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TopFeat/results view top loci #1337

Merged
merged 18 commits into from
Jun 27, 2023
Merged

TopFeat/results view top loci #1337

merged 18 commits into from
Jun 27, 2023

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jarvisraymond-uchicago
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@jarvisraymond-uchicago jarvisraymond-uchicago commented Jun 20, 2023 •
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Jira Ticket: VADC-511

New Features

This adds the Top Loci table to the ResultsPheWeb visualization. The functionality includes:

  • Sorting
  • Filtering
  • Download of Manhattan Plot data in TSV format

Additionally the Results view has been organized into separate folders for the ResultsPheWeb, and the TopLociTable. Tests have been written and test data placed in the TestData folder.

Bug Fixes

In some cases the Results view would crash the application instead of showing an error message if the data received from the API call was missing values. This has been fixed using the conditional operator, i.e.

let results = data?.outputs?.parameters?.filter(
      (entry) => entry.name === 'pheweb_json_index',
    );

Design

image

Implementation

output

thanh-nguyen-dang and others added 14 commits June 12, 2023 13:03
@thanh-nguyen-dang @jarvisraymond-uchicago
feat(no-access): add no access message (#1301)
ab238f4
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Initial commit
319b0cb
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Fixed title for AF
f16fb9d
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Got search to work on first column
c23cfc8
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Got search to work on remaining columns
96d2fc7
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Formatted code
a36a052
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Seperated out logic for filtering into sepe…
9d91cb0 
…rate file
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Ran linter
5ffaade
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Moved files into seperate folder
4249cf2
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Wrote unit tests
8c62cc3
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Ran formatter
b02e15b
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Ran formatter and npm test
d7ef5c7
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Added comments back for ESLINT ignores
28f2d9e
@jarvisraymond-uchicago
feat(resultsViewTopLoci): Reverted unintentially changed file
5821877
@jarvisraymond-uchicago jarvisraymond-uchicago marked this pull request as ready for review June 20, 2023 19:55
pieterlukasse
pieterlukasse reviewed Jun 21, 2023
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nice work @jarvisraymond-uchicago !

I tested locally and it works pretty well. I did find some minor sorting and filtering issues that would be good to address though. Please see comments.

src/Analysis/GWASResults/Views/Results/ResultsPheWeb/TopLociTable/TopLociTable.jsx Outdated Show resolved Hide resolved
src/Analysis/GWASResults/Views/Results/ResultsPheWeb/TopLociTable/TopLociTable.jsx Show resolved Hide resolved
src/Analysis/GWASResults/Views/Results/ResultsPheWeb/TopLociTable/TopLociTable.jsx Outdated Show resolved Hide resolved
@jarvisraymond-uchicago jarvisraymond-uchicago merged commit c64c8b1 into feat/vadc_sprint10 Jun 27, 2023
@jarvisraymond-uchicago jarvisraymond-uchicago deleted the feat/resultsViewTopLoci branch June 27, 2023 12:56
pieterlukasse pushed a commit that referenced this pull request Jul 31, 2023
@jarvisraymond-uchicago @thanh-nguyen-dang @pieterlukasse
TopFeat/results view top loci (#1337)
f432dea 
* feat(no-access): add no access message (#1301)

* feat(resultsViewTopLoci): Initial commit

* feat(resultsViewTopLoci): Fixed title for AF

* feat(resultsViewTopLoci): Got search to work on first column

* feat(resultsViewTopLoci): Got search to work on remaining columns

* feat(resultsViewTopLoci): Formatted code

* feat(resultsViewTopLoci): Seperated out logic for filtering into seperate file

* feat(resultsViewTopLoci): Ran linter

* feat(resultsViewTopLoci): Moved files into seperate folder

* feat(resultsViewTopLoci): Wrote unit tests

* feat(resultsViewTopLoci): Ran formatter

* feat(resultsViewTopLoci): Ran formatter and npm test

* feat(resultsViewTopLoci): Added comments back for ESLINT ignores

* feat(resultsViewTopLoci): Reverted unintentially changed file

* feat(resultsViewTopLoci): Updated search function to remove commas and added additional pageSizeOptions

