v0.2.0 #480

jarmoza announced in Announcements

jarmoza
Jun 27, 2023

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 Ability to upload file and store it as data via landing page #5
@surchs made their first contribution in Example data #27
@rmanaem made their first contribution in Refactored annot-categorical component so it's ready for the store #241
@alyssadai made their first contribution in Create LICENSE #279
@yarikoptic made their first contribution in codespell: workflow, config, typos fixed #410
@Remi-Gau made their first contribution in [INFRA] add dependabot #417
@dependabot made their first contribution in Bump codespell-project/actions-codespell from 1 to 2 #418

Changes

Removal of nextPageAccessible getter by @jarmoza in Removal of nextPageAccessible getter #258
Create LICENSE by @alyssadai in Create LICENSE #279
Implemented mutation to change column to category mapping by @rmanaem in Implemented mutation to change column to category mapping #283
Implement getCategories store getter by @surchs in Implement getCategories store getter #284
Implement getColumnDescription getter by @surchs in Implement getColumnDescription getter #289
Implement value description getter by @surchs in Implement value description getter #290
createColumnToCategoryMap mutation + required getter + test by @jarmoza in createColumnToCategoryMap mutation + required getter + test #291
Implemented getColumnNames getter by @rmanaem in Implemented getColumnNames getter #292
setCurrentPage mutation + unit test for store refactor by @jarmoza in setCurrentPage mutation + unit test for store refactor #296
Implementation of nextPage getter for refactor + unit test by @jarmoza in Implementation of nextPage getter for refactor + unit test #297
index page refactor by @surchs in index page refactor #302
Implementation of isPageAccessible getter for refactor by @jarmoza in Implementation of isPageAccessible getter for refactor #299
action to process a new dataTable by @surchs in action to process a new dataTable #303
Data dictionary refactor for Store refactor + Tests by @jarmoza in Data dictionary refactor for Store refactor + Tests #312
Update to Vuex syntax for getters and unit tests by @jarmoza in Update to Vuex syntax for getters and unit tests #321
Components and their tests are nominally refactored for store by @jarmoza in Components and their tests are nominally refactored for store #323
Mutations should have a single payload parameter by @jarmoza in Mutations should have a single payload parameter #325
Swapping in refactored store by @jarmoza in Swapping in refactored store #326
Basic app launch post-refactor by @jarmoza in Basic app launch post-refactor #327
Navbar/next page button/page accessibility update for refactor by @jarmoza in Navbar/next page button/page accessibility update for refactor #328
Updates to Index page for data table + data dictionary for store refactor by @jarmoza in Updates to Index page for data table + data dictionary for store refactor #329
Adjusting e2e tests + support code for Phase 1 store refactor by @jarmoza in Adjusting e2e tests + support code for Phase 1 store refactor #330
Build static by @surchs in Build static #335
New mutation setHeuristic for phase 2 store refactor by @jarmoza in New mutation setHeuristic for phase 2 store refactor #337
New 'getHeuristic' getter for phase 2 store refactor by @jarmoza in New 'getHeuristic' getter for phase 2 store refactor #342
Only run index & categ e2e tests for now by @jarmoza in Only run index & categ e2e tests for now #343
Refactor getter 'getAnnotationComponent' by @jarmoza in Refactor getter 'getAnnotationComponent' #345
getMappedColumns Getter for Phase 2 Store Refactor by @jarmoza in getMappedColumns Getter for Phase 2 Store Refactor #349
New getter for category explanation text for the phase 2 store refactor by @jarmoza in New getter for category explanation text for the phase 2 store refactor #351
getOptions getter for Phase 2 store refactor by @jarmoza in getOptions getter for Phase 2 store refactor #353
