From b76b352419e4c57d41d8fed8b7a07b983f22a76e Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 01/14] edit tests for human subset

---
 tests/test_illumina.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_illumina.py b/tests/test_illumina.py
index dd51b9b5..e7bc33c2 100644
--- a/tests/test_illumina.py
+++ b/tests/test_illumina.py
@@ -412,7 +412,7 @@ def test_updates_changed_study_permissions(
 
     @m.context("When data are multiplexed")
     @m.context("When data contain a human subset")
-    @m.it("Removes managed access permissions")
+    @m.it("Update managed access permissions to restricted human access group")
     def test_updates_human_permissions_mx(
         self, illumina_synthetic_irods, illumina_synthetic_mlwh
     ):

From 6c16a95356e6284566bc2a11b55b6a4b8dc3ed5f Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 02/14] add new permissions for human

---
 tests/test_illumina.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_illumina.py b/tests/test_illumina.py
index e7bc33c2..98012d86 100644
--- a/tests/test_illumina.py
+++ b/tests/test_illumina.py
@@ -425,7 +425,10 @@ def test_updates_human_permissions_mx(
             AC("irods", perm=Permission.OWN, zone=zone),
             AC("ss_4000", perm=Permission.READ, zone=zone),
         ]
-        new_permissions = [AC("irods", perm=Permission.OWN, zone=zone)]
+        new_permissions = [
+            AC("irods", perm=Permission.OWN, zone=zone),
+            AC("ss_4000_human", perm=Permission.READ, zone=zone),               
+        ]
 
         for obj in [DataObject(path), DataObject(qc_path)]:
             obj.add_permissions(*old_permissions)

From 43085968b84b6f998183dcfa9c8c8052937e9a12 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 03/14] add human irods group for human subset

---
 src/npg_irods/illumina.py      |  4 ++--
 src/npg_irods/metadata/lims.py | 10 +++++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/npg_irods/illumina.py b/src/npg_irods/illumina.py
index 2067b9ed..4cf1a59c 100644
--- a/src/npg_irods/illumina.py
+++ b/src/npg_irods/illumina.py
@@ -234,7 +234,7 @@ def empty_acl(*args):
         for fc in flowcells:
             secondary_metadata.extend(sample_fn(fc.sample))
             secondary_metadata.extend(study_fn(fc.study))
-            acl.extend(acl_fn(fc.sample, fc.study, zone=zone))
+            acl.extend(acl_fn(c.subset, fc.sample, fc.study, zone=zone))
 
     # Remove duplicates
     secondary_metadata = sorted(set(secondary_metadata))
@@ -248,7 +248,7 @@ def empty_acl(*args):
         cons_update = ensure_consent_withdrawn(item)
     elif any(c.contains_nonconsented_human() for c in components):  # Illumina specific
         log.info("Non-consented human data", path=item)
-        xahu_update = ensure_consent_withdrawn(item)
+        xahu_update = update_permissions(item, acl)
     else:
         perm_update = update_permissions(item, acl)
 
diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index 0346ddda..c618df07 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -168,7 +168,7 @@ def make_reduced_study_metadata(study: Study) -> list[AVU]:
     return [avu_if_value(TrackedStudy.ID, study.id_study_lims)]
 
 
-def make_sample_acl(sample: Sample, study: Study, zone=None) -> list[AC]:
+def make_sample_acl(seq:SeqConcept, sample: Sample, study: Study, zone=None) -> list[AC]:
     """Returns an ACL for a given Sample in a Study.
 
     This method takes into account all factors influencing access control, which are:
@@ -192,8 +192,12 @@ def make_sample_acl(sample: Sample, study: Study, zone=None) -> list[AC]:
     Returns:
         An ACL
     """
-    irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}"
-    perm = Permission.NULL if sample.consent_withdrawn else Permission.READ
+    print(seq)
+    if seq is not None and seq.value == "human":
+        irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}_human"
+    else:
+        irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}"
+    perm = Permission.NULL if sample.consent_withdrawn or (seq is not None and seq.value == "xahuman") else Permission.READ
 
     return [AC(irods_group, perm, zone=zone)]
 

From 70cf526d38ffc112dad1627c7ff93d6d95e95867 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 04/14] add xahuman to testing config

---
 tests/conftest.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tests/conftest.py b/tests/conftest.py
index 50b42191..832bb0f1 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1029,6 +1029,13 @@ def illumina_synthetic_irods(tmp_path):
             *run_pos,
             AVU(tag, 1),
         ),
+        "12345/12345#1_xahuman.cram": (
+            AVU(idp, "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
+            AVU(cmp, '{"id_run":12345, "position":1, "tag_index":1, "subset":"xahuman"}'),
+            AVU(cmp, '{"id_run":12345, "position":2, "tag_index":1, "subset":"xahuman"}'),
+            *run_pos,
+            AVU(tag, 1),
+        ),
         "12345/12345#2.cram": (
             AVU(idp, "0b3bd00f1d186247f381aa87e213940b8c7ab7e5"),
             AVU(cmp, '{"id_run":12345, "position":1, "tag_index":2}'),

