AnalysisAdaptor.pm 5.33 KB
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=pod

=head1 NAME

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    Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor
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=head1 SYNOPSIS

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    $analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
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    $analysis_adaptor = $analysis_object->adaptor;
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=head1 DESCRIPTION

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    Module to encapsulate all db access for persistent class Analysis.
    There should be just one such adaptor per application and database connection.

=head1 LICENSE

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    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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    Copyright [2016-2020] EMBL-European Bioinformatics Institute
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    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.
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=head1 CONTACT

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    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
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=cut


package Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;

use strict;
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use warnings;
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use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::URLFactory;
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use Bio::EnsEMBL::Hive::Utils ('throw');
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use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
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sub default_table_name {
    return 'analysis_base';
}


sub default_insertion_method {
    return 'INSERT';
}


sub object_class {
    return 'Bio::EnsEMBL::Hive::Analysis';
}
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=head2 fetch_by_logic_name_or_url

    Description: given a URL gets the analysis from URLFactory, otherwise fetches it from the db

=cut

sub fetch_by_logic_name_or_url {
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    my $self                = shift @_; # can either be $self or class name
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    my $logic_name_or_url   = shift @_;

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    if($logic_name_or_url =~ m{^\w*://}) {
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        return Bio::EnsEMBL::Hive::URLFactory->fetch($logic_name_or_url, ref($self) && $self->db);
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    } else {
        return $self->fetch_by_logic_name($logic_name_or_url);
    }
}


=head2 fetch_by_url_query

    Description: fetches the analysis either by logic_name or by dbID (either coming from the tail of the URL)

=cut

sub fetch_by_url_query {
    my ($self, $field_name, $field_value) = @_;

    if(!$field_name or !$field_value) {

        return;

    } elsif($field_name eq 'logic_name') {

        return $self->fetch_by_logic_name($field_value);

    } elsif($field_name eq 'dbID') {

        return $self->fetch_by_dbID($field_value);

    }
}


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=head2 fetch_all_by_pattern

  Arg [1]    : (optional) string $pattern
  Example    : my $first_fifteen_analyses_and_two_more = $analysis_adaptor->fetch_all_by_pattern( '1..15,analysis_X,21' );
  Example    : my $two_open_ranges = $analysis_adaptor->fetch_all_by_pattern( '..7,10..' );
  Example    : my $double_exclusion = $analysis_adaptor->fetch_all_by_pattern( '1..15-3..5+4' );
  Example    : my $blast_related_with_exceptions = $analysis_adaptor->fetch_all_by_pattern( 'blast%-12-%funnel' );
  Description: Fetches an arrayref of non-repeating Analyses objects by interpreting a pattern.
                The pattern can contain individual analyses_ids, individual logic_names,
                open and closed ranges of analysis_ids, wildcard patterns of logic_names,
                merges (+ or ,) and exclusions (-) of the above subsets.
  Exceptions : none
  Caller     : both beekeeper.pl (for scheduling) and runWorker.pl (for specialization)

=cut

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sub fetch_all_by_pattern {
    my ($self, $pattern) = @_;

    my $analyses;

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    if( not defined($pattern) ) {

        $analyses = $self->fetch_all();

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    } elsif( $pattern=~/[+\-,]/ ) {     # merging by inclusion/exclusion, and maintaining uniqueness
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        my @syll = split(/([+\-,])/, $pattern);

        my %uniq = map { ($_->dbID => $_) } @{ $self->fetch_all_by_pattern( shift @syll ) };   # initialize with the first syllable

        while(@syll) {
            my $operation   = shift @syll;
            my $subpattern  = shift @syll;
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            foreach my $analysis (@{ $self->fetch_all_by_pattern( $subpattern ) }) {
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                if($operation eq '-') {
                    delete $uniq{$analysis->dbID};
                } elsif ($operation eq '+' or $operation eq ',') {
                    $uniq{$analysis->dbID} = $analysis;
                } else {
                    throw( "Complex pattern '$pattern' not recognized" );
                }
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            }
        }

        $analyses = [ values %uniq ];

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    } elsif( $pattern=~/^\d+$/ ) {
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        $analyses = $self->fetch_all_by_analysis_id( $pattern );

    } elsif( $pattern=~/^(\d+)\.\.(\d+)$/ ) {

        $analyses = $self->fetch_all( "analysis_id BETWEEN $1 AND $2" );

    } elsif( $pattern=~/^(\d+)\.\.$/ ) {

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        $analyses = $self->fetch_all( "$1<=analysis_id" );
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    } elsif( $pattern=~/^\.\.(\d+)$/ ) {

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        $analyses = $self->fetch_all( "analysis_id<=$1" );
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    } elsif( $pattern=~/^\w+$/) {

        $analyses = $self->fetch_all_by_logic_name( $pattern );

    } elsif( $pattern=~/^[\w\%]+$/) {

        $analyses = $self->fetch_all( "logic_name LIKE '$pattern'" );

    } else {

        throw( "Pattern '$pattern' not recognized" );

    }

    return $analyses;
}


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