Add node v16 dependency info by @surchs in Add node v16 dependency info #356
Getter getMissingValues for Phase 2 Store Refactor by @jarmoza in Getter getMissingValues for Phase 2 Store Refactor #355
Missing values table items refactor + component test fix by @jarmoza in Missing values table items refactor + component test fix #357
mutation 'changeMissingStatus' for Phase 2 Store Refactor by @jarmoza in mutation 'changeMissingStatus' for Phase 2 Store Refactor #359
Added and configured lint staged and lint workflow by @rmanaem in Added and configured lint staged and lint workflow #362
Added and configured cd workflow by @rmanaem in Added and configured cd workflow #361
getUniqueValues getter for Phase 2 Store Refactor by @jarmoza in getUniqueValues getter for Phase 2 Store Refactor #363
changeMissingStatus getter Fix + Check for Unique Values by @jarmoza in changeMissingStatus getter Fix + Check for Unique Values #365
selectCategoricalOption mutation for Phase 2 Store Refactor by @jarmoza in selectCategoricalOption mutation for Phase 2 Store Refactor #366
e2e node version update by @jarmoza in e2e node version update #370
getHarmonizedPreview getter for Phase 2 Refactor by @jarmoza in getHarmonizedPreview getter for Phase 2 Refactor #368
Feature for Phase 2 Refactor: Transform Heuristics for continuous values are now selectable by column by @jarmoza in Feature for Phase 2 Refactor: Transform Heuristics for continuous values are now selectable by column #372
Refactor: handle controlled terms as objects by @surchs in Refactor: handle controlled terms as objects #374
Phase 2 Store Refactor - Integration Part 1 - Annotation page access, tabs refactor, column-category unlinking by @jarmoza in Phase 2 Store Refactor - Integration Part 1 - Annotation page access, tabs refactor, column-category unlinking #375
Phase 2 refactor: New getter getSelectedCategoricalOption by @jarmoza in Phase 2 refactor: New getter getSelectedCategoricalOption #378
Phase 2 refactor: Column linking/unlinking alters data dictionary by @jarmoza in Phase 2 refactor: Column linking/unlinking alters data dictionary #379
Replace remaining getSelectedOption instances and fix optional chaining bug with new getter by @jarmoza in Replace remaining getSelectedOption instances and fix optional chaining bug with new getter #380
Phase 2 Refactor: Missing values functionality + integration with Annotation page by @jarmoza in Phase 2 Refactor: Missing values functionality + integration with Annotation page #382
Old tool group component removal, old store removal, and store field rename by @jarmoza in Old tool group component removal, old store removal, and store field rename #383
Implemented updateAnnotationCount mutation by @rmanaem in Implemented updateAnnotationCount mutation #389
Capitalized references of description in store and updated affected unit tests by @rmanaem in Capitalized references of description in store and updated affected unit tests #391
Fixed the bug that made download page unreachable from annotation page by @rmanaem in Fixed the bug that made download page unreachable from annotation page #396
Bumped cypress version to 12.9.0 by @rmanaem in Bumped cypress version to 12.9.0 #397
Categorical Select bugfix + Rework of initialization of data dictionary columns for data types by @jarmoza in Categorical Select bugfix + Rework of initialization of data dictionary columns for data types #395
Removed range and string options from transformationHeuristics by @rmanaem in Removed range and string options from transformationHeuristics #401
Refactored download button by @rmanaem in Refactored download button #404
Removal of old download components and related functionality by @jarmoza in Removal of old download components and related functionality #409
Refactored e2e tests by @rmanaem in Refactored e2e tests #405
codespell: workflow, config, typos fixed by @yarikoptic in codespell: workflow, config, typos fixed #410
[INFRA] add dependabot by @Remi-Gau in [INFRA] add dependabot #417