* feat(resultsViewTopLoci): Wrote custom sorting function for variant

* feat(resultsViewTopLoci): Updated sort functions for AF and PVAL to parse Number before sort

* feat(resultsViewTopLoci): Simplified sort method for variant

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>
@pieterlukasse pieterlukasse mentioned this pull request Jul 31, 2023
Merged
pieterlukasse pushed a commit that referenced this pull request Aug 1, 2023
@jarvisraymond-uchicago @thanh-nguyen-dang @pieterlukasse
TopFeat/results view top loci (#1337)
6308e59 
* feat(no-access): add no access message (#1301)

* feat(resultsViewTopLoci): Initial commit

* feat(resultsViewTopLoci): Fixed title for AF

* feat(resultsViewTopLoci): Got search to work on first column

* feat(resultsViewTopLoci): Got search to work on remaining columns

* feat(resultsViewTopLoci): Formatted code

* feat(resultsViewTopLoci): Seperated out logic for filtering into seperate file

* feat(resultsViewTopLoci): Ran linter

* feat(resultsViewTopLoci): Moved files into seperate folder

* feat(resultsViewTopLoci): Wrote unit tests

* feat(resultsViewTopLoci): Ran formatter

* feat(resultsViewTopLoci): Ran formatter and npm test

* feat(resultsViewTopLoci): Added comments back for ESLINT ignores

* feat(resultsViewTopLoci): Reverted unintentially changed file

* feat(resultsViewTopLoci): Updated search function to remove commas and added additional pageSizeOptions

* feat(resultsViewTopLoci): Wrote custom sorting function for variant

* feat(resultsViewTopLoci): Updated sort functions for AF and PVAL to parse Number before sort

* feat(resultsViewTopLoci): Simplified sort method for variant

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>
tianj7 pushed a commit that referenced this pull request Aug 10, 2023
@jarvisraymond-uchicago @thanh-nguyen-dang @tianj7
TopFeat/results view top loci (#1337)
9cc9cc4 
* feat(no-access): add no access message (#1301)

* feat(resultsViewTopLoci): Initial commit

* feat(resultsViewTopLoci): Fixed title for AF

* feat(resultsViewTopLoci): Got search to work on first column

* feat(resultsViewTopLoci): Got search to work on remaining columns

* feat(resultsViewTopLoci): Formatted code

* feat(resultsViewTopLoci): Seperated out logic for filtering into seperate file

* feat(resultsViewTopLoci): Ran linter

* feat(resultsViewTopLoci): Moved files into seperate folder

* feat(resultsViewTopLoci): Wrote unit tests

* feat(resultsViewTopLoci): Ran formatter

* feat(resultsViewTopLoci): Ran formatter and npm test

* feat(resultsViewTopLoci): Added comments back for ESLINT ignores

* feat(resultsViewTopLoci): Reverted unintentially changed file

* feat(resultsViewTopLoci): Updated search function to remove commas and added additional pageSizeOptions

* feat(resultsViewTopLoci): Wrote custom sorting function for variant

* feat(resultsViewTopLoci): Updated sort functions for AF and PVAL to parse Number before sort

* feat(resultsViewTopLoci): Simplified sort method for variant

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>
tianj7 added a commit that referenced this pull request Aug 15, 2023
@tianj7 @jarvisraymond-uchicago
@mfshao @nss10 @ocshawn @thanh-nguyen-dang @pieterlukasse @qiongl-CTDS
BRH-553 (#1383)
7e3a264 
* workspace changes

* Feat/support nested field names (#1324)

* feat(supportNestedFieldNames): Added solution described in ticket, unable to populate summary field using example described in ticket

