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] 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 4cf1a59..1f42adc 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 f8a67d2..9961ca8 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 bbe8895..3ebfb82 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