Fix/gwas id bug #1056
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Fix/gwas id bug #1056
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kmhernan
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Aug 11, 2022
kmhernan
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Aug 11, 2022
alilahrime
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Aug 18, 2022
* feat(gwas-ui-demo): integrate middleware endpts, add status list and modal template * add manifest object * feat(gwas-ui-demo): move filter to prev step & change dispay of statuses * feat(gwas-ui-demo): form submit conditions * fix: naming of GWAS app * fix: change correct naming * feat(gwas-ui-demo): refactor workflow list & add prefixed id * feat(gwas-ui-demo): refactor covar delete & edit btn layout * feat(gwas-ui-demo): change source id hot fix * feat(gwas-ui-demo): change step description & template * feat(gwas-ui-demo): refactor queries for cohort definitions and concepts, add loading status * feat(gwas-ui-demo): add loading fetch logic and submission and cancel for gwas workflows * fix: update packages-lock.json * feat(gwas-ui-demo): filter empty cohort defs & default page size * feat(gwas-ui-demo): redirect to wts login if no creds * feat(gwas-ui-demo): fetch sources after wts & fix covariate removal * feat(gwas-ui-demo): comment cohort concept filter * feat(gwas-ui-demo): resolve eslint errors * fix(stylelint): remove !important * feat(gwas-ui-demo): remove comment, cancel status * feat(gwas-ui-demo): remove comments and unneeded declarations * feat(gwas-ui-demo): update gwas template version * feat(gwas-ui-demo): add conservative querying config * feat(gwas-ui-demo): delete old gwas app * feat(gwas-ui-demo): linter changes * feat(gwas-ui-demo): refetch workflow status list every minute * feat(gwas-ui-demo): fix interval * feat(gwas-ui-demo): uninstall react-is * feat(gwas-ui-demo): add job status refetch interval * feat(gwas-ui-demo): run eslint * feat(dev): add atlas icram content security to dev html * feat(PXP-9868): change gwas description, add spinners * feat(gwas-ui-demo): add quantitative vs case control selection * feat(PXP-9943): add hare dropdown to quant gwas * patch extra exception handling part missing part from PR #994 * feat(gwas-ui-demo): add gwas type descriptions * feat(gwas-ui-demo): add reset btn for gwas type * feat(gwas-ui-demo): add first 4 steps for case control * feat(gwas-ui-demo): add separate hare dropdowns, update req bodies * adding extra stats review step to case-control flow (#999) * feat(gwas-ui-demo): add details and notification to quant final step, refactor hare fetches in case/control * feat(gwas-ui-demo): remove isBinary from forms * feat(gwas-ui-demo): add info button placeholders * feat(gwas-ui-demo): make review header smaller * fix(gwas-ui-demo): fix covariate delete in case control * feat(gwas-ui-demo): add job name to quant req * filtering concepts to allow only continuous ones to be selected (#1000) * fix(gwas-ui-demo): feedback step changes, add cohort button, remove delete * feat(gwas-ui-demo): add info button text to most of quant * adding a event listener to capture messages posted by the app (#1002) * adding a event listener to capture messages posted by the app This generic solution allows for any future app to use postMessage to keep user session alive * adjust HARE concept id (#1004) * Fix/case control hare (#1005) * fix(casecontrol): hare concept ID and boolean function * fix(requests): add queryConfig to stop spurious requests from being triggered * adjust concept type filter to reflect new type (#1006) * feat add workflow name (#1008) * adding overlap check (#1009) * Chore/update text workflow steps (#1010) * change text/styling in pipeline wizard * update text and style for GWASUIApp Co-authored-by: Craig Barnes <craigrbarnes@uchicago.edu> * using new cohort-middleware endpoint for fetching covariates by concept type (#1011) * Fix/gwas submission params (#1013) * chore(template): update template name * fix(hare): pass hare population parameter * fix(casecontrol): lots of bug fixing for submission (#1014) * Fix/gwas state issues (#1015) * fix(reset): reset more state vars * fix(nextButton): add next button disabled logic for case-control * fix(quant-ui): persist current table page after selection, start filter functionality * separating value from description in hare dropdown & merging case-control dropdowns (#1018) * separating value from description in hare dropdown * change to ensure dropdown description is updated when the data is refreshed * merge case and control HARE dropdowns into a single selection ...showing the cohort sizes in the dropdown. Also aligned both wizards to use similar code, e.g. calling a function for the description * fix dropdown width issue ...and better naming * fix(PXP-10058): widen jobs submitted on pipeline selection page * Add HARE concept id in submit & make HARE selection mandatory (#1022) * add HARE concept id to submit workflow call * making HARE selection