reformatted with black ahhhhhhhhhhhh

wtsi-npg · Jan 12, 2024 · 5d51bec · 5d51bec
1 parent 18b4461
commit 5d51bec
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Showing 3 changed files with 15 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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)]: