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These should be class-wide attributes, not per instance
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@muffato @tgrego
muffato authored and tgrego committed Jan 23, 2020
1 parent dce11ed commit b14f8a7
Showing 1 changed file with 41 additions and 41 deletions.
82 changes: 41 additions & 41 deletions modules/Bio/EnsEMBL/Hive/HivePipeline.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,26 @@ use Bio::EnsEMBL::Hive::Utils::URL;
use Bio::EnsEMBL::Hive::Accumulator;
use Bio::EnsEMBL::Hive::NakedTable;

use constant {
TWEAK_ERROR_MSG => {
PARSE_ERROR => 'Tweak cannot be parsed',
ACTION_ERROR => 'Action is not supported',
FIELD_ERROR => 'Field not recognized',
VALUE_ERROR => 'Invalid value',
},
TWEAK_ACTION => {
'=' => 'SET',
'+' => 'SET',
'?' => 'SHOW',
'#' => 'DELETE',
},
TWEAK_OBJECT_TYPE => {
PIPELINE => 'Pipeline',
ANALYSIS => 'Analysis',
RESOURCE_CLASS => 'Resource class',
},
};


sub hive_dba { # The adaptor for HivePipeline objects
my $self = shift @_;
Expand Down Expand Up @@ -186,26 +206,6 @@ sub new { # construct an attached or a detached Pipeline object
# warn "Created a standalone pipeline";
}

$self->{TWEAK_ERROR_MSG} = {
PARSE_ERROR => "Tweak cannot be parsed",
ACTION_ERROR => "Action is not supported",
FIELD_ERROR => "Field not recognized",
VALUE_ERROR => "Invalid value",
};

$self->{TWEAK_ACTION} = {
'=' => "SET",
'+' => "SET",
'?' => "SHOW",
'#' => "DELETE",
};

$self->{TWEAK_OBJECT_TYPE} = {
PIPELINE => "Pipeline",
ANALYSIS => "Analysis",
RESOURCE_CLASS => "Resource class",
};

Bio::EnsEMBL::Hive::TheApiary->pipelines_collection->add( $self );

return $self;
Expand Down Expand Up @@ -577,8 +577,8 @@ sub apply_tweaks {
my $hash_pair = $pwp_collection->find_one_by('param_name', $param_name);
my $value = $hash_pair ? $hash_pair->{'param_value'} : undef;
my $tweakStructure;
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{PIPELINE};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{PIPELINE};
$tweakStructure->{Object}->{Id} = undef;
$tweakStructure->{Object}->{Name} = undef;
$tweakStructure->{Return}->{Field} = $param_name;
Expand Down Expand Up @@ -619,11 +619,11 @@ sub apply_tweaks {
} elsif($tweak=~/^pipeline\.(\w+)(\?|=(.+))$/) {
my ($attrib_name, $operator, $new_value_str) = ($1, $2, $3);
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{PIPELINE};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{PIPELINE};
$tweakStructure->{Object}->{Id} = undef;
$tweakStructure->{Object}->{Name} = undef;
$tweakStructure->{Return}->{Field} = $attrib_name;
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};

if($self->can($attrib_name)) {
my $old_value = stringify( $self->$attrib_name() );
Expand All @@ -640,7 +640,7 @@ sub apply_tweaks {
}

} else {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{FIELD_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{FIELD_ERROR};
push @response, "Tweak.Error \tCould not find the pipeline-wide '$attrib_name' method\n";
}
push @{$responseStructure->{Tweaks}}, $tweakStructure;
Expand All @@ -657,8 +657,8 @@ sub apply_tweaks {
my $old_value = $analysis->parameters;
my $param_hash = destringify( $old_value );
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{ANALYSIS};
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{ANALYSIS};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Id} = defined $analysis->dbID ? $analysis->dbID + 0 : undef;
$tweakStructure->{Object}->{Name} = $analysis_name;
$tweakStructure->{Return}->{Field} = $param_name;
Expand Down Expand Up @@ -706,8 +706,8 @@ sub apply_tweaks {
foreach my $analysis (@$analyses) {
my $analysis_name = $analysis->logic_name;
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{ANALYSIS};
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{ANALYSIS};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Id} = defined $analysis->dbID ? $analysis->dbID + 0 : undef;
$tweakStructure->{Object}->{Name} = $analysis_name;
$tweakStructure->{Return}->{Field} = $attrib_name;
Expand Down Expand Up @@ -791,10 +791,10 @@ sub apply_tweaks {

