v0.3.0

What's Changed

• Created citation file from template by @jarmoza in #479
• [MAINT] Linter fixes for new eslint-plugin-cypress version by @jarmoza in #483
• [ENH] Updated branding and shortcuts for navbar by @jarmoza in #490
• [MAINT] Updated navbar documentation link by @rmanaem in #497
• [ENH] Added appzi by @rmanaem in #510
• [REF] Change dependabot default label by @surchs in #528
• [MNT] Instructed dependabot to ignore semver-major for eslint-plugin-prettier by @rmanaem in #532
• [MNT] Removed the test case for checking next page's url by @rmanaem in #546
• [MNT] Refactored annot-explanation component by @rmanaem in #555
• [MNT] Remove uuid dependency by @surchs in #557
• [MNT] Capitalized age heuristics by @rmanaem in #562
• [MNT] Implemented getColumnsForCategory and getUniqueColumnValues by @rmanaem in #569
• [ENH] Added lintfix script to package.json by @rmanaem in #570
• [ENH] Add assessment tool categorization workflow by @surchs in #574
• [CI] Bumped cd workflow node-version to 18 by @rmanaem in #581
• [ENH] Added Subject ID/Participant ID to JSON output file by @rmanaem in #584
• [ENH] Implemented annoatation workflow for healthy controls by @rmanaem in #586
• [REF] Refactored getJSONOutput getter to handle participantID explicitly by @rmanaem in #587
• [ENH] Added Assessment Tool annoatatoins to the JSON output file by @rmanaem in #588
• [ENH] Moved tool and diagnosis terms into separate json files by @rmanaem in #590
• [MNT] Reworked routing for the app by @rmanaem in #598
• [ENH] Added all valid diagnosis options by @rmanaem in #599
• [FIX] Updated diagnosisTerms.json by @rmanaem in #600
• [ENH] Impemented validation for output JSON by @rmanaem in #602
• [MNT] Renamed examples files by @rmanaem in #608
• [ENH] Aligned assessment tool workflow UI elements by @rmanaem in #622
• [DOC] Add link to docs by @surchs in #624
• [ENH] Clean up the home page by @surchs in #621
• [MNT] Removed prettier by @surchs in #625
• [FIX] read value description from user dictionary correctly by @surchs in #623
• [ENH] Improved column highlighting in assessment tool workflow by @rmanaem in #627
• [ENH] Changed the favicon to neurobagel logo by @rmanaem in #634
• [ENH] Added logo to navbar by @rmanaem in #635
• [MNT] Updated diagnosisTerms.json by @rmanaem in #638
• [DOC] Provide welcome text on home page by @surchs in #639
• [DOC] Add minimal instruction for annotation workflow by @surchs in #643
• [ENH] Added beta badge to navbar by @rmanaem in #646
• [ENH] Implemented tooltip for beta badge by @rmanaem in #648
• [DOC] Removed non-installation instructions/info from README.md by @rmanaem in #647
• [FIX] allow users to use the browser-back button by @surchs in #650
• [MNT] Updated help text and category explanations of the annotation page by @rmanaem in #654
• [ENH] Implemented styling for table rows of annot-single-tool component by @rmanaem in #655
• [ENH] Add validation to data dictionary before download by @surchs in #671
• [ENH] Add session ID as a new category for annotation by @surchs in #675
• [DOC] Update Copyright holders by @surchs in #693
• [FIX] Remove existing annotations from data dictionaries by @surchs in #715
• [MNT] Add plausible by @surchs in #721
• [ENH] Preview of the data dictionary by @Manya-tech in #699
• [MNT] Instructed dependabot to ignore major version updates for braces by @rmanaem in #764
• [MNT] Fix badge link formatting in README.md by @alyssadai in #800
• [MNT] Modified the deployment process to trigger on release by @rmanaem in #802
• [ENH] Added clearer descriptions by @rmanaem in #827
• [MNT] Removed FromInt age transformation by @rmanaem in #829
• [ENH] Made requirement of age annotation more prominent by @rmanaem in #830
• [ENH] Implemented Annotate Another Dataset button by @rmanaem in #832
• [ENH] Implemented custom filtering function by @rmanaem in #831
• [ENH] Enabled functionality to remove unmapped assessment tools and columns by @rmanaem in #833
• [REF] Add assessment terms from SNOMED by @surchs in #836
• [FIX] Addressed the issue with missing mutations by @rmanaem in #837
• [FIX] Update outdated docs links by @alyssadai in #839
• [MNT] Update labels in dependabot.yml by @alyssadai in #841

New Contributors

• @Manya-tech made their first contribution in #699
• @neurobagel-bot made their first contribution in #810

Full Changelog: 0.2.0...v0.3.0

v0.2.0

What's Changed

0.2.0 - New data dictionary output, Refactor of Vuex store, and Expansion of Cypress testing coverage

Overview

• Annotation tool now outputs a modified BIDS data dictionary that includes Neurobagel annotations section per participants.tsv column (In versions 0.1.x, a fully transformed version of participants.tsv was outputted. See the description of 0.1.x below for more details.)
• Assessment tool categorization is temporarily removed until new version of assessment tool annotation is added
• Continuous value columns now can be annotated with the following transformation heuristics: bounded value, european decimal value, float value, and integer value
• Categorical value columns (currently Diagnosis and Sex) can now be annotated with a set of labels via Snomed and BIDS controlled vocabularies (see categoricalOptions in store/index.js)
• Vuex store has been refactored to accommodate all of the changes for this release
• Testing coverage has greatly increased. e2e and page-level tests have been refactored for the changes in this release, and there are now unit tests for all getters, mutations, and actions in the Vuex store
• Though the annotation tool's output is still accessible via the Download page, preview of the file's contents has been removed. (This will be implemented for the new data dictionary in an upcoming release.
• Updated figures, descriptions, install/deployment, and page instructions in README.md

