Merge pull request #755 from wtsi-npg/devel

pull from devel to master to create release 97.0.0

.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
+      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
+      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_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

Changes

@@ -1,5 +1,17 @@
 LIST OF CHANGES
 
+release 97.0.0
+ - Change CI workflow to standard file name
+ - Change to Perl versions from Perlbrew
+ - Add Perl 5.34.1 to the test matrix
+ - Switched the default LIMS driver in samplesheet generation from 'xml'
+   to 'ml_warehouse'.
+ - Added 'lims_driver_type' attribute to npg::samplesheet.
+ - Updated the tests for samplesheet generation, which are using the xml
+   LIMS driver, to set the driver type explicitly.
+ - In samplesheet generation, dropped a special case of MiSeq instruments
+   without a batch; last use in production was over 5 years ago.
+
 release 96.0.0
  - Fixed a regression in the npg_move_runfolder script,
    which made it unusable.

MANIFEST

@@ -1,4 +1,3 @@
-.github/workflows/testing_and_building_repos.yml
 bin/event_notifications
 bin/illumina_instruments_uptime
 bin/npg_daemon_control
@@ -1468,6 +1467,5 @@ t/useragent.pm
 t/util.pm
 wtsi_local/httpd.conf
 wtsi_local/httpd_sfweb.conf
-
 META.yml
 META.json

lib/npg/samplesheet.pm

@@ -15,6 +15,7 @@ use st::api::lims;
 use st::api::lims::samplesheet;
 use npg_tracking::util::config qw(get_config_staging_areas);
 use npg_tracking::util::abs_path qw(abs_path);
+use WTSI::DNAP::Warehouse::Schema;
 
 with 'npg_tracking::glossary::run';
 
@@ -62,12 +63,25 @@ still retained in the relevant custom fields.
 my$config=get_config_staging_areas();
 Readonly::Scalar my $SAMPLESHEET_PATH => $config->{'samplesheets'}||q(samplesheets/);
 Readonly::Scalar my $MIN_COLUMN_NUM   => 3;
-Readonly::Scalar my $DEFAULT_LIMS_DRIVER_TYPE => 'xml';
+Readonly::Scalar my $DEFAULT_LIMS_DRIVER_TYPE => 'ml_warehouse';
 
 ##################################################################
 ####################### Public attributes ########################
 ##################################################################
 
+=head2 lims_driver_type
+
+LIMs driver type to use, defaults to ml_warehouse.
+
+=cut
+
+has 'lims_driver_type' => (
+  'isa'      => 'Str',
+  'required' => 0,
+  'is'       => 'ro',
+  'default'  => $DEFAULT_LIMS_DRIVER_TYPE,
+);
+
 =head2 id_run
 
 An optional attribute
@@ -157,6 +171,22 @@ sub _build_npg_tracking_schema {
   return $s
 }
 
+=head2 mlwh_schema
+ 
+DBIx schema class for ml_warehouse access.
+
+=cut
+
+has 'mlwh_schema' => (
+  'isa'        => 'WTSI::DNAP::Warehouse::Schema',
+  'is'         => 'ro',
+  'required'   => 0,
+  'lazy_build' => 1,
+);
+sub _build_mlwh_schema {
+  return WTSI::DNAP::Warehouse::Schema->connect();
+}
+
 =head2 run
 
 An attribute, DBIx object for a row in the run table of the tracking database.
@@ -180,7 +210,6 @@ An attribute, an array of st::api::lims type objects.
 
 This attribute should normally be provided by the caller via the
 constuctor. If the attribute is not provided, it it built automatically.
-XML st::api::lims driver is used to access LIMS data.
 
 =cut
 
@@ -191,17 +220,20 @@ has 'lims' => (
 );
 sub _build_lims {
   my $self=shift;
-  my $id = $self->run->batch_id;
-  if ($id=~/\A\d{13}\z/smx) {
-    load_class 'st::api::lims::warehouse';
-    return [st::api::lims->new(
-      position => 1,
-      driver   => st::api::lims::warehouse->new(position=>1, tube_ean13_barcode=>$id)
-    )];
+
+  my $ref = {driver_type => $self->lims_driver_type};
+  my $batch_id = $self->run->batch_id;
+  if ($self->lims_driver_type eq $DEFAULT_LIMS_DRIVER_TYPE) {
+    $ref->{'id_flowcell_lims'} = $batch_id;
+    $ref->{'mlwh_schema'} = $self->mlwh_schema;
+  } elsif ($self->lims_driver_type eq 'xml') {
+    $ref->{'batch_id'} = $batch_id;
+  } else {
+    croak sprintf 'Lazy-build for driver type %s is not inplemented',
+      $self->lims_driver_type;
   }
-  return [st::api::lims->new(
-            batch_id => $id,
-            driver_type => $DEFAULT_LIMS_DRIVER_TYPE)->children];
+
+  return [st::api::lims->new($ref)->children];
 };
 
 =head2 output
@@ -592,6 +624,8 @@ __END__
 
 =item open
 
+=item WTSI::DNAP::Warehouse::Schema
+
 =back
 
 =head1 INCOMPATIBILITIES
@@ -604,7 +638,7 @@ David K. Jackson E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2019,2020 Genome Research Ltd.
+Copyright (C) 2019,2020, 2023 Genome Research Ltd.
 
 This file is part of NPG.