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Dev/download data file dataflow #544

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24446e6
avoid downloadData to delete and download
EreboPSilva Feb 23, 2026
f484c99
Added better reporting
EreboPSilva Mar 4, 2026
50cbeda
Fix HiveDownloadData to correctly handle pre-existing files
EreboPSilva Mar 6, 2026
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2 changes: 2 additions & 0 deletions modules/Bio/EnsEMBL/Analysis/Hive/Config/StarScallopRnaseq.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -436,6 +436,8 @@ sub pipeline_analyses {
-parameters => {
output_dir => $self->o('input_dir'),
download_method => $self->o('download_method'),
read_length_table => $self->o('read_length_table'),

uncompress => 0,
},
-flow_into => {
Expand Down
52 changes: 51 additions & 1 deletion modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/HiveDownloadData.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,35 @@ sub param_defaults {
sub fetch_input {
my ($self) = @_;

# Early exit if file already present and verified
my $filepath = catfile($self->param_required('output_dir'), basename($self->param_required('url')));
if (-e $filepath && $self->param_is_defined('md5sum')) {
my $digest = Digest::MD5->new();
open(my $fh, $filepath) || $self->throw("Could not open '$filepath': $!");
binmode $fh;
my $md5sum = $digest->addfile($fh)->hexdigest;
close($fh) || $self->throw("Could not close '$filepath': $!");
if ($md5sum eq $self->param('md5sum')) {
$self->say_with_header("File '$filepath' already exists and md5sum matches, skipping download", 1);
my $final_file = $self->param('uncompress') ? ($filepath =~ /^(\S+)\.\w+$/)[0] : $filepath;

my $already_processed = 0;
eval {
my $sth = $self->db->dbc->prepare('SELECT read_length FROM '.$self->param('read_length_table').' WHERE fastq = ?');
$sth->execute(basename($final_file));
my $row = $sth->fetchrow_arrayref;
$already_processed = 1 if $row;
$sth->finish;
};

unless ($already_processed) {
$self->dataflow_output_id({filename => $final_file}, $self->param('_branch_to_flow_to'));
}
$self->input_job->autoflow(0);
$self->complete_early("File already present and verified");
}
}

if ($] =~ '^5.024') {
$self->throw("Perl 5.24 doesn't work with this module. If you manage to make it work, please submit a pull-request");
}
Expand Down Expand Up @@ -249,9 +278,30 @@ sub pre_cleanup {
my ($self) = @_;

my $filepath = catfile($self->param_required('output_dir'), basename($self->param_required('url')));

if (-e $filepath) {
unlink $filepath;
if ($self->param_is_defined('md5sum')) {
my $digest = Digest::MD5->new();
open(my $fh, $filepath) || $self->throw("Could not open '$filepath': $!");
binmode $fh;
my $md5sum = $digest->addfile($fh)->hexdigest;
close($fh) || $self->throw("Could not close '$filepath': $!");

unless ($md5sum eq $self->param('md5sum')) {
$self->say_with_header("File '$filepath' exists but md5sum mismatch (expected: ".$self->param('md5sum').", got: $md5sum), removing for re-download");
unlink $filepath or $self->warning("Could not remove '$filepath': $!");
}
# if md5 matches: do nothing here, fetch_input handles the early exit
}
else {
$self->say_with_header("File '$filepath' already exists but no md5sum defined, removing it to force a clean download");
unlink $filepath or $self->warning("Could not remove '$filepath': $!");
}
}
else {
$self->say_with_header("File '$filepath' does not exist, nothing to clean up");
}
}

1;