From 9d8d6076eef416db7614bb55ff48cbd48dfb40d5 Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Fri, 15 Dec 2023 10:13:01 +0000
Subject: [PATCH] Dropped platform-specific ACL rules.

This pr builds on
https://github.com/wtsi-npg/perl-irods-wrap/pull/297,
where all existing rules are consolidated in one method.
---
 lib/WTSI/NPG/HTS/Illumina/AlnDataObject.pm    | 66 -------------------
 .../NPG/HTS/Illumina/AlnDataObjectTest.pm     | 52 ++++-----------
 2 files changed, 12 insertions(+), 106 deletions(-)

diff --git a/lib/WTSI/NPG/HTS/Illumina/AlnDataObject.pm b/lib/WTSI/NPG/HTS/Illumina/AlnDataObject.pm
index dabee96f..c2efff8f 100644
--- a/lib/WTSI/NPG/HTS/Illumina/AlnDataObject.pm
+++ b/lib/WTSI/NPG/HTS/Illumina/AlnDataObject.pm
@@ -156,72 +156,6 @@ sub reference {
   return $reference;
 }
 
-=head2 contains_nonconsented_human
-
-  Arg [1]      None
-
-  Example    : $obj->contains_nonconsented_human
-  Description: Return true if the file contains human data not having
-               explicit consent. This is indicated by alignment results
-               returned by the subset method.
-
-  Returntype : Bool
-
-=cut
-
-sub contains_nonconsented_human {
-  my ($self) = @_;
-
-  my $contains_nonconsented_human =
-    any { $_->has_subset and ($_->subset eq $HUMAN or
-                              $_->subset eq $XAHUMAN)
-        } $self->composition->components_list;
-
-  if ($contains_nonconsented_human) {
-    $self->debug('subset indicates onconsented human sequence in ',
-                 $self->str);
-  }
-
-  return $contains_nonconsented_human;
-}
-
-override 'update_group_permissions' => sub {
-  my ($self, $strict_groups) = @_;
-
-  # super must be called explicitly in order to fire the before/after
-  # methods on update_group_permissions (these are defined in the
-  # superclass)
-  super();
-
-  if ($self->contains_nonconsented_human) {
-    my $path = $self->str;
-
-    my @groups = $self->get_groups($WTSI::NPG::iRODS::READ_PERMISSION);
-    $self->info('Ensuring permissions removed for nonconsented human on ',
-                "'$path': for groups ", pp(\@groups));
-    my @failed_groups;
-
-    foreach my $group (@groups) {
-      try {
-        $self->set_permissions($WTSI::NPG::iRODS::NULL_PERMISSION, $group);
-      } catch {
-        push @failed_groups, $group;
-        $self->error("Failed to remove permissions for group '$group' from ",
-                     "'$path': ", $_);
-      };
-    }
-
-    my $num_groups = scalar @groups;
-    my $num_errors = scalar @failed_groups;
-    if ($num_errors > 0) {
-      $self->logcroak("Failed to remove $num_errors / $num_groups group ",
-                      "permissions from '$path': ", pp(\@failed_groups));
-    }
-  }
-
-  return $self;
-};
-
 sub _build_composition {
   my ($self) = @_;
 
diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm
index bf0865b9..b7db088c 100644
--- a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm
+++ b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm
@@ -179,13 +179,20 @@ sub setup_test : Test(setup) {
 
         my $num_reads = 10000;
 
-        my @avus;
-        push @avus, TestAnnotator->new->make_primary_metadata
-          ($obj->composition,
+        my $composition = $obj->composition;
+        my $component = $composition->get_component(0);
+        my %args = (
            is_paired_read => 1,
            is_aligned     => $obj->is_aligned,
            num_reads      => $num_reads,
-           reference      => $obj->reference);
+           reference      => $obj->reference, 
+        );
+        my $ta = TestAnnotator->new();
+
+        my @avus;
+        push @avus, $ta->make_primary_metadata($composition, %args),
+          $ta->make_alignment_metadata(
+            $component, $num_reads, $obj->reference, $obj->is_aligned);
 
         foreach my $avu (@avus) {
           my $attribute = $avu->{attribute};
@@ -259,41 +266,6 @@ sub position : Test(12) {
   }
 }
 
-sub contains_nonconsented_human : Test(12) {
-  my $irods = WTSI::NPG::iRODS->new(environment          => \%ENV,
-                                    strict_baton_version => 0);
-
-  foreach my $format (qw[bam cram]) {
-    foreach my $path (sort grep { /17550/ } keys %file_composition) {
-      my $full_path = "/seq/17550/$path.$format";
-      my @initargs = _build_initargs(\%file_composition, $path);
-
-      my $obj = WTSI::NPG::HTS::Illumina::AlnDataObject->new
-        ($irods, $full_path, @initargs);
-
-      my $ss = $obj->subset;
-      if (not $ss) {
-        ok(!$obj->contains_nonconsented_human,
-           "$full_path is not nonconsented human");
-      }
-      elsif ($ss eq 'nonhuman' or
-             $ss eq 'yhuman'   or
-             $ss eq 'phix') {
-        ok(!$obj->contains_nonconsented_human,
-           "$full_path is not nonconsented human ($ss)");
-      }
-      elsif ($ss eq 'human' or
-             $ss eq 'xahuman') {
-        ok($obj->contains_nonconsented_human,
-           "$full_path is nonconsented human ($ss)");
-      }
-      else {
-        fail "Unexpected alignment_filter '$ss'";
-      }
-    }
-  }
-}
-
 sub is_restricted_access : Test(12) {
   my $irods = WTSI::NPG::iRODS->new(environment          => \%ENV,
                                     strict_baton_version => 0);
@@ -423,7 +395,7 @@ sub nonconsented_human_access_revoked : Test(6) {
                           expected_groups_before => [$public_group,
                                                      'ss_10',
                                                      'ss_100'],
-                          expected_groups_after  => [] # all access removed
+                          expected_groups_after  => ['ss_619_human']
                          });
   }
 }