-
Notifications
You must be signed in to change notification settings - Fork 28
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #255 from Ensembl/TapToJson
Added new module DataCheckTapToJson to convert datacheck tap output t…
- Loading branch information
Showing
6 changed files
with
259 additions
and
95 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| =head1 LICENSE | ||
| Copyright [2018-2020] EMBL-European Bioinformatics Institute | ||
| Licensed under the Apache License, Version 2.0 (the "License"); | ||
| you may not use this file except in compliance with the License. | ||
| You may obtain a copy of the License at | ||
| http://www.apache.org/licenses/LICENSE-2.0 | ||
| Unless required by applicable law or agreed to in writing, software | ||
| distributed under the License is distributed on an "AS IS" BASIS, | ||
| WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| See the License for the specific language governing permissions and | ||
| limitations under the License. | ||
| =head1 NAME | ||
| Bio::EnsEMBL::DataCheck::Pipeline::ConvertTapToJson | ||
| =head1 DESCRIPTION | ||
| Parse one or more TAP-format output files into a single JSON file. | ||
| By default, only failures are included in the JSON file, and the | ||
| results are indexed by datacheck name. Results for passing datachecks | ||
| can be included by setting '-json_passed => 1', and can be indexed by the | ||
| species name/database by setting '-json_by_species => 1'. | ||
| =cut | ||
|
|
||
| package Bio::EnsEMBL::DataCheck::Pipeline::ConvertTapToJson; | ||
|
|
||
| use strict; | ||
| use warnings; | ||
| use feature 'say'; | ||
|
|
||
| use JSON; | ||
| use Path::Tiny; | ||
| use TAP::Parser; | ||
|
|
||
| use base ('Bio::EnsEMBL::Hive::Process'); | ||
|
|
||
| sub param_defaults { | ||
| my $self = shift; | ||
|
|
||
| return { | ||
| output_dir => undef, | ||
| json_output_file => undef, | ||
| json_by_species => 0, | ||
| json_passed => 0 | ||
| }; | ||
| } | ||
|
|
||
| sub fetch_input { | ||
| my $self = shift; | ||
|
|
||
| # Whether we are parsing a single TAP-format file or a directory | ||
| # of them, we need a single json output file. If the output_dir | ||
| # is not specified, the output will go to STDOUT - which isn't | ||
| # really useful in a pipeline context, but this code can be used | ||
| # in standalone mode on the command line as well. | ||
| if ( | ||
| $self->param_is_defined('output_dir') && | ||
| ! $self->param_is_defined('json_output_file') | ||
| ) { | ||
| my $filename = 'results'; | ||
| $filename .= '_passed' if $self->param('json_passed'); | ||
| $filename .= '_by_species' if $self->param('json_by_species'); | ||
| $filename .= '.json'; | ||
| my $output_file = path($self->param('output_dir'), $filename); | ||
| $self->param('json_output_file', $output_file->stringify); | ||
| } | ||
| } | ||
|
|
||
| sub run { | ||
| my $self = shift; | ||
|
|
||
| my $tap = $self->param_required('tap'); | ||
| my $output_file = $self->param('json_output_file'); | ||
| my $passed = $self->param('json_passed'); | ||
| my $by_species = $self->param('json_by_species'); | ||
|
|
||
| $self->parse_results($tap, $output_file, $by_species, $passed); | ||
| } | ||
|
|
||
| sub write_output { | ||
| my $self = shift; | ||
|
|
||
| $self->dataflow_output_id( | ||
| { json_output_file => $self->param('json_output_file') }, 1 | ||
| ); | ||
| } | ||
|
|
||
| sub parse_results { | ||
| my ($self, $tap, $output_file, $by_species, $passed) = @_; | ||
|
|
||
| my @tap_files; | ||
| if (-d $tap) { | ||
| @tap_files = map { $_->stringify } path($tap)->children; | ||
| } else { | ||
| push @tap_files, $tap; | ||
| } | ||
|
|
||
| my %results; | ||
| my $datacheck; | ||
| my $species; | ||
| my $test; | ||
| my %tests; | ||
|
|
||
| foreach my $tap_file (@tap_files) { | ||
| my $tap = path($tap_file)->slurp; | ||
| my $parser = TAP::Parser->new( { tap => $tap } ); | ||
|
|
||
| while (my $result = $parser->next) { | ||
| if ($result->is_comment) { | ||
| if ($result->as_string =~ /^# Subtest: (.+)/) { | ||
| $datacheck = $1; | ||
| } | ||
| } elsif ($result->is_unknown) { | ||
| if ($result->as_string =~ /^\s+# Subtest: (.+)/) { | ||
| $species = $1; | ||
| %tests = (); | ||
| } elsif ($result->as_string =~ /^\s{8}((?:not ok|# No tests run).*)/) { | ||
| $test = $1; | ||
| $tests{$test} = []; | ||
| } elsif ($result->as_string =~ /^\s{8}((?:ok|.* # SKIP).*)/ && $passed) { | ||
| $test = $1; | ||
| $tests{$test} = []; | ||
| } elsif ($result->as_string =~ /^\s{8}#\s(\s*.*)/) { | ||
| if (defined $test) { | ||
| push @{$tests{$test}}, $1; | ||
| } else { | ||
| warn "Premature diagnostication: diagnostics incomplete ". | ||
| "for $species because they cannot be linked to a test"; | ||
| } | ||
| } elsif ($result->as_string =~ /^\s{4}((?:ok|not ok))/) { | ||
| my $ok = $1 eq 'ok' ? 1 : 0; | ||
| if (!$ok || $passed) { | ||
| my %datacheck_tests = %tests; | ||
| if ($by_species) { | ||
| $results{$species}{$datacheck}{'ok'} = $ok; | ||
| $results{$species}{$datacheck}{'tests'} = \%datacheck_tests; | ||
| } else { | ||
| $results{$datacheck}{$species}{'ok'} = $ok; | ||
| $results{$datacheck}{$species}{'tests'} = \%datacheck_tests; | ||
| } | ||
| } | ||
| $test = undef; | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| my $json = JSON->new->canonical->pretty->encode(\%results); | ||
|
|
||
| if ($output_file) { | ||
| path($output_file)->parent->mkpath; | ||
| path($output_file)->spew($json) | ||
| } else { | ||
| say $json; | ||
| } | ||
| } | ||
|
|
||
| 1; |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.