Next page button component tests - Clean branch by @jarmoza in Next page button component tests - Clean branch #414
[ENH] Updated Diagnosis options by @rmanaem in [ENH] Updated Diagnosis options #428
Getter for json output for discrete (categorical) value columns by @jarmoza in Getter for json output for discrete (categorical) value columns #426
[ENH] Implemented getter to create JSON representation of continuous column by @rmanaem in [ENH] Implemented getter to create JSON representation of continuous column #430
[ENH] Meta-getter for JSON output from download page by @jarmoza in [ENH] Meta-getter for JSON output from download page #431
[ENH] Restore download functionality for refactor/new meta getter by @jarmoza in [ENH] Restore download functionality for refactor/new meta getter #433
[ENH] Merging dev branch into master post-refactor by @jarmoza in [ENH] Merging dev branch into master post-refactor #437
Updated cd.yaml by @rmanaem in Updated cd.yaml #440
Bump codespell-project/actions-codespell from 1 to 2 by @dependabot in Bump codespell-project/actions-codespell from 1 to 2 #418
Bump actions/stale from 6 to 8 by @dependabot in Bump actions/stale from 6 to 8 #419
Bump terser from 4.8.0 to 4.8.1 by @dependabot in Bump terser from 4.8.0 to 4.8.1 #421
Bump ua-parser-js from 0.7.31 to 0.7.35 by @dependabot in Bump ua-parser-js from 0.7.31 to 0.7.35 #422
Bump loader-utils from 1.4.0 to 1.4.2 by @dependabot in Bump loader-utils from 1.4.0 to 1.4.2 #448
Bump parse-path and @nuxt/telemetry by @dependabot in Bump parse-path and @nuxt/telemetry #423
Bump nth-check and nuxt by @dependabot in Bump nth-check and nuxt #449
Bump json5 from 1.0.1 to 1.0.2 by @dependabot in Bump json5 from 1.0.1 to 1.0.2 #450
Bump decode-uri-component from 0.2.0 to 0.2.2 by @dependabot in Bump decode-uri-component from 0.2.0 to 0.2.2 #451
Bump follow-redirects from 1.14.7 to 1.15.2 by @dependabot in Bump follow-redirects from 1.14.7 to 1.15.2 #452
[MAINT] Instructed dependabot to ignore nuxt and vue major updates by @rmanaem in [MAINT] Instructed dependabot to ignore nuxt and vue major updates #455
Bump papaparse from 5.3.1 to 5.4.1 by @dependabot in Bump papaparse from 5.3.1 to 5.4.1 #458
Bump cy-verify-downloads from 0.1.8 to 0.1.14 by @dependabot in Bump cy-verify-downloads from 0.1.8 to 0.1.14 #456
Bump eslint-plugin-prettier from 4.0.0 to 4.2.1 by @dependabot in Bump eslint-plugin-prettier from 4.0.0 to 4.2.1 #459
[ENH] Updates to README for descriptions, how-to-use instructions, screenshots, and badges by @jarmoza in [ENH] Updates to README for descriptions, how-to-use instructions, screenshots, and badges #447
Bump bootstrap-vue from 2.21.2 to 2.23.1 by @dependabot in Bump bootstrap-vue from 2.21.2 to 2.23.1 #463
Bump eslint from 8.11.0 to 8.43.0 by @dependabot in Bump eslint from 8.11.0 to 8.43.0 #462
Bump cypress from 12.9.0 to 12.14.0 by @dependabot in Bump cypress from 12.9.0 to 12.14.0 #461
Bump husky from 7.0.4 to 8.0.3 by @dependabot in Bump husky from 7.0.4 to 8.0.3 #460
[MAINT] Instructed dependabot to ignore webpack major version updates by @rmanaem in [MAINT] Instructed dependabot to ignore webpack major version updates #465
Bump editorconfig from 0.15.3 to 1.0.2 by @dependabot in Bump editorconfig from 0.15.3 to 1.0.2 #470
Bump bootstrap from 4.6.1 to 5.3.0 by @dependabot in Bump bootstrap from 4.6.1 to 5.3.0 #469
Bump lint-staged from 13.1.2 to 13.2.2 by @dependabot in Bump lint-staged from 13.1.2 to 13.2.2 #467
Bump vue-select from 3.18.3 to 3.20.2 by @dependabot in Bump vue-select from 3.18.3 to 3.20.2 #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 Ability to upload file and store it as data via landing page #5
@surchs made their first contribution in Example data #27
@rmanaem made their first contribution in Refactored annot-categorical component so it's ready for the store #241

Changes

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

This discussion was created from the release v0.2.0.

Replies: 1 comment

Remi-Gau
Jun 27, 2023
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