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Added a new optional parameter to methods returning lists of runs and run count - the name of the manufacturer. If this name is undefined in the parameters hash, it defaults to 'Illumina'. To avoid code repetition, consolidated queries for listing and counting runs, which previously were in six different places. Simplified the logic of retrieving cached lists and counts of runs vs computing new values.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,5 @@ | ||
| ######### | ||
| # Author: rmp | ||
| # Created: 2006-10-31 | ||
| # | ||
| package npg::model::run_status_dict; | ||
|
|
||
| use strict; | ||
| use warnings; | ||
| use base qw(npg::model); | ||
|
|
@@ -43,70 +40,6 @@ sub init { | |
| return 1; | ||
| } | ||
|
|
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| sub runs { | ||
| my ($self, $params ) = @_; | ||
| $params ||= {}; | ||
| $params->{id_instrument_format} ||= q{all}; | ||
|
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||
| my $pkg = 'npg::model::run'; | ||
| my $query = qq(SELECT @{[join q(, ), map { "r.$_" } $pkg->fields()]} | ||
| FROM @{[$pkg->table()]} r, | ||
| run_status rs | ||
| WHERE rs.id_run = r.id_run | ||
| AND rs.iscurrent = 1 | ||
| AND rs.id_run_status_dict = ?); | ||
|
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||
| if ( $params->{id_instrument} && $params->{id_instrument} =~ /\d+/xms ) { | ||
| $query .= qq[ AND id_instrument = $params->{id_instrument}]; | ||
| } else { | ||
| if ( $params->{id_instrument_format} ne q{all} && $params->{id_instrument_format} =~ /\A\d+\z/xms ) { | ||
| $query .= qq[ AND r.id_instrument_format = $params->{id_instrument_format}]; | ||
| } | ||
| } | ||
| $query .= q( ORDER BY r.id_run DESC); | ||
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||
| $query = $self->util->driver->bounded_select($query, | ||
| $params->{len}, | ||
| $params->{start}); | ||
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| return $self->gen_getarray($pkg, $query, $self->id_run_status_dict()); | ||
| } | ||
|
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||
| sub count_runs { | ||
| my ( $self, $params ) = @_; | ||
| $params ||= {}; | ||
| $params->{id_instrument_format} ||= q{all}; | ||
| $self->{count_runs} ||= {}; | ||
|
|
||
| if ( ! defined $self->{count_runs}->{id_instrument_format} ) { | ||
|
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| my $pkg = 'npg::model::run'; | ||
| my $query = qq(SELECT COUNT(*) | ||
| FROM @{[$pkg->table()]} r, | ||
| run_status rs | ||
| WHERE rs.id_run = r.id_run | ||
| AND rs.iscurrent = 1 | ||
| AND rs.id_run_status_dict = ?); | ||
|
|
||
| if ( $params->{id_instrument} && $params->{id_instrument} =~ /\d+/xms ) { | ||
| $query .= qq[ AND id_instrument = $params->{id_instrument}]; | ||
| } else { | ||
| if ( $params->{id_instrument_format} ne q{all} && $params->{id_instrument_format} =~ /\A\d+\z/xms ) { | ||
| $query .= qq[ AND r.id_instrument_format = $params->{id_instrument_format}]; | ||
| } | ||
| } | ||
|
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||
| my $ref = $self->util->dbh->selectall_arrayref($query, {}, $self->id_run_status_dict()); | ||
|
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||
| if ( defined $ref->[0] && | ||
| defined $ref->[0]->[0] ) { | ||
| $self->{count_runs}->{ $params->{id_instrument_format} } = $ref->[0]->[0]; | ||
| } | ||
| } | ||
|
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||
| return $self->{count_runs}->{ $params->{id_instrument_format} } || 0; | ||
| } | ||
|
|
||
| sub run_status_dicts_sorted { | ||
| my ( $self ) = @_; | ||
|
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||
|
|
@@ -155,20 +88,6 @@ npg::model::run_status_dict | |
| my $arRunStatusDicts = $oRunStatusDict->run_status_dicts(); | ||
| =head2 runs - arrayref of npg::model::runs with a current status having this id_run_status_dict | ||
| my $arRuns = $oRunStatusDict->runs(); | ||
| Takes an optional hash of params, id_instrument_format => (all,1,2,3..) (defaults to all) | ||
| If this is given, the runs returned will only be for instruments of that format | ||
| =head2 count_runs - Count the runs with this rsd as their current status | ||
| my $iCountRuns = $oRunStatusDict->count_runs(); | ||
| Takes an optional hash of params, id_instrument_format => (all,1,2,3..) (defaults to all) | ||
| If this is given, the count of runs returned will only be for instruments of that format | ||
| =head2 run_status_dicts_sorted | ||
| Use instead of generated run_status_dicts to get a temporal ordered, current list | ||
|
|
@@ -185,11 +104,17 @@ Use instead of generated run_status_dicts to get a temporal ordered, current lis | |
| =head1 AUTHOR | ||
| Roger Pettett, E<lt>[email protected]E<gt> | ||
| =over | ||
| =item Roger Pettett | ||
| =item Marina Gourtovaia | ||
| =back | ||
| =head1 LICENSE AND COPYRIGHT | ||
| Copyright (C) 2008 GRL, by Roger Pettett | ||
| Copyright (C) 2006-2012,2013,2014,2025 Genome Research Ltd. | ||
| This file is part of NPG. | ||
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