From 34b0fca32a04592932fead13183f82b5ccf346ae Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 05/14] reformatted with black ahhhhhhhhhhhh

---
 src/npg_irods/metadata/lims.py | 10 ++++++++--
 tests/conftest.py              |  8 ++++++--
 tests/test_illumina.py         |  2 +-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index c618df07..384369ed 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -168,7 +168,9 @@ def make_reduced_study_metadata(study: Study) -> list[AVU]:
     return [avu_if_value(TrackedStudy.ID, study.id_study_lims)]
 
 
-def make_sample_acl(seq:SeqConcept, sample: Sample, study: Study, zone=None) -> list[AC]:
+def make_sample_acl(
+    seq: SeqConcept, sample: Sample, study: Study, zone=None
+) -> list[AC]:
     """Returns an ACL for a given Sample in a Study.
 
     This method takes into account all factors influencing access control, which are:
@@ -197,7 +199,11 @@ def make_sample_acl(seq:SeqConcept, sample: Sample, study: Study, zone=None) ->
         irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}_human"
     else:
         irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}"
-    perm = Permission.NULL if sample.consent_withdrawn or (seq is not None and seq.value == "xahuman") else Permission.READ
+    perm = (
+        Permission.NULL
+        if sample.consent_withdrawn or (seq is not None and seq.value == "xahuman")
+        else Permission.READ
+    )
 
     return [AC(irods_group, perm, zone=zone)]
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 832bb0f1..e7520c16 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1031,8 +1031,12 @@ def illumina_synthetic_irods(tmp_path):
         ),
         "12345/12345#1_xahuman.cram": (
             AVU(idp, "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
-            AVU(cmp, '{"id_run":12345, "position":1, "tag_index":1, "subset":"xahuman"}'),
-            AVU(cmp, '{"id_run":12345, "position":2, "tag_index":1, "subset":"xahuman"}'),
+            AVU(
+                cmp, '{"id_run":12345, "position":1, "tag_index":1, "subset":"xahuman"}'
+            ),
+            AVU(
+                cmp, '{"id_run":12345, "position":2, "tag_index":1, "subset":"xahuman"}'
+            ),
             *run_pos,
             AVU(tag, 1),
         ),
diff --git a/tests/test_illumina.py b/tests/test_illumina.py
index 98012d86..035f61e9 100644
--- a/tests/test_illumina.py
+++ b/tests/test_illumina.py
@@ -427,7 +427,7 @@ def test_updates_human_permissions_mx(
         ]
         new_permissions = [
             AC("irods", perm=Permission.OWN, zone=zone),
-            AC("ss_4000_human", perm=Permission.READ, zone=zone),               
+            AC("ss_4000_human", perm=Permission.READ, zone=zone),
         ]
 
         for obj in [DataObject(path), DataObject(qc_path)]:

From bcb0804090bdb512025e8234628aecdacc94e702 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 06/14] seqconcept unique to illumina

---
 src/npg_irods/ont.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/npg_irods/ont.py b/src/npg_irods/ont.py
index 3ebfb82e..bbe88956 100644
--- a/src/npg_irods/ont.py
+++ b/src/npg_irods/ont.py
@@ -505,7 +505,7 @@ def _do_secondary_metadata_and_perms_update(
 
     acl = []
     for fc in flowcells:
-        acl.extend(make_sample_acl(fc.sample, fc.study, zone=zone))
+        acl.extend(make_sample_acl(None, fc.sample, fc.study, zone=zone))
 
     recurse = item.rods_type == Collection
     cons_update = perm_update = False

From e6d96461a679db17202777cf596d32848188c0c4 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 07/14] add arg to method comment

---
 src/npg_irods/metadata/lims.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index 384369ed..a141ecc7 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -186,6 +186,7 @@ def make_sample_acl(
     Note that this function does not check that the sample is in the study.
 
     Args:
+        seq: Sequencing terminology, unique to illumina  
         sample: A sample, which will be used to confirm consent, which modifies the
                 ACL.
         study: A study, which will provide permissions for the ACL.
@@ -194,7 +195,6 @@ def make_sample_acl(
     Returns:
         An ACL
     """
-    print(seq)
     if seq is not None and seq.value == "human":
         irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}_human"
     else:

From 5225c1a381e19b3e540046899481cedc8bb7cdcf Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 08/14] black apaaaaaain

---
 src/npg_irods/metadata/lims.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index a141ecc7..e18ef556 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -186,7 +186,7 @@ def make_sample_acl(
     Note that this function does not check that the sample is in the study.
 
