Testing external contributor PR #195#197
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* 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) * 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 (#84) * update to @gen3/ff 0.10.85 (#85) * Update README.md (#86) add unrelated-histories information * Fix docker start (#88) * fix Docker not starting * fix Docker not starting * update env files (#89) * Release 0.10.89 (#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (#93) * update apps config path (#94) * add theme colors into safelist (#95) * update to 0.10.91 (#96) * fix version to 0.10.91 (#97) * update to 0.10.92 (#104) * update to node 22.11, gen3FF 0.10.94 (#107) * update git node version * update gen3 to 0.11.11 * add favicon (#109) * add favicon * add favicon --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Add Datadog/remove faro (#105) * add Datadog/remove faro * remove Grafana * update gen3 to 0.11.18 * update gen3 to 0.11.19 and add footer links * update to Gen3 FEF 0.11.43 (#127) * add GradioApp support (#128) * add GradioApp support * fix default * update dependencies * update more dependencies * update more dependencies * add the hugging face apps (#129) * update tailwind paths for Gen3/frontend (#136) * fix default * update package-lock * fix build error * remove gradio * remove older tailwind path * update gen3 version and package lock * update gen3 to 0.11.47 * update gen3 to 0.11.48 remove unneeded cookies-next * Feat/footer (#139) * add the hugging face apps * Update README for clarity on Gen3 Data Commons * update development configuration * darken footer * partially revert footer changed (#140) * update docker image for faster builds (#141) * Changes to landingPage (#142) * Revert landingPage change (#143) * Update from old Gen3 Docs to new Gen3 Docs link (#146) * Update Gen3 docs link Update the default Documentation link from the old Gen3 docs site (https://gen3.org/resources/user/) to the new Gen3 docs site (https://docs.gen3.org/) * Update to new docs link Change the workspace docs reference from the old docs (https://gen3.org/resources/user/analyze-data/) to the new docs (https://docs.gen3.org/gen3-resources/user-guide/analyze-data/) * Update to v0.11.58 (#147) * add height to tailwind config * add package * add height to tailwind config * update to 0.11.55 * update deps * update to v0.11.58 * update to 0.11.59 (#148) * update node version in ci * update to nextjs 15.5.7 (#153) * Add Authz Middleware (#156) * update to new auth model * update to 0.12.0 * Setup for data dog * Add missing icons and update tailwind config (#158) * add missing icons * update app with dataDog * update tailwind config * update tailwind config * refactor data dog * update to NextJS 15.5.9 (#162) * Add linkWithIconAndTooltip custom cell renderer (#166) * fix a bug when app page is not found react expecting null * Update middleware to use code generation (#167) * update to NextJS 15.5.9 * fix fetchArboristResources to use the correct endpoint * get working scanPaths and update middleware * set NODE_ENV for dev and prod builds * update to 0.12.5 * update to 0.12.5 * new package-lock.json * add package lock * new package-lock.json part 2 * update dependencies * update dependencies (#169) * update dependencies (#171) * update gen3 to 12.10 * update to node24 (#173) * Remove authz_default.json (#176) * remove support for authz_default.json and update tools to fail if @gen3/toolsff not built or fails * update to @gen3 0.12.12, remove authz record from workspace entry * dont load datadog if values are not set, add comment for adding values * Update copyright year and owner in LICENSE file (#181) * Change license to Apache Software License 2.0 (#182) Updated the license to Apache Software License 2.0 and modified copyright year. * Bump Node.js version to 24.13.0 and update Dockerfile and CI workflow accordingly. (#185) * GFF-281: pull config and mount on volume (#98) * update Dockerfile * update hostname * update hostname * update hostname * update hostname * update hostname * update labnding page * update landing page * update middleware config and Dockerfile * add Dockerfile.main and update workflow to specify Dockerfile location * bump dependencies to version 0.12.16 and update Dockerfile with volume configuration changes * add header metadata configuration file for Gen3 Data Commons * update start script, middleware config, and Dockerfile for standalone server setup and permissions adjustments * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update workflow to use Dockerfile.config and add new icons to gen3.json config * update icons * update workflow to include override tag name and add deployment instructions to documentation * bump dependencies to version 0.12.17 * add debug log to print Datadog application ID environment variable * integrate Datadog initialization with public runtime configuration inputs * remove unnecessary debug logs and update middleware matcher configuration * Associate Tailwind theme names to mantine CSS variables and load theme dynamically. (#187) * Add initial configuration for Canine Data