Releases

Version 111.1 by chaney08 on 2022/03/22 19:26

Collaboratory 2 release (2022-03-22) (Released)

Collaboratory.Lab

  • Improved environment variables (more details in FAQ):
    • Added variables for the Docker image version
    • Support for environment variables has been added for URLs specifying an execution site (e.g. lab.ch.ebrains.eu/...). Up to now, environment variables were only supported fo URLs to the generic lab.ebrains.eu/...
  • Added a new extension in the Lab to monitor HPC jobs launched through the Unicore interface. More info here.
    • To activate the extension in the JupyterLab context menu: View -> Activate Command Palette -> PyUnicore Task Stream
  • Added support for the SWIG tool. SWIG allows C/C++ libraries to be accessed in Python.

Collaboratory.Wiki

  • Updated footer.

Collaboratory.Office

  • Added a plugin that will open the collab a document is contained in. Read more.

Collaboratory.Drive 

  • Added a button that will open the collab a document is contained in. Read more.

OpenShift Dev cluster

  • The NFS disk storage for all persistent volumes is being increased. 

Collaboratory 2 release (2022-02-22) (Released)

Collaboratory.Lab

  • A new R kernel has been implemented in the Lab. Users can now select this kernel to use the R language in notebooks.
  • The ebrains-drive lib is now available by default in new notebooks. The "pip install" command is no longer needed for Collaboratory.Drive integration.

Collaboratory 2 release (2022-02-16) (Released)

Collaboratory.IAM

  • When EBRAINS users log in the first time, they have occasionally seen an error message. This is resolved by this deployment.

Collaboratory.Lab

  • We have fixed an issue with SSL certificates while using certain Python modules (e.g. requests) in the Lab.

Collaboratory 2 release (2022-02-08) (Released)

Collaboratory.Wiki

  • All common navigation elements in a collab (Drive, Team, Lab, Bucket) are now grouped together at the top of the left navigation panel.

Collaboratory.Lab

  • Updated JupyterLab image to use latest version
    • Adds a debugger to the Lab, allowing users to debug their notebooks.
    • Includes native git integration
    • Allows the user to install extensions to JupyterLab
  • Fixed issues with notebook exports (and re-enabled native PDF export)
  • Added nbgitpuller support
  • Set bash as the default shell in the terminal
  • Updated the JupyterLab extension to make Lab URL query parameters available (now works with direct links to a specific openshift cluster)
  • Reduced Docker image size to improve Collaboratory Lab load times.
  • Fixed unknown user id issue in the Lab container
  • Updated Jupyter Hub version

Collaboratory 2 release (2022-01-25) (Delayed, Released 27th)

Collaboratory.Wiki

  • Adding a new API to delete collabs. Details found here after release.
  • The "Get Collab" API has been updated, you can now use this API to search for exact title. Details found here after release.
  • Updates to the maintenance banner. 

Collaboratory 2 release (2022-01-17) (Released)

Collaboratory.Lab

  • We are re-enabling the Juelich site selection for running your Notebooks on.

Collaboratory 2 release (2022-01-11) (Released)

Collaboratory.Wiki

  • The new Toast that appears if you have not filled in your PLUS profile has been updated to take into account more scenarios. The message and links will change dynamically based on a users situation.
  • Upgrading XWiki to latest patch version.
  • New policy released regarding collabs. Read more

Collaboratory.Drive

  • File uploads are now limited to 1GB or below in size.

Collaboratory 2 release (2021-12-14) (Released)

Collaboratory.Lab

  • Idle Labs are now kept running for up to 12 hours before being automatically closed. 
  • The Lab is aware of a new permission regarding user quotas. Lab users will be asked to grant the Lab this permission in their next session.
  • The "Experimental" image is now becoming the Official EBRAINS image while the current  "Official EBRAINS" image will now be deprecated.
  • The option to choose the Julich site is temporarily being disabled.

Collaboratory.Wiki

  • Removed inactive EBRAINS user accounts from the results of user searches. These include the list displayed when trying to add a user to a collab's Team.
  • The wording of the email received when you need to re-verify your account has been updated.
  • You can no longer create collabs with duplicate titles.
  • When using the "Collabs" search, filters will no longer be applied by default; instead you now need to select what filters you want to apply.
  • A "Toast" popup will now remind you to fill out your PLUS profile if you have not already done so.

