Feat/combine gwas workflow view1 #1117

jarvisraymond-uchicago · 2022-10-11T15:07:42Z

Jira Ticket: VADC-215

New Features

This adds the first view for the new GWAS workflow and adds a story book for the new version of the CohortSelect. The required files for the first view have been copied to a Util and a new Shared folder, so the new workflow won't be dependent on the old workflows. The underlying logic was copied from Case Control GWAS Step 1.

Bug Fixes

This fixes the "ghost" button warning and resolves eslint issues that were in GWASContainer.jsx

Design

Implementation

StoryBook

…s and shared folder

…electStudyPopulation and updated refs

…X space element

…e to parent

…yPopulation

…ner.jsx and cohortMiddlewareApi

…ner.jsx props

…ogic from GWASContainer

…lass so style changes do not impact other workflows

…lect

…tainer.jsx

…story book and app

…elect.stories

…slint-disable-next-line in CohortSelect.jsx

…ectly aligned

pieterlukasse

thanks @jarvisraymond-uchicago ! I left some comments.

src/Analysis/GWASV2/GWASContainer.jsx

src/Analysis/GWASV2/SelectStudyPopulation/Utils/CohortDefinitions.jsx

src/Analysis/GWASV2/SelectStudyPopulation/Utils/CohortSelect.jsx

src/Analysis/GWASV2/Shared/SearchBar.jsx

…pulationCohort per PR review recommendation

…hortSelected

…hortSelected from CohortDefinations.jsx

…hortSelected from CohortSelect.jsx

… in SearchBar.jsx

… in CohortSelect.jsx

jarvisraymond-uchicago · 2022-10-14T13:39:32Z

thanks @jarvisraymond-uchicago ! I left some comments.

Thank you! Per your suggestions:

The selectCaseCohort state in GWASContainer.jsx has been updated to selectedStudyPopulationCohort and the setter to setSelectedStudyPopulationCohort per your recommendation
The state has been updated to selectedStudyPopulationCohort and the setter to setSelectedStudyPopulationCohort per your recommendation
The cohortDefinations.jsx component should be specific to SelectStudyPopulation. The var and prop otherCohortSelected has been removed.
The reference to otherCohortSelected has been removed from CohortSelect.jsx now.
The fields prop in SearchBar.jsx has been updated to field now

