Platform news
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Updated packages in R image
In order to add a new package to the R Docker image we had to upgrade some of the existing package versions. Hopefully these upgrades will be welcome but there’s a small possibility they might cause issues with existing code so please be on the look out for this. The…
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Automatically run failed dependencies when submitting jobs
Previously, when submitting jobs to run the platform would reject requests if any of the requested action’s dependencies had previously failed. This required users to explicitly request those failed dependencies to be re-run. This was cumbersome, and was not the same behaviour as when running actions locally on user’s machines…
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Updated disclosure control guidance
We have recently made some updates to our disclosure control guidance. This is important for both researchers requesting release of outputs and those who review them. We have made the following changes, which are summarised in more detail below:
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User, project, and organisation Event Logs added
OpenSAFELY Jobs has been updated with new Event Log pages for users, projects, and organisations. These pages provide specific information about current Job Requests, and allow users to see a complete audit log of all previous Job Requests. Examples of new Event Log pages include: The global OpenSAFELY Job Server…
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New
opensafely cleancommandWe have added a command to the opensafely command line tool: opensafely clean This command will safely remove any leftover OpenSAFELY docker artifacts from your system. Specifically, it removes old images, job containers, and file volumes that may have been created when running jobs locally on a user’s computer. Users who…
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Improved access to OpenSAFELY Jobs from secure environments
OpenSAFELY Jobs is used by researchers from within the secure environments (such as TPP level 4) to support the review and output checking of files. We’ve added an easier way for users to log in to OpenSAFELY Jobs from the TPP secure environment, by implementing auto-generated single use tokens. Previously,…
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Updates to the OpenSAFELY Jobs home page
OpenSAFELY Jobs home page has been updated to create a personalised dashboard for users. Once logged in, users will now be able to view: Alongside the new home page, users are now able to access a personalised list of: For visitors to the website who don’t have an account, a…
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Introducing the
opensafely execcommand for interactive sessionsThere is new opensafely exec command in recent versions of the opensafely tool. It is designed to aid in development of analysis code using the published OpenSAFELY docker images. The need to add your your work-in-progress code to project.yaml in order to test it is awkward. This leads some users to use their own…
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New build of the OpenSAFELY R image
We have just published a new build of the R image. No action needed, but more information below! What has not changed? This is not a semantic change – the same versions of the same set of libraries are installed. However the way the image is built has been reworked, in order to…
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Using compressed data files by default
Using compressed files is now the default recommendation in documentation and templates. On the backends, where datasets can be very large, using uncompressed files significantly slows execution and consumes more disk space. The research-template has been updated to generate csv.gz files from cohortextractor by default, and the examples…
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