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Add UndoEdaStudy step to remove EDA metadata before undoing a single rnaSeq dataset #89

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Add UndoEdaStudy step to remove EDA metadata before undoing a single rnaSeq dataset #89

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25 changes: 25 additions & 0 deletions Main/lib/perl/WorkflowSteps/UndoEdaStudy.pm
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
package ApiCommonWorkflow::Main::WorkflowSteps::UndoEdaStudy;

@ISA = (ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep);

use strict;
use ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep;

sub run {
my ($self, $test, $undo) = @_;

my $extDbRlsSpec = $self->getParamValue('extDbRlsSpec');
my $gusConfigFile = $self->getParamValue('gusConfigFile');

my $workflowDataDir = $self->getWorkflowDataDir();
my $logFile = "$workflowDataDir/undoEdaStudy.log";

if ($undo) {
$self->runCmd($test, "undoEdaStudy.pl --extDbRlsSpec '$extDbRlsSpec' --gusConfigFile $gusConfigFile");
$self->runCmd(0, "rm -f $logFile");
} else {
$self->runCmd($test, "echo 'EDA study metadata loaded for $extDbRlsSpec' > $logFile");
}
}

1;
14 changes: 14 additions & 0 deletions Main/lib/xml/workflowTemplates/rnaseq.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,13 @@
<depends name="dumpPseudogenes"/>
<depends name="${name}_ebi_rnaSeq_loadDataset"/>
</subgraph>

<step name="${name}_ebi_rnaSeq_undoEdaStudy"
stepClass="ApiCommonWorkflow::Main::WorkflowSteps::UndoEdaStudy">
<paramValue name="extDbRlsSpec">${organismAbbrev}_${name}_ebi_rnaSeq_RSRC|${version}</paramValue>
<paramValue name="gusConfigFile">$$gusConfigFile$$</paramValue>
<depends name="${name}_ebi_rnaSeq_experiment"/>
</step>
</datasetTemplate>


Expand Down Expand Up @@ -199,6 +206,13 @@
<depends name="${name}_rnaSeq_experiment_CDS"/>
</subgraph>

<step name="${name}_rnaSeq_undoEdaStudy"
stepClass="ApiCommonWorkflow::Main::WorkflowSteps::UndoEdaStudy">
<paramValue name="extDbRlsSpec">${organismAbbrev}_${name}_rnaSeq_RSRC|${version}</paramValue>
<paramValue name="gusConfigFile">$$gusConfigFile$$</paramValue>
<depends name="${name}_analyze_rnaSeq_experiment"/>
</step>

</datasetTemplate>

<datasetTemplate class="longReadRnaSeqExperiment">
Expand Down