Merge branch 'master' into PLAT-997-efs-volume-mounting

.github/workflows/check-internal-links.yml

@@ -19,9 +19,12 @@ jobs:
         run: |
           git submodule update --init --recursive
       # Fail the build in PRs, but not for Netlify previews or production builds
-      - name: Replace credentials
+      - name: Fail build on error
         run: |
           sed -Ei 's/onBroken([A-Za-z]+): "warn"/onBroken\1: "throw"/g' docusaurus.config.js
+      - name: Faster builds
+        run: |
+          sed -Ei 's/experimental_faster: "false"/experimental_faster: "true"/g' docusaurus.config.js
       # Install and build Docusaurus website
       - name: Build Docusaurus website
         run: |

changelog/seqera-enterprise/v23.4.0.mdx

@@ -1,6 +1,6 @@
 ---
 title: Seqera Enterprise v23.4.0
-date: 2024-08-02
+date: 2024-02-08
 tags: [seqera enterprise]
 ---
 

changelog/seqera-enterprise/v24.1.3.mdx

@@ -1,6 +1,6 @@
 ---
 title: Seqera Enterprise v24.1.3
-date: 2024-07-01
+date: 2024-08-22
 tags: [seqera enterprise]
 ---
 

changelog/seqera-enterprise/v24.1.4.mdx

@@ -1,6 +1,6 @@
 ---
 title: Seqera Enterprise v24.1.4
-date: 2024-07-01
+date: 2024-08-21
 tags: [seqera enterprise]
 ---
 

changelog/seqera-enterprise/v24.1.7.mdx

@@ -1,6 +1,6 @@
 ---
 title: Seqera Enterprise v24.1.7
-date: 2024-10-03
+date: 2024-11-03
 tags: [seqera enterprise]
 ---
 

