pull from devel to master to create Release 3.24.1

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Referenced from:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/run-tests.yml

@@ -71,7 +71,7 @@ jobs:
           # singularity so that paths used are misleading/unclear
 
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: "Install OS dependencies"
         run: |
@@ -94,7 +94,7 @@ jobs:
           echo DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/$(id -u)/bus" >> $GITHUB_ENV
 
       - name: "Cache Singularity images"
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.SINGULARITY_CACHEDIR }}
           key: ${{ runner.os }}-singularity
@@ -134,18 +134,16 @@ jobs:
 
       - name: "Cache Perl"
         id: cache-perl
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         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
+          ./scripts/install_perlbrew.sh
 
           source ${{ env.PERL_CACHE }}/etc/bashrc
           perlbrew available

Changes

@@ -1,5 +1,20 @@
 Unreleased 
 
+Release 3.24.1 (2024-10-04)
+
+ - Fix handling of undefined data release strategy
+ - Improve error handling when listing collections (add early returns).
+ - Move Perlbrew install to a script so that it can be used by both
+   GitHub Actions and Docker.
+ - Added .github/dependabot.yml file to auto-update GitHub actions
+ - Following a release on 07/09/2024, see https://metacpan.org/dist/App-perlbrew/changes
+   the checksum of the script served by https://install.perlbrew.pl had changed.
+   https://install.perlbrew.pl is a redirect to raw
+   https://github.com/gugod/App-perlbrew/blob/master/perlbrew-install, so
+   the change originates from GitHub and can be trusted. Our CI flow compares
+   the checksum of the downloaded script to the expected value. We now store
+   an updated expected checksum value, which corresponds to the latest release.
+
 Release 3.24.0 (2024-09-02)
 
  - populate_wtsi_irods_groups now sets ss_<STUDY_ID>_human group membership if

bin/populate_wtsi_irods_groups.pl

@@ -166,7 +166,8 @@ sub _uid_to_irods_uid {
     @members = map { _uid_to_irods_uid($_) }
                map { @{ $group2uids->{$_} || [$_] } } @dags;
   }
-  elsif ($study->data_release_strategy ne $MANAGED_TYPE) {
+  elsif (defined $study->data_release_strategy and
+    $study->data_release_strategy ne $MANAGED_TYPE) {
     @members = @public;
   }
   else {

lib/WTSI/NPG/iRODS/BatonClient.pm

@@ -918,37 +918,35 @@ sub _list_collection {
   my $response = $self->communicate($spec);
   $self->validate_response($response);
 
-  my @all_specs;
+  if ($response->{error}) {
+    if ($response->{error}->{code} == $ITEM_DOES_NOT_EXIST) {
+      return (undef, undef);
+    }
 
-  if ($response->{error} &&
-      $response->{error}->{code} == $ITEM_DOES_NOT_EXIST) {
-    @all_specs = (undef, undef);
+    $self->logconfess('Error listing collection: ', $self->encode($response));
   }
-  else {
-    my @object_specs;
-    my @collection_specs;
 
-    if (!exists $response->{contents}) {
-      $self->logconfess('The returned path spec did not have ',
-                        'a "contents" key: ', $self->encode($response));
-    }
+  my @object_specs;
+  my @collection_specs;
 
-    my @contents = @{delete $response->{contents}};
-    push @collection_specs, $response;
+  if (!exists $response->{contents}) {
+    $self->logconfess('The returned path spec did not have ',
+      'a "contents" key: ', $self->encode($response));
+  }
 
-    foreach my $path (@contents) {
-      if (exists $path->{data_object}) {
-        push @object_specs, $path;
-      }
-      else {
-        push @collection_specs, $path;
-      }
-    }
+  my @contents = @{delete $response->{contents}};
+  push @collection_specs, $response;
 
-    @all_specs = (\@object_specs, \@collection_specs);
+  foreach my $path (@contents) {
+    if (exists $path->{data_object}) {
+      push @object_specs, $path;
+    }
+    else {
+      push @collection_specs, $path;
+    }
   }
 
-  return @all_specs;
+  return (\@object_specs, \@collection_specs);
 }
 
 # Return two arrays of path specs, given a collection path to recurse

scripts/install_perlbrew.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+set -ex
+
+PERLBREW_ROOT=${PERLBREW_ROOT:-"/app/perlbrew"}
+export PERLBREW_ROOT
+
+PERLBREW_SHA256="8f254651d2eee188199b3355228eb67166974716081b794ca93b69c8f949c38d"
+curl -sSL https://install.perlbrew.pl -o ./perlbrew.sh
+sha256sum ./perlbrew.sh | grep "$PERLBREW_SHA256"
+/bin/bash ./perlbrew.sh
+rm ./perlbrew.sh

scripts/perlbrew.sha256

@@ -0,0 +1 @@
+8f254651d2eee188199b3355228eb67166974716081b794ca93b69c8f949c38d  perlbrew.sh