
+ coordinate system in which they are stored in the
+ database. In order to convert the features to a
+ particular coordinate system use the transfer() or
+ transform() method. If none of the features are
+ found in the database a reference to an empty list is
+ returned.
+ Returntype : listref of Bio::EnsEMBL::Features
+ Exceptions : thrown if $id arg is not provided
+ does not exist
+ Caller : general
+ Status : Stable
- my @dbnames = @{ $self->list_dbnames };
+=cut
- for (my $i = 0; $i < @dbnames; $i++) {
- if ($dbnames[$i] eq $dbname) {
- return $i;
- }
- }
-}
+sub fetch_all_by_dbID_list {
+ my ( $self, $id_list_ref, $slice ) = @_;
+ if ( !defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY' ) {
+ throw("id_list list reference argument is required");
+ }
-=head2 get_peptide
+ if ( !@{$id_list_ref} ) { return [] }
- Arg [1] : Bio::EnsEMBL::ArchiveStableId $arch_id
- Example : none
- Description : Retrieves the peptide string for given ArchiveStableId. If its
- not a peptide or not in the database returns undef.
- Returntype : string or undef
- Exceptions : none
- Caller : Bio::EnsEMBL::ArchiveStableId->get_peptide, general
- Status : At Risk
- : under development
+ # Construct a constraint like 't1.table1_id = 123'
+ my @tabs = $self->_tables();
+ my ( $name, $syn ) = @{ $tabs[0] };
-=cut
+ # Ensure that we do not exceed MySQL's max_allowed_packet (defaults to
+ # 1 MB) splitting large queries into smaller queries of at most 256 KB
+ # (32768 8-bit characters). Assuming a (generous) average dbID string
+ # length of 16, this means 2048 dbIDs in each query.
+ my $max_size = 2048;
-sub get_peptide {
- my $self = shift;
- my $arch_id = shift;
- if ( lc( $arch_id->type() ) ne 'translation' ) {
- return undef;
- }
+ my %id_list;
+ $id_list{$_}++ for @{$id_list_ref};
+ my @id_list = keys %id_list;
- my $sql = qq(
- SELECT pa.peptide_seq
- FROM peptide_archive pa, gene_archive ga
- WHERE ga.translation_stable_id = ?
- AND ga.translation_version = ?
- AND ga.peptide_archive_id = pa.peptide_archive_id
- );
+ my @out;
- my $sth = $self->prepare($sql);
- $sth->bind_param( 1, $arch_id->stable_id, SQL_VARCHAR );
- $sth->bind_param( 2, $arch_id->version, SQL_SMALLINT );
- $sth->execute();
+ while (@id_list) {
+ my @ids;
+ my $id_str;
- my ($peptide_seq) = $sth->fetchrow_array();
- $sth->finish();
+ if ( scalar(@id_list) > $max_size ) {
+ @ids = splice( @id_list, 0, $max_size );
+ } else {
+ @ids = @id_list;
+ @id_list = ();
+ }
- return $peptide_seq;
-} ## end sub get_peptide
+ if ( scalar(@ids) > 1 ) {
+ $id_str = " IN (" . join( ',', @ids ) . ")";
+ } else {
+ $id_str = " = " . $ids[0];
+ }
+ my $constraint = "${syn}.${name}_id $id_str";
-=head2 get_current_release
+ push @out, @{ $self->generic_fetch($constraint, undef, $slice) };
+ }
- Example : my $current_release = $archive_adaptor->get_current_release;
- Description : Returns the current release number (as found in the meta table).
- Return type : Int
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+ return \@out;
+} ## end sub fetch_all_by_dbID_list
-=cut
+# might not be a good idea, but for convenience
+# shouldnt be called on the BIG tables though
-sub get_current_release {
+sub fetch_all {
my $self = shift;
+ return $self->generic_fetch();
+}
- unless ($self->{'current_release'}) {
- my $mca = $self->db->get_MetaContainer;
- my ($release) = @{ $mca->list_value_by_key('schema_version') };
- $self->{'current_release'} = $release;
- }
- return $self->{'current_release'};
+#_tables
+#
+# Args : none
+# Example : $tablename = $self->_table_name()
+# Description: ABSTRACT PROTECTED
+# Subclasses are responsible for implementing this
+# method. It should list of [tablename, alias] pairs.
+# Additionally the primary table (with the dbID,
+# analysis_id, and score) should be the first table in
+# the list. e.g:
+# ( ['repeat_feature', 'rf'],
+# ['repeat_consensus', 'rc']);
+# used to obtain features.
+# Returntype : list of [tablename, alias] pairs
+# Exceptions : thrown if not implemented by subclass
+# Caller : BaseFeatureAdaptor::generic_fetch
+#
+
+sub _tables {
+ throw( "abstract method _tables not defined "
+ . "by implementing subclass of BaseAdaptor" );
}
-=head2 get_current_assembly
+#_columns
+#
+# Args : none
+# Example : $tablename = $self->_columns()
+# Description: ABSTRACT PROTECTED
+# Subclasses are responsible for implementing this
+# method. It should return a list of columns to be
+# used for feature creation.