* Style/gwas pipeline padding (#1111) * style(gwasPipelinePadding): removed <hr /> element from CovariateReview and added inline styles to better vertically center tutorial button on GWASCaseControl * style(gwasPipelinePadding): removed <hr /> element from OutcomeSelectReview and added inline styles to GWASQuantitative * style(gwasPipelinePadding): added class and style for asterisks * style(gwasPipelinePadding): removed unneeded obj for housing styles in GWASQuantitative * style(gwasPipelinePadding): refactored code to avoid using negative margin values * style(gwasPipelinePadding): converted inline styles to use a class * style(gwasPipelinePadding): converted inline styles for no padding to use a class * style(gwasPipelinePadding): converted inline styles for no padding to use a class for GWASQuantitative * style(gwasPipelinePadding): made class name for asterisk consistent with rest of codebase * style(gwasPipelinePadding): fixed formatting issue in GWASQuantitative.jsx * style(gwasPipelinePadding): ran eslint to format files * style(gwasPipelinePadding): removed top spacing on Dichotomous selection and capitalized Cohort * style(gwasPipelinePadding): offset asterisk spacing per stakeholder advisement * style(gwasPipelinePadding): removed additional top padding in CustomDichotomousSelect.jsx * feat(VADC-261): add combined gwas steps template (#1114) * feat(VADC-261): add combined gwas steps template * fix(VADC-261): change step 4 label * fix(VADC-261): typo * Improve workflow list refresh (#1113) * improve workflow list fetch mechanism and decrease interval add storybook test for workflow list add refetchInterval to workflow list and update test add "phase" to workflow and to keys of useQuery and change test ... this will ensure the endpoint is called again if the status of the workflow changes set workflow list refresh interval to 5s * removing old reference to refreshWorkflows * Feat/combine gwas workflow view1 (#1117) * feat(CombineGWASWorkflowView1): Added bolerplate files * feat(CombineGWASWorkflowView1): created working prototype * feat(CombineGWASWorkflowView1): updated layout to better match design * feat(CombineGWASWorkflowView1): updated code organization to use utils and shared folder * feat(CombineGWASWorkflowView1): moved util files to utils folder in SelectStudyPopulation and updated refs * feat(CombineGWASWorkflowView1): formatted CSS and removed unneeded JSX space element * feat(CombineGWASWorkflowView1): Cleaned up CSS * feat(CombineGWASWorkflowView1): Updated text in button and moved state to parent * feat(CombineGWASWorkflowView1): updated child to use state from parent * feat(CombineGWASWorkflowView1): Fixed Eslint issues on AddCohortButton * feat(CombineGWASWorkflowView1): Fixed Eslint issues on CohortDefinitions * feat(CombineGWASWorkflowView1): Fixed Eslint issues on CohortDefinations * feat(CombineGWASWorkflowView1) Resolved ESLINT issues with SelectStudyPopulation * feat(CombineGWASWorkflowView1) Resolved ESLINT issues with GWASContainer.jsx and cohortMiddlewareApi * feat(CombineGWASWorkflowView1) Resolved ESLINT issues with GWASContainer.jsx props * feat(CombineGWASWorkflowView1) Removed unneeded steps component and logic from GWASContainer * feat(CombineGWASWorkflowView1) Added workflow specific wrapping CSS class so style changes do not impact other workflows * feat(CombineGWASWorkflowView1): created a story book to mock CohortSelect * feat(CombineGWASWorkflowView1): removed unneeded imports from GWASContainer.jsx * feat(CombineGWASWorkflowView1): set button styles so they render for story book and app * feat(CombineGWASWorkflowView1): Formatted code for clarity in CohortSelect.stories * feat(CombineGWASWorkflowView1): Added clarifying comment to explain eslint-disable-next-line in CohortSelect.jsx * feat(CombineGWASWorkflowView1): organized CSS * feat(CombineGWASWorkflowView1): ran stylelint auto fix for css files * feat(CombineGWASWorkflowView1): ensure form field and button are perfectly aligned * feat(CombineGWASWorkflowView1): updated state name to selectedStudyPopulationCohort per PR review recommendation * feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCohortSelected * feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCohortSelected from CohortDefinations.jsx * feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCohortSelected from CohortSelect.jsx * feat(CombineGWASWorkflowView1): updated var name from fields to field in SearchBar.jsx * feat(CombineGWASWorkflowView1): updated var name from fields to field in CohortSelect.jsx Co-authored-by: Jarvis <113449836+jarvisraymond-uchicago@users.noreply.github.com> Co-authored-by: Ali Lahrime <90918464+alilahrime@users.noreply.github.com>

jarvisraymond-uchicago added 5 commits October 10, 2022 13:40

feat(CombineGWASWorkflowView1): Added bolerplate files

0666675

feat(CombineGWASWorkflowView1): created working prototype

5268a18

feat(CombineGWASWorkflowView1): updated layout to better match design

8f4fef0

feat(CombineGWASWorkflowView1): updated code organization to use util…

6272f2a

…s and shared folder

feat(CombineGWASWorkflowView1): moved util files to utils folder in S…

2f085af

…electStudyPopulation and updated refs

jarvisraymond-uchicago changed the base branch from master to feat/vadc_sprint20 October 11, 2022 15:12

