3 | Petronas

Release notes


30 november 2022
When upgrading, you might need to add the otp_secret column to the user table manually in the database. This is most likely the case when using PostgresQL for your database.
  • Feature
    • TOTP Multi-Factor-Authenticator has been added. Admins can enforce that all users enable MFA (PR#376, Issue#355).
    • The server support email is now settable in the configuration file, used to be fixed at [email protected] (PR#330, Issue#319).
    • You can now request all tasks assigned by a given user (PR#326, Issue#43).
    • When pickles are used the task info is shown in the node logs (PR#366, Issue#171).
  • Change
    • The[TAG] is tagged with the vantage6-client version that is already in the image (PR#389, Issue#233).
    • The infrastructure base image has been updated to improve build time (PR#406, Issue#250).


3 november 2022
  • Bugfix
    • Fixed a bug in the local proxy server which made algorithm containers crash in case the client.create_new_task method was used (PR#382).
    • Fixed a bug that crashed the node when a non existing image was send in a task (PR#375).

3.4.0 & 3.4.1

25 oktober 2022
  • Feature
    • Add columns to the SQL database on startup (PR#365, ISSUE#364). This simpifies the upgrading proces when a new column is added in the new release, as you do no longer need to manually add columns. When downgrading the columns will not be deleted.
    • Docker wrapper for Parquet files (PR#361, ISSUE#337). Parquet provides a way to store tabular data with the datatypes included which is an advantage over CSV.
    • When the node starts, or when the client is verbose initialized a banner to cite the vantage6 project is added (PR#359, ISSUE#356).
    • In the client a waiting for results method is added (PR#325, ISSUE#8). Which allows you to automatically poll for results by using client.wait_for_results(...), for more info see help(client.wait_for_results).
    • Added Github releases (PR#358, ISSUE#357).
    • Added option to filter GET /role by user id (PR#328, ISSUE#213). E.g.: client.role.list(user=...).
  • Change
  • Bugfix
    • Improve checks for non-existing resources in unittests (PR#320, ISSUE#265). Flask did not support negative ints, so the tests passed due to another 404 response.
    • client.node.list does no longer filter by offline nodes (PR#321, ISSUE#279).
This version is also the first version to be released with container images for both ARM and x86 architecture.
3.4.1 is a rebuild from 3.4.0 in which the all dependencies are fixed, as the build led to a broken server image.


  • Bugfix
    • The function client.util.change_my_password() was updated (Issue #333)


  • Bugfix
    • Temporary fix for a bug that prevents the master container from creating tasks in an encrypted collaboration. This temporary fix disables the parallel encryption module in the local proxy. This functionality will be restored in a future release.
This version is also the first version where the User Interface is available in the right version. From this point onwards, the user interface changes will also be part of the release notes.


  • Feature
    • The release pipeline has been expanded to automatically push new Docker images of node/server to the harbor2 service.
  • Bugfix
    • The VPN IP address for a node was not saved by the server using the PATCH /node endpoint, while this functionality is required to use the VPN
Note that 3.3.4 was only released on PyPi and that version is identical to 3.3.5. That version was otherwise skipped due to a temporary mistake in the release pipeline.


  • Bugfix
    • Token refresh was broken for both users and nodes. (Issue#306, PR#307)
    • Local proxy encrpytion was broken. This prefented algorithms from creating sub tasks when encryption was enabled. (Issue#305, PR#308)


  • Bugfix
    • vpn_client_image and network_config_image are settable through the node configuration file. (PR#301, Issue#294)
    • The option --all from vnode stop did not stop the node gracefully. This has been fixed. It is possible to force the nodes to quit by using the --force flag. (PR#300, Issue#298)
    • Nodes using a slow internet connection (high ping) had issues with connecting to the websocket channel. (PR#299, Issue#297)


  • Bugfix
    • Fixed faulty error status codes from the /collaboration endpoint (PR#287).
    • Default roles are always returned from the /role endpoint. This fixes the error when a user was assigned a default role but could not reach anything (as it could not view its own role) (PR#286).
    • Performance upgrade in the /organization endpoint. This caused long delays when retrieving organization information when the organization has many tasks (PR#288).
    • Organization admins are no longer allowed to create and delete nodes as these should be managed at collaboration level. Therefore, the collaboration admin rules have been extended to include create and delete nodes rules (PR#289).
    • Fixed some issues that made 3.3.0 incompatible with 3.3.1 (Issue#285).