mandatory for 1st wizard * making HARE selection mandatory for 2nd wizard * fix(gwas-ui): remove extra workflow lists, add cohort btn reposition * refactor(gwas-ui): remove comments, add prop type * Fix warnings (#1023) * solutions to get rid of warnings - "useForm" warning in dev mode - Cannot update a component (`CaseControlGWAS`) while rendering a different component (`ConceptsStatsByHare`). ..."useForm" warning happened because the `form.setFieldsValue` was called in the wrong step of the wizard, when no form was rendered yet ...the other warning happened because previous code was trying to update a state item of the outer component while its own rendering was still taking place... ALSO: improved some naming, fixed some typos. * fix issue where fetchConceptStatsByHare was not being called after changing cohort * fix(hare): pass concept value name (#1024) * fix(hare): pass concept value name * fix(typo): add missing brackets * refactor(gwas-ui): add first step to quant & case control, move fetches * fix covariates in submit request by using the selectedCovariates state variable (#1025) * refactor(casecontrol): add control cohort & covariate step * fix(gwas-ui): add separate file for static jsx labels * View logs for failed jobs (#1026) * add view logs option for failed status * let's not use var but let * feat(gwas-ui): add props and imports to cov select component * fix(VADC-29): delete covariate mutation from step handler * fix(VADC-29): remove handleNext, resolve quant cov selection bug * refactor(gwas-ui): add gwas type select, delete handleNext * refactor(gwas-ui-cc): break up cohortSelect, add custom dichotomous template * fix(gwas-ui-cc): disable other cohort table in cd select * feat(gwas-ui): add reusable search, reformat covariates, add more hare select logic * feat(gwas-ui): add hare select in cc, misc styling * fix(gwas-ui-cc): resolve most eslint errors in refactor * feat(gwas-ui): parametrize hare select in workflow params * fix(gwas-ui): comment out refactor * simplified CustomDichotomousSelect by removing edit option and added 1st storybook example * Revert "fix(gwas-ui): comment out refactor" This reverts commit 1b456d0. * putting back react-is was removed by mistake?? * revert styling change * update storybook and add MSW https://mswjs.io/ * fix Covariates.jsx and respective storybook test * basic storybook test for CustomDichotomousSelect * (WIP) new storybook for WorkflowParameters * downgrade storybook this helped fix webpack issues. Now both webpack AND storybook work (even at the same time!). The storybook version I now get when running is 6.4.19 instead of 6.5.9 * added init values for WorkflowParameters test/story * feat(gwas-refactor): add case control submission progress * feat(gwas-refactor): display success w/ status * test for GWASFormSubmit * feat(gwas-ui-demo): add outcome selection review to quant * feat read argo template version from config (#1037) * feat(gwas-refactor): add quant to final step & workflow params * feat(gwas-refactor): complete quant submission * fix harebreakdown description * add validation for numPCs and HARE selection in Case-control flow * add/fix validation for numPCs and HARE selection in Quantitative flow * feat(gwas-refactor): update submit req body for selected concepts * fix use gwasTemplate for template_version * feat add react tour (#1042) * feat(gwas-refactor): eslint changes, update req body * fix(gwas-refactor): typo * Revert "feat add react tour (#1042)" This reverts commit 351b55c. * feat add react tour (#1044) * fix(gwas-submission): use concept value name (#1045) * feat(text): slight changes to user facing text in case-control (#1047) * fix add space for parameter name and input, add missing tour button (#1049) * fix gwas ui eslint errors (#1050) * fix(eslint): delete previous case control and quantitative * fix(eslint): import/prop validation, camelcase, consistent returns * fix(eslint): custom dichotomous removal * fix(eslint): fix all current eslint errors, include cd removal * fix(eslint): escape quotes * fix(gwas-ui): remove babel-eslint, sync plugins * fix(eslint): eslint resolved after syncing babel * fix(gwas-ui): revert dev html w/ clinical trials * fix(package): updated lock * chore(dep): update trim newlines * fix(deps): rebuild lock * fix(dep): remove trimlines dep * fix(deps): handle trim newlines issue within default-browser-id deps * fix(dep): meow * Fix/gwas id bug (#1056) * fix(typo): uiid vs uuid oof * refactor(cleanup): move & rename files, remove comments, cov delete * fix(eslint): defaultProps > defaultPropTypes * fix(gwas-ui): fix bugs & pr feedback (#1058) Co-authored-by: Andrew Prokhorenkov <aprokh@uchicago.edu> Co-authored-by: Kyle Hernandez <kmhernan84@gmail.com> Co-authored-by: pieterlukasse <pieterlukasse@gmail.com> Co-authored-by: UchicagoZchen138 <86243966+UchicagoZchen138@users.noreply.github.com> Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> Co-authored-by: Craig Barnes <craigrbarnes@uchicago.edu> Co-authored-by: UchicagoZchen138 <zchen138@uchicago.edu>
