Added new module DataCheckTapToJson to convert datacheck tap output t…

…o json to display as html through datacheck service

lib/Bio/EnsEMBL/DataCheck/Pipeline/DataCheckTapToJson.pm

@@ -0,0 +1,104 @@
+=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::DataCheckSummary
+
+=head1 DESCRIPTION
+Store summary of datacheck results, and optionally send it via email.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Pipeline::DataCheckTapToJson;
+
+use strict;
+use warnings;
+use feature 'say';
+
+use JSON;
+use Path::Tiny;
+use Pod::Usage;
+use TAP::Parser;
+
+
+use base ('Bio::EnsEMBL::Hive::Process');
+sub run {
+
+  my $self = shift;
+
+  my $output_dir   = $self->param('output_dir');
+  my @tap_files = map { $_->stringify } path($output_dir)->children;
+
+  my %results;
+  my $datacheck;
+  my $species;
+  my $test;
+  my %tests;
+  my $passed = 1;
+  my $by_species = 1;
+
+  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);
+  my $basename = path($output_dir)->basename;
+  my $output_file = $output_dir . '/' . $basename . '.json';
+  path($output_file)->parent->mkpath;
+  path($output_file)->spew($json)
+
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Pipeline/DbDataChecks_conf.pm

@@ -198,6 +198,7 @@ sub pipeline_analyses {
                                   ['RunDataChecks']
                                 ),
                               'A->1' => ['DataCheckSummary'],
+
                             },
       -rc_name           => 'default',
     },
@@ -300,9 +301,17 @@ sub pipeline_analyses {
       -max_retry_count   => 0,
       -rc_name           => 'default',
       -flow_into         => {
-                              '1' => ['?table_name=result'],
+                              '1' => ['?table_name=result', 'DataCheckTapToJson'],
                             },
     },
+    {
+      -logic_name        => 'DataCheckTapToJson',
+      -module            => 'Bio::EnsEMBL::DataCheck::Pipeline::DataCheckTapToJson',
+      -analysis_capacity => 10,
+      -max_retry_count   => 0,
+      -rc_name           => 'default',
+    },
+
 
   ];
 }