  • Feature
    • Login requirements have been updated. Passwords are now required to have sufficient complexity (8+ characters, and at least 1 uppercase, 1 lowercase, 1 digit, 1 special character). Also, after 5 failed login attempts, a user account is blocked for 15 minutes (these defaults can be changed in a server config file).
    • Added endpoint /password/change to allow users to change their password using their current password as authentication. It is no longer possible to change passwords via client.user.update() or via a PATCH /user/{id} request.
    • Added the default roles 'viewer', 'researcher', 'organization admin' and 'collaboration admin' to newly created servers. These roles may be assigned to users of any organization, and should help users with proper permission assignment.
    • Added option to filter get all roles for a specific user id in the GET /role endpoint.
    • RabbitMQ has support for multiple servers when using vserver start. It already had support for multiple servers when deploying via a Docker compose file.
    • When exiting server logs or node logs with Ctrl+C, there is now an additional message alerting the user that the server/node is still running in the background and how they may stop them.
  • Change
    • Node proxy server has been updated
    • Updated PyJWT and related dependencies for improved JWT security.
    • When nodes are trying to use a wrong API key to authenticate, they now receive a clear message in the node logs and the node exits immediately.
    • When using vserver import, API keys must now be provided for the nodes you create.
    • Moved all swagger API docs from YAML files into the code. Also, corrected errors in them.
    • API keys are created with UUID4 instead of UUID1. This prevents that UUIDs created milliseconds apart are not too similar.
    • Rules for users to edit tasks were never used and have therefore been deleted.
  • Bugfix
    • In the Python client, client.organization.list() now shows pagination metadata by default, which is consistent all other list() statements.
    • When not providing an API key in vnode new, there used to be an unclear error message. Now, we allow specifying an API key later and provide a clearer error message for any other keys with inadequate values.
    • It is now possible to provide a name when creating a name, both via the Python client as via the server.
    • A GET /role request crashed if parameter organization_id was defined but not include_root. This has been resolved.
    • Users received an 'unexpected error' when performing a GET /collaboration?organization_id=<id> request and they didn't have global collaboration view permission. This was fixed.
    • GET /role/<id> didn't give an error if a role didn't exist. Now it does.


  • Feature
    • Horizontal scaling for the vantage6-server instance by adding support for RabbitMQ.
    • It is now possible to connect other docker containers to the private algorithm network. This enables you to attach services to the algorithm network using the docker_services setting.
    • Many additional select and filter options on API endpoints, see swagger docs endpoint (/apidocs). The new options have also been added to the Python client.
    • Users are now always able to view their own data
    • Usernames can be changed though the API
  • Bugfix
    • (Confusing) SQL errors are no longer returned from the API.
    • Clearer error message when an organization has multiple nodes for a single collaboration.
    • Node no longer tries to connect to the VPN if it has no vpn_subnet setting in its configuration file.
    • Fix the VPN configuration file renewal
    • Superusers are no longer able to post tasks to collaborations its organization does not participate in. Note that superusers were never able to view the results of such tasks.
    • It is no longer possible to post tasks to organization which do not have a registered node attach to the collaboration.
    • The vnode create-private-key command no longer crashes if the ssh directory does not exist.
    • The client no longer logs the password
    • The version of the alpine docker image (that is used to set up algorithm runs with VPN) was fixed. This prevents that many versions of this image are downloaded by the node.
    • Improved reading of username and password from docker registry, which can be capitalized differently depending on the docker version.
    • Fix error with multiple-database feature, where default is now used if specific database is not found


  • Feature
    • Algorithm-to-algorithm communication can now take place over multiple ports, which the algorithm developer can specify in the Dockerfile. Labels can be assigned to each port, facilitating communication over multiple channels.
    • Multi-database support for nodes. It is now also possible to assign multiple data sources to a single node in Petronas; this was already available in Harukas 2.2.0. The user can request a specific data source by supplying the database argument when creating a task.
    • The CLI commands vserver new and vnode new have been extended to facilitate configuration of the VPN server.
    • Filter options for the client have been extended.
    • Roles can no longer be used across organizations (except for roles in the default organization)
    • Added vnode remove command to uninstall a node. The command removes the resources attached to a node installation (configuration files, log files, docker volumes etc).
    • Added option to specify configuration file path when running vnode create-private-key.
  • Bugfix
    • Fixed swagger docs
    • Improved error message if docker is not running when a node is started
    • Improved error message for vserver version and vnode version if no servers or nodes are running
    • Patching user failed if users had zero roles - this has been fixed.
    • Creating roles was not possible for a user who had permission to create roles only for their own organization - this has been corrected.


