Development#1285
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feat: enable CAS based import & extend molecule:clean to query for CAS metadata
* feat: refactor support bubble to block spamming. - use google recaptcha v3 for bot detection - implement rate limiting on support bubble submissions - add server-side validation for gibberish content * copilot review comment fix * decrease the ratelimit * fix: tidy up recaptcha from composer * fix: composer warning suppressed, psr-5 warning resolved --------- Co-authored-by: Venkata Nainala <mailcs76@gmail.com>
* configure laravel CSP * include composer.lock changes * fix pinting issues * Update app/Support/Csp/Policies/NmrxivPolicy.php Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix pinting issues * Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix pinting issues * fix: moved csp-report endpoint to admin routes and removed unused socialite orcid package * chore: pint updates * fix: ziggyvue import updates and also added link to the csp-report in the admin view * chore: prettier formating added * build dev image for CSP --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chandu Nainala <mailcs76@gmail.com>
remove the ziggy.js file
…s dashboard (#1277) * feat: Enable search and filtering on projects dashboard - update code to unify project badge logic - move the project badge to a reusable component * prettier formating * run prettier * copilot review changes * add one time command to update project statuses * fix: unmatched return type error fix * fix: style changes to filter button * fix: manifest json regenerated * chore: pint formatting changes * fix: composer update * fix: npm audit fixes --------- Co-authored-by: Venkata Nainala <mailcs76@gmail.com>
* fix: modify nmrxiv policy to fix csp issues * fix:remove single policy addition and make multiple additions for font-src directive * pint formatting * updated policy to include missing directives * update ORCID API endpoint in csp policy * more formatting and removal of duplicates. * NMRIUM_URL * add nmrium in frame-src and connect-src directives * revert dev build tag change * revert missing tags for dev-latest images * deploy latest csp changes * fix:revert dev-build changes
* add test coverage workflow * add .env.ci * use postgres instead of mysql for testing * add meilisearch test config and adjust redis to local for ci * remove healtchecks for redis and meilisearch services * fix the db mismatch issues in CI * fix filesystem driver issue * rectify .env file name * add .env.ci.test with correct DB_PASSWORD * skip ELNSubmissionTrackingTest.php test that requires external API access in CI environment * ELNSubmissionTrackingTest * fixx failing tests * update Code cov token * update test-coverage workflow and .env.ci.test * fix LicenseFactory issue * update composer install command and revert license factory changes * fix env for mielisearch in ci * run test for every commit/sync/pr/merge to dev and main branch * linting fix * skip ELNSubmissionTrackingTest and allow read and write permission for code coverage * inherit secrets * Update PostgreSQL image version to 17 --------- Co-authored-by: Chandu Nainala <mailcs76@gmail.com>
* add test coverage workflow * add .env.ci * use postgres instead of mysql for testing * add meilisearch test config and adjust redis to local for ci * remove healtchecks for redis and meilisearch services * fix the db mismatch issues in CI * fix filesystem driver issue * rectify .env file name * add .env.ci.test with correct DB_PASSWORD * skip ELNSubmissionTrackingTest.php test that requires external API access in CI environment * ELNSubmissionTrackingTest * fixx failing tests * update Code cov token * update test-coverage workflow and .env.ci.test * fix LicenseFactory issue * update composer install command and revert license factory changes * fix env for mielisearch in ci * run test for every commit/sync/pr/merge to dev and main branch * linting fix * skip ELNSubmissionTrackingTest and allow read and write permission for code coverage * inherit secrets * feat: add tests for models * chore: pint formatting of some tests * fix: failing tests due to URL generation and storage issues * run pint formatting * fix: failing tests * run pint formatting * revert test database name --------- Co-authored-by: Chandu Nainala <mailcs76@gmail.com>
* feat: add comprehensive project tests and factories * fix: add unit tests for NMRiumModel * pint formatting * composer update symfony/http-foundation * Update app/Events/ProjectMemberAdded.php Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update app/Events/AddingProjectMember.php Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Initial plan (#1296) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> * :void * Initial plan (#1297) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> * revert copilot changes * fix failing tests * revert db name in phpunit.xml * run lint --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: Chandu Nainala <mailcs76@gmail.com>
* chore: csp optimization remove csp routes and commands, update policy to remove unused sources * review changes * pint and formatting --------- Co-authored-by: Chandu Nainala <mailcs76@gmail.com>
* fix: overdue embargo handling state and notices * composer update
* fix: dashboard search box loading issue * fix: include case sensitive search in dashboard search box * composer update
…o development # Conflicts: # composer.lock
![github-code-quality[bot]](https://avatars.githubusercontent.com/u/9919?s=60&v=4){kind=small}
| datasetDetails.studySlug + | ||
| "/" + | ||
| datasetDetails.datasetSlug; | ||
| let safeDatasetUrl = datasetUrl; |
Extract PublicSiteHeader, deposit CTA helpers, and public nav config so public pages share consistent navigation and branding.
Register /faqs as a named Inertia route alongside other public pages.
Redesign welcome, about, legal, and browse pages to use PublicSiteHeader, unified footer, and shared empty-state styling.
Consolidate structure drawing helpers and align search, predict, and upload flows with the updated public search interface.
Improve notification badge placement and tighten header action spacing.
Assert welcome, about, FAQs, legal, and projects routes render expected components.
Dedupe and pre-bundle openchemlib for reliable structure editor loading.
Increase memory_limit for queue-heavy workloads and add supervisord Horizon worker plus .env.example notes for local Sail setups.
Add scheduled repair command and enrichment inspectors, and invoke them from submission and project processing jobs when metadata is incomplete.
Surface backup failures clearly and align job tests with the revised backup workflow.
Ensure invite flows and API resources respect updated authorization rules for collaborators and reviewers.
Introduce normalized text search endpoints under v1/search, keep deprecated routes for compatibility, and refresh OpenAPI documentation.
Expose /search for catalog browsing, wire unified search to the new API, and share pagination and fetch utilities across public search views.
Improve public Inertia layouts, citation and access dialogs, and compound browsing while keeping shared header navigation consistent.
Extend dashboard query handling and refresh the projects index with search, pagination, and workspace-aware filtering.
Factories often create projects without attaching the owner to project_users, so dashboard sharing UI now reports owner correctly via userProjectRole.
Exercise repair command dispatch paths, inspector query methods, and ProcessProject unique lock TTL to satisfy Codecov patch thresholds.
* feat(ui): add shared public site header and navigation utilities Extract PublicSiteHeader, deposit CTA helpers, and public nav config so public pages share consistent navigation and branding. * feat(pages): add dedicated FAQs Inertia page and route Register /faqs as a named Inertia route alongside other public pages. * refactor(ui): adopt shared header and refresh public-facing pages Redesign welcome, about, legal, and browse pages to use PublicSiteHeader, unified footer, and shared empty-state styling. * refactor(search): improve unified search and structure editor UX Consolidate structure drawing helpers and align search, predict, and upload flows with the updated public search interface. * style(ui): polish authenticated app layout header controls Improve notification badge placement and tighten header action spacing. * test: add feature coverage for public Inertia pages Assert welcome, about, FAQs, legal, and projects routes render expected components. * chore(build): update frontend lockfiles and Vite openchemlib config Dedupe and pre-bundle openchemlib for reliable structure editor loading. * fix(tests): use RefreshDatabase for public Inertia page tests Routes for welcome, about, FAQs, legal, and public projects pages query the database for stats; migrations must run in CI for valid Inertia responses. * fix(tests): use SSR Inertia assertions for public page tests The test suite renders Inertia via the root Blade template (data-page), not X-Inertia JSON. Use assertInertiaPageComponent to match existing tests.
Increase memory_limit for queue-heavy workloads and add supervisord Horizon worker plus .env.example notes for local Sail setups.
Surface backup failures clearly and align job tests with the revised backup workflow. Co-authored-by: Nisha Sharma <nisha.sharma@uni-jena.de>
* fix(compounds): repair missing compound info during processing Add scheduled repair command and enrichment inspectors, and invoke them from submission and project processing jobs when metadata is incomplete. * test(compounds): expand coverage for repair and inspector helpers Exercise repair command dispatch paths, inspector query methods, and ProcessProject unique lock TTL to satisfy Codecov patch thresholds.
* fix(auth): align project and study policies with member access Ensure invite flows and API resources respect updated authorization rules for collaborators and reviewers. * fix(tests): align reviewer coverage with current review UI Return owner from userProjectRole when the user owns the project but is not on the members pivot, and match policy PR tests to Project/Show until the public browse refactor lands.
…o development # Conflicts: # resources/js/Pages/Public/Compounds.vue # resources/js/Shared/Footer.vue # resources/js/Shared/PublicSiteHeader.vue # resources/js/Shared/UnifiedSearch.vue # resources/js/Utils/publicNavItems.js # tests/Feature/AboutPageTest.php # tests/Feature/FaqsPageTest.php # tests/Feature/LegalPagesTest.php # tests/Feature/Project/ProjectControllerAdditionalCoverageTest.php # tests/Feature/PublicProjectsPageTest.php # tests/Feature/WelcomePageTest.php
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Fixes #1326
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Fixes #608