5.4.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.3.0

Notes to tag/commit: 5.4.0

Generated: 2023-02-11

New Features

• VLMD submission: Initial implementation of VLMD submission interface (#1092)
• VLMD submission: add /data-dictionary-submission page to data portal
  (#1092)
• Bug fix for virtual tour: #1217
  (#1227)
• Unified flow table selection:
  #1215 (#1227)
• disable retries of failed requests at a global level for the GWAS app,
  align storybook request config , throw web service errors:
  #1216 (#1227)
• Fix SelectCohort errors: #1218
  (#1227)
• Added and reverted addition of React Library (following accidental merge)

Bug Fixes

• Removes ref to non-working server in TestSchema.sh (#1226)

Dependency Updates

• Adds: (#1233)
• "@testing-library/jest-dom": "^5.16.5", (#1233)
• "@testing-library/react": "^12.1.5", (#1233)
• Updates Node from 14 to 16: (#1233)
• node-version: '16' (#1233)
• Bumps glob-parent from 3.1.0 to
  5.1.2. (#1105)

Improvements

• Update the default createdby image (#1230)
• Fix misleading use of fetch() response .ok when calling /auth/proxy
  (#1220)

5.3.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.2.2

Notes to tag/commit: 5.3.0

Generated: 2023-01-25

New Features

• Support hiding DICOM pop-out buttons for N/A DICOM images. (#1173)
• Add new config field guppyConfig.manifestMapping.useFilterForCounts to
  data explorer. Set to true to use the explore filter to query for file
  counts. This requires the fields that has been specified in the explorer
  tab of a certain index must have all those fields injected into its
  corresponding File index (#1173)
• VADC-378 Integrate the virtual tour into the new GWAS (#1207). This
  integrates the virtual tour into the new GWAS app (#1211)
• VADC-393: fix query config import (#1202). Imports queryConfig from
  cohortMiddlewareApi.js instead of react-query for cohort listing. (#1211)
• VADC-373: Feat/gwas unified flow style steps2 and3 (#1203). This updates
  the styles for views 2.1, 2.2, 3.1 and 3.2, so that the buttons are to be
  positioned on the top right above the charts. (#1211)
• VADC-366: Feat/gwas unified flow outcome card (#1201). This adds an outcome
  card that shows in the the sidebar after a user selects an outcome. It has
  been styled to match the design. (#1211)
• VADC-364: Feat/gwas style sidebars (#1195). This styles the sidebars.
  (#1211)
• VADC-382: feat: add JEST tests for dichotomous(case/control) scenario
  (#1191). Adds new JEST tests for SelectHareDropDown component, adds
  documentation to main README.md on how to run JEST unit tests and (#1211)
• removes some unnecessary code (#1211)
• Homepage: added options to exclude File nodes from the charts (#1208)
• This is the sprint branch for sprint 25 and includes new functionality,
  features and revisions including: (#1179)
• Add Scrolling functionality to Attrition Table (#1179)
• FE for View 4.1 - Modal (#1179)
• Cleanup - change inline styles to CSS referenced via class names (#1179)
• Cleanup - Configure GWAS (#1179)
• FE for View 4.2 - Congratulations (#1179)
• Change Text in Progress Bar to always say "Select" and not "Edit" for each
  step (#1179)
• Cleanup - Move isEnterOrSpace to Shared Folder. Rename Shared Folder to
  Utils (#1179)
• Add Selected Hare Functionality to Configure GWAS (#1179)
• Cherry Pick FE Code and Deploy to QA (#1179)
• Integrate histogram into GWAS++ flow (#1179)

Deployment Changes

• New portal config options to exclude File nodes from the charts added: use
  "graphql.chartNodesExcludeFiles" to exclude File nodes from graphql
  chart, or use "components.index.homepageChartNodesExcludeFiles" to
  exclude File nodes from homepage chart. Note both of them are default to
  false so you have to explicitly set them to true to enable them (#1208)

Improvements

• Prevent portal from updating _unique_id to
  ${commonsName}_${x._unique_id}_${index} to bring consistency to the id of
  the studies regardless of their order in MDS (#1205)
• block access to some files (#1199)
• updatedprops passed to some antd components since some of them will be
  deprecated (#1196)
• Access Request (Study/Workspace): now can prevent user from creating extra
  tickets if they already have a same request pending (#1189)
• Access Request (Study/Workspace): Improved message display (#1189)

Bug Fixes

• Hook was calling multiple times for every checkbox click (#1209)

Dependency Updates

• update trim-newlines to 3.0.1 (#1196)
• update gen3-ui-component to 0.11.2 (#1196)
• update guppy to 0.15.4 (#1196)
• update isomorphic-fetch to 3.0.0 (#1196)

5.2.2

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.2.1

Notes to tag/commit: 5.2.2

Generated: 2022-12-21

Bug Fixes

• Discovery: disable filter button if studies are still loading (#1187)
• Fixed an Aggregate authz related bug where a null response from a key in
  wts/aggregate/authz/mapping is gracefully handled by Data-Portal (#1186)