Commons Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * Refactor Mantine theme handling to dynamically support CSS variables and theme merging * remove canine config * Remove CSS variables support and related environment configuration * Remove debugging console logs from Tailwind config * Update LICENSE to include full Apache License v2.0 text --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * update gen3 to 0.12.22 * update version number * Update discovery.json (#189) Update docs links to use new Gen3 docs sites * Add Test Config for CI (#186) * Add Test Config for CI * Add fix * revery ci * Fix * Set `NODE_ENV` to `test` in Dockerfile.test * Update image name for test * Add compute_tag job * Add integration tests * File issue * Reduce workflows * Revert the change * Merge into single workflow * Revert change * Update integration_tests.yaml * Switch to `start_with_config.sh` for Dockerfile.config, update shell to Bash in start.sh, standardize `npm prune` flags in Dockerfiles. --------- Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> * Skip CI image build and integration tests for forked repository (#191) * Skip CI image build and integration tests for forked repository * Update integration_tests.yaml * Update ci_image_build_push.yaml * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 (#192) * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 * Remove unused `CustomRowRenderers` and associated registration logic * Add configuration for clinical data analysis and update Gen3 explorer settings - Introduced `clinicalDataAnalysis.json` and `analysisTools.json` for supporting clinical and cohort analysis. - Updated `explorer.json` with new fields, tabs, and chart configurations for subjects and files. - Adjusted development environment API settings. * Bump `lodash` and `@types/lodash` to v4.17.23 * Fix workflow fork check * Update package lock remove victory and validator (#196) * Update package lock remove victory and validator * add back victory --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Update to version 0.12.25 (#197) * Update to version 0.12.25 * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump `@gen3/core` and `@gen3/frontend` to version 0.12.26 and update `package-lock.json`. * Update node to 24.14.0 and npm to 11.9.0 * Add dependabot for frontend packages * Update update_dependencies.yaml * update to Gen3 0.12.27 (uc-cdis#202) * Update integration_tests.yaml * test fix for non gen3 directory builds * Fix dependabot failures (uc-cdis#205) * test fix for non gen3 directory builds 2 * move dependbot files to correct location * move dependbot files to correct location 2 * fix yaml errors * fix yaml errors * fix yaml errors * fix yaml errors * Log publicConfig for debugging (uc-cdis#209) * Log publicConfig for debugging * Use server-side environment variables for publicConfig initialization. * Add IGV app registration and update Gen3 dependencies to v0.12.30 (uc-cdis#210) * Enhance GitHub Actions workflow with dynamic tag computation and Dockerfile selection logic" (uc-cdis#211) * Update Dockerfile path in GitHub Actions to "Dockerfile.config" * Enhance GitHub Actions workflow with dynamic tag computation and Dockerfile selection logic. * Update to 0.12.31 (uc-cdis#213) * MC2DP-725: handle auth wildcards for sub directories * update color vars * Update to 0.12.31 (uc-cdis#216) * fix login cionfig values * Bump @gen3 dependencies to version 0.12.32 in package.json and packag… (uc-cdis#218) * Bump @gen3 dependencies to version 0.12.32 in package.json and package-lock.json * Update README with node version requirement * add .npmrc enforcing node version * set global DD verable names * cleanup env files * add cron to automaticly open prs to sync forked repos * Bump Gen3 dependencies to version 0.12.33 and replace `pluralize` with `pluralize-ts`. * run npm audit fix, update package lock * Update to React 19.2 (uc-cdis#224) * Update `react` and `react-dom` to v19.2.4, switch Gen3 dependencies to local `.yalc` references, and adjust `package-lock.json` dependencies. * Bump `@gen3/core`, `@gen3/frontend`, and `@gen3/toolsff` to v0.12.34; update `react` and `react-dom` to v19.2.14; add GraphiQL dependency and styles. * add login page to next config for local dev * (MC2DP-649): enable config of 404 and 403 pages * (MC2DP-649): update FF to 0.12.35 * (MC2DP-649): fix missing comma * MC2DP-739: change config to new default config * MC2DP-739: update to latest ff * update package lock * fix authentication logic error, remove unused feature * remove comment * move things around * remove files that should not change --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> 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> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Krishna Agarwal <159047652+krishnaa05@users.noreply.github.com> Co-authored-by: smvgarcia <111767892+smvgarcia@users.noreply.github.com> Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> Co-authored-by: krishna <krishnaa@uchicago.edu> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
ocshawn
added a commit
that referenced