cmlsn
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Nov 29, 2022
* feat(gwas-ui-demo): integrate middleware endpts, add status list and modal template * add manifest object * feat(gwas-ui-demo): move filter to prev step & change dispay of statuses * feat(gwas-ui-demo): form submit conditions * fix: naming of GWAS app * fix: change correct naming * feat(gwas-ui-demo): refactor workflow list & add prefixed id * feat(gwas-ui-demo): refactor covar delete & edit btn layout * feat(gwas-ui-demo): change source id hot fix * feat(gwas-ui-demo): change step description & template * feat(gwas-ui-demo): refactor queries for cohort definitions and concepts, add loading status * feat(gwas-ui-demo): add loading fetch logic and submission and cancel for gwas workflows * fix: update packages-lock.json * feat(gwas-ui-demo): filter empty cohort defs & default page size * feat(gwas-ui-demo): redirect to wts login if no creds * feat(gwas-ui-demo): fetch sources after wts & fix covariate removal * feat(gwas-ui-demo): comment cohort concept filter * feat(gwas-ui-demo): resolve eslint errors * fix(stylelint): remove !important * feat(gwas-ui-demo): remove comment, cancel status * feat(gwas-ui-demo): remove comments and unneeded declarations * feat(gwas-ui-demo): update gwas template version * feat(gwas-ui-demo): add conservative querying config * feat(gwas-ui-demo): delete old gwas app * feat(gwas-ui-demo): linter changes * feat(gwas-ui-demo): refetch workflow status list every minute * feat(gwas-ui-demo): fix interval * feat(gwas-ui-demo): uninstall react-is * feat(gwas-ui-demo): add job status refetch interval * feat(gwas-ui-demo): run eslint * feat(dev): add atlas icram content security to dev html * feat(PXP-9868): change gwas description, add spinners * feat(gwas-ui-demo): add quantitative vs case control selection * feat(PXP-9943): add hare dropdown to quant gwas * patch extra exception handling part missing part from PR #994 * feat(gwas-ui-demo): add gwas type descriptions * feat(gwas-ui-demo): add reset btn for gwas type * feat(gwas-ui-demo): add first 4 steps for case control * feat(gwas-ui-demo): add separate hare dropdowns, update req bodies * adding extra stats review step to case-control flow (#999) * feat(gwas-ui-demo): add details and notification to quant final step, refactor hare fetches in case/control * feat(gwas-ui-demo): remove isBinary from forms * feat(gwas-ui-demo): add info button placeholders * feat(gwas-ui-demo): make review header smaller * fix(gwas-ui-demo): fix covariate delete in case control * feat(gwas-ui-demo): add job name to quant req * filtering concepts to allow only continuous ones to be selected (#1000) * fix(gwas-ui-demo): feedback step changes, add cohort button, remove delete * feat(gwas-ui-demo): add info button text to most of quant * adding a event listener to capture messages posted by the app (#1002) * adding a event listener to capture messages posted by the app This generic solution allows for any future app to use postMessage to keep user session alive * adjust HARE concept id (#1004) * Fix/case control hare (#1005) * fix(casecontrol): hare concept ID and boolean function * fix(requests): add queryConfig to stop spurious requests from being triggered * adjust concept type filter to reflect new type (#1006) * feat add workflow name (#1008) * adding overlap check (#1009) * Chore/update text workflow steps (#1010) * change text/styling in pipeline wizard * update text and style for GWASUIApp Co-authored-by: Craig Barnes <craigrbarnes@uchicago.edu> * using new cohort-middleware endpoint for fetching covariates by concept type (#1011) * Fix/gwas submission params (#1013) * chore(template): update template name * fix(hare): pass hare population parameter * fix(casecontrol): lots of bug fixing for submission (#1014) * Fix/gwas state issues (#1015) * fix(reset): reset more state vars * fix(nextButton): add next button disabled logic for case-control * fix(quant-ui): persist current table page after selection, start filter functionality * separating value from description in hare dropdown & merging case-control dropdowns (#1018) * separating value from description in hare dropdown * change to ensure dropdown description is updated when the data is refreshed * merge case and control HARE dropdowns into a single selection ...showing the cohort sizes in the dropdown. Also aligned both wizards to use similar code, e.g. calling a function for the description * fix dropdown width issue ...and better naming * fix(PXP-10058): widen jobs submitted on pipeline selection page * Add HARE concept id in submit & make HARE selection mandatory (#1022) * add HARE concept id to submit workflow call * making HARE selection mandatory for 1st wizard * making HARE selection mandatory for 2nd wizard * fix(gwas-ui): remove extra workflow lists, add cohort btn reposition * refactor(gwas-ui): remove comments, add prop type * Fix warnings (#1023) * solutions to get rid of warnings - "useForm" warning