+# Returntype : list of strings
+# Exceptions : thrown if not implemented by subclass
+# Caller : BaseFeatureAdaptor::generic_fetch
+#
- Example : my $current_assembly = $archive_adaptor->get_current_assembly;
- Description : Returns the current assembly version (as found in the meta
- table).
- Return type : String
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+sub _columns {
+ throw( "abstract method _columns not defined "
+ . "by implementing subclass of BaseAdaptor" );
+}
-=cut
-sub get_current_assembly {
- my $self = shift;
+# _default_where_clause
+#
+# Arg [1] : none
+# Example : none
+# Description: May be overridden to provide an additional where
+# constraint to the SQL query which is generated to
+# fetch feature records. This constraint is always
+# appended to the end of the generated where clause
+# Returntype : string
+# Exceptions : none
+# Caller : generic_fetch
+#
- unless ($self->{'current_assembly'}) {
- my $mca = $self->db->get_MetaContainer;
- my ($assembly) = @{ $mca->list_value_by_key('assembly.default') };
- $self->{'current_assembly'} = $assembly;
- }
+sub _default_where_clause { return '' }
- return $self->{'current_assembly'};
-}
+# _left_join
-=head2 lookup_current
+# Arg [1] : none
+# Example : none
+# Description: Can be overridden by a subclass to specify any left
+# joins which should occur. The table name specigfied
+# in the join must still be present in the return
+# values of.
+# Returntype : a {'tablename' => 'join condition'} pair
+# Exceptions : none
+# Caller : general
+#
- Arg[1] : Bio::EnsEMBL::ArchiveStableId $arch_id -
- the stalbe ID to find the current version for
- Example : if ($self->lookup_version($arch_id) {
- $arch_id->version($arch_id->current_version);
- $arch_id->db_name($self->dbc->dbname);
- Description : Look in [gene|transcript|translation]_stable_id if you can find
- a current version for this stable ID. Set
- ArchiveStableId->current_version if found.
- Return type : Boolean (TRUE if current version found, else FALSE)
- Exceptions : none
- Caller : general
- Status : At Risk
- : under development
+sub _left_join { return () }
-=cut
-sub lookup_current {
- my $self = shift;
- my $arch_id = shift;
+#_final_clause
- my $type = lc( $arch_id->type );
+# Arg [1] : none
+# Example : none
+# Description: May be overriden to provide an additional clause
+# to the end of the SQL query used to fetch feature
+# records. This is useful to add a required ORDER BY
+# clause to the query for example.
+# Returntype : string
+# Exceptions : none
+# Caller : generic_fetch
+
+sub _final_clause { return '' }
- unless ($type) {
- warning("Can't lookup current version without a type.");
- return 0;
- }
+<<<<<<< ArchiveStableIdAdaptor.pm
+#_objs_from_sth
+=======
my $sql = qq(
SELECT version FROM ${type}
WHERE stable_id = ?
@@ -1454,58 +793,44 @@ sub lookup_current {
$arch_id->current_version($version);
return 1;
}
+>>>>>>> 1.40
+
+# Arg [1] : DBI::row_hashref $hashref containing key-value pairs
+# for each of the columns specified by the _columns method
+# Example : my @feats = $self->_obj_from_hashref
+# Description: ABSTRACT PROTECTED
+# The subclass is responsible for implementing this
+# method. It should take in a DBI row hash reference
+# and return a list of created features in contig
+# coordinates.
+# Returntype : list of Bio::EnsEMBL::*Features in contig coordinates
+# Exceptions : thrown if not implemented by subclass
+# Caller : BaseFeatureAdaptor::generic_fetch
+
+sub _objs_from_sth {
+ throw( "abstract method _objs_from_sth not defined "
+ . "by implementing subclass of BaseAdaptor" );
+}
- # didn't find a current version
- return 0;
-} ## end sub lookup_current
-
-
-# infer type from stable ID format
-sub _resolve_type {
+sub dump_data {
my $self = shift;
- my $arch_id = shift;
-
- my $stable_id = $arch_id->stable_id();
- my $id_type;
-
- # first, try to infer type from stable ID format
- #
- # Anopheles IDs
- if ($stable_id =~ /^AGAP.*/) {
- if ($stable_id =~ /.*-RA/) {
- $id_type = "Transcript";
- } elsif ($stable_id =~ /.*-PA/) {
- $id_type = "Translation";
- } else {
- $id_type = "Gene";
- }
+ my $data = shift;
+
+ my $dumper = Data::Dumper->new([$data]);
+ $dumper->Indent(0);
+ $dumper->Terse(1);
+ my $dump = $dumper->Dump();
+# $dump =~ s/'/\\'/g;
+ # $dump =~ s/^\$VAR1 = //;
+ return $dump;
+}
- # standard Ensembl IDs
- } elsif ($stable_id =~ /.*G\d+$/) {
- $id_type = "Gene";
- } elsif ($stable_id =~ /.*T\d+$/) {
- $id_type = "Transcript";
- } elsif ($stable_id =~ /.*P\d+$/) {
- $id_type = "Translation";
- } elsif ($stable_id =~ /.*E\d+$/) {
- $id_type = "Exon";
-
- # if guessing fails, look in db
- } else {
- my $sql = qq(
- SELECT type from stable_id_event
- WHERE old_stable_id = ?
