Feat: add "Execution" view to results app to enable a view of the (parsed/interpreted) workflow logs#72
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* merge all changes back into master (#15) * initial setup changes setting homepage and logo (#3) * feat(gwasAppSetup): Initial commit (#5) * feat(gwasAppSetup): Initial commit * feat(gwasAppSetup): Fixed 508 issues * feat(gwasAppSetup): Got storybook to work and added CI test * feat(gwasAppSetup): Edited CI test to match Spike CI test * Chore/update 0.10.78 (#6) * Update/release 0 10 67 (#57) * update version to v0.10.61 * update version to v0.10.67 * update version to v0.10.67 * Update ci.yaml * update build to use start.sh for automation (#59) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update to 0.10.73 (#63) * Chore/update docker (#64) * update Dockerfile * update .env files * Chore/update 0.10.74 (#66) * update Dockerfile * update .env files * update to gen3.2 0.10.74 * Added Loading.tsx component and integrated Suspense (#65) * Added Loading.tsx component and integrated Suspense * Moved Loading.tsx to components folder and updated _app.tsx * update to 0.10.77 (#67) * update to 0.10.78 (#68) --------- Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Advaith Mahendrakar <120632885+AdvaithMahendrakar12@users.noreply.github.com> * VADC-1644: add test support for RTKQuery (#8) * add cohortAp and hooks * add teamProjectHooks.ts * setup jest test storybook with rtkQuery hooks * add test support for RTKQ add teamProjectHooks.test * clean up test * clean up test * add sharp * add sharp * update to 0.10.79 * revert CohortDefinitions refactor test-utils * add error to useProjectHooks * remove hook story * remove cohortApi to keep PR smaller * Update vadc email (#10) * Update navigation.json all email references that currently are vadc@lists.uchicago.edu → change to vadc-support@gen3.org * Update TeamProjectModal.tsx all email references that currently are vadc@lists.uchicago.edu → change to vadc-support@gen3.org * feat(resultsAppSetup): Commented out all JS files, deleted all CSS fi… (#11) * feat(resultsAppSetup): Commented out all JS files, deleted all CSS files and modified * feat(resultsAppSetup): renamed all .stories.jsx files to .oldStories.tsx * feat(resultsAppSetup): created placeholder setup for app * feat(resultsAppSetup): resolved ESLINT errors * feat(resultsAppSetup): fixed compilation error * feat(resultsAppSetup): updated files to avoid typescript errors * feat(resultsAppSetup): changed placeholder variable so it doesn't render in UI * VADC-1613: GWASUIApp: Phenotype Selection View (#13) Port GWASUIApp: Add Phenotype Selection View for selecting Outcome Phenotype and Covariate Phenotype to new framework. add lint-fix command to package json * Chore/merge base fork (#14) * Update/release 0 10 67 (#57) * update version to v0.10.61 * update version to v0.10.67 * update version to v0.10.67 * Update ci.yaml * update build to use start.sh for automation (#59) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update to 0.10.73 (#63) * Chore/update docker (#64) * update Dockerfile * update .env files * Chore/update 0.10.74 (#66) * update Dockerfile * update .env files * update to gen3.2 0.10.74 * Added Loading.tsx component and integrated Suspense (#65) * Added Loading.tsx component and integrated Suspense * Moved Loading.tsx to components folder and updated _app.tsx * update to 0.10.77 (#67) * update to 0.10.78 (#68) * update to 0.10.79 (#71) add sharp add testing support * update to 0.10.80 (#73) * add mantine theme that uses config colors (#76) * add mantine theme that uses config colors * run lint fix --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update to 0.10.81 (#77) * try and fix build * try and fix build --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Advaith Mahendrakar <120632885+AdvaithMahendrakar12@users.noreply.github.com> * VADC-1646: cohort middleware api (#9) * add tests for cohortApi * add getSourceId query * add more queries * add more queries: histogram * add all used queries * add all used queries * add sample data to nextJS API routes * fix lint error * remove comma * VADC-1684: workflow api for the results app (#12) * start of workflowApi * add presigned URLs, monthly * add api endpoints for development/testing * add endpoint data and test * update test typing * add tests for presignedURLs * ad test for fetch from presigned url returns 401 * add documentation * fix name of cohortUtils.ts * fix bad conflict resolution --------- Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> * add missing login image (#7) update first time use modal text Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> --------- Co-authored-by: Jarvis <113449836+jarvisraymond-uchicago@users.noreply.github.com> Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Advaith Mahendrakar <120632885+AdvaithMahendrakar12@users.noreply.github.com> Co-authored-by: smvgarcia <111767892+smvgarcia@users.noreply.github.com> * use old dockerfile (#16) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update dockerfile (#17) * use old dockerfile * update dockerfile --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * add ff path for qa (#18) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * add ff path for qa (#19) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fix basepath for images in next (#20) * fix basepath for images in next * fix docker loading config file * fix loading of images that already have path added --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * bump gen3 version to 82 (#21) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Vadc data commons integration (#23) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * lock fix --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fix build errors (#24) * fix lint errors * fix build errors --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Fix/security (#25) * fix spacing issues for precommit * fix exeptions for precommit --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) * upstream update (#26) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * Chore/upstream update (#27) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * Update README.md (uc-cdis#86) add unrelated-histories information * Fix docker start (uc-cdis#88) * fix Docker not starting * fix Docker not starting * update env files (uc-cdis#89) * VADC-1741: add atlas page (#28) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Release 0.10.89 (uc-cdis#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * npm cleanup and remove ff directory (#29) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update ContentDatabase paths (uc-cdis#93) * Chore/fork sync (#30) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) * Update README.md (uc-cdis#86) add unrelated-histories information * Fix docker start (uc-cdis#88) * fix Docker not starting * fix Docker not starting * update env files (uc-cdis#89) * Release 0.10.89 (uc-cdis#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (uc-cdis#93) * overwrite dockerfile q :q exit help end * dockerfile fix --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * VADC-1740: update storybook (#32) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Set up user permission for Apps on QA (#33) * VADC-1755: setup permision for atlas * VADC-1755: setup permision for Gen3 GWAS --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * point atlas to correct url (#34) * point atlas to correct url (#35) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fix env dev file (#36) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update to 0.10.91 (uc-cdis#96) * atlas fix iframe url (#37) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * VADC-1670: Results App Page Setup (#38) * fix version to 0.10.91 (uc-cdis#97) * VADC-1761: change how user refresh is triggered (#39) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * update to 0.10.92 (uc-cdis#104) * update Gen3 FF to 0.10.92 (#43) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) * Update README.md (uc-cdis#86) add unrelated-histories information * Fix docker start (uc-cdis#88) * fix Docker not starting * fix Docker not starting * update env files (uc-cdis#89) * Release 0.10.89 (uc-cdis#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (uc-cdis#93) * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * update to 0.10.91 (uc-cdis#96) * fix version to 0.10.91 (uc-cdis#97) * update to 0.10.92 (uc-cdis#104) * fix syntax * revert navigation * remove duplicates/fix name --------- Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * add dataLibrary config (#44) * (VADC-1776): Update logo and text on home page (#49) * VADC-1776: Update logo and text on home page * add VA logo to footer --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * VADC-1776: Make VA logo smaller file (#50) * Remove va footer logo (#52) Remove va footer logo * VADC-1781: update logo (#53) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * (CADC-1664): GWASResults: Hometable Initial Setup (#55) * GWASResults: Hometable Initial Setup * fix Team Project selector * add back button to apps * fix iframe url on OHDSI Atlas * CADC-1787: add OCC logo to footer (#56) * update to node 22.11, gen3FF 0.10.94 (uc-cdis#107) * Feat: add PLP app steps and fix CSRF issue (#51) New Features Initial version of PLP steps in frontend-framework. Includes PLP Attrition table and integration with argo-wrapper /submit endpoint Bug Fixes adds missing 'x-csrf-token': csrfToken, header (needed for POST requests) Deployment changes depends on specific versions of cohort-middleware and argo-wrapper (TODO - add release numbers) * (CADC-1666): Create Input Details Page (#59) * CADC-1666: Create Input Details Page * CADC-1666: Job Details Table (#61) * CADC-1796: Remove the word GWAS and change the URL (#63) * CADC-1671: Results App Page Download Buttons (#62) * (CADC-1801): add a logo to the browser tab too for QA (#64) * Feat/plp improvements (#60) * feat: multiple improvments to PLP app - add remaining size, training set and test set sizes to submit modal - limit test set relative size - update Randomforest parameters - add CommaSeparatedNumberInput type with tooltip - add labels and better styling - add Lasso parameters and improve the RandomForest ones - introduce multiselect for CRITERION - add SVM model option * feat: improve SVM form * feat: improve checkbox style in LassoParameters * fix: add back "seed" field * feat: added real state and dispatch to SelectModelAndParameters storybook * tmp: temporarily setting session update time to 30min instead of 5min to test... * fix: change arguments to arrays instead of csv strings * fix: change initial value of percentageOfDataToUseAsTest to null * fix: adjust testset size calculation * fix: adjust code to deal with percentageOfDataToUseAsTest being empty * fix: show -- for empty date * fix: set default model parameters at mount/init * feat: update PLP icon * fix: fix the finishedAt date in results table for