jarvisraymond-uchicago added 20 commits October 11, 2022 10:21

feat(CombineGWASWorkflowView1): formatted CSS and removed unneeded JS…

a6c3c4a

…X space element

feat(CombineGWASWorkflowView1): Cleaned up CSS

1f3b9c8

feat(CombineGWASWorkflowView1): Updated text in button and moved stat…

9a841bf

…e to parent

feat(CombineGWASWorkflowView1): updated child to use state from parent

36713cd

feat(CombineGWASWorkflowView1): Fixed Eslint issues on AddCohortButton

8a81b4b

feat(CombineGWASWorkflowView1): Fixed Eslint issues on CohortDefinitions

234e8a5

feat(CombineGWASWorkflowView1): Fixed Eslint issues on CohortDefinations

f67318f

feat(CombineGWASWorkflowView1) Resolved ESLINT issues with SelectStud…

cbf2613

…yPopulation

feat(CombineGWASWorkflowView1) Resolved ESLINT issues with GWASContai…

be2beb7

…ner.jsx and cohortMiddlewareApi

feat(CombineGWASWorkflowView1) Resolved ESLINT issues with GWASContai…

c8c1d1e

…ner.jsx props

feat(CombineGWASWorkflowView1) Removed unneeded steps component and l…

4aa2ec8

…ogic from GWASContainer

feat(CombineGWASWorkflowView1) Added workflow specific wrapping CSS c…

6981fe2

…lass so style changes do not impact other workflows

feat(CombineGWASWorkflowView1): created a story book to mock CohortSe…

3b8f050

…lect

feat(CombineGWASWorkflowView1): removed unneeded imports from GWASCon…

35d1e9b

…tainer.jsx

feat(CombineGWASWorkflowView1): set button styles so they render for …

2288685

…story book and app

feat(CombineGWASWorkflowView1): Formatted code for clarity in CohortS…

c204deb

…elect.stories

feat(CombineGWASWorkflowView1): Added clarifying comment to explain e…

f73abf3

…slint-disable-next-line in CohortSelect.jsx

feat(CombineGWASWorkflowView1): organized CSS

fc43bfd

feat(CombineGWASWorkflowView1): ran stylelint auto fix for css files

4737b26

feat(CombineGWASWorkflowView1): ensure form field and button are perf…

33cdd51

…ectly aligned

jarvisraymond-uchicago requested review from alilahrime and pieterlukasse October 12, 2022 15:47

jarvisraymond-uchicago marked this pull request as ready for review October 12, 2022 15:47

pieterlukasse requested a review from cemile-ctds October 13, 2022 14:12

pieterlukasse reviewed Oct 13, 2022

View reviewed changes

jarvisraymond-uchicago added 6 commits October 13, 2022 16:08

feat(CombineGWASWorkflowView1): updated state name to selectedStudyPo…

8c90e12

…pulationCohort per PR review recommendation

feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCo…

3fa60cf

…hortSelected

feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCo…

154ad27

…hortSelected from CohortDefinations.jsx

feat(CombineGWASWorkflowView1): removed unneeded var and prop otherCo…

fd0904e

…hortSelected from CohortSelect.jsx

feat(CombineGWASWorkflowView1): updated var name from fields to field…

59caba1

… in SearchBar.jsx

feat(CombineGWASWorkflowView1): updated var name from fields to field…

a03f30d

… in CohortSelect.jsx

pieterlukasse approved these changes Oct 14, 2022

View reviewed changes

pieterlukasse merged commit 2f36e85 into feat/vadc_sprint20 Oct 14, 2022

pieterlukasse deleted the feat/CombineGWASWorkflowView1 branch October 14, 2022 13:42

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Feat/combine gwas workflow view1 #1117

Feat/combine gwas workflow view1 #1117

jarvisraymond-uchicago commented Oct 11, 2022 •

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jarvisraymond-uchicago commented Oct 14, 2022 •

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Feat/combine gwas workflow view1 #1117

Feat/combine gwas workflow view1 #1117

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jarvisraymond-uchicago commented Oct 11, 2022 • edited Loading

New Features

Bug Fixes

Design

Implementation

StoryBook

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