Collaboratory.Bucket (Data-proxy)

  • file picker option added in the data-proxy. Data Proxy front UI can be parametrized with 2 query parameters: redirect_uri  and redirect_title . Once the user has selected files/folders in the UI, and clicks on the redirect button, he is redirected to the specified redirect_uri. The redirect_title is optional and allows to customize the redirect button in the UI.
  • There is a new query parameter folder . When the user browses a bucket, the folder parameter is updated. That allows the user to share a link to a specific folder.
  • Public buckets are now visible to anyone authenticated in the UI
  • Public / Private toggle is visible to everyone but disabled by default. Only administrators can update the bucket privacy status.

Collaboratory 2 release (2021-12-07) (Released)

Collaboratory.Lab

  • The Lab now loads the Drive of the selected collab before loading the Drive of other collabs the user has access to. This reduces the time it takes for the selected collab's Drive to be accessible when starting up the Lab. This applies both to users opening the Lab from the Wiki navigation or from a link to a specific notebook.
  • Notebooks can be exported to various views from the File > Export Notebook as menu. Some of those export options were no longer working and have been removed.

Collaboratory.Wiki

  • The guided tour of the Wiki for users logging in the first time has been removed. Instead, feel free to check out individual tool tutorials that you can find on our documentation page.

Collaboratory 2 release (2021-11-10) (Released)

Collaboratory.Drive

  • We are deploying an upgrade to the Drive which should resolve multiple issues and adds new features including:
    • It improves Drive performance which had caused issues with Lab sessions left idling by users.
    • Its web interface updates dynamically when new files are created/deleted/renamed in a sub-folder of a collab's Drive.
    • It adds a new search file by filename in a given collab's Drive.
    • It adds a new "column view" in the web UI for browsing files in a collab's Drive.
    • Its web UI groups the public (shared) links and smart (internal) links to be managed via a common button and pop-up.
    • Its web UI adds color tagging to individual files.

Collaboratory.Lab

  • The new version provides access to Lab sessions with more RAM for authorized users. Authorization can be requested by contacting https://ebrains.eu/support with a motivation.

Collaboratory 2 release (2021-10-19) (Released)

Collaboratory.Lab

  • We have now added the ability for users to request larger amounts of memory for notebooks. For now, the best way to gain access to these larger notebooks is to contact support to request access.

Collaboratory.Bucket

  • Users now have the ability to copy files from one bucket to another. You can do this when initially creating a bucket or at any time after creation via the Bucket UI.

Collaboratory 2 release (2021-10-11) (Released)

Collaboratory.Lab

  • We are adding a new Python kernel to the Collaboratory Lab in which pre-installed neuroscience tools are readily available. The new kernel is the one with "EBRAINS" in its name. Available tools in that kernel can be listed with the command "module avail". The new kernel will be available in the experimental Docker image of the Lab.

Collaboratory 2 release (2021-09-14) (Released)

Collaboratory.Wiki

  • Collabs will now have a "Contact Administrator" button that allows users to send a message to the administrators of a collab. The administrators will receive the message along with the details of the user that has sent the message. 

Collaboratory 2 release (2021-09-03) (Released)

Collaboratory.Wiki

  • A new API is available to retrieve users emails based off a username, this is only available to users with the appropriate rights and will be detailed in the Wiki API .
  • The User API will now also return the "mitreid-sub", a unique identifier carried over from Collaboratory 1 that will be maintained in Collaboratory 2.
  • The GET Users endpoint is now only available for authenticated users.

Collaboratory 2 release (2021-08-31) (Released)

Collaboratory 1

  • Account creation has been removed from Collaboratory 1 in preparation for Collaboratory 1 shutdown.

Collaboratory.IAM

  • Users registering on Collaboratory 2 will now have a 16 digit numerical "Mitreid-sub" generated. This allows services using the "mitreid-sub" on Collaboratory 1 to continue using this field on Collaboratory 2.

Collaboratory.Wiki

  • The collab creation form has been updated. When users click on "Create" they will now see a popup window informing them of the progress of the collab creation.