Contributors

• @jarmoza made their first contribution in #5
• @surchs made their first contribution in #27
• @rmanaem made their first contribution in #241
• @alyssadai made their first contribution in #279
• @yarikoptic made their first contribution in #410
• @Remi-Gau made their first contribution in #417
• @dependabot made their first contribution in #418

Changes

• Removal of nextPageAccessible getter by @jarmoza in #258
• Create LICENSE by @alyssadai in #279
• Implemented mutation to change column to category mapping by @rmanaem in #283
• Implement getCategories store getter by @surchs in #284
• Implement getColumnDescription getter by @surchs in #289
• Implement value description getter by @surchs in #290
• createColumnToCategoryMap mutation + required getter + test by @jarmoza in #291
• Implemented getColumnNames getter by @rmanaem in #292
• setCurrentPage mutation + unit test for store refactor by @jarmoza in #296
• Implementation of nextPage getter for refactor + unit test by @jarmoza in #297
• index page refactor by @surchs in #302
• Implementation of isPageAccessible getter for refactor by @jarmoza in #299
• action to process a new dataTable by @surchs in #303
• Data dictionary refactor for Store refactor + Tests by @jarmoza in #312
• Update to Vuex syntax for getters and unit tests by @jarmoza in #321
• Components and their tests are nominally refactored for store by @jarmoza in #323
• Mutations should have a single payload parameter by @jarmoza in #325
• Swapping in refactored store by @jarmoza in #326
• Basic app launch post-refactor by @jarmoza in #327
• Navbar/next page button/page accessibility update for refactor by @jarmoza in #328
• Updates to Index page for data table + data dictionary for store refactor by @jarmoza in #329
• Adjusting e2e tests + support code for Phase 1 store refactor by @jarmoza in #330
• Build static by @surchs in #335
• New mutation setHeuristic for phase 2 store refactor by @jarmoza in #337
• New 'getHeuristic' getter for phase 2 store refactor by @jarmoza in #342
• Only run index & categ e2e tests for now by @jarmoza in #343
• Refactor getter 'getAnnotationComponent' by @jarmoza in #345
• getMappedColumns Getter for Phase 2 Store Refactor by @jarmoza in #349
• New getter for category explanation text for the phase 2 store refactor by @jarmoza in #351
• getOptions getter for Phase 2 store refactor by @jarmoza in #353
• Add node v16 dependency info by @surchs in #356
• Getter getMissingValues for Phase 2 Store Refactor by @jarmoza in #355
• Missing values table items refactor + component test fix by @jarmoza in #357
• mutation 'changeMissingStatus' for Phase 2 Store Refactor by @jarmoza in #359
• Added and configured lint staged and lint workflow by @rmanaem in #362
• Added and configured cd workflow by @rmanaem in #361
• getUniqueValues getter for Phase 2 Store Refactor by @jarmoza in #363
• changeMissingStatus getter Fix + Check for Unique Values by @jarmoza in #365
• selectCategoricalOption mutation for Phase 2 Store Refactor by @jarmoza in #366
• e2e node version update by @jarmoza in #370
• getHarmonizedPreview getter for Phase 2 Refactor by @jarmoza in #368
• Feature for Phase 2 Refactor: Transform Heuristics for continuous values are now selectable by column by @jarmoza in #372
• Refactor: handle controlled terms as objects by @surchs in #374
• Phase 2 Store Refactor - Integration Part 1 - Annotation page access, tabs refactor, column-category unlinking by @jarmoza in #375
• Phase 2 refactor: New getter getSelectedCategoricalOption by @jarmoza in #378
• Phase 2 refactor: Column linking/unlinking alters data dictionary by @jarmoza in #379
• Replace remaining getSelectedOption instances and fix optional chaining bug with new getter by @jarmoza in #380
• Phase 2 Refactor: Missing values functionality + integration with Annotation page by @jarmoza in #382
• Old tool group component removal, old store removal, and store field rename by @jarmoza in #383
• Implemented updateAnnotationCount mutation by @rmanaem in #389
• Capitalized references of description in store and updated affected unit tests by @rmanaem in #391
• Fixed the bug that made download page unreachable from annotation page by @rmanaem in #396
• Bumped cypress version to 12.9.0 by @rmanaem in #397
• Categorical Select bugfix + Rework of initialization of data dictionary columns for data types by @jarmoza in #395
• Removed range and string options from transformationHeuristics by @rmanaem in #401
• Refactored download button by @rmanaem in #404
• Removal of old download components and related functionality by @jarmoza in #409
• Refactored e2e tests by @rmanaem in #405
• codespell: workflow, config, typos fixed by @yarikoptic in #410
• [INFRA] add dependabot by @Remi-Gau in #417
• Next page button component tests - Clean branch by @jarmoza in #414
• [ENH] Updated Diagnosis options by @rmanaem in #428
• Getter for json output for discrete (categorical) value columns ...