* feat(supportNestedFieldNames): Ran linter

* feat(supportNestedFieldNames): Reverted auto formatting

* feat(supportNestedFieldNames): Added other changed file without auto formating

* feat(supportNestedFieldNames): Added nested search with lodash get to DiscoveryListView ln 130

* feat(supportNestedFieldNames): Updated files to remove unintentional auto formatting

* feat(supportNestedFieldNames): Refactored to use jsonpath

* feat(supportNestedFieldNames): Fixed issue with empty resourceFieldValues rendering in details view

* feat(supportNestedFieldNames): Updated parameter passed to search functionality so search will still work

* feat(supportNestedFieldNames): Updated parameter passed to search functionality to parse all array values

* feat(supportNestedFieldNames): Removed unneeded comments

* feat(supportNestedFieldNames): Updated discoverydetails logic to not render fields when array contains a single empty string

* feat(supportNestedFieldNames): Wrote function to parse array containing an array for displaying multiple values in a single place in the detail view

* feat(supportNestedFieldNames): Renamed function for clarity

* feat(supportNestedFieldNames): Reverted unneeded auto formatting from prettier and ran eslint

* feat(supportNestedFieldNames): Added jsonpath query for headerField in DiscoveryDetails.tsx

* feat(supportNestedFieldNames): Reverted unintentional auto formatting

* feat(supportNestedFieldNames): Added logic to formatSearchIndex so JSON Path values can be used in search in Discovery.tsx

* Update src/Discovery/DiscoveryListView.tsx

Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>

* feat(supportNestedFieldNames): Removed console logs and added support for nested searchableFields

* feat(supportNestedFieldNames): Ran linter

* feat(supportNestedFieldNames): clarified comment

* Update src/Discovery/Discovery.tsx

Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>

* Update src/Discovery/Discovery.tsx

Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>

* Update src/Discovery/Discovery.tsx

Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>

* use jsonpath to check if group is empty

* increase mds query limit

* update docs

* aggregation

* update for na fields

* fix test

* change concat char

---------

Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>
Co-authored-by: Mingfei Shao <mshao1@uchicago.edu>

* Feat/UI changes paymodel (#1368)

* Make UI changes for the new hatchery pay model updates
* Changing the position of the missing paymodels alert
* remove unnecessary null check

* HP-1179: Updates to Study Registration / VLMD Submission page to support nested fields (#1365)

* HP-1179: Updates to Study Registration / VLMD Submission page to support nested fields

* HP-1179: fix typo in cedar id

* HP-1179: update clinicaltrials.gov api to classic endpoint

* HP-1179: update CSP

* HP-1179: dont create metadata clinicaltrials_gov if it does not exist

---------

Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>

* Feat/home table column management menu (#1304)

* feat(no-access): add no access message (#1301)

* feat(homeTableColumnManagementMenu): Initial commit

* feat(homeTableColumnManagementMenu): Fixed bug due to hasOnlyBoolValues not returning computational output

* feat(homeTableColumnManagementMenu): Ran linter

* feat(homeTableColumnManagementMenu): Formatted CSS and reverted unintentionally changed file

* feat(homeTableColumnManagementMenu): Ran stylelint

* feat(homeTableColumnManagementMenu): Ran eslint new

* feat(homeTableColumnManagementMenu): Changed method name for clarity

* feat(homeTableColumnManagementMenu): Refactored toggleSwitch functions into a single re-usable function

* feat(homeTableColumnManagementMenu): Reverted changes: refactoring doesn't address filtering resets

* feat(homeTableColumnManagementMenu): Refactored again to address dynamic filtering for toggleColumn

* feat(homeTableColumnManagementMenu): Renamed variables for clarity in toggleColumn function

* feat(homeTableColumnManagementMenu): Clarified comment

* feat(homeTableColumnManagementMenu): ran linter

* feat(homeTableColumnManagementMenu): Renamed folder to HomeTableState, created separate file to hold function UpdateColumnManagement.js

