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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

1.7.0 - 2022-09-02

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.

1.6.0 - 2022-04-22

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.

1.5.1 - 2021-12-24

Changed

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

1.5.0 - 2021-12-20

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.
  • Domains' ontologies and use cases are now verified when created.

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.

1.4.0 - 2021-11-06

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.

1.3.3 - 2021-11-02

This release is paired with the APE Web DOI release.

1.3.2 - 2021-08-09

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.

1.3.1 - 2021-08-09

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.

1.3.0 - 2021-07-28

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.

1.2.0 - 2021-07-06

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.

1.1.0 - 2021-05-28

Added

  • A link to the official running instance of APE Web in the README.
  • CHANGELOG.md file.
  • Terms and conditions page.
  • Endpoint to GET global run parameters limits.
  • Endpoint to PUT new global run parameters limits.
  • Front-end gets run parameters limits from back-end.
  • Admin page allows configuring the global run parameters limits.
  • Back-end checks if a workflow run does not exceed the configured run parameters limits.
  • Project version is shown in footer.

Changed

  • Removed required steps to install APE 1.1.7 to local Maven repository, replaced with instructions to optionally use a different version of APE when compiling the back-end.
  • Update the footer links to point to the APE Web GitHub repository.
  • Reduced the size of the headers on the admin page.

Removed

  • Vacancies link in footer.
  • PostCSS (because it was not used).
  • Sass (all CSS is now in Less).

Fixed

  • Domain upload creating corrupted domains.
  • "Sign out" button in header.
  • "Go to login" on admin page's unauthorized result.
  • Max run duration being the max length/steps when downloading configuration files.
  • Unknown "text" HTML element error on explore page.

1.0.0 - 2021-05-03

Added

  • Public and private domains.
  • User accounts.
  • Administrator accounts.
  • Domain creation page.
  • Domain edit page.
  • Explore page.
    • Configure and run APE.
    • Uploading and downloading workflow run configurations.
    • Preset use case run configurations.
    • Constraint sketcher.
    • Workflow comparison.
    • Workflow bash script downloading.
    • Workflow graph PNG downloading.
  • Administration page.
    • Add topics.
    • Approve user accounts.