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4.0.0 to 4.1.0

This document describes the upgrade instructions from 4.0.0 to 4.1.0.

Configuration changes​

New optional environment variables have been added to support forwarding browser cookies (e.g., SSO session tokens) to actions as secrets. If you do not need this feature, no changes are required. To enable cookie forwarding, you must add the following to your docker-compose file:

aerie_ui:
  environment:
    PUBLIC_ACTION_INCLUDE_CREDENTIALS: 'true'  # include browser cookies in action server requests

aerie_action:
  environment:
    ACTION_COOKIE_NAMES: 'ssosession'  # comma-separated list of cookie names to forward
    ACTION_CORS_ALLOWED_ORIGIN: 'https://YOUR_HOST_NAME'  # origin of your PlanDev UI (required for cross-origin)

Forwarded cookies are available in action code under actionsAPI.config.SECRETS.cookies:

const ssoToken = actionsAPI.config.SECRETS.cookies.ssosession;

See the Actions documentation for more details on cookie requirements and secrets in actions.

Other changes​

PlanDev: Fixed issues with procedure generation​

PlanDev v4.0.0 contained some regressions with procedural constraints and goals - namely, some static fields were incorrectly being included as procedure parameters in the JAR, and the JAR was incorrectly named <NAME>Mapper.jar instead of just <NAME>.jar. These have both been fixed in this release

SeqDev: .seq.json filetype association​

For the SeqDev editor, we have changed the default association for .seq.json files so they are edited as JSON files rather than sequence files, since SeqJson is usually an outputFormat rather than an inputFormat. However, since this is a user-configurable database setting, existing users will need to update it if they want this change. In Hasura/Postgres, update the table ui.file_extension_content_type of the row where file_extension = .seq.json to have content_type value of JSON.

SeqDev: SeqN language improvements​

For SeqDev users, this release includes a new release of the aerie-sequence-languages library (v1.0.1), which will only work with SeqDev v4.1.0 (this release) and above. It includes some improvements to handling of control characters and special characters in SeqN strings, and automatic replacement of unsupported "curly quotes" (“”) in SeqN documents.

This is a non-breaking API change, but users with custom sequencing adaptations should update this library and rebuild/reupload their adaptation. If your sequencing adaptation overrides the list of SeqDev/SeqN extensions or other SeqN parsing code, you may need to make some code changes to take advantage of these improvements. See PRs #20, #21 & #22 for details.

SeqDev: Known SeqN inconsistency​

An existing inconsistency in the SeqN language definition was discovered: escaped special characters like "\n" or "\t" in metadata keys are serialized into SeqJson differently than values - values are escaped while keys are "double-escaped". For example, @METADATA "key\t" "val\t" in SeqN becomes "metadata": { "\\t": "\t" } in SeqJSON. This was left unchanged due to unknown downstream effects, but we may consider changing it in a future release - contact us if you have concerns.