Improvements

• Discovery: filter AND/OR logic toggle button will not be disabled (#1187)

5.2.1

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.2.0

Notes to tag/commit: 5.2.1

Generated: 2022-12-19

Bug Fixes

• Workspace: do callback within debounce time (#1183)

Improvements

• Hiding DICOM Viewer button for the imaging studies that doesn't have one
  (#1174)

5.2.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.1.0

Notes to tag/commit: 5.2.0

Generated: 2022-12-16

Improvements

• Discovery: add advSearchFilters.displayName config to customize Filter
  button title (#1160)
• Discovery: enlarged search bar size (#1160)
• Discovery: add Reset button to filter component (#1160)
• Discovery: add AND/OR toggle to filter component, defaults to AND
  (#1160)
• Discovery: Filter component won't shrink smaller than its size (#1160)
• Study Registration: update "Data Repository" tag in metadata during
  registration (#1160)
• Move linter configs so they can be shared by npm commands and super-linter
  GH action (#1175)
• Misc: security updates (#1162)
• WTS is a useful service for other backend components that need to access
  gen3 services using a token bound to a specific user account. (#1095)
• Update the guide to run data-portal locally (#1151)

New Features

• This is VADC Sprint Branch for Sprint 24. (#1158)
• 331: Combine GWAS Workflows: Style View 2.0 (#1158)
• 341: Combine GWAS Workflows: File Organization for components and methods
  for Sprint 24 (#1158)
• 329: Combine GWAS Workflows: Move logic from Children Components to Wrapper
  Components (#1158)
• 307: Integrate Euler diagram into GWAS App (#1158)
• 361: Try out auto-complete dropdowns instead of searchable tables for
  Custom Dichotomous view (#1158)
• Refactored the github actions steps into ci.yaml, (#1147)
• Added Security pipeline steps (#1147)
• Added NPM Unit Test steps (#1147)
• Added inputs to run pre and post npm test commands (#1147)
• Removed the Python Poetry test step. (#1147)
• Removed the travis.yaml file since it is no longer needed. (#1147)
• This addresses tickets: (#1143)
• Combine GWAS Workflows: FE for View 3.0 - Select Continous or Dichotomous
  with Cards- separate wiring than 217 (#1143)
• Combine GWAS Workflows: FE for View - FE for View 3.2 (#1143)
• Combine GWAS Workflows: FE for View 2.2 - Dichotomous (#1143)
• Combine GWAS Workflows: FE for View 2.1 - Continuous and View 3.1 (#1143)
• Combine GWAS Workflows: FE for View 2.0 - Select Continuous or Dichotomous
  (#1143)
• Combine GWAS Workflows: Update attrition table to use new state management
  architecture (#1143)
• Combine GWAS Workflows: Update Props, parameters and logic for Attrition
  Table for Quantitative Use Case Only (#1143)
• Combine GWAS Workflows: Update Props, parameters and logic for Attrition
  Table for Case/Control Use Case Only (#1143)
• This implements the features associated with tickets for VADC Sprint 21
  Frontend Work: (#1131)
• gwas V2 workflow progress bar (#1131)
• Add new command that only runs eslint on edited files in current git branch
  (#1131)
• Add Attrition Table below Steps (basic setup & styling only) (#1131)
• UI feature - Euler diagram for evaluating cohort selections in dichotomous
  covariate or dichotomous outcome steps (#1131)

Dependency Updates

• WTS becomes a dependency for data-portal in general, instead of just for
  the /workspace subsection of the portal. (#1095)
• The change IS backwards compatible, since this is controlled by a new
  optional "feature flag" called workspaceTokenServiceRefreshTokenAtLogin.
  If this is set to true it will refresh the WTS token directly at portal
  login (recommended mode). If not set, this refresh happens only when the
  user enters the workspace section of the portal (default/old/previous
  mode). (#1095)
• Added "@upsetjs/venn.js": "^1.4.2" (#1131)
• Requires dependencies overrides: (#1131)
• "uglify-js": "3.14.3", (#1131)
• "ansi-regex": "3.0.1" (#1131)
• Bumps @xmldom/xmldom from 0.7.5 to
  0.7.6. (#1122)

Deployment Changes

• this change assumes WTS is already a core/central service. The dependency
  is hereby moved to the homepage (instead of the ./workspace page) (#1095)

Bug Fixes

• Updates eslint-new to continue parsing when files have been deleted (#1143)
• Handle null values in discovery page (#1140)

5.1.0: GA4 support and GWAS update

Release Notes

For: uc-cdis/data-portal

Notes since tag: 5.0.0

Notes to tag/commit: 5.1.0

Generated: 2022-10-26

New Features

• Add Google Analytics 4 (GA4) tag support (#1127)
• This makes the whole of the cards on the Gen3 GWAS clickable. (#1109)
• It also allows for the user to navigate to them using their keyboard (by
  pressing the tab key) and trigger them using either the space bar or enter
  key. Adds a hover state for the cards modeled after hover state used on
  cards on previous page (App selection UI) (#1109)
• Include basic ADA accessibility code (tabIndex and aria-labels) (#1109)
• Removes checkbox interaction (#1109)

