APE Web 1.7.0

Added

• SLTLx editor. It allows writing SLTLx formulas to use as constraints for workflows.

Changed

• Update front-end Docker container Node.js version 14 -> 16.
• Update APE dependency version 1.1.12 -> 2.0.3.
• Update front-end dependencies, most notably:
  • Ant Design 4.7.0 -> 4.20.6
  • Next.js 9.5.5 -> 12.1.5
  • React 16.14.0 -> 17.0.2
  • ESLint 7.32.0 -> 8.18.0
  • TypeScript 4.4.4 -> 4.7.4
  • eslint-config-airbnb-typescript 11.4.0 -> 17.0.0
• Update back-end dependencies.
  • spring boot 2.3.4 -> 2.6.7
  • owlapi 5.1.17 -> 5.1.20
  • gson 8.6 -> 9.0
  • spring boot starter data mongodb 2.6.2 -> 2.6.7
  • log4j-core 2.17.0 -> 2.17.2
  • log4j-api 2.17.0 -> 2.17.2
  • graphviz-java 0.17.0 -> 0.18.1
  • springmockk 2.0.3 -> 3.1.1
  • json 20200518 -> 20220320
• Update Travis CI Node.js version 14 -> 16.
• Replace placeholder values in .env file of the front-end with working values.

APE Web 1.6.0

Added

• Domain verification. Domains' ontology and core configuration are verified with an empty run, and use cases are verified to run and give at least one workflow result.

Fixed

• Buttons "Go back home" and "Go to domain" after creating a domain are now properly centered.

APE Web 1.5.1

Changed

• Force all dependencies to use log4j and slf4j version 2.17.0.

APE Web 1.5.0

IMPORTANT: this version might still be vulnerable to CVE-2021-44228. Please use version 1.5.1 or later instead.

Added

• Clear buttons to clear all input data, output data, constraints on the explore page.
• Domains can now be permanently deleted in the domain edit page.

Changed

• Update back-end Kotlin version from 1.3.72 -> 1.6.0.
• Update APE dependency version 1.1.9 -> 1.1.12 (includes log4j vulnerability fix).

Fixed

• Remove "tab" as suggestion for separating data taxonomy roots as this also moves the user to the next input field.
• Some dependencies were updated to fix vulnerability issues.
• When there are many inputs, outputs, or constraints on the explore page; a scrollbar will now appear inside the workflow input box to prevent the workflow result from appearing far below.

APE Web 1.4.0

Added

• The domain name is now shown on the domain explore page.
• Notification explaining how to navigate the workflows on the explore page appears when the user selects more workflows for the first time.

Changed

• Update APE dependency to 1.1.9.
• Change "CWL (beta)" download to "Abstract CWL" download.
• Make it possible to configure the size limit of file uploads in the .env files (default: 10MB).
• Run parameter field "Max duration (s)" is now "Max duration (seconds)".
• Improved tooltips on the domain creation page.
• Improved tooltips on the domain edit page.

Fixed

• OntologyTreeSelect's dropdown is now wider to fit all items.
• OntologyTreeSelect now better handles items with the same name.
• Several errors surrounding the constraint sketcher.
• APE synthesis flag messages sometimes being empty.
• OntologyTreeSelect search function.
• First tree node in OntologyTreeSelect not expanding by default.
• Run parameter fields are now required.

APE Web 1.3.3 - DOI release

Release needed to obtain a DOI

APE Web 1.3.2

Fixed

• Public domains can be explored again without logging in.
• Add missing "no access" result page when trying to explore a domain a user does not have access to.

APE Web 1.3.1

IMPORTANT: this version has an issue where exploring domains is not possible without being logged in (even public domains). Please use version 1.3.2 instead.

Added

• The current ontology, tools annotations, use case config, and use case constraints files of a domain can now be downloaded on the domain edit page.

Changed

• Visibility and "use strict tool annotations" fields on create domain page now have default values.
• File uploads when creating and editing domains now filter accepted file types in the file dialog.
• User is now redirected to the home page after successfully creating a domain.

Fixed

• Uploading use case run configuration and constraints file on the create domain page.
• Uploading new a use case run configuration or constraints file on the domain edit page.
• NaN value in run parameters when a use case run configuration does not contain a value for the parameter.
• HTML "text" tag error on the explore page.
• Incorrect unauthorized response when exploring private domains.
• Add missing "use strict tools annotations" field to the domain edit page.

APE Web 1.3.0

Added

• Column to public domains list which shows the owner of the domain.
• Official domains are shown with an "official" topic.

Changed

• Update APE dependency to 1.1.8.
• Rewrote workflow visualization code to fix overlapping nodes.

Fixed

• Filtering domains based on their topics.
• Less console errors when a domain has no use case.

APE Web 1.2.0

Added

• Grant or revoke administrator privileges to / from users in the administrator page.
• Manage access to a domain in the domain edit page.
• Endpoint for changing the administrator status of users.
• (Admin only) endpoint for getting a list of all users.
• Endpoint to get all users with certain access to a domain.
• Endpoint to set a user's access to a domain.
• Endpoint to transfer the ownership of a domain.

Changed

• More specific error messages are shown when a workflow run / synthesis gets interrupted.
• Change occurrences of "APE Web View" to "APE Web".
• Moved front-end Docker container from Node.js 12 to Node.js 14.
• Logging of back-end tests is less verbose (information about the tests themselves is not affected).
• User's email addresses are no longer included in responses from the back-end by default (previously email addresses were also only given when necessary).

Fixed

• Test application.properties of back-end was in the wrong location.
• The 403 result on the domain edit page now redirects to the home page instead of a non-existent page.