* feat(homeTableColumnManagementMenu): changed ColumnManagement obj var names to sound more boolean

* feat(homeTableColumnManagementMenu): Wrote method to generate switch JSX, fixed broken test, ran linter

* feat(homeTableColumnManagementMenu): Ran linter, fixed broken storybook story

* feat(homeTableColumnManagementMenu): updated test for Manage Columns to programmatically determined num of expected switches

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Feat/input details view (#1306)

* feat(no-access): add no access message (#1301)

* feat(inputDetailsView): Initial commit

* feat(inputDetailsView): Ran linter

* Feat/home table column management menu (#1304)

* feat(no-access): add no access message (#1301)

* feat(homeTableColumnManagementMenu): Initial commit

* feat(homeTableColumnManagementMenu): Fixed bug due to hasOnlyBoolValues not returning computational output

* feat(homeTableColumnManagementMenu): Ran linter

* feat(homeTableColumnManagementMenu): Formatted CSS and reverted unintentionally changed file

* feat(homeTableColumnManagementMenu): Ran stylelint

* feat(homeTableColumnManagementMenu): Ran eslint new

* feat(homeTableColumnManagementMenu): Changed method name for clarity

* feat(homeTableColumnManagementMenu): Refactored toggleSwitch functions into a single re-usable function

* feat(homeTableColumnManagementMenu): Reverted changes: refactoring doesn't address filtering resets

* feat(homeTableColumnManagementMenu): Refactored again to address dynamic filtering for toggleColumn

* feat(homeTableColumnManagementMenu): Renamed variables for clarity in toggleColumn function

* feat(homeTableColumnManagementMenu): Clarified comment

* feat(homeTableColumnManagementMenu): ran linter

* feat(homeTableColumnManagementMenu): Renamed folder to HomeTableState, created separate file to hold function UpdateColumnManagement.js

* feat(homeTableColumnManagementMenu): changed ColumnManagement obj var names to sound more boolean

* feat(homeTableColumnManagementMenu): Wrote method to generate switch JSX, fixed broken test, ran linter

* feat(homeTableColumnManagementMenu): Ran linter, fixed broken storybook story

* feat(homeTableColumnManagementMenu): updated test for Manage Columns to programmatically determined num of expected switches

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* feat(inputDetailsView): Added logic for row specific API call

* feat(inputDetailsView): Added comment explaining how to output covariates, formatted code

* feat(inputDetailsView): Added comment explaining how to output covariates, formatted code

* feat(inputDetailsView): Wrote method to parse covariates and return JSX for each

* feat(inputDetailsView): Added fall backs for missing data

* feat(inputDetailsView): refactored for code clarity

* feat(inputDetailsView): fixed bug due to missing conditional

* feat(inputDetailsView): Ran ESLINT new

* feat(inputDetailsView): Removed unneeded console statement

* feat(inputDetailsView): Removed unneeded JSON logging to DOM

* feat(inputDetailsView): Wrote storybook and input unit test

* feat(inputDetailsView): Created separate data for the tests, made test pass with null data for mocked failure json

* feat(inputDetailsViews): Began writing JobDetails.test.jsx

* feat(inputDetailsView): Added JEST test for job details

* feat(inputDetailsView): Formatted code

* feat(inputDetailsView): Updated failure JSON test data to have all shown fields null

* feat(inputDetailsView): cleaned up code

* feat(inputDetailsView): made test approach consistent

* feat(inputDetailsView): made test approach consistent and work

* feat(inputDetailsView): Ran linters

* feat(inputDetailsView): Removed unneeded storybook template

* feat(inputDetailsView): Updated output string and console.error per PR review

* feat(inputDetailsView): Simplified processing function

* feat(inputDetailsView): Added corrections from PR

* feat(inputDetailsView): Added corrections from PR for JobDetails.js

* feat(inputDetailsView): Ran linter

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* feat: add pheweb_plots.js

 Duplicated from https://github.com/statgen/locuszoom-hosted/blob/c153d3ba465be5b171d073c0aa785e86c1cde109/assets/js/util/pheweb_plots.js