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May 8, 2026
* 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) * 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 (#84) * update to @gen3/ff 0.10.85 (#85) * Update README.md (#86) add unrelated-histories information * Fix docker start (#88) * fix Docker not starting * fix Docker not starting * update env files (#89) * Release 0.10.89 (#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (#93) * update apps config path (#94) * add theme colors into safelist (#95) * update to 0.10.91 (#96) * fix version to 0.10.91 (#97) * update to 0.10.92 (#104) * update to node 22.11, gen3FF 0.10.94 (#107) * update git node version * update gen3 to 0.11.11 * add favicon (#109) * add favicon * add favicon --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Add Datadog/remove faro (#105) * add Datadog/remove faro * remove Grafana * update gen3 to 0.11.18 * update gen3 to 0.11.19 and add footer links * update to Gen3 FEF 0.11.43 (#127) * add GradioApp support (#128) * add GradioApp support * fix default * update dependencies * update more dependencies * update more dependencies * add the hugging face apps (#129) * update tailwind paths for Gen3/frontend (#136) * fix default * update package-lock * fix build error * remove gradio * remove older tailwind path * update gen3 version and package lock * update gen3 to 0.11.47 * update gen3 to 0.11.48 remove unneeded cookies-next * Feat/footer (#139) * add the hugging face apps * Update README for clarity on Gen3 Data Commons * update development configuration * darken footer * partially revert footer changed (#140) * update docker image for faster builds (#141) * Changes to landingPage (#142) * Revert landingPage change (#143) * Update from old Gen3 Docs to new Gen3 Docs link (#146) * Update Gen3 docs link Update the default Documentation link from the old Gen3 docs site (https://gen3.org/resources/user/) to the new Gen3 docs site (https://docs.gen3.org/) * Update to new docs link Change the workspace docs reference from the old docs (https://gen3.org/resources/user/analyze-data/) to the new docs (https://docs.gen3.org/gen3-resources/user-guide/analyze-data/) * Update to v0.11.58 (#147) * add height to tailwind config * add package * add height to tailwind config * update to 0.11.55 * update deps * update to v0.11.58 * update to 0.11.59 (#148) * update node version in ci * update to nextjs 15.5.7 (#153) * Add Authz Middleware (#156) * update to new auth model * update to 0.12.0 * Setup for data dog * Add missing icons and update tailwind config (#158) * add missing icons * update app with dataDog * update tailwind config * update tailwind config * refactor data dog * update to NextJS 15.5.9 (#162) * Add linkWithIconAndTooltip custom cell renderer (#166) * fix a bug when app page is not found react expecting null * Update middleware to use code generation (#167) * update to NextJS 15.5.9 * fix fetchArboristResources to use the correct endpoint * get working scanPaths and update middleware * set NODE_ENV for dev and prod builds * update to 0.12.5 * update to 0.12.5 * new package-lock.json * add package lock * new package-lock.json part 2 * update dependencies * update dependencies (#169) * update dependencies (#171) * update gen3 to 12.10 * update to node24 (#173) * Remove authz_default.json (#176) * remove support for authz_default.json and update tools to fail if @gen3/toolsff not built or fails * update to @gen3 0.12.12, remove authz record from workspace entry * dont load datadog if values are not set, add comment for adding values * Update copyright year and owner in LICENSE file (#181) * Change license to Apache Software License 2.0 (#182) Updated the license to Apache Software License 2.0 and modified copyright year. * Bump Node.js version to 24.13.0 and update Dockerfile and CI workflow accordingly. (#185) * GFF-281: pull config and mount on volume (#98) * update Dockerfile * update hostname * update hostname * update hostname * update hostname * update hostname * update labnding page * update landing page * update middleware config and Dockerfile * add Dockerfile.main and update workflow to specify Dockerfile location * bump dependencies to version 0.12.16 and update Dockerfile with volume configuration changes * add header metadata configuration file for Gen3 Data Commons * update start script, middleware config, and Dockerfile for standalone server setup and permissions adjustments * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update workflow to use Dockerfile.config and add new icons to gen3.json config * update icons * update workflow to include override tag name and add deployment instructions to documentation * bump dependencies to version 0.12.17 * add debug log to print Datadog application ID environment variable * integrate Datadog initialization with public runtime configuration inputs * remove unnecessary debug logs and update middleware matcher configuration * Associate Tailwind theme names to mantine CSS variables and load theme dynamically. (#187) * Add initial configuration for Canine Data Commons Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * Refactor