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 by @jarmoza in #426
• [ENH] Implemented getter to create JSON representation of continuous column by @rmanaem in #430
• [ENH] Meta-getter for JSON output from download page by @jarmoza in #431
• [ENH] Restore download functionality for refactor/new meta getter by @jarmoza in #433
• [ENH] Merging dev branch into master post-refactor by @jarmoza in #437
• Updated cd.yaml by @rmanaem in #440
• Bump codespell-project/actions-codespell from 1 to 2 by @dependabot in #418
• Bump actions/stale from 6 to 8 by @dependabot in #419
• Bump terser from 4.8.0 to 4.8.1 by @dependabot in #421
• Bump ua-parser-js from 0.7.31 to 0.7.35 by @dependabot in #422
• Bump loader-utils from 1.4.0 to 1.4.2 by @dependabot in #448
• Bump parse-path and @nuxt/telemetry by @dependabot in #423
• Bump nth-check and nuxt by @dependabot in #449
• Bump json5 from 1.0.1 to 1.0.2 by @dependabot in #450
• Bump decode-uri-component from 0.2.0 to 0.2.2 by @dependabot in #451
• Bump follow-redirects from 1.14.7 to 1.15.2 by @dependabot in #452
• [MAINT] Instructed dependabot to ignore nuxt and vue major updates by @rmanaem in #455
• Bump papaparse from 5.3.1 to 5.4.1 by @dependabot in #458
• Bump cy-verify-downloads from 0.1.8 to 0.1.14 by @dependabot in #456
• Bump eslint-plugin-prettier from 4.0.0 to 4.2.1 by @dependabot in #459
• [ENH] Updates to README for descriptions, how-to-use instructions, screenshots, and badges by @jarmoza in #447
• Bump bootstrap-vue from 2.21.2 to 2.23.1 by @dependabot in #463
• Bump eslint from 8.11.0 to 8.43.0 by @dependabot in #462
• Bump cypress from 12.9.0 to 12.14.0 by @dependabot in #461
• Bump husky from 7.0.4 to 8.0.3 by @dependabot in #460
• [MAINT] Instructed dependabot to ignore webpack major version updates by @rmanaem in #465
• Bump editorconfig from 0.15.3 to 1.0.2 by @dependabot in #470
• Bump bootstrap from 4.6.1 to 5.3.0 by @dependabot in #469
• Bump lint-staged from 13.1.2 to 13.2.2 by @dependabot in #467
• Bump vue-select from 3.18.3 to 3.20.2 by @dependabot in #466

Full Changelog: https://github.com/neurobagel/annotation_tool/commits/0.2.0

0.1.x - Annotation tool prototype

Contributors

• @jarmoza made their first contribution in #5
• @surchs made their first contribution in #27
• @rmanaem made their first contribution in #241

Changes

• Ability to upload file and store it as data via landing page by @jarmoza in #5
• Example data by @surchs in #27
• Landing page file loading, Clickable columns on Categorization Page, and Vuex Store by @jarmoza in #28
• Blank annotation for mockup image by @jarmoza in #33
• Navigation and state by @jarmoza in #42
• move examples to their own root dir by @surchs in #54
• Transparent category colors and some related UI polish for the categorization page by @jarmoza in #47
• Page state preservation for Categorization page, Palette/Table clicking simplification, and general cleanup for landing and categorization pages by @jarmoza in #61
• New global store version + new dynamic styling for categorization page by @jarmoza in #66
• [STYLE] add ESLint and prettier by @surchs in #75
• [FEAT] add explanation component by @surchs in #76
• [FEAT] display categorized columns on the annotation page by @surchs in #77
• Initial work to integrate annotation page components and global store by @jarmoza in #84
• Creating a layout for the tool and moving navbar to the layout by @jarmoza in #86
• [FEAT] add discrete value annotation by @surchs in #87
• Prevents blank lines from tsv data passing through the annotation process by @jarmoza in #90
• Adding download page and hooking it into annotation tool workflow by @jarmoza in #91
• [FEAT] add vocabulary annotation by @surchs in #92
• [FIX] pass the original and annotated dataTable to components by @surchs in #97
• Changing annotation table status check to see if it differs from original table by @jarmoza in #98
• add example dataset to illustrate transformations by @surchs in #99
• Styling improvements for demo by @jarmoza in #100
• Post demo cleanup - Annotation page component overhaul and formatting by @jarmoza in #108
• Initial missing values implementation by @jarmoza in #110
• Implement missing values component by @surchs in #123
• Implement missing values discrete by @surchs in #132
• Fixes for unique explanation component ID and client-only tags by @jarmoza in #145
• Assessment Tool Groups UI on Categorization Page by @jarmoza in #144
• Assessment tool group tabs and enhanced functionality by @jarmoza in #150
• Implement missing values vocabulary by @surchs in #143
• Precommit hooks via husky by @jarmoza in #156
• Missing value functionality for assessment tool groups + related changes by @jarmoza in #159
• Annotation tool now outputs JSON files reflecting the annotated table by @jarmoza in #163
• First Cypress End to End Testing Implementation by @jarmoza in #165
• Remove the old mockup image by @surchs in #168
• Initial page-specific tests for the Annotation page by @jarmoza in #182
• Update output format to data model by @surchs in #191
• Fix for categorical double save bug on annotation page by @jarmoza in #196
• File select cancellation fix + condition cleanup by @jarmoza in #197
• Explanation component test added by @surchs in #219
• Refactor and test missing value component by @surchs in #222
• Split cypress test actions by @surchs in #226
• Continuous value component refactor by @surchs in #224
• Refactor of category-select-table component by @jarmoza in #229
• Column linking table refactor + component test by @jarmoza in #230
• Refactored annot-categorical component so it's ready for the store by @rmanaem in #241
• Refactored annot-columns component so it's ready for the store by @rmanaem in #249
• Next page accessibility/navbar/layout refactor + All page refactor by @jarmoza in #233
• Refactor annotation-tab component by @surchs in #242