* chore: add required d3 libraries for PheWeb

* fix: update PheWeb code to make it compatible with our stack

* feat: code and storybook for PheWeb Manhattan

* fix: eslint fixes for PheWeb Manhattan

* feat: move Manhattan test data

* feat: rename SharedComponents folder to Components

* feat: improve accessibility by adding a SVG <details> to PheWeb plot

* Fix/directory name change fix (#1319)

* feat(no-access): add no access message (#1301)

* fix(directoryNameChangeFix): fixes issue with wrong directory name in filepaths

* fix(directoryNameChangeFix): ran linter

* fix(directoryNameChangeFix): reverted unintentionally changed file

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* feat: Results view with switch between PNG and PheWeb Manhattan

* fix: change part of PheWeb rendering into synchronous code

...instead of window.addEventListener("load", function() {

* fix: eslint fixes in Results view and PheWeb code

* fix: move from SharedComponents to Components

* feat: add downloadManhattanPlot for PheWeb viz

* fix: download larger image

* feat: improve test by using variable for s3 location

* feat: working test for ResultsPng

* fix: fix the ManhattanPlot storybook test

* feat: extra storybook test for possible error in ResultsPheWeb

* fix: apply fix proposed by @ocshawn

Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com>

* feat: improve exception handling in getWorkflowDetails

* Update src/Analysis/GWASResults/Views/Results/ResultsPheWeb.jsx

Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com>

* fix: add license NOTICE for the PheWeb library

...which requires the copyright notice to be included when using the code

* feat: improve Pheweb tooltip by adding a background color

* fix: fixed exception handling for ManhattanPlot

* fix: fix linting issues in GWASResults Results view

* feat: change PheWeb tooltip text to white

* fix: remove linkout to locuszoom

* feat: integrate argo-wrapper call to retry failed workflows

* fix: adjust expected response type to text

* feat: improved storybook for Home table

...and included a mock for the retry workflow endpoint

* feat: add extra storybook scenario for failed retry

* feat: use antd notification instead of alert

* feat: run eslint on ActionsDropDown

* feat: updated JEST test for ActionsDropdown

* Feat/attrition table input details (#1329)

* feat(no-access): add no access message (#1301)

* feat(attritionTableInputDetails): initial commit

* feat(attritionTableInputDetails): Created table that successfully prints to screen

* feat(attritionTableInputDetails): Created app specific CSS file for attrition table

* feat(attritionTableInputDetails): Fixed imports for JobDetails.test.jsx

* feat(attritionTableInputDetails): Wrote unit test

* feat(attritionTableInputDetails): Fixed linting issues

* feat(attritionTableInputDetails): Added working storybook logic for Attrition Table

* feat(attritionTableInputDetails): removed depracted comment

* feat(attritionTableInputDetails): formatted code for clarity remove unneeded print statement

* feat(attritionTableInputDetails): Updated string for null dates

* feat(attritionTableInputDetails): Ran auto formatter

* feat(attritionTableInputDetails): Reverted file to sprint10 version

* feat(attritionTableInputDetails): Reverted unintentionally changed file

* feat(attritionTableInputDetails): Updated AttritionTable to find objects that match group name instead of relying on array indexing

* feat(attritionTableInputDetails): Resolved eslint issue

* feat(attritionTableInputDetails): Reverted ActionsDropdown.test.jsx to version in sprint10 branch

* feat(attritionTableInputDetails): manually reverted ActionsDropdown.test.jsx

* feat(attritionTableInputDetails): ran eslint on ActionsDropdown to auto format it

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* TopFeat/results view top loci (#1337)

* feat(no-access): add no access message (#1301)