changelog/seqera-enterprise/v24.1_major.mdx

@@ -0,0 +1,96 @@
+---
+title: Seqera Enterprise v24.1_major
+date: 2024-07-04
+tags: [seqera enterprise]
+---
+
+Seqera Platform Enterprise version 24.1 introduces three new features: Data Studios (in public preview), Data Explorer, and managed identities. A number of bug fixes and performance enhancements are included in this major release.
+
+## Data Studios
+
+[Data Studios](https://docs.seqera.io/platform/24.2/data_studios) closes the loop from development to deployment and insights, allowing you to create, manage, and share notebook environments in Seqera with the click of a button. Data Studios makes it seamless to work across teams with multi-user support, built-in authentication, and automatic snapshots as you work.
+
+- Host a combination of container images and compute environments for interactive analysis using your preferred tools, like Jupyter notebooks, RStudio, and Visual Studio Code IDEs.
+- Checkpoints provide a stable point-in-time snapshot.
+- Collaborate and share data in real time.
+
+Data Studios is available as a public preview. [Contact support](https://support.seqera.io) to request access to this feature. 
+
+## Data Explorer
+
+[Data Explorer](https://docs.seqera.io/platform/24.2/data/data-explorer) allows you to browse and interact with remote data repositories from organization workspaces in Seqera Platform. It supports AWS S3, Azure Blob Storage, and Google Cloud Storage repositories.
+
+Data Explorer is now Generally Available (GA) and supports multi-file and multi-folder download. This allows users to download entire datasets of pipeline results to share with their team.
+
+## Extended data roles
+
+User roles provide flexibility for admins to provide users with the permissions they need, without compromising security. The **Connect** user role has been added to the existing user roles with functionality related to Data Studios:
+
+- **Connect**: Open a connection to a running data studio session and interact with the contents.
+- **Maintain**: Create, update, start, stop, configure, and delete data studio sessions.
+- **View**: List, search, and view the status, configuration, and details of data studios.
+- **Launch**: Open a connection to a running data studio session and interact with the contents.
+
+See [User roles](https://docs.seqera.io/platform/24.2/orgs-and-teams/roles) for more information.
+
+## Managed identities
+
+Managed identities offer significant advantages for High-Performance Computing (HPC) environments by enabling granular access control for individual workspace users. Unlike traditional SSH credentials that grant all workspace users access to HPC clusters with the same service account, managed identities ensure each user’s activity is logged under their own credentials.
+
+See [Managed identities](https://docs.seqera.io/platform/24.2/credentials/managed_identities) for more information. 
+
+## Other feature improvements
+
+- A redesigned [pipeline launch form](https://docs.seqera.io/platform/24.2/getting-started/quickstart-demo/launch-pipelines) provides an improved workflow and an interface to create and edit run parameters as raw JSON/YAML. Enable the new launch form per workspace via [environment variable](https://docs.seqera.io/platform/24.2/enterprise/configuration/overview#core-features).
+- Retrieve reports from primary compute environment on Nextflow CLI runs. See [Configure reports for Nextflow CLI runs](https://docs.seqera.io/platform/24.2/reports/overview#configure-reports-for-nextflow-cli-runs) for more information. 
+- The standard email login can be disabled via `tower.yml` or an environment variable, provided an alternative OIDC provider is set up first. See [Basic configuration](https://docs.seqera.io/platform/24.2/enterprise/configuration/overview#basic-configuration) for more information.
+
+## Breaking changes
+
+**MariaDB driver: New MySQL connection parameter required**
+
+MariaDB driver 3.x requires a special parameter in the connection URL to connect to a MySQL database:
+
+`jdbc:mysql://<domain>:<port>/tower?permitMysqlScheme=true`
+
+All deployments using a MySQL database (regardless of version: 5.6, 5.7, or 8) should be updated accordingly when upgrading to Platform version 24.1 or later.
+
+**MariaDB driver: No truncation support for MySQL 5.6**
+
+The MariaDB driver has dropped support for the `jdbcCompliantTruncation` parameter, which was true by default and set the `STRICT_TRANS_TABLES` SQL mode. The `STRICT_TRANS_TABLES` mode produces an error when the value of a VARCHAR column exceeds its limit, instead of truncating it to fit. Most common installations of MySQL 5.7 and 8 already include this mode at the server level, but the Docker container version of MySQL 5.6 does not.
+
+The SQL mode must be set explicitly through the connection URL for deployments still using MySQL 5.6:
+
+`jdbc:mysql://<domain>:<port>/tower?permitMysqlScheme=true&sessionVariables=sql_mode='STRICT_TRANS_TABLES,NO_ENGINE_SUBSTITUTION'`
+
+**Micronaut property key changes**
+
+The property that determines the expiration time of the JWT access token (used for authenticating web sessions and Nextflow-Platform interactions) has changed:
+
+| Previous                                                         | New                                                          |
+| ---------------------------------------------------------------- | ------------------------------------------------------------ |
+| `micronaut.security.token.jwt.generator.access-token.expiration` | `micronaut.security.token.generator.access-token.expiration` |
+
+Enterprise deployments that have customized this value previously will need to adopt the new format.
+
+## Upgrade steps 
+
+1. This version includes an update to the Platform Enterprise H8 cache. **Do not start the upgrade while any pipelines are in a `running` state as active run data may be lost.**
+1. This version requires a database schema update. Make a backup of your Platform database prior to upgrade.
+1. If you are upgrading from a version older than 23.4.1, update your installation to version [23.4.4](https://docs.seqera.io/changelog/seqera-enterprise/v23.4_major) first, before updating to 24.1 with the steps below.
+1. For recommended Platform memory settings, add the following environment variable to your Platform configuration values (`tower.env`, `configmap.yml`, etc.):
+    ```bash 
+    JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144
+    ```
+1. See [Upgrade installation](https://docs.seqera.io/platform/24.2/enterprise/upgrade) for database backup and installation upgrade guidance.
+
+:::info
+Docker Compose deployments require downtime while upgrading services. Restarting the application may take several minutes. See [Docker compose deployment](https://docs.seqera.io/platform/24.2/enterprise/docker-compose) for more information.
+
+For Kubernetes deployments, apply the 24.1 `tower-cron.yml` to your cron pod and wait for the cron pod to be running before applying the `tower-svc.yml` to your backend pod and restarting the service. If the cron pod update is interrupted, you may need to restore the instance from your DB backup and start again. See [Kubernetes deployment](https://docs.seqera.io/platform/24.2/enterprise/kubernetes) for more information. 
+
+For custom deployments with third-party services such as ArgoCD, [contact support](https://support.seqera.io) for assistance during upgrade. 
+::: 
+
+
+[gcp-vm-instance-template]: https://cloud.google.com/compute/docs/instance-templates