- OR new_stable_id = ?
- );
- my $sth = $self->prepare($sql);
- $sth->execute($stable_id, $stable_id);
- ($id_type) = $sth->fetchrow_array;
- $sth->finish;
- }
+sub get_dumped_data {
+ my $self = shift;
+ my $data = shift;
- warning("Couldn't resolve stable ID type.") unless ($id_type);
-
- $arch_id->type($id_type);
+ $data =~ s/\n|\r|\f|\\//g;
+ return eval ($data);
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 2806b5e1a2..4ae77b004e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -79,6 +79,29 @@ sub new {
return $self;
}
+=head2 start_equals_end
+
+ Arg [1] : (optional) boolean $newval
+ Example : $bfa->start_equals_end(1);
+ Description: Getter/Setter for the start_equals_end flag. If set
+ to true sub _slice_fetch will use a simplified sql to retrieve 1bp slices.
+ Returntype : boolean
+ Exceptions : none
+ Caller : Pipeline
+ Status : Stable
+
+=cut
+
+sub start_equals_end {
+ my ( $self, $value ) = @_;
+
+ if ( defined($value) ) {
+ $self->{'start_equals_end'} = $value;
+ }
+ return $self->{'start_equals_end'};
+}
+
+
=head2 clear_cache
Args : None
@@ -623,41 +646,46 @@ COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
$constraint .= " AND " if ($constraint);
- if ( !$slice->is_circular() ) {
- # Deal with the default case of a non-circular chromosome.
- $constraint .=
- "${tab_syn}.seq_region_id IN ("
- . join( ',', @sr_ids )
- . ") AND "
- . "${tab_syn}.seq_region_start <= $slice_end AND "
- . "${tab_syn}.seq_region_end >= $slice_start";
+
+ $constraint .= "${tab_syn}.seq_region_id IN ("
+ . join( ',', @sr_ids ) . ") AND";
+
+ #faster query for 1bp slices where SNP data is not compressed
+ if ( $self->start_equals_end && $slice_start == $slice_end ) {
+ $constraint .=
+ " AND ${tab_syn}.seq_region_start = $slice_end" .
+ " AND ${tab_syn}.seq_region_end = $slice_start";
+
} else {
- # Deal with the case of a circular chromosome.
- if ( $slice_start > $slice_end ) {
- $constraint .=
- "${tab_syn}.seq_region_id IN ("
- . join( ',', @sr_ids )
- . ") AND ( ${tab_syn}.seq_region_start >= $slice_start "
- . "OR ${tab_syn}.seq_region_start <= $slice_end "
- . "OR ${tab_syn}.seq_region_end >= $slice_start "
- . "OR ${tab_syn}.seq_region_end <= $slice_end "
- . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";
-
- } else {
- $constraint .=
- "${tab_syn}.seq_region_id IN ("
- . join( ',', @sr_ids )
- . ") AND ((${tab_syn}.seq_region_start <= $slice_end "
- . "AND ${tab_syn}.seq_region_end >= $slice_start) "
- . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
- . "AND (${tab_syn}.seq_region_start <= $slice_end "
- . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
- }
- }
- if ( $max_len && !$slice->is_circular ) {
- my $min_start = $slice_start - $max_len;
- $constraint .= " AND ${tab_syn}.seq_region_start >= $min_start";
+ if ( !$slice->is_circular() ) {
+ # Deal with the default case of a non-circular chromosome.
+ $constraint .= " ${tab_syn}.seq_region_start <= $slice_end AND "
+ . "${tab_syn}.seq_region_end >= $slice_start";
+
+ if ( $max_len ) {
+ my $min_start = $slice_start - $max_len;
+ $constraint .= " AND ${tab_syn}.seq_region_start >= $min_start";
+ }
+
+ } else {
+ # Deal with the case of a circular chromosome.
+ if ( $slice_start > $slice_end ) {
+ $constraint .= " ( ${tab_syn}.seq_region_start >= $slice_start "
+ . "OR ${tab_syn}.seq_region_start <= $slice_end "
+ . "OR ${tab_syn}.seq_region_end >= $slice_start "
+ . "OR ${tab_syn}.seq_region_end <= $slice_end "
+ . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";
+
+ } else {
+ $constraint .= " ((${tab_syn}.seq_region_start <= $slice_end "
+ . "AND ${tab_syn}.seq_region_end >= $slice_start) "
+ . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
+ . "AND (${tab_syn}.seq_region_start <= $slice_end "
+ . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
+ }
+ }
+
}
my $fs = $self->generic_fetch( $constraint, undef, $slice );
--
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