* feat(resultsViewTopLoci): Initial commit

* feat(resultsViewTopLoci): Fixed title for AF

* feat(resultsViewTopLoci): Got search to work on first column

* feat(resultsViewTopLoci): Got search to work on remaining columns

* feat(resultsViewTopLoci): Formatted code

* feat(resultsViewTopLoci): Seperated out logic for filtering into seperate file

* feat(resultsViewTopLoci): Ran linter

* feat(resultsViewTopLoci): Moved files into seperate folder

* feat(resultsViewTopLoci): Wrote unit tests

* feat(resultsViewTopLoci): Ran formatter

* feat(resultsViewTopLoci): Ran formatter and npm test

* feat(resultsViewTopLoci): Added comments back for ESLINT ignores

* feat(resultsViewTopLoci): Reverted unintentially changed file

* feat(resultsViewTopLoci): Updated search function to remove commas and added additional pageSizeOptions

* feat(resultsViewTopLoci): Wrote custom sorting function for variant

* feat(resultsViewTopLoci): Updated sort functions for AF and PVAL to parse Number before sort

* feat(resultsViewTopLoci): Simplified sort method for variant

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* fix: escape invalid SVG/XML characters in PheWeb code

* fix: add symbollic allele example in alt field

... and corresponding exception handling in case any other issue causes invalid
SVG/XML in the future

* Feat/maintain selected row results app (#1348)

* feat(no-access): add no access message (#1301)

* feat(maintainSelectedRowResultsApp): Added styles and logic to support maintaining bck color of selected row

* feat(maintainSelectedRowResultsApp): ran stylelint

* feat(maintainSelectedRowResultsApp): Updated storybook so it works

* feat(maintainSelectedRowResultsApp): Removed unneeded file and reverted unintentionally changed file

* feat(maintainSelectedRowResultsApp): Reverted unintentionally changed file to version in target branch

* feat(maintainSelectedRowResultsApp): Removed unneeded console logs

* feat(maintainSelectedRowResultsApp): Added functionality so row is selected on click

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Feat/results view header (#1349)

* feat(no-access): add no access message (#1301)

* feat(resultsViewHeader): Updated pageTitle prop to include selectedRow name on Results page

* feat(resultsViewHeader): Reverted unintentionally changed file

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Feat/two attrition tables (#1350)

* feat(no-access): add no access message (#1301)

* feat(twoAttritionTables): Created separate component to modularize attrition table

* feat(twoAttritionTables): Added prop types to Attrition table

* feat(twoAttritionTables): Renamed test for AttritionTableWrapper

* feat(twoAttritionTables): Refactored test for AttritionTableWrapper

* feat(twoAttritionTables): Resolved linting issues

* feat(twoAttritionTables): Reverted file to master

* feat(twoAttritionTables): Reverted file to sprint branch version

* feat(twoAttritionTables): Refactored test to validate correct output of data

* feat(twoAttritionTables): simplified error messaging logic

* feat(twoAttritionTables): Ran linter

* feat(twoAttritionTables): Added support for capitalized type columns and Outcome Phenotype label

* feat(twoAttritionTables): Ran linter

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Changed the manhattan plot key

* Feat/job details table update (#1361)

* feat(no-access): add no access message (#1301)

* feat(jobDetailsTableUpdate): Wrote totalSizes calculator

* feat(jobDetailsTableUpdate): Formatted code

* feat(jobDetailsTableUpdate): Added notes from discussion with Pieter as comments and commented example code

* feat(jobDetailsTableUpdate): refactored to use null instead of sentinel values and conditionally render table rows in JobDetails

* feat(jobDetailsTableUpdate): formatted code and updated teset

* feat(jobDetailsTableUpdate): Updated tests to test new functionality better

* feat(jobDetailsTableUpdate): Updated tests

* feat(jobDetailsTableUpdate): Reverted file to sprint version

* feat(jobDetailsTableUpdate): Began working on logic to removeOutcomeFromVariablesData function