Improvements

• GA init and tracking logic update (#1127)
• this allows for devs running local node js version > 14 to also get all the
  tests to pass (#1119)
• Removing Veracode scanning pipeline (#1121)
• Removing Veracode scanning pipeline (#1116)
• Apply the discovery detail active-tab fix to the back button. (#1112)
• Addition of hover state and accessibility code (#1109)

Dependency Updates

• Replace react-ga with react-ga4 (#1127)
• updated node js to 16.x in Dockerfile and Travis CI tests (#1119)

Bug Fixes

• fixed unhandled promise rejection, which fixes a failing unit test (#1119)
• fixed failing unit test for UserProfile (#1119)
• Fix discovery page errors when tags are empty (#1118)
• Discovery: fixed a bug which causes study with authz == null incorrectly
  showing as OTHER accessibility level (#1110)
• Fix discovery page errors when features.authorization is enabled but
  features.authorization.supportedValues is not configured (#1108)

VA-2022.11

VA specific release

⚠️ This release is meant for the VA project.

What's Changed since last VA release

Full Changelog: 5.0.0...VA-2022.11

Relevant history of 5.0.0
https://github.com/uc-cdis/data-portal/commits/5.0.0/src/Analysis

Relevant history of VA-2022.11
https://github.com/uc-cdis/data-portal/commits/VA-2022.11/src/Analysis

List of relevant PRs:

• fix attrition table style (#1104)
• Makes whole cards clickable in GWASUIApp.jsx (#1109)
• Style/gwas pipeline padding (#1111)
• Improve workflow list refresh (#1113)

5.0.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 4.0.0

Notes to tag/commit: 5.0.0

Bug Fixes

• return local arborist if no externally connected commons (#1106)
• updating Guppy to version 0.15.2 to fix bug with download TSV/CSV formats
  button in Explorer (#1102)
• fixes the bug where an attrition row would not always update: when removing
  a covariate just above another one that is 100% missing, the latter one
  would get the counts of the previous one (i.e. the counts were not updated)
  (#1103)
• fix the column type for dichotomous covariate (#1101)
• update corresponding storybook test (#1101)
• reactour for next in quant (#1100)
• Add clinicalTrialFields in studyRegistrationConfig that was
  accidentally deleted in portal_confg.md. (#1099)
• make cohort overlap message more apparent (#1093)

New Features

• add attrition table to gwas ui (#1098)
• Add Workspace Registration feature where users can have an option to
  request for workspace access directly from dataportal (#1067)

Breaking Changes

• Replaced loading the data in iframes in Workspace page with Redirect
  component. (#1067)
• Deprecating the use of default-workspaces i. e an individual commons will
  no longer be able to deploy standalone jupyterhub images, they may use
  hatchery service instead. (#1067)
• studyRegistrationConfig in gitops.json must now be placed within the
  regsitrationConfigs.features block [Refer this
  PR] (#1067)

Improvements

• reactour for attrition table (#1100)
• Created a new /403Error page to redirect all users for a non-workspace
  related Unauthorized requests (#1067)
• reactour wording (#1094)

4.0.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 3.33.0

Notes to tag/commit: 4.0.0

Generated: 2022-09-16

New Features

• "True Access" for aggregate discovery component (#1089)

Improvements

• Make Discovery access icons more configurable (#1089)

Deployment Changes

• Use "discoveryUseAggWTS" in "featureFlags" to enable "True Access" for aggregate discovery
• "True Access" for aggregate discovery depends on WTS 0.4.0+

Breaking Changes

• Discovery component will now require a supportedValues section in its discoveryConfig.features.authorization config (e.g. uc-cdis/cdis-manifest#5138, see testing in qa-heal https://ctds-planx.atlassian.net/browse/BRH-254)
• Discovery component will now require a studies section in its discoveryConfig config, by default it can be a empty list [], fro example: "studies: []"

3.33.0

Release Notes

For: uc-cdis/data-portal

Notes since tag: 3.32.1

Notes to tag/commit: a9f2369

Bug Fixes

• spacing issue in case control step 2 (#1090)
• final step null variable error (#1090)
• covariates in step 5 does not disable if there's only 1 covariate left
  (#1088)
• outcome covariate shown in outcome section of final step (#1088)
• outcome covariate not shown in covariate section of final step (#1088)
• hide reactour in step 4 of case control when covariate table is empty
  (#1088)
• text changes, placeholder table for when no covariates selected (#1085)
• dichotomous variable deletion (#1082)

Improvements

• HARE dropdown now automatically removes overlap between case/cohort and
  reports only the non-overlapping populations sizes. (#1087)

Video

• https://user-images.githubusercontent.com/86243966/190019777-58aa70f4-78eb-4747-b667-27a6a46b3b4f.mov
  (#1088)

New Features

• unique dichotomous variable name (#1082)