Collaboratory 2 release (2021-08-17) (Released)

Collaboratory.IAM

  • Users can check in the Wiki for their past login events (or from the wiki > user profile icon > basic profile > logs). The IAM update will pass the correct IP address from which the user logged in, instead of displaying the IP address 127.0.0.1.

Collaboratory.Lab

  • Added a form for the user to select the Fenix site to run notebooks on.
  • Activated the Fenix Jülich Supercomputing Centre execution site.
  • Users visiting the Lab before visiting the Drive will now receive an appropriate error message.
  • New environment variables have been added in the Notebook environment with:
    • the notebook filename,
    • the name of the collab containing the notebook file in its Drive,
    • the Fenix site where the notebook is executed, and
    • the Docker image in which the notebook is executed.
  • View our sample notebook on how to access these variables. NOTE: This notebook will not work until after tonight's deployment.
  • Read the FAQ for creating your own custom environment variables.

Collaboratory 2 release (2021-08-03) (Released)

Collaboratory.Wiki

  • Change 2 endpoints of the Collaboratory Wiki API to also accept a Keycloak sub unique identifier as a search parameter.

Collaboratory 2 release (2021-07-20) (Released)

Collaboratory.Wiki

  • Collaboratory deletion now removes the associated Drive from the name, preventing duplicate Drives.
  • Copying links from the Identity manager now works correctly.
  • Backend changes made in preparation for future releases. 
  • Complete redesign of the Documentation which you will find in The Collaboratory collab.

Collaboratory 2 release (2021-07-06) (Released)

Collaboratory.Lab

  • Fixes and improvements to pyplot and matplotlib.
  • Added NGL Viewer to interactively view molecular structures.
  • Fixed permission issues in the notebook docker images that was were causing some libraries to throw warnings, the .cache dir is now writeable.
  • Images have been cleaned by removing unnecessary libraries.

Collaboratory.IAM

  • Fixed an issue where a user would occasionally be unable to delete a newly created collab.

Collaboratory.Drive

  • Fixed an issue where linking directly to a document in a newly created private collab would provide an "Unable to view file" error. 

Collaboratory 2 release (2021-06-22) (Released)

Collaboratory.Lab

  • Official EBRAINS Docker image: Added R and rpy2.
  • Experimental Docker image for EBRAINS tool developers: NFS Mount will now be available for developers. Added gcc10 and image optimisations. 

Collaboratory 2 release (2021-06-14) (Released)

Collaboratory.Wiki 

  • Fixed an issue causing new collabs to not have a Drive present.

Collaboratory 2 release (2021-06-10) (Released)

Collaboratory.Wiki 

  • A small bug fix for the collab search page.

Collaboratory 2 release (2021-06-08) (Released)

As well as individual services, we have also changed how announcements are made, if more than one announcement is being made you now see an arrow to the left of the announcement banner that you can use to switch between announcements.

Collaboratory.Wiki 

  • Added more filters to Collab search, you can now filter on collabs where you are a viewer, an editor or an admin.
  • Collab Creation and collab settings forms have been updated, more descriptions have been added and the private or public collab choice is now a radio button.
  • Instructions on how to get your collab as a highlighted collab have been published, if you visit the collab search page you will find a link to this new page just above the highlighted collabs.
  • The collab page editor has been replaced by a full page editor instead of the current inline editor being used.

Collaboratory.Lab

  • Users can now choose between 2 different images when launching a notebook, most users should keep using the Official EBRAINS image, however tool developers can now work on the experimental image.

Collaboratory.Bucket

  • The ability for users to create permanent links is now available via the UI by right clicking on any file and choosing "Manage public link".

Collaboratory 2 release (2021-05-11) (Released)

The Collaboratory release on 11th May represents a large change in the functionality of the collab search page. Please contact support if you encounter any issues with this new functionality, thank you.