my $analysis_name = $analysis->logic_name;
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{ANALYSIS};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{ANALYSIS};
$tweakStructure->{Object}->{Id} = defined $analysis->dbID ? $analysis->dbID + 0 : undef;
$tweakStructure->{Object}->{Name} = $analysis_name;
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};
$tweakStructure->{Return}->{Field} = $attrib_name;
if( $attrib_name eq 'resource_class' ) {
$tweakStructure->{Return}->{OldValue} = $analysis->resource_class ? $analysis->resource_class->name : undef;
Expand All @@ -807,7 +807,7 @@ sub apply_tweaks {
push @response, "Tweak.Show \tanalysis[$analysis_name].resource_class ::\t(missing value)\n";
}
} elsif($operator eq '#') {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{ACTION_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{ACTION_ERROR};
push @response, "Tweak.Error \tDeleting of ResourceClasses is not supported\n";
} else {
$tweakStructure->{Return}->{NewValue} = $new_value_str;
Expand Down Expand Up @@ -838,12 +838,12 @@ sub apply_tweaks {
$tweakStructure->{Return}->{NewValue} = $tweakStructure->{Return}->{OldValue};
push @response, "Tweak.Show \tanalysis[$analysis_name].is_excluded ::\t".$analysis_stats->is_excluded()."\n";
} elsif($operator eq '#') {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{ACTION_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{ACTION_ERROR};
push @response, "Tweak.Error \tDeleting of excluded status is not supported\n";
} else {
$tweakStructure->{Return}->{NewValue} = $new_value_str;
if(!($new_value =~ /^[01]$/)) {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{VALUE_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{VALUE_ERROR};
push @response, "Tweak.Error \tis_excluded can only be 0 (no) or 1 (yes)\n";
} elsif ($new_value == $analysis_stats->is_excluded()) {
push @response, "Tweak.Info \tanalysis[$analysis_name].is_excluded is already $new_value, leaving as is\n";
Expand All @@ -861,7 +861,7 @@ sub apply_tweaks {
$tweakStructure->{Return}->{NewValue} = $tweakStructure->{Return}->{OldValue};
push @response, "Tweak.Show \tanalysis[$analysis_name].$attrib_name ::\t$old_value\n";
} elsif($operator eq '#') {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{ACTION_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{ACTION_ERROR};
push @response, "Tweak.Error \tDeleting of Analysis attributes is not supported\n";
} else {
$tweakStructure->{Return}->{NewValue} = stringify($new_value);
Expand All @@ -870,7 +870,7 @@ sub apply_tweaks {
$need_write = 1;
}
} else {
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{FIELD_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{FIELD_ERROR};
push @response, "Tweak.Error \tAnalysis does not support '$attrib_name' attribute\n";
}

Expand All @@ -887,10 +887,10 @@ sub apply_tweaks {
foreach my $rc (@$resource_classes) {
my $rc_name = $rc->name;
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{RESOURCE_CLASS};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{RESOURCE_CLASS};
$tweakStructure->{Object}->{Id} = defined $rc->dbID ? $rc->dbID + 0 : undef;
$tweakStructure->{Object}->{Name} = $rc_name;
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};

if(my $rd = $self->collection_of( 'ResourceDescription' )->find_one_by('resource_class', $rc, 'meadow_type', $meadow_type)) {
my ($submission_cmd_args, $worker_cmd_args) = ($rd->submission_cmd_args, $rd->worker_cmd_args);
Expand All @@ -913,8 +913,8 @@ sub apply_tweaks {
foreach my $rc (@$resource_classes) {
my $rc_name = $rc->name;
my $tweakStructure;
$tweakStructure->{Object}->{Type} = $self->{TWEAK_OBJECT_TYPE}->{RESOURCE_CLASS};
$tweakStructure->{Action} = $self->{TWEAK_ACTION}->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Type} = TWEAK_OBJECT_TYPE->{RESOURCE_CLASS};
$tweakStructure->{Action} = TWEAK_ACTION->{substr($operator, 0, 1)};
$tweakStructure->{Object}->{Id} = defined $rc->dbID ? $rc->dbID + 0 : undef;
$tweakStructure->{Object}->{Name} = $rc_name;

Expand Down Expand Up @@ -950,7 +950,7 @@ sub apply_tweaks {

} else {
my $tweakStructure;
$tweakStructure->{Error} = $self->{TWEAK_ERROR_MSG}->{PARSE_ERROR};
$tweakStructure->{Error} = TWEAK_ERROR_MSG->{PARSE_ERROR};
push @response, "Tweak.Error \tFailed to parse the tweak\n";
push @{$responseStructure->{Tweaks}}, $tweakStructure;
}
Expand Down

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