     Args:
-        seq: Sequencing terminology, unique to illumina  
+        seq: Sequencing terminology, unique to illumina
         sample: A sample, which will be used to confirm consent, which modifies the
                 ACL.
         study: A study, which will provide permissions for the ACL.

From c3986ec73e79279ddf0f8e6abe0b4f902f342fae Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 09/14] add xahuman

---
 tests/test_locate_data_objects.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_locate_data_objects.py b/tests/test_locate_data_objects.py
index bf36ac71..4582be1e 100644
--- a/tests/test_locate_data_objects.py
+++ b/tests/test_locate_data_objects.py
@@ -20,6 +20,7 @@ def test_illumina_updates(
                 "12345#1.cram",
                 "12345#1_human.cram",
                 "12345#1_phix.cram",
+                "12345#1_xahuman.cram",
                 "12345#2.cram",
                 "12345#888.cram",
                 "12345.cram",

From 0179b839846ee8da4f10deb8ecde87703c1437c8 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 10/14] update comment for right info

---
 src/npg_irods/metadata/lims.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index e18ef556..f8a67d2e 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -186,7 +186,7 @@ def make_sample_acl(
     Note that this function does not check that the sample is in the study.
 
     Args:
-        seq: Sequencing terminology, unique to illumina
+        seq: Platform-independent concepts
         sample: A sample, which will be used to confirm consent, which modifies the
                 ACL.
         study: A study, which will provide permissions for the ACL.

From e7365d6a7e843d532de24577b54adb4350daf1d9 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 10:54:07 +0000
Subject: [PATCH 11/14] make seqsubset optional argument

---
 src/npg_irods/illumina.py      |  2 +-
 src/npg_irods/metadata/lims.py | 17 ++++++++---------
 src/npg_irods/ont.py           |  2 +-
 3 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/src/npg_irods/illumina.py b/src/npg_irods/illumina.py
index 4cf1a59c..1f42adc7 100644
--- a/src/npg_irods/illumina.py
+++ b/src/npg_irods/illumina.py
@@ -234,7 +234,7 @@ def empty_acl(*args):
         for fc in flowcells:
             secondary_metadata.extend(sample_fn(fc.sample))
             secondary_metadata.extend(study_fn(fc.study))
-            acl.extend(acl_fn(c.subset, fc.sample, fc.study, zone=zone))
+            acl.extend(acl_fn(fc.sample, fc.study, c.subset, zone=zone))
 
     # Remove duplicates
     secondary_metadata = sorted(set(secondary_metadata))
diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index f8a67d2e..9961ca80 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -37,7 +37,7 @@
 
 from npg_irods.db.mlwh import Sample, Study
 from npg_irods.metadata.common import (
-    SeqConcept,
+    SeqSubset,
     ensure_avus_present,
     avu_if_value,
 )
@@ -169,7 +169,7 @@ def make_reduced_study_metadata(study: Study) -> list[AVU]:
 
 
 def make_sample_acl(
-    seq: SeqConcept, sample: Sample, study: Study, zone=None
+    sample: Sample, study: Study, subset: SeqSubset=None, zone=None
 ) -> list[AC]:
     """Returns an ACL for a given Sample in a Study.
 
@@ -186,7 +186,7 @@ def make_sample_acl(
     Note that this function does not check that the sample is in the study.
 
     Args:
-        seq: Platform-independent concepts
+        subset: Subset of sequence reads
         sample: A sample, which will be used to confirm consent, which modifies the
                 ACL.
         study: A study, which will provide permissions for the ACL.
@@ -195,15 +195,14 @@ def make_sample_acl(
     Returns:
         An ACL
     """
-    if seq is not None and seq.value == "human":
+    if subset is not None and subset is subset.XAHUMAN:
+        return []
+
+    if subset is not None and subset is subset.HUMAN:
         irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}_human"
     else:
         irods_group = f"{STUDY_IDENTIFIER_PREFIX}{study.id_study_lims}"
-    perm = (
-        Permission.NULL
-        if sample.consent_withdrawn or (seq is not None and seq.value == "xahuman")
-        else Permission.READ
-    )
+    perm = Permission.NULL if sample.consent_withdrawn else Permission.READ
 
     return [AC(irods_group, perm, zone=zone)]
 
diff --git a/src/npg_irods/ont.py b/src/npg_irods/ont.py
index bbe88956..3ebfb82e 100644
--- a/src/npg_irods/ont.py
+++ b/src/npg_irods/ont.py
@@ -505,7 +505,7 @@ def _do_secondary_metadata_and_perms_update(
 
     acl = []
     for fc in flowcells:
-        acl.extend(make_sample_acl(None, fc.sample, fc.study, zone=zone))
+        acl.extend(make_sample_acl(fc.sample, fc.study, zone=zone))
 
     recurse = item.rods_type == Collection
     cons_update = perm_update = False

From b19b85ba4b1585cbd241c04a36be424acecaea34 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 12:10:45 +0000
Subject: [PATCH 12/14] black = pain