  • Feature
    • Direct algorithm-to-algorithm communication has been added. Via a VPN connection, algorithms can exchange information with one another.
    • Pagination is added. Metadata is provided in the headers by default. It is also possible to include them in the output body by supplying an additional parameterinclude=metadata. Parameters page and per_page can be used to paginate. The following endpoints are enabled:
      • GET /result
      • GET /collaboration
      • GET /collaboration/{id}/organization
      • GET /collaboration/{id}/node
      • GET /collaboration/{id}/task
      • GET /organization
      • GET /role
      • GET /role/{id}/rule
      • GET /rule
      • GET /task
      • GET /task/{id}/result
      • GET /node
    • API keys are encrypted in the database
    • Users cannot shrink their own permissions by accident
    • Give node permission to update public key
    • Dependency updates
  • Bugfix
    • Fixed database connection issues
    • Don't allow users to be assigned to non-existing organizations by root
    • Fix node status when node is stopped and immediately started up
    • Check if node names are allowed docker names


31 Oktober 2022
  • Bugfix
    • Encryption module in the local proxy server has been fixed

2.3.0 - 2.3.4

  • Feature
    • Allows for horizontal scaling of the server instance by adding support for RabbitMQ. Note that this has not been released for version 3(!)
  • Bugfix
    • Performance improvements on the /organization endpoint


  • Feature
    • Multi-database support for nodes. It is now possible to assign multiple data sources to a single node. The user can request a specific data source by supplying the database argument when creating a task.
    • The mailserver now supports TLS and SSL options
  • Bugfix
    • Nodes are now disconnected more gracefully. This fixes the issue that nodes appear offline while they are in fact online
    • Fixed a bug that prevented deleting a node from the collaboration
    • A role is now allowed to have zero rules
    • Some http error messages have improved
    • Organization fields can now be set to an empty string

2.1.2 and 2.1.3

  • Bugfix
    • Changes to the way the application interacts with the database. Solves the issue of unexpected disconnects from the DB and thereby freezing the application.


  • Bugfix
    • Updating the country field in an organization works again\
    • The client.result.list(...) broke when it was not able to deserialize one of the in- or outputs.


  • Feature
    • Custom algorithm environment variables can be set using the algorithm_env key in the configuration file. See this Github issue.
    • Support for non-file-based databases on the node. See this Github issue.
    • Added flag --attach to the vserver start and vnode start command. This directly attaches the log to the console.
    • Auto updating the node and server instance is now limited to the major version. See this Github issue.
      • e.g. if you've installed the Trolltunga version of the CLI you will always get the Trolltunga version of the node and server.
      • Infrastructure images are now tagged using their version major. (e.g. trolltunga or harukas )
      • It is still possible to use intermediate versions by specifying the --image option when starting the node or server. (e.g. vserver start --image )
  • Bugfix


  • Bugfix
    • Fixed a bug that prevented the usage of secured registry algorithms


  • Feature
    • Role/rule based access control
      • Roles consist of a bundle of rules. Rules profided access to certain API endpoints at the server.
      • By default 3 roles are created: 1) Container, 2) Node, 3) Root. The root role is assigned to the root user on the first run. The root user can assign rules and roles from there.
    • Major update on the python-client. The client also contains management tools for the server (i.e. to creating users, organizations and managing permissions. The client can be imported from from vantage6.client import Client .
    • You can use the agrument verbose on the client to output status messages. This is usefull for example when working with Jupyter notebooks.
    • Added CLI vserver version , vnode version , vserver-local version and vnode-local version commands to report the version of the node or server they are running
    • The logging contains more information about the current setup, and refers to this documentation and our Discourd channel
  • Bugfix
    • Issue with the DB connection. Session management is updated. Error still occurs from time to time but can be reset by using the endpoint /health/fix . This will be patched in a newer version.


  • Feature
    • The node is now compatible with the Harbor v2.0 API


  • Bug fixes
    • Fixed a bug that ignored the --system flag from vnode start
    • Logging output muted when the --config option is used in vnode start
    • Fixed config folder mounting point when the option --config option is used in vnode start


  • Bug fixes
    • starting the server for the first time resulted in a crash as the root user was not supplied with an email address.
    • Algorithm containers could still access the internet through their host. This has been patched.


