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Update pinned version, support new BE - #15
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* feat: refactor Drug widgets * feat: simplify list of widgets * feat: update diseases * feat: update disease sections * fix: lint issue * feat: migrate target profile
* feat: refactor Drug widgets * feat: simplify list of widgets * feat: update diseases * feat: update disease sections * fix: lint issue * feat: migrate target profile * feat: create api types * feat: run codegen * feat: variant widgets migration * feat: remove comments * feat: credible set sections * feat: credible set sections * fix: molqtl query * feat: update credible set widgets * feat: update study sections
* feat: refactor Drug widgets * feat: simplify list of widgets * feat: update diseases * feat: update disease sections * fix: lint issue * feat: migrate target profile * feat: create api types * feat: run codegen * feat: variant widgets migration * feat: remove comments * feat: credible set sections * feat: credible set sections * fix: molqtl query * feat: update credible set widgets * feat: evidence sections * feat: update study sections
Small typo
…and tooltips (#804)
…erience (#807) Co-authored-by: HelenaCornu <hcornu@ebi.ac.uk>
* feat(previews):use gh cli for fork pr checkout for deployment * feat(previews):use gh cli for fork pr checkout for deployment
* show download error message in bibliography widgets * do not wait for timer if have response
* feat(gwas):add credible set counts * feat(gwas):fix typo
* chore: update/validate EFO identifiers * chore: update/validate EFO identifiers in OTAR project description
…widget (#956) * improve colors and expanded row highlighting * use new widget * darker grey for na bars
* [Platform]: Update dependencies and enhance Associations Toolkit with Gene Enrichment Analysis features * Modify biome.json to include platform source in coverage exclusions * Update yarn.lock for dependency version upgrades * Add AnalysisMenu component to AssociationsView * Integrate GeneEnrichmentAnalysisModal and GeneEnrichmentProvider in DiseaseAssociations * fix: Update biome.json coverage exclusions and upgrade dependencies in yarn.lock * [Platform]: Implement Gene Enrichment Analysis features * Add GeneEnrichmentAnalysisForm component for library selection * Integrate library fetching logic in GeneEnrichmentProvider * Update reducer to handle library fetch actions * Modify GeneEnrichmentAnalysisModal to display the new form * Adjust AnalysisMenu to conditionally render based on context state * Update DiseaseAssociations to utilize the new modal structure * [Platform]: Enhance Gene Enrichment Analysis components * Update GeneEnrichmentAnalysisForm to include gene set source selection * Refactor GeneEnrichmentAnalysisModal to use Dialog component for improved UI * Modify reducer to manage libraries and loading states * Improve form layout and styling for better user experience * Implement Gene Enrichment Analysis features: add actions and reducer for analysis inputs and runs, replace GeneEnrichmentAnalysisForm with AnalysisContainer, and introduce new components for analysis form and results display. Also, add GSEA API integration for running analyses. * Enhance Gene Enrichment Analysis UI: Introduce results table and tree view components for better visualization of analysis results. Update modal dimensions based on results availability and refine GSEA API response structure. * Enhance AnalysisContainer and introduce RunHistorySidebar: Add functionality for managing analysis runs, including selection and deletion. Refactor main content rendering logic and improve UI layout for better user experience. * ref: update buttons text and help text * Refactor Gene Enrichment Analysis components: Enhance UI layout and functionality across multiple components, including the introduction of a sunburst visualization for analysis results. Update modal dimensions and improve state management in the reducer. Add utility functions for color mapping and pathway hierarchy management. * Integrate Plotly sunburst visualization in Gene Enrichment Analysis: Add new components for Plotly sunburst chart and results display, enhance filtering options, and update package dependencies for improved data visualization. Refactor existing components to accommodate new functionality. * Remove sunburst visualization from AnalysisResults component: Comment out the sunburst rendering logic to streamline the display options for analysis results. * Update GeneEnrichmentAnalysis component text and reorganize SunburstFilters layout: Change GSEA label to full form and reposition NES Range filter for improved clarity and usability. * Enhance Gene Enrichment Analysis components: Implement scroll lock functionality in modal, improve zoom and pan controls in Plotly sunburst chart, and update interaction hints in results display. Refactor layout and labels for better clarity and usability across various components. * Update ResultsTable component to open links in a new tab for improved user experience. * Update OtPopper component to increase zIndex for improved layering in UI. * Enhance Gene Enrichment Analysis components: Add activeRunId prop to AnalysisResults for better tracking of analysis runs, implement reset functionality in PlotlySunburstChart, and improve layout and sorting options in ResultsTreeView for enhanced usability. * Update API URLs in Gene Enrichment Analysis components to use production endpoints for GSEA and libraries, enhancing deployment readiness. * Add configuration for API base URL in Gene Enrichment Analysis components and refactor API calls to use the new constant. Update text labels for clarity in AnalysisForm component. * "Overlap Genes" to "Overlapping Genes" in ResultsTable component * Add library display names for Gene Enrichment Analysis components * Add tooltips to columns in ResultsTable * Update ResultsTreeView component to replace faFlask icon with faFile and modify legend * ResultsTreeView: change label from "root pathways" to "top-level pathways" * ResultsTreeView: update icon colors for significant and non-significant nodes * ResultsTable: append current date to data downloader file * ResultsTreeView: adjust icon colors for parent and terminal pathways * Add tooltips for NES, P-value, FDR, and gene count in ResultsTreeView * GeneEnrichmentAnalysisModal: link to GSEA docs in html * InputOverlap type and integrate it into analysis results * [Platform]: revert accidental biome.json platform/src inclusion Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * [Platform]: Implement row metrics for associations and update table layout components * Add novelty metrics and detail panel to associations toolkit * Refactor Associations state management to include enableIndirect functionality * Refactor Associations context management: replace AssociationsStateContext with dedicated contexts for query, URL, and data handling * Refactor Associations components to streamline state management and improve code structure * Refactor Associations components to replace useAotfContext with specific hooks for query, URL, and data management * feat: add new table components for Associations Toolkit - Implemented TableBody component to render table rows and handle focus state. - Created TableCell component for individual cell rendering with tooltip support. - Added TableFooter component for pagination and legend display. - Developed TableHeader component to manage header rendering and sorting functionality. - Introduced useAssociationsData hook for data fetching and state management. - Added static data sources for associations with detailed metadata. * feat: Add RequiredControl and SliderControl components for enhanced user input options feat: Implement