From c138254c14da8528f7b2cbb763867499a53d67c7 Mon Sep 17 00:00:00 2001 From: zaynab butt Date: Thu, 25 Jan 2024 11:43:16 +0000 Subject: [PATCH] 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 1f42adc..b714928 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 bb26531..b283d8d 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 e7520c1..0c6afba 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 035f61e..69eeff0 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 206c46a..95a1ba2 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