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add debug
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@teharrison
teharrison committed Jun 14, 2017
1 parent 9a016ee commit 6b589fa
Showing 1 changed file with 23 additions and 12 deletions.
35 changes: 23 additions & 12 deletions src/MGRAST/lib/resources/inbox.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -412,6 +412,9 @@ sub validate_metadata {
sub seq_stats {
my ($self, $uuid) = @_;

my $post = $self->get_post_data(['debug']);
my $debug = $post->{'debug'} ? 1 : 0;

my $response = {
id => $self->{wf_info}{user_id},
user => $self->{wf_info}{user_name},
Expand All @@ -429,7 +432,7 @@ sub seq_stats {
$self->{wf_info}{job_name} = $self->{wf_info}{user_id}."_seqstats";
$self->{wf_info}{task_list} = $self->json->encode(\@tasks);

my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth);
my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth, $debug);
$self->add_node_action(undef, $node, $job, 'stats');

# return data
Expand All @@ -443,8 +446,10 @@ sub sff_to_fastq {
my ($self) = @_;

# get and validate sequence file
my $post = $self->get_post_data(['sff_file']);
my $uuid = exists($post->{'sff_file'}) ? $post->{'sff_file'} : "";
my $post = $self->get_post_data(['sff_file', 'debug']);
my $uuid = exists($post->{'sff_file'}) ? $post->{'sff_file'} : "";
my $debug = $post->{'debug'} ? 1 : 0;

unless ($uuid) {
$self->return_data( {"ERROR" => "this request type requires the sff_file parameter"}, 400 );
}
Expand All @@ -453,7 +458,7 @@ sub sff_to_fastq {
$self->{wf_info}{job_name} = $self->{wf_info}{user_id}."_sff2fastq";
$self->{wf_info}{task_list} = $self->json->encode(\@tasks);

my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth);
my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth, $debug);
$self->add_node_action($uuid, undef, $job, 'sff2fastq');

# return data
Expand All @@ -471,11 +476,13 @@ sub demultiplex {
my ($self) = @_;

# get and validate files
my $post = $self->get_post_data(['seq_file', 'index_file', 'index_file_2', 'barcode_file']);
my $post = $self->get_post_data(['seq_file', 'index_file', 'index_file_2', 'barcode_file', 'debug']);
my $seq_file = exists($post->{'seq_file'}) ? $post->{'seq_file'} : "";
my $index_file = exists($post->{'index_file'}) ? $post->{'index_file'} : "";
my $index2_file = exists($post->{'index_file_2'}) ? $post->{'index_file_2'} : "";
my $bar_file = exists($post->{'barcode_file'}) ? $post->{'barcode_file'} : "";
my $debug = $post->{'debug'} ? 1 : 0;

unless ($seq_file && $bar_file) {
$self->return_data( {"ERROR" => "this request type requires both the seq_file and barcode_file parameters"}, 400 );
}
Expand All @@ -493,7 +500,7 @@ sub demultiplex {
$self->{wf_info}{job_name} = $self->{wf_info}{user_id}."_demultiplex";
$self->{wf_info}{task_list} = $self->json->encode(\@tasks);

my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth);
my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth, $debug);
$self->add_node_action($seq_file, undef, $job, 'demultiplex');
$self->add_node_action($bar_file, undef, $job, 'demultiplex');
if ($index_file) {
Expand All @@ -517,11 +524,13 @@ sub pairjoin {
my ($self) = @_;

# get and validate sequence files
my $post = $self->get_post_data(['pair_file_1', 'pair_file_2', 'output', 'retain']);
my $post = $self->get_post_data(['pair_file_1', 'pair_file_2', 'output', 'retain', 'debug']);
my $pair1_file = exists($post->{'pair_file_1'}) ? $post->{'pair_file_1'} : "";
my $pair2_file = exists($post->{'pair_file_2'}) ? $post->{'pair_file_2'} : "";
my $outprefix = exists($post->{'output'}) ? $post->{'output'} : $self->uuidv4();
my $retain = exists($post->{'retain'}) ? $post->{'retain'} : 0;
my $retain = $post->{'retain'} ? 1 : 0;
my $debug = $post->{'debug'} ? 1 : 0;

unless ($pair1_file && $pair2_file) {
$self->return_data( {"ERROR" => "this request type requires both the pair_file_1 and pair_file_2 parameters"}, 400 );
}
Expand All @@ -535,7 +544,7 @@ sub pairjoin {
$self->{wf_info}{job_name} = $self->{wf_info}{user_id}."_pairjoin";
$self->{wf_info}{task_list} = $self->json->encode(\@tasks);

my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth);
my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth, $debug);
$self->add_node_action($pair1_file, undef, $job, "pairjoin");
$self->add_node_action($pair2_file, undef, $job, "pairjoin");

Expand All @@ -553,13 +562,15 @@ sub pairjoin_demultiplex {
my ($self) = @_;

# get and validate sequence files
my $post = $self->get_post_data(['pair_file_1', 'pair_file_2', 'index_file', 'index_file_2', 'barcode_file', 'retain']);
my $post = $self->get_post_data(['pair_file_1', 'pair_file_2', 'index_file', 'index_file_2', 'barcode_file', 'retain', 'debug']);
my $pair1_file = exists($post->{'pair_file_1'}) ? $post->{'pair_file_1'} : "";
my $pair2_file = exists($post->{'pair_file_2'}) ? $post->{'pair_file_2'} : "";
my $index_file = exists($post->{'index_file'}) ? $post->{'index_file'} : "";
my $index2_file = exists($post->{'index_file_2'}) ? $post->{'index_file_2'} : "";
my $bar_file = exists($post->{'barcode_file'}) ? $post->{'barcode_file'} : "";
my $retain = exists($post->{'retain'}) ? $post->{'retain'} : 0;
my $retain = $post->{'retain'} ? 1 : 0;
my $debug = $post->{'debug'} ? 1 : 0;

unless ($pair1_file && $pair2_file) {
$self->return_data( {"ERROR" => "this request type requires both the pair_file_1 and pair_file_2 parameters"}, 400 );
}
Expand All @@ -572,7 +583,7 @@ sub pairjoin_demultiplex {
$self->{wf_info}{job_name} = $self->{wf_info}{user_id}."_pairjoin_demultiplex";
$self->{wf_info}{task_list} = $self->json->encode(\@tasks);

my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth);
my $job = $self->submit_awe_template($self->{wf_info}, $Conf::mgrast_submission_workflow, $self->token, $self->user_auth, $debug);
$self->add_node_action($pair1_file, undef, $job, "pairjoin_demultiplex");
$self->add_node_action($pair2_file, undef, $job, "pairjoin_demultiplex");
$self->add_node_action($bar_file, undef, $job, "pairjoin_demultiplex");
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