* feat(jobDetailsTableUpdate): Wrote logic to remove outcome from covariates row

* feat(jobDetailsTableUpdate): Renamed final size to total size

* feat(jobDetailsTableUpdate): Renamed final size to total size

* feat(jobDetailsTableUpdate): formatted code

* feat(jobDetailsTableUpdate): Refactored to use new architecture, working prototype

* feat(jobDetailsTableUpdate): Ran linter

* feat(jobDetailsTableUpdate): Refactored tests so they pass

* feat(jobDetailsTableUpdate): Fixed linting issues

* feat(jobDetailsTableUpdate): Removed unneeded object from JobDetails test

* feat(jobDetailsTableUpdate): Ran linter on test code

* feat(jobDetailsTableUpdate): Ran linter and removed unneeded console log

* feat(jobDetailsTableUpdate): Ran linter

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Feat/qq plot (#1363)

* feat(no-access): add no access message (#1301)

* feat(qqPlot): Added working prototype

* feat(qqPlot): Refactored directory structure, wrote CSS to show button

* feat(qqPlot): Have QQ Plot rendering in Application with test data

* feat(qqPlot): Styled modal

* feat(qqPlot): Ran eslint-new

* feat(qqPlot): Removed console logs and formatted code

* feat(qqPlot): Added logic to disabled View QQ Plot button and show tooltip

* feat(qqPlot): Began working on storybook

* feat(qqPlot): Updated storybook to have unique ID and ref for QQ plot API response

* feat(qqPlot): Removed ref to removed function for displayTop in QQPlotModal

* feat(qqPlot): Added inline styles so storybook looks pleasant

* feat(qqPlot): Replaced excessive es-lint comments with a single es-lint ignore for file

* feat(qqPlot):  wrote very simple unit test

* feat(qqPlot): Ran stylelint and resolved issues, ran ESLINT, resolved issues

* feat(qqPlot): Removed unneeded cruft from Results.jsx

* feat(qqPlot): removed unintentionally changed file, formatted code

* feat(qqPlot): removed unneeded ESLINT comments

* feat(qqPlot): Ran linter

* feat(qqPlot): Reverted file

* feat(qqPlot): Updated inline style to use className

* feat(qqPlot): Ran linter

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* Fix/results app home table fix (#1367)

* feat(no-access): add no access message (#1301)

* fix(resultsAppHomeTableFix): Added code to prevent application crashing in case of user sorting when finishedAt is null

* fix(resultsAppHomeTableFix): Fixed issue with filterByDateRange excluding selection for same day due to granularity of comparison

* fix(resultsAppHomeTableFix): Ran linter

* fix(resultsAppHomeTableFix): Reverted file to sprint branch version

* fix(resultsAppHomeTableFix): Updated import order for consistency, removed unintentional conditional change

* fix(resultsAppHomeTableFix): Formatted code for clarity

* fix(resultsAppHomeTableFix): Moved individual functions for tableDataProcessing into a single file to make importing more terse

* fix(resultsAppHomeTableFix): Removed unneeded line break

---------

Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>

* fix: adjust labels shown in GWAS Results Input view

* fix(gwasAppButtonWidth): Updated CSS for progress bar buttons. Update should be isolated to progress bar (#1341)

* fix: fix failing unit test for JobDetails

* fix: Handle workspace page when no default paymodel exists (#1373)

* Feat/vadc sprint15 (#1377)

* Feat/add back button (#1375)

* feat(addBackButton): Removed selector to hide back button

* feat(addBackButton): Wrote logic to toggle back button and refactored to use reusable function

* feat(addBackButton): Renamed file based on new usage

* feat(addBackButton): Formatted code for readability

* feat(addBackButton): Added comment per reviewers request to clarify code

* feat(addBackButton): Renamed file and removed comment per reviewer's request

* Fix/hiccup hometable (#1376)

