Moved skip statements

Ensembl · Jun 30, 2022 · a1d0a9e · a1d0a9e
1 parent 96dad5e
commit a1d0a9e
Showing 1 changed file with 44 additions and 44 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/APPRISCompareSource.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/APPRISCompareSource.pm
@@ -29,53 +29,53 @@ use File::Spec;
 extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
-  NAME           => 'APPRISCompareSource',
-  DESCRIPTION    => 'APPRIS load match input data in files',
-  GROUPS         => ['geneset_support_level'],
-  DATACHECK_TYPE => 'critical',
-  DB_TYPES       => ['core'],
-  TABLES         => ['transcript_attrib']
+    NAME           => 'APPRISCompareSource',
+    DESCRIPTION    => 'APPRIS load match input data in files',
+    GROUPS         => [ 'geneset_support_level' ],
+    DATACHECK_TYPE => 'critical',
+    DB_TYPES       => [ 'core' ],
+    TABLES         => [ 'transcript_attrib' ]
 };
 
-sub skip_tests {
-  if ( ! defined($ENV{'APPRIS_FILE_PATH'}) ) {
-    return( 1, "No APPRIS_FILE_PATH base dit set" );
-  }
-}
-
 sub tests {
-  my ($self) = @_;
-  my $helper = $self->dba->dbc->sql_helper;
-  my $mca = $self->dba->get_adaptor('MetaContainer');
-  my $assembly_default = $mca->get_assemnly_default;
-  my $production_name = $mca->get_production_name;
-  my $schema_version = $mca->get_schema_version;
-
-  # TODO manage the extra parameter to pass to the test a `base_path` value.
-  # File format : .../Mus_musculus.GRCm38.e93.appris_data.principal.txt
-  my $file = File::Spec->catfile($ENV{'APPRIS_FILE_PATH'},
-      join('.', ucfirst($production_name), $assembly_default, "e".$schema_version, 'appris_data', 'principal', 'txt'));
-  my $desc_1 = 'APPRIS file content match imported transcript_attrib';
-  my $sql_1 = q/
-    SELECT UPPER(value), count(*)
-    FROM transcript_attrib
-    JOIN attrib_type a using (attrib_type_id)
-    WHERE a.code = 'appris'
-    GROUP BY value;
-  /;
-  my $attribs_counts = $helper->execute( -SQL => $sql_1 );
-  my $cut = `cut -f3 $file | sed -r 's/[:]+//g' |sort | uniq -c | awk '{ print $2 " " $1}' `;
-  my @data=split(/\n/, $cut);
-  my @line;
-  my %filecounts;
-  foreach my $token (@data) {
-    @line = split(/ /, $token);
-    $filecounts{$line[0]} = $line[1];
-  };
-  foreach my $attrib_count (@$attribs_counts) {
-    my ($count, $code) = @$attrib_count;
-    is($count, $filecounts{ $code }, $desc_1);
-  }
+    my ($self) = @_;
+    SKIP: {
+
+        my $helper = $self->dba->dbc->sql_helper;
+        my $mca = $self->dba->get_adaptor('MetaContainer');
+        my $assembly_default = $mca->get_assemnly_default;
+        my $production_name = $mca->get_production_name;
+        my $schema_version = $mca->get_schema_version;
+        my $file = File::Spec->catfile($ENV{'APPRIS_FILE_PATH'},
+        join('.', ucfirst($production_name), $assembly_default, "e" . $schema_version, 'appris_data', 'principal', 'txt'));
+
+        skip 'No APPRIS_FILE_PATH dir set', 1 unless defined($ENV{'APPRIS_FILE_PATH'});
+
+        skip 'No file for current version of database', 1 unless -e $file;
+        # TODO manage the extra parameter to pass to the test a `base_path` value.
+        # File format : .../Mus_musculus.GRCm38.e93.appris_data.principal.txt
+        my $desc_1 = 'APPRIS file content match imported transcript_attrib';
+        my $sql_1 = q/
+            SELECT UPPER(value), count(*)
+            FROM transcript_attrib
+            JOIN attrib_type a using (attrib_type_id)
+            WHERE a.code = 'appris'
+            GROUP BY value;/;
+
+        my $attribs_counts = $helper->execute(-SQL => $sql_1);
+        my $cut = `cut -f3 $file | sed -r 's/[:]+//g' |sort | uniq -c | awk '{ print $2 " " $1}' `;
+        my @data = split(/\n/, $cut);
+        my @line;
+        my %filecounts;
+        foreach my $token (@data) {
+            @line = split(/ /, $token);
+            $filecounts{$line[0]} = $line[1];
+        };
+        foreach my $attrib_count (@$attribs_counts) {
+            my ($count, $code) = @$attrib_count;
+            is($count, $filecounts{ $code }, $desc_1);
+        }
+    }
 }
 
 1;