---
 src/npg_irods/metadata/lims.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index 9961ca80..5fbea4e8 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -169,7 +169,7 @@ def make_reduced_study_metadata(study: Study) -> list[AVU]:
 
 
 def make_sample_acl(
-    sample: Sample, study: Study, subset: SeqSubset=None, zone=None
+    sample: Sample, study: Study, subset: SeqSubset = None, zone=None
 ) -> list[AC]:
     """Returns an ACL for a given Sample in a Study.
 

From a61a36c4d8efbf1452932f4880951880be8009c9 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Wed, 24 Jan 2024 13:41:25 +0000
Subject: [PATCH 13/14] import SeqConcept

---
 src/npg_irods/metadata/lims.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index 5fbea4e8..bb265319 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -37,6 +37,7 @@
 
 from npg_irods.db.mlwh import Sample, Study
 from npg_irods.metadata.common import (
+    SeqConcept,
     SeqSubset,
     ensure_avus_present,
     avu_if_value,

From c138254c14da8528f7b2cbb763867499a53d67c7 Mon Sep 17 00:00:00 2001
From: zaynab butt <zb3@sanger.ac.uk>
Date: Thu, 25 Jan 2024 11:43:16 +0000
Subject: [PATCH 14/14] update comments

---
 src/npg_irods/illumina.py      | 4 ++--
 src/npg_irods/metadata/lims.py | 4 ++--
 tests/conftest.py              | 2 +-
 tests/test_illumina.py         | 4 ++--
 tests/test_pacbio.py           | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/npg_irods/illumina.py b/src/npg_irods/illumina.py
index 1f42adc7..b7149281 100644
--- a/src/npg_irods/illumina.py
+++ b/src/npg_irods/illumina.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 2024 Genome Research Ltd. All rights reserved.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -234,7 +234,7 @@ def empty_acl(*args):
         for fc in flowcells:
             secondary_metadata.extend(sample_fn(fc.sample))
             secondary_metadata.extend(study_fn(fc.study))
-            acl.extend(acl_fn(fc.sample, fc.study, c.subset, zone=zone))
+            acl.extend(acl_fn(fc.sample, fc.study, subset=c.subset, zone=zone))
 
     # Remove duplicates
     secondary_metadata = sorted(set(secondary_metadata))
diff --git a/src/npg_irods/metadata/lims.py b/src/npg_irods/metadata/lims.py
index bb265319..b283d8da 100644
--- a/src/npg_irods/metadata/lims.py
+++ b/src/npg_irods/metadata/lims.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2021, 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2021, 2022, 2023, 2024 Genome Research Ltd. All rights reserved.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -187,10 +187,10 @@ def make_sample_acl(
     Note that this function does not check that the sample is in the study.
 
     Args:
-        subset: Subset of sequence reads
         sample: A sample, which will be used to confirm consent, which modifies the
                 ACL.
         study: A study, which will provide permissions for the ACL.
+        subset: Subset of sequence reads.
         zone: The iRODS zone.
 
     Returns:
diff --git a/tests/conftest.py b/tests/conftest.py
index e7520c16..0c6afba8 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2020, 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2020, 2022, 2023, 2024 Genome Research Ltd. All rights reserved.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/tests/test_illumina.py b/tests/test_illumina.py
index 035f61e9..69eeff0a 100644
--- a/tests/test_illumina.py
+++ b/tests/test_illumina.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 2024 Genome Research Ltd. All rights reserved.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -412,7 +412,7 @@ def test_updates_changed_study_permissions(
 
     @m.context("When data are multiplexed")
     @m.context("When data contain a human subset")
-    @m.it("Update managed access permissions to restricted human access group")
+    @m.it("Updates managed access permissions to restricted human access group")
     def test_updates_human_permissions_mx(
         self, illumina_synthetic_irods, illumina_synthetic_mlwh
     ):
diff --git a/tests/test_pacbio.py b/tests/test_pacbio.py
index 206c46a4..95a1ba29 100644
--- a/tests/test_pacbio.py
+++ b/tests/test_pacbio.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 2024 Genome Research Ltd. All rights reserved.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by