* fix(hiccupHometable): Began writing unit test

* fix(hiccupHometable): Wrote unit test

* fix(hiccupHometable): Formatted code for clarity

* fix(hiccupHometable): updated test description

* fix: adjust subtractDates to deal with empty end date

* fix: adjust to return -- when endDate is still empty

...per discussion / review request

* Fix: Portal updates to match new hatchery changes (#1374)

* Fix: Portal updates to match new hatchery changes
* Ensure workspace launch is disabled only in commons where paymodels are available

* update all minor version dependencies (#1366)

* "@babel/core": "^7.22.9",
* "@emotion/react": "^11.11.1",
* "@fortawesome/react-fontawesome": "^0.2.0",
* "@gen3/guppy": "^0.16.1",
* "@gen3/ui-component": "^0.11.4",
* "clipboard-plus": "^1.1.0",
* "core-js": "^3.31.1",
* "echarts": "^5.4.3",
* "echarts-for-react": "^3.0.2",
* "enzyme": "^3.11.0",
* "enzyme-adapter-react-16": "^1.15.7",
* "js-search": "^2.0.1",
* "jszip": "^3.10.1",
* "lodash": "^4.17.21",
* "mock-local-storage": "^1.1.24",
* "prop-types": "^15.8.1",
* "react-query": "^3.39.3",
* "react-virtualized": "^9.22.5",
* "recharts": "^2.7.2",
* "redux": "^4.2.1",
* "redux-thunk": "^2.4.2",
* "regenerator-runtime": "^0.13.11",
* "semver": "^7.5.4",
* "@babel/eslint-parser": "^7.22.9",
* "@babel/plugin-proposal-object-rest-spread": "^7.20.7",
* "@babel/plugin-transform-modules-commonjs": "^7.22.5",
* "@babel/plugin-transform-runtime": "^7.22.9",
* "@babel/preset-env": "^7.22.9",
* "@babel/preset-react": "^7.22.5",
* "@babel/runtime-corejs3": "^7.22.6",
* "@storybook/cli": "^7.1.1",
* "@testing-library/jest-dom": "^5.17.0",
* "@types/core-js": "^2.5.5",
* "@types/enzyme": "^3.10.13",
* "@types/react-redux": "^7.1.25",
* "@types/regenerator-runtime": "^0.13.1",
* "babel-plugin-dev-expression": "^0.2.3",
* "eslint-plugin-import": "^2.27.5",
* "eslint-plugin-jsx-a11y": "^6.7.1",
* "eslint-plugin-react": "~7.33.0",
* "eslint-plugin-react-hooks": "^4.6.0",
* "eslint-plugin-storybook": "^0.6.13",
* "jest-localstorage-mock": "^2.4.26",
* "msw-storybook-addon": "^1.8.0",
* "postcss": "^8.4.27",
* "redux-mock-store": "^1.5.4",
* "relay-compiler-webpack-plugin": "^9.1.0",
* "stylelint": "^15.10.2",

* PXP-11018: render some html tags in study descriptions (#1369)

* PXP-11018: render some html tags in study descriptions

* PXP-11041: Discovery page: remove empty “Tags by category” component (#1381)

Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>

* fix fomatting

* PXP-11042: Discovery page update tooltip text (#1382)

* address comments and fix logic

* linting change

---------

Co-authored-by: Jarvis <113449836+jarvisraymond-uchicago@users.noreply.github.com>
Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>
Co-authored-by: Mingfei Shao <mshao1@uchicago.edu>
Co-authored-by: Sai Shanmukha Narumanchi <nss10@outlook.com>
Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com>
Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
Co-authored-by: Thanh Dang Nguyen <thanhnd@uchicago.edu>
Co-authored-by: pieterlukasse <pieterlukasse@gmail.com>
Co-authored-by: qiongl-CTDS <51421191+qiongl-CTDS@users.noreply.github.com>
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@jarvisraymond-uchicago @pieterlukasse @thanh-nguyen-dang