platform_versioned_docs/version-24.1/enterprise/_images/README.md

@@ -0,0 +1,6 @@
+# Source locations
+
+The images under this folder are both generated from source files in the Seqera company Google Drive. If you're a Seqera employee, search for the following in Google Drive for the respective source files:
+
+- "Seqera reference architecture" for the source file of 'seqera_reference_architecture.png'.
+- "References, Architectures & Diagrams" for the source file of 'seqera_reference_architecture_aws.png'.

platform_versioned_docs/version-24.2/data_studios/index.mdx

@@ -106,6 +106,17 @@ Checkpoint files in the compute environment work directory may be shared by mult
 The cleanup process is a best effort and not guaranteed. Seqera attempts to remove the checkpoint, but it can fail if, for example, the compute environment credentials used do not have sufficient permissions to delete objects from storage buckets.
 :::
 
+## Session volume automatic resizing
+
+By default, a session allocates an initial 2 GB of storage. Available disk space is continually monitored and if the available space drops below a 1 GB threshold, the file system is dynamically-resized to include an additional 2 GB of available disk space.
+
+This approach ensures that a session doesn't initially include unnecessary free disk space, while providing the flexibility to accommodate installation of large software packages required for data analysis.
+
+The maximum storage allocation for a session is limited by the compute environment disk boot size. By default, this is 30 GB. This limit is shared by all sessions running in the same compute environment.
+
+If the maximum allocation size is reached, it is possible to reclaim storage space using a snapshot. 
+
+Stop the active session to trigger a snapshot from the active volume. Data Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space.
 
 <!-- links -->
 [contact]: https://support.seqera.io/

platform_versioned_docs/version-24.2/enterprise/_images/README.md

@@ -0,0 +1,6 @@
+# Source locations
+
+The images under this folder are both generated from source files in the Seqera company Google Drive. If you're a Seqera employee, search for the following in Google Drive for the respective source files:
+
+- "Seqera reference architecture" for the source file of 'seqera_reference_architecture.png'.
+- "References, Architectures & Diagrams" for the source file of 'seqera_reference_architecture_aws.png'.

platform_versioned_docs/version-24.2/troubleshooting_and_faqs/data_studios_troubleshooting.mdx

@@ -39,10 +39,5 @@ The running container in the AWS Batch compute environment inherits the memory l
 
 By default, AWS Batch compute environments that are created with Batch Forge restrict access to S3 to the working directory only, unless additional **Allowed S3 Buckets** are specified. If the compute environment does not have write access to the mounted dataset, it will be mounted as read-only.
 
-## Allocated storage for the data studio is exceeded
-
-A data studio is allocated a 5 GB overlay filesystem partition by default for installing software packages and other local configuration. This limit is irrespective of the boot disk size of the container. If you exceed the available storage space, you cannot reliably make local changes to the data studio container until you free up disk space.
-
-Each time you stop and start a data studio, an additional 5 GB allocation is provided. If you are experiencing a disk size limitation, as a workaround you can stop and restart the data studio.
 
 [contact]: https://seqera.io/contact-us/