From d4ef6406de9e2f21bc705a85ddea8c50598f985e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Jul 2024 18:50:29 +0000 Subject: [PATCH 1/7] Bump setuptools from 68.2.2 to 70.0.0 Bumps [setuptools](https://github.com/pypa/setuptools) from 68.2.2 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](https://github.com/pypa/setuptools/compare/v68.2.2...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index e5c5957..5be56f3 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1545,11 +1545,12 @@ }, "setuptools": { "hashes": [ - "sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87", - "sha256:b454a35605876da60632df1a60f736524eb73cc47bbc9f3f1ef1b644de74fd2a" + "sha256:54faa7f2e8d2d11bcd2c07bed282eef1046b5c080d1c32add737d7b5817b1ad4", + "sha256:f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0" ], + "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==68.2.2" + "version": "==70.0.0" }, "sevenbridges-python": { "hashes": [ From 636409d18e3fcb3831058537a0d206b0d2990d4e Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Tue, 16 Jul 2024 11:26:32 -0600 Subject: [PATCH 2/7] [IBCDPE-1006] Upgrades to v24.1.1 This PR upgrades our tower_version to v24.1.1. This will introduce a change which prevents compute environments from failing to be created. --- config/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/config.yaml b/config/config.yaml index 0700274..b7d49b1 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -3,7 +3,7 @@ profile: {{ var.profile | default() }} region: {{ var.region | default("us-east-1") }} aws_infra_templates_root_url: https://raw.githubusercontent.com/Sage-Bionetworks/aws-infra admincentral_cf_bucket: bootstrap-awss3cloudformationbucket-19qromfd235z9 -tower_version: v23.4.3 +tower_version: v24.1.1 default_stack_tags: Department: IBC Project: Infrastructure From 47bc308c7b90e42fe54b8194915d6d879eab4114 Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Tue, 16 Jul 2024 13:48:09 -0600 Subject: [PATCH 3/7] [IBCDPE-1006] Updates mysql DBUrl This adds a missing parameter to the TOWER_DB_URL. Documentation from Seqera [here](https://docs.seqera.io/platform/24.1.1/enterprise/release_notes/enterprise_latest#breaking-changes). --- templates/nextflow-aurora-mysql.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/nextflow-aurora-mysql.yaml b/templates/nextflow-aurora-mysql.yaml index bedd1b6..ac53365 100644 --- a/templates/nextflow-aurora-mysql.yaml +++ b/templates/nextflow-aurora-mysql.yaml @@ -406,7 +406,7 @@ Outputs: Value: !Join - '' - - !Sub 'jdbc:mysql://${AuroraCluster.Endpoint.Address}:' - - !Sub '${AuroraCluster.Endpoint.Port}/${DBName}' + - !Sub '${AuroraCluster.Endpoint.Port}/${DBName}?permitMysqlScheme=true' Export: Name: !Sub '${AWS::Region}-${AWS::StackName}-DBUrl' From 4011501bbfd367e55f35b9ceca3ce917e63345eb Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Wed, 17 Jul 2024 13:30:02 -0600 Subject: [PATCH 4/7] [IBCDPE-1017] Adds Vesteinn Thorsson (ISB) to `iatlas-project` This PR adds access to the `iatlas-project` workspace for Vesteinn Thorsson (PI at ISB). --- config/projects-prod/iatlas-project.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/config/projects-prod/iatlas-project.yaml b/config/projects-prod/iatlas-project.yaml index 4cecd0f..1c68f5b 100644 --- a/config/projects-prod/iatlas-project.yaml +++ b/config/projects-prod/iatlas-project.yaml @@ -22,6 +22,7 @@ parameters: - "{{stack_group_config.tower_viewer_arn_prefix}}/steven_vensko@med.unc.edu" - "{{stack_group_config.tower_viewer_arn_prefix}}/cheimann@isbscience.org" - "{{stack_group_config.tower_viewer_arn_prefix}}/clarisse.lau@isbscience.org" + - "{{stack_group_config.tower_viewer_arn_prefix}}/vesteinn.thorsson@isbscience.org" AccountAdminArns: - "{{stack_group_config.sso_admin_role.arn}}" - !stack_output_external sagebase-github-oidc-workflows-prod-nextflow-infra::ProviderRoleArn From cfba5272b1e3e035c374fe1628401f1870afc794 Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Wed, 17 Jul 2024 13:32:13 -0600 Subject: [PATCH 5/7] Update nextflow-tower-config-bucket.yaml --- templates/nextflow-tower-config-bucket.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/templates/nextflow-tower-config-bucket.yaml b/templates/nextflow-tower-config-bucket.yaml index 4877337..e22dbf2 100644 --- a/templates/nextflow-tower-config-bucket.yaml +++ b/templates/nextflow-tower-config-bucket.yaml @@ -69,6 +69,7 @@ Resources: - "*@sagebionetworks.org" - "cheimann@isbscience.org" - "clarisse.lau@isbscience.org" + - "vesteinn.thorsson@isbscience.org" trustedEmails: - "benjamin_vincent@med.unc.edu" - "dbortone@email.unc.edu" From 00360464ba948ce78799834245a40bbb53907219 Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Wed, 17 Jul 2024 13:37:28 -0600 Subject: [PATCH 6/7] remove project access for clarisse --- config/projects-prod/iatlas-project.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/config/projects-prod/iatlas-project.yaml b/config/projects-prod/iatlas-project.yaml index 1c68f5b..16e875a 100644 --- a/config/projects-prod/iatlas-project.yaml +++ b/config/projects-prod/iatlas-project.yaml @@ -21,7 +21,6 @@ parameters: - "{{stack_group_config.tower_viewer_arn_prefix}}/dbortone@email.unc.edu" - "{{stack_group_config.tower_viewer_arn_prefix}}/steven_vensko@med.unc.edu" - "{{stack_group_config.tower_viewer_arn_prefix}}/cheimann@isbscience.org" - - "{{stack_group_config.tower_viewer_arn_prefix}}/clarisse.lau@isbscience.org" - "{{stack_group_config.tower_viewer_arn_prefix}}/vesteinn.thorsson@isbscience.org" AccountAdminArns: - "{{stack_group_config.sso_admin_role.arn}}" From 636a92c722992bebca4d5a71ee00fc405a494c03 Mon Sep 17 00:00:00 2001 From: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Date: Wed, 17 Jul 2024 13:38:00 -0600 Subject: [PATCH 7/7] remove allow-list access for clarisse --- templates/nextflow-tower-config-bucket.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/templates/nextflow-tower-config-bucket.yaml b/templates/nextflow-tower-config-bucket.yaml index e22dbf2..43893c4 100644 --- a/templates/nextflow-tower-config-bucket.yaml +++ b/templates/nextflow-tower-config-bucket.yaml @@ -68,7 +68,6 @@ Resources: - "*@sagebase.org" - "*@sagebionetworks.org" - "cheimann@isbscience.org" - - "clarisse.lau@isbscience.org" - "vesteinn.thorsson@isbscience.org" trustedEmails: - "benjamin_vincent@med.unc.edu"