in dev mode - Cannot update a component (`CaseControlGWAS`) while rendering a different component (`ConceptsStatsByHare`). ..."useForm" warning happened because the `form.setFieldsValue` was called in the wrong step of the wizard, when no form was rendered yet ...the other warning happened because previous code was trying to update a state item of the outer component while its own rendering was still taking place... ALSO: improved some naming, fixed some typos. * fix issue where fetchConceptStatsByHare was not being called after changing cohort * fix(hare): pass concept value name (#1024) * fix(hare): pass concept value name * fix(typo): add missing brackets * refactor(gwas-ui): add first step to quant & case control, move fetches * fix covariates in submit request by using the selectedCovariates state variable (#1025) * refactor(casecontrol): add control cohort & covariate step * fix(gwas-ui): add separate file for static jsx labels * View logs for failed jobs (#1026) * add view logs option for failed status * let's not use var but let * feat(gwas-ui): add props and imports to cov select component * fix(VADC-29): delete covariate mutation from step handler * fix(VADC-29): remove handleNext, resolve quant cov selection bug * refactor(gwas-ui): add gwas type select, delete handleNext * refactor(gwas-ui-cc): break up cohortSelect, add custom dichotomous template * fix(gwas-ui-cc): disable other cohort table in cd select * feat(gwas-ui): add reusable search, reformat covariates, add more hare select logic * feat(gwas-ui): add hare select in cc, misc styling * fix(gwas-ui-cc): resolve most eslint errors in refactor * feat(gwas-ui): parametrize hare select in workflow params * fix(gwas-ui): comment out refactor * simplified CustomDichotomousSelect by removing edit option and added 1st storybook example * Revert "fix(gwas-ui): comment out refactor" This reverts commit 1b456d0. * putting back react-is was removed by mistake?? * revert styling change * update storybook and add MSW https://mswjs.io/ * fix Covariates.jsx and respective storybook test * basic storybook test for CustomDichotomousSelect * (WIP) new storybook for WorkflowParameters * downgrade storybook this helped fix webpack issues. Now both webpack AND storybook work (even at the same time!). The storybook version I now get when running is 6.4.19 instead of 6.5.9 * added init values for WorkflowParameters test/story * feat(gwas-refactor): add case control submission progress * feat(gwas-refactor): display success w/ status * test for GWASFormSubmit * feat(gwas-ui-demo): add outcome selection review to quant * feat read argo template version from config (#1037) * feat(gwas-refactor): add quant to final step & workflow params * feat(gwas-refactor): complete quant submission * fix harebreakdown description * add validation for numPCs and HARE selection in Case-control flow * add/fix validation for numPCs and HARE selection in Quantitative flow * feat(gwas-refactor): update submit req body for selected concepts * fix use gwasTemplate for template_version * feat add react tour (#1042) * feat(gwas-refactor): eslint changes, update req body * fix(gwas-refactor): typo * Revert "feat add react tour (#1042)" This reverts commit 351b55c. * feat add react tour (#1044) * fix(gwas-submission): use concept value name (#1045) * feat(text): slight changes to user facing text in case-control (#1047) * fix add space for parameter name and input, add missing tour button (#1049) * fix gwas ui eslint errors (#1050) * fix(eslint): delete previous case control and quantitative * fix(eslint): import/prop validation, camelcase, consistent returns * fix(eslint): custom dichotomous removal * fix(eslint): fix all current eslint errors, include cd removal * fix(eslint): escape quotes * fix(gwas-ui): remove babel-eslint, sync plugins * fix(eslint): eslint resolved after syncing babel * fix(gwas-ui): revert dev html w/ clinical trials * fix(package): updated lock * chore(dep): update trim newlines * fix(deps): rebuild lock * fix(dep): remove trimlines dep * fix(deps): handle trim newlines issue within default-browser-id deps * fix(dep): meow * Fix/gwas id bug (#1056) * fix(typo): uiid vs uuid oof * refactor(cleanup): move & rename files, remove comments, cov delete * fix(eslint): defaultProps > defaultPropTypes * fix(gwas-ui): fix bugs & pr feedback (#1058) Co-authored-by: Andrew Prokhorenkov <aprokh@uchicago.edu> Co-authored-by: Kyle Hernandez <kmhernan84@gmail.com> Co-authored-by: pieterlukasse <pieterlukasse@gmail.com> Co-authored-by: UchicagoZchen138 <86243966+UchicagoZchen138@users.noreply.github.com> Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> Co-authored-by: Craig Barnes <craigrbarnes@uchicago.edu> Co-authored-by: UchicagoZchen138 <zchen138@uchicago.edu>
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Bug Fixes
fix typo for id variable in custom dichotomous variable object
addressed feedback on file naming and folder structure
New features
covariate deletion in case control and quant