  • Features
    • Cross language serialization. Enabling algorithm developers to write algorithms that are not language dependent.
    • Reset password is added to the API. For this purpose two endpoints have been added: /recover/lostand recover/reset . The server config file needs to extended to be connected to a mail-server in order to make this work.
    • User table in the database is extended to contain an email address which is mandatory.
  • Bug fixes
    • Collaboration name needs to be unique
    • API consistency and bug fixes:
      • GET organization was missing domain key
      • PATCH /organization could not patch domain
      • GET /collaboration/{id}/node has been made consistent with /node
      • GET /collaboration/{id}/organization has been made consistent with /organization
      • PATCH /user root-user was not able to update users
      • DELETE /user root-user was not able to delete users
      • GET /task null values are now consistent: [] is replaced by null
      • POST, PATCH, DELETE /node root-user was not able to perform these actions
      • GET /node/{id}/task output is made consistent with the
  • other
    • questionairy dependency is updated to 1.5.2
    • vantage6-toolkit repository has been merged with the vantage6-client as they were very tight coupled.


  • Features
    • new command vnode clean to clean up temporary docker volumes that are no longer used
    • Version of the individual packages are printed in the console on startup
    • Custom task and log directories can be set in the configuration file
    • Improved CLI messages
    • Docker images are only pulled if the remote version is newer. This applies both to the node/server image and the algorithm images
    • Client class names have been simplified (UserClientProtocol -> Client)
  • Bug fixes
    • Removed defective websocket watchdog. There still might be disconnection issues from time to time.


  • Updated Command Line Interface (CLI)
    • The commands vnode list , vnode start and the new commandvnode attach are aimed to work with multiple nodes at a single machine.
    • System and user-directories can be used to store configurations by using the --user/--system options. The node stores them by default at user level, and the server at system level.
    • Current status (online/offline) of the nodes can be seen using vnode list , which also reports which environments are available per configuration.
    • Developer container has been added which can inject the container with the source. vnode start --develop [source]. Note that this Docker image needs to be build in advance from the development.Dockerfile and tag devcon.
    • vnode config_file has been replaced by vnode files which not only outputs the config file location but also the database and log file location.
  • New database model
    • Improved relations between models. Thereby updating the Python API, see here.
    • Input for the tasks is now stored in the result table. This was required as the input is encrypted individually for each organization (end-to-end encryption (E2EE) between organizations).
    • The Organization model has been extended with the public_key (String) field. This field contains the public key from each organization, which is used by the E2EE module.
    • The Collaboration model has been extended with the encrypted (Boolean) field which keeps track if all messages (tasks, results) need to be E2EE for this specific collaboration.
    • The Task keeps track of the initiator (organization) of the organization. This is required to encrypt the results for the initiator.
  • End to end encryption
    • All messages between all organizations are by default be encrypted.
    • Each node requires the private key of the organization as it needs to be able to decrypt incoming messages. The private key should be specified in the configuration file using the private_key label.
    • In case no private key is specified, the node generates a new key an uploads the public key to the server.
    • If a node starts (using vnode start), it always checks if the public_key on the server matches the private key the node is currently using.
    • In case your organization has multiple nodes running they should all point to the same private key.
    • Users have to encrypt the input and decrypt the output, which can be simplified by using our client vantage6.client.Client for Python or vtg::Client for R.
    • Algorithms are not concerned about encryption as this is handled at node level.
  • Algorithm container isolation
    • Containers have no longer an internet connection, but are connected to a private docker network.
    • Master containers can access the central server through a local proxy server which is both connected to the private docker network as the outside world. This proxy server also takes care of the encryption of the messages from the algorithms for the intended receiving organization.
    • In case a single machine hosts multiple nodes, each node is attached to its own private Docker network.
  • Temporary Volumes
    • Each algorithm mounts temporary volume, which is linked to the node and the run_id of the task
    • The mounting target is specified in an environment variable TEMPORARY_FOLDER. The algorithm can write anything to this directory.
    • These volumes need to be cleaned manually. (docker rm VOLUME_NAME)
    • Successive algorithms only have access to the volume if they share the same run_id . Each time a user creates a task, a new run_id is issued. If you need to share information between containers, you need to do this through a master container. If a master container creates a task, all slave tasks will obtain the same run_id.
  • RESTful API
    • All RESTful API output is HATEOS formatted. (wiki)
  • Local Proxy Server
    • Algorithm containers no longer receive an internet connection. They can only communicate with the central server through a local proxy service.
    • It handles encryption for certain endpoints (i.e. /task, the input or /result the results)
  • Dockerized the Node
    • All node code is run from a Docker container. Build versions can be found at our Docker repository: . Specific version can be pulled using tags.
    • For each running node, a Docker volume is created in which the data, input and output is stored. The name of the Docker volume is: vantage-NODE_NAME-vol . This volume is shared with all incoming algorithm containers.
    • Each node is attached to the public network and a private network: vantage-NODE_NAME-net.