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Adding in compilation tests to ensure all perl modules compile #99

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Adding in compilation tests to ensure all perl modules compile #99

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9 changes: 5 additions & 4 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -54,11 +54,12 @@ build-test-script:
echo 'script_dir=$$(dirname "$$(readlink -f "$$0")")' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'export KB_DEPLOYMENT_CONFIG=$$script_dir/../deploy.cfg' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'export KB_AUTH_TOKEN=`cat /kb/module/work/token`' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'export PERL5LIB=$$script_dir/../$(LIB_DIR):$$PATH:$$PERL5LIB' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'export PERL5LIB=$$script_dir/../$(LIB_DIR):$$PERL5LIB' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
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$PATH contains the paths of various executables, but no paths to perl libraries.

echo 'cd $$script_dir/..' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'echo "running test scripts!"' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'prove -lvrm $(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'prove -lvm --ext pl $(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'echo "running perl .t tests"' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'prove -I $(TEST_DIR)/lib -lvrm -j9 $(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'echo "running .pl tests"' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'prove -I $(TEST_DIR)/lib -lvm --ext pl $(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
chmod +x $(TEST_DIR)/$(TEST_SCRIPT_NAME)

deploy-mfatoolkit:
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24 changes: 12 additions & 12 deletions cpanfile
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@@ -1,12 +1,12 @@
requires 'Config::IniFiles';
requires 'Cpanel::JSON::XS';
requires 'Data::Dumper::Concise';
requires 'Devel::Cover';
requires 'JSON::MaybeXS';
requires 'Path::Tiny';
requires 'Ref::Util';
requires 'Template::Plugin::JSON';
requires 'Template';
requires 'Test::Most';
requires 'Test::Output';
requires 'Try::Tiny';
requires 'Cpanel::JSON::XS', '>= 4.19';
requires 'Data::Dumper::Concise', '>= 2.023';
requires 'JSON::MaybeXS', '>= 1.004000';
requires 'Path::Tiny', '>= 0.112';
requires 'Ref::Util', '>= 0.204';
requires 'Template::Plugin::JSON', '>= 0.08';
requires 'Template', '>= 2.26';
requires 'Term::ANSIColor', '>= 5.00';
requires 'Test::Most', '>= 0.35';
requires 'Test::Output', '>= 1.031';
requires 'Test::Compile', '>= 2.3.1';
requires 'Try::Tiny', '>= 0.30';
35 changes: 0 additions & 35 deletions lib/Bio/KBase/ObjectAPI/KBaseFBA/BooleanGeneExpressionData.pm
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This file was deleted.

35 changes: 0 additions & 35 deletions lib/Bio/KBase/ObjectAPI/KBaseFBA/BooleanGeneExpressionDataCollection.pm
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29 changes: 29 additions & 0 deletions test/00_test_compile.t
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@@ -0,0 +1,29 @@
use Test::Most;
use Test::Compile;
use KBaseTestContext;

my $base_dir = KBaseTestContext->base_dir();
my $test = Test::Compile->new();

# check all .pm and .pl files compile
$test->all_files_ok( $base_dir );

# check the test files are also OK
my @all_t_files = all_t_files( $test, $base_dir );
for ( @all_t_files ) {
ok $test->pl_file_compiles( $_ ), $_ . ' compiles';
}

$test->done_testing();

sub all_t_files {
my ( $test, @dirs ) = @_;

@dirs = @dirs ? @dirs : ( $base_dir );

my @t_files;
for my $file ( $test->_find_files( @dirs ) ) {
push @t_files, $file if $file =~ /\.t$/;
}
return @t_files;
}
28 changes: 20 additions & 8 deletions test/bio_kbase_templater.t
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Expand Up @@ -41,7 +41,8 @@ subtest 'populate_template' => sub {
{ thing => 'world' },
), 'valid output, includes template vars, output to STDOUT';
};
my @content = map { s/(^\s*|\s*$)//g; $_ } grep { /\S/ } split /[\n\r]/, $stdout;

my @content = parse_template_string( $stdout );
cmp_deeply
\@content,
[ "Hello world", "G'day sport!" ],
Expand All @@ -55,8 +56,7 @@ subtest 'populate_template' => sub {
\$string
), 'valid output, no template vars, saved to scalar ref';


@content = map { s/(^\s*|\s*$)//g; $_ } grep { /\S/ } split /[\n\r]/, $string;
@content = parse_template_string( $string );
cmp_deeply
\@content,
[ "Hello", "G'day sport!" ],
Expand All @@ -73,7 +73,7 @@ subtest 'populate_template' => sub {
\$string
), 'valid output, includes template vars, saved to scalar ref';

@content = map { s/(^\s*|\s*$)//g; $_ } grep { /\S/ } split /[\n\r]/, $string;
@content = parse_template_string( $string );
cmp_deeply
\@content,
[ "Hello world", "G'day sport!" ],
Expand All @@ -90,10 +90,7 @@ subtest 'populate_template' => sub {
$temp_file->stringify,
), 'valid output, includes template vars, saved to a file';

@content = map { s/(^\s*|\s*$)//g; $_ }
grep { /\S/ }
split /[\n\r]/, $temp_file->slurp_utf8;

@content = parse_template_string( $temp_file->slurp_utf8 );
cmp_deeply
\@content,
[ "Hello world", "G'day sport!" ],
Expand All @@ -106,4 +103,19 @@ subtest 'populate_template' => sub {

};

sub parse_template_string {
my ( $template_string ) = @_;

return
# remove leading and trailing whitespace
map { my $line = $_;
$line =~ s/(^\s*|\s*$)//g;
$line;
}
# ensure the line has non-whitespace content
grep { /\S/ }
# split on any line break type
split /[\n\r]+/, $template_string;
}

done_testing;
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