running workflows * fix: fix wofklow details endpoint usage; remove "observation" from outcome window * small card text changes * fix: adjust RandomForest params * fix: change MAX_LEAF_NODES to number * Update ResourceBrowser.tsx (#67) * fix: remove prefix from team project name display * fix: improve MAX_SAMPLES in RandomForest params page * fix: change MAX_LEAF_NODES to list type * feat: enable ResultsPng * tmp: change BOOTSTRAP bool to list[] * fix: add some basic image src check * fix: add snyk comment / ignore * feat: convert ResultsPng to TS * feat: working mock endpoint for plot * feat: better styling for results plot * feat: move download all button to right side * fix: change last 3 params of RandomForest to lists * fix: fix the quoted numbers problem * feat: support other roc plots in results * fix: fix for SVM parameters that should be a list * feat: add back button; restore .trim() * fix: fix accessibility issue in tab list by removing spaces from value used in ARIA * feat: remove unused image * feat: add better mock plot * tmp: testing short updateSessionTime --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Andrew Prokhorenkov <aprokh@uchicago.edu> * (CADC-1814): Add Analysis tab for Notebooks * update git node version * update gen3 to 0.11.11 * Upstream integration (#71) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) * Update README.md (uc-cdis#86) add unrelated-histories information * Fix docker start (uc-cdis#88) * fix Docker not starting * fix Docker not starting * update env files (uc-cdis#89) * Release 0.10.89 (uc-cdis#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (uc-cdis#93) * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * update to 0.10.91 (uc-cdis#96) * fix version to 0.10.91 (uc-cdis#97) * update to 0.10.92 (uc-cdis#104) * update to node 22.11, gen3FF 0.10.94 (uc-cdis#107) * update package lock * update docker * update docker and node ci version * update package lock * update gen3 --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * Upstream integration (#72) * update to eslint 9 (#78) * cleanup navigation to point ot pages, update gen3 to 0.10.82, rename workspace config (#79) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * fixs for precommit security check * fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (uc-cdis#84) * update to @gen3/ff 0.10.85 (uc-cdis#85) * Update README.md (uc-cdis#86) add unrelated-histories information * Fix docker start (uc-cdis#88) * fix Docker not starting * fix Docker not starting * update env files (uc-cdis#89) * Release 0.10.89 (uc-cdis#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (uc-cdis#93) * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * update to 0.10.91 (uc-cdis#96) * fix version to 0.10.91 (uc-cdis#97) * update to 0.10.92 (uc-cdis#104) * update to node 22.11, gen3FF 0.10.94 (uc-cdis#107) * update git node version * update gen3 to 0.11.11 * update pacage lock --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> * add favicon (uc-cdis#109) * add favicon * add favicon --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Add Datadog/remove faro (uc-cdis#105) * add Datadog/remove faro * remove Grafana * CADC-1823: UI refreshing too often on protected content pages (#73) * CADC-1823: reset sessionConfig to defalt values (#74) * CADC-1824: Remove notebooks from the Analysis tab in QA (#75) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * CADC-1826: Workspaces- 'no pay model' (#76) Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * (CADC-1821): Incorporate caps bar on PLP App and Results App (#77) * update gen3 to 0.11.18 * fix placement of workflow info (#78) * update gen3 to 0.11.19 and add footer links * add PLP notebook to analysis page (#80) Co-authored-by: sara volk de garcia <smvgarcia@uchicago.edu> * Update analysisTools.json (#81) * update to 0.11.27 to fix logout issue (#82) * fix(submit): No dashes in model name (#83) * Update JobSubmitModal.tsx (uc-cdis#84) * (CADC-1853): Add runtime to results app (uc-cdis#85) * CADC-1853: Add runtime to results app * CADC-1853: fix storybook ada error --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * CADC-1881: PLP Fix Frontend not passing model parameters (uc-cdis#86) * update to Gen3 FEF 0.11.43 (uc-cdis#127) * add GradioApp support (uc-cdis#128) * add GradioApp support * fix default * update dependencies * update more dependencies * update more dependencies * cleanup unused files * fix build * feat: upgrade storybook to v9 note: these changes were made automatically by the upgrade script `npx storybook@latest upgrade` * roll back changes for ada * disab le a11y * disable stories * cleanup * cleanup * remove dd app --------- Co-authored-by: Jarvis <113449836+jarvisraymond-uchicago@users.noreply.github.com> Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Advaith Mahendrakar <120632885+AdvaithMahendrakar12@users.noreply.github.com> Co-authored-by: smvgarcia <111767892+smvgarcia@users.noreply.github.com> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: pieterlukasse <pieterlukasse@gmail.com> Co-authored-by: Andrew Prokhorenkov <aprokh@uchicago.edu> Co-authored-by: sara volk de garcia <smvgarcia@uchicago.edu> Co-authored-by: J. Q. <55899496+jawadqur@users.noreply.github.com> Co-authored-by: vzpgb <45467497+vzpgb@users.noreply.github.com>
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Link to JIRA ticket if there is one: https://ctds-planx.atlassian.net/browse/VPODC-237
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