Mantine theme handling to dynamically support CSS variables and theme merging * remove canine config * Remove CSS variables support and related environment configuration * Remove debugging console logs from Tailwind config * Update LICENSE to include full Apache License v2.0 text --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * update gen3 to 0.12.22 * update version number * Update discovery.json (#189) Update docs links to use new Gen3 docs sites * Add Test Config for CI (#186) * Add Test Config for CI * Add fix * revery ci * Fix * Set `NODE_ENV` to `test` in Dockerfile.test * Update image name for test * Add compute_tag job * Add integration tests * File issue * Reduce workflows * Revert the change * Merge into single workflow * Revert change * Update integration_tests.yaml * Switch to `start_with_config.sh` for Dockerfile.config, update shell to Bash in start.sh, standardize `npm prune` flags in Dockerfiles. --------- Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> * Skip CI image build and integration tests for forked repository (#191) * Skip CI image build and integration tests for forked repository * Update integration_tests.yaml * Update ci_image_build_push.yaml * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 (#192) * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 * Remove unused `CustomRowRenderers` and associated registration logic * Add configuration for clinical data analysis and update Gen3 explorer settings - Introduced `clinicalDataAnalysis.json` and `analysisTools.json` for supporting clinical and cohort analysis. - Updated `explorer.json` with new fields, tabs, and chart configurations for subjects and files. - Adjusted development environment API settings. * Bump `lodash` and `@types/lodash` to v4.17.23 * Fix workflow fork check * Update package lock remove victory and validator (#196) * Update package lock remove victory and validator * add back victory --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Update to version 0.12.25 (#197) * Update to version 0.12.25 * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump `@gen3/core` and `@gen3/frontend` to version 0.12.26 and update `package-lock.json`. * Update node to 24.14.0 and npm to 11.9.0 * Add dependabot for frontend packages * Update update_dependencies.yaml * update to Gen3 0.12.27 (uc-cdis#202) * Update integration_tests.yaml * test fix for non gen3 directory builds * Fix dependabot failures (uc-cdis#205) * test fix for non gen3 directory builds 2 * move dependbot files to correct location * move dependbot files to correct location 2 * fix yaml errors * fix yaml errors * fix yaml errors * fix yaml errors * Log publicConfig for debugging (uc-cdis#209) * Log publicConfig for debugging * Use server-side environment variables for publicConfig initialization. * Add IGV app registration and update Gen3 dependencies to v0.12.30 (uc-cdis#210) * Enhance GitHub Actions workflow with dynamic tag computation and Dockerfile selection logic" (uc-cdis#211) * Update Dockerfile path in GitHub Actions to "Dockerfile.config" * Enhance GitHub Actions workflow with dynamic tag computation and Dockerfile selection logic. * Update to 0.12.31 (uc-cdis#213) * MC2DP-725: handle auth wildcards for sub directories * update color vars * Update to 0.12.31 (uc-cdis#216) * fix login cionfig values * Bump @gen3 dependencies to version 0.12.32 in package.json and packag… (uc-cdis#218) * Bump @gen3 dependencies to version 0.12.32 in package.json and package-lock.json * Update README with node version requirement * add .npmrc enforcing node version * set global DD verable names * cleanup env files * add cron to automaticly open prs to sync forked repos * Bump Gen3 dependencies to version 0.12.33 and replace `pluralize` with `pluralize-ts`. * run npm audit fix, update package lock * Update to React 19.2 (uc-cdis#224) * Update `react` and `react-dom` to v19.2.4, switch Gen3 dependencies to local `.yalc` references, and adjust `package-lock.json` dependencies. * Bump `@gen3/core`, `@gen3/frontend`, and `@gen3/toolsff` to v0.12.34; update `react` and `react-dom` to v19.2.14; add GraphiQL dependency and styles. * add login page to next config for local dev * (MC2DP-649): enable config of 404 and 403 pages * (MC2DP-649): update FF to 0.12.35 * (MC2DP-649): fix missing comma * MC2DP-739: change config to new default config * MC2DP-739: update to latest ff * update package lock * fix authentication logic error, remove unused feature * remove comment * move things around * update next version * update FF to 0.12.41 * fix package lock --------- Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> 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> Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Krishna Agarwal <159047652+krishnaa05@users.noreply.github.com> Co-authored-by: smvgarcia <111767892+smvgarcia@users.noreply.github.com> Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> Co-authored-by: krishna <krishnaa@uchicago.edu> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
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