Merge pull request #18 from jmtcsngr/devel

merge from devel to master

.github/workflows/perlbrew.sha256

@@ -0,0 +1 @@
+c3996e4fae37a0ae01839cdd73752fb7b17e81bac2a8b39712463a7d518c4945  perlbrew.sh

.github/workflows/run-tests.yml

@@ -0,0 +1,127 @@
+name: "Unit tests"
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l -e -o pipefail {0}
+
+    env:
+      PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
+      NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
+      WSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
+      WSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
+
+
+    strategy:
+      matrix:
+        perl: ["5.26.3", "5.34.1"]
+
+    services:
+       mysql:
+         image: mysql:8.0
+         ports:
+           - 3306:3306
+         env:
+           MYSQL_ALLOW_EMPTY_PASSWORD: yes
+           MYSQL_ROOT_PASSWORD: null
+           MYSQL_DATABASE: npgt
+         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=10s --health-retries=5 
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Change dbhost to 127.0.0.1
+        run: |
+            sed -i s/localhost/127.0.0.1/ ${GITHUB_WORKSPACE}/data/config.ini
+
+      - name: set timezone
+        run: |
+            sudo timedatectl set-timezone Europe/London 
+
+      - name: "Install OS dependencies"
+        run: |
+          sudo apt-get update
+          # https://github.com/actions/runner-images/issues/2139
+          sudo apt-get remove -y nginx libgd3
+          sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl
+
+      - name: "Cache Perl"
+        id: cache-perl
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.PERL_CACHE }}
+          key: ${{ runner.os }}-${{ matrix.perl }}-perl
+
+      - name: "Install Perlbrew"
+        if: steps.cache-perl.outputs.cache-hit != 'true'
+        run: |
+          curl -sSL https://install.perlbrew.pl -o perlbrew.sh
+          sha256sum -c .github/workflows/perlbrew.sha256
+          export PERLBREW_ROOT=${{ env.PERL_CACHE }}
+          sh perlbrew.sh
+            
+          source ${{ env.PERL_CACHE }}/etc/bashrc
+          perlbrew available
+          perlbrew install --notest perl-${{ matrix.perl }}
+          perlbrew use perl-${{ matrix.perl }}
+          perlbrew install-cpanm
+
+      - name: "Initialize Perlbrew"
+        run: |
+          echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile"
+
+      - name: "Install Perl dependencies"
+        run: |
+          cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          
+          cpanm --quiet --notest Module::Build
+          cpanm --quiet --notest Alien::Tidyp
+          
+          ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
+             perl-dnap-utilities \
+             ml_warehouse
+
+          cpanm --installdeps --notest .
+
+      - name: "Log install failure"
+        if: ${{ failure() }}
+        run: |
+          find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
+
+      - name: "Archive CPAN logs on failure"
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: cpan_log
+          path: ~/.cpanm/work/*/build.log
+          retention-days: 5
+
+      - name: "Run tests"
+        run: |
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          
+          export TEST_AUTHOR=1
+          perl Build.PL
+          ./Build test --verbose
+          ./Build install
+
+      - name: "Build distribution"
+        run: |
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          export TEST_AUTHOR=1
+          
+          ./Build dist
+          export DIST_FILE=$(ls npg-tracking-*.tar.gz)
+          export MD5_FILE=$DIST_FILE.md5
+          md5sum $DIST_FILE > $MD5_FILE
+          export SHA256_FILE=$DIST_FILE.sha256
+          shasum -a 256 $DIST_FILE > $SHA256_FILE

Build.PL

@@ -121,24 +121,25 @@ my $builder = $class->new(
                 'base'                            => '2.12',
                 'Carp'                            => '1.04',
                 'CGI'                             => '3.52',
-                'Class::Accessor'                 => '0.31',
                 'Class::Load'                     => 0,
                 'Class::Std'                      => '0.0.8',
                 'ClearPress'                      => '>= 473.3.3',
                 'Config::Any'                     => 0,
                 'Config::Auto'                    => 0,
                 'Crypt::CBC'                      => 0,
                 'Cwd'                             => 0,
+                'Data::UUID'                      => 0,
                 'Date::Parse'                     => '2.27',
                 'DateTime'                        => '0.5',
                 'DateTime::TimeZone'              => 0,
                 'DateTime::Format::MySQL'         => 0,
                 'DateTime::Format::Strptime'      => '1.0702',
-                'DBD::mysql'                      => 0,
+                'DBD::mysql'                      => '== 4.050',
                 'DBI'                             => '1.608',
                 'DBIx::Class'                     => '0.08119',
                 'DBIx::Class::Core'               => 0,
                 'DBIx::Class::Schema'             => 0,
+                'DBIx::Class::Schema::Loader'     => 0,
                 'DBIx::Class::InflateColumn::DateTime' => 0,
                 'Digest::MD5'                     => 0,
                 'Digest::SHA'                     => 0,
@@ -208,9 +209,9 @@ my $builder = $class->new(
                 'SQL::Translator'                 => '0.11006',
                 'Sys::Hostname'                   => '1.11',
                 'Template'                        => '2.19',
+                'Text::CSV'                       => '0',
                 'Try::Tiny'                       => 0,
                 'URI::Escape'                     => 0,
-                'URI::URL'                        => 0,
                 'utf8'                            => 0,
                 'warnings'                        => '1.05',
                 'XML::LibXML'                     => '1.70',
@@ -219,6 +220,7 @@ my $builder = $class->new(
 
                 'WTSI::DNAP::Utilities::Loggable'  => '>= 0.5.3',
                 'WTSI::DNAP::Utilities::Timestamp' => '0',
+                'WTSI::DNAP::Warehouse::Schema'    => '0',
             },
          );