Collaboratory.Wiki

  • Large update to the collab search page functionality
    • Look and feel has been improved
    • You will now see "Highlighted collabs" when initially arriving on the page
    • You can now filter by "My favourite" collabs - Showing only those collabs that you have favourited (Small heart symbol on top right of a collab page)

Collaboratory.Lab

  • Neuron installation has been fixed and updated to latest version.
  • The "Copy shareable link" menu entry in the file browser of the Lab should now produce a correct URL without manual intervention.
  • You can now use Environment variables populated from a URL, more information

Collaboratory.Bucket

  • The ability for users to create permanent links is now available  (Via API only for now): API Documentation

Collaboratory 2 release (2021-04-28) (Partially released)

Due to the problem described in the "Drive issue" announcement, the Collaboratory release was delayed from 27th April to the 28th April

Collaboratory.Wiki

  • The new "Bucket" menu is now available in all collabs
  • Various UI fixes.
  • Collapsible macro styles have been updated.
  • Fixed some issues with our Search functionality. 
  • Favourite collabs API has been developed for future integration into the UI.
  • Added a report button to collabs, you can now report unused or inappropriate collabs.
  • Issue for some users getting permission denied messages when they should not has been resolved.

There was an issue during the release of the Lab, as such, the following has not yet been released and will be released on a different day.

Collaboratory.Lab

  • Nueron installation has been fixed and updated to latest version.
  • The "Copy shareable link" button should now work without manual intervention.

Collaboratory 2 release (2021-04-13) (Released)

Collaboratory.Wiki

  • The new "Bucket" menu will be available in every new collab created, and will be rolled out to existing collab's in the coming days.
  • Users logged into the wiki, should now automatically be logged into the lab in an iFrame instead of needing to login again. 

Collaboratory 2 release (2021-03-30) (Released)

The release going ahead on the 30th March will contain numerous upgrades and fixes throughout the Collaboratory Drive, Wiki and Lab.

Collaboratory.Drive

  • Incorrect name formats are now automatically fixed
  • Improvements to Automated tests.

Collaboratory.Lab

  • Current Notebook image was rebuilt with extra extensions.  These are :  nbgitpuller,ipywidgets, jupyterlab-plotly, jupyter-matplotlib

Collaboratory.Wiki

  • The "Favourite" button was moved to the top right of a collab page.
  • New API added, this will allow users to get the Collab(CollabObject) via the DriveId - More information
  • Highlighted Collabs is now a responsive design.
  • Improvements to Automated tests.

Note: This release will cause all running containers to be reset.

Wiki update (2021-03-02) (Released)

As well as numerous bug fixes and small improvements to the Wiki, we are also upgrading the current version of XWiki(Version 10.11.9) to the most recent version of XWiki (Version 12.10.2). We are also adding a few fixes to its integration in the Wiki front end . A new feature was added: a new "Like" (Represented by a :heart:) feature that is now available on Collab pages. For now, it can be used to show support and approval for any Collab page you like and use, in the future, we will be expanding upon this functionality.  

If you would like to see new features or feel certain functionality is required to improve the Collaboratory, please join the Collaboratory user group, once joined, please do not hesitate to make your suggestions. 

EBRAINS ticketing system (2021-03-02) (Released)

The categories of tickets are being aligned to the description of services on the EBRAINS.eu website. We are using this opportunity to also upgrade the ticketing system to a more recent version.

Collaboratory 2 release (2021-02-17) (Released)

The release going ahead on 17th February has the following enhancements.
 

  1. Mounting a new "Shared" drive for the ability to easily share links from Seafile. So going forward, any links that need to be shared should be generated in the "Shared " drive. The original "/drive" will be kept so it does not break any of the already existing links.
  2. OnlyOffice is being upgraded to the latest version. This should solve the issue listed below in the "Files locked in the Drive " section. The section will remain temporarily until it is verified this issue is fully fixed.
  3. Seafile file system is being increased

Collaboratory 1 maintenance (Released)

Collaboratory 1 services will be down from 18:00 CET (my timezone) Thursday Jan 7 for maintenance. The services are being re-hosted from the EPFL/BBP infrastructure to the Fenix infrastructure. The OIDC authentication service will be reactivated first (within 30 minutes); all other services will follow in the evening. Once the Collaboratory 1 services are back online, you may find that files added to the storage within the last days do not initially appear. This will be remedied overnight as we synchronize the storage. Thank you for your patience and understanding.

As a reminder the Collaboratory 1 services are deprecated and will be shut down in September 2021.

If you encounter issues with Collaboratory 1 after Friday 12:00 CET, please contact https://ebrains.eu/support

The re-hosting was completed on Thursday evening. Some services relying on the Collaboratory 1 may need to be restarted to take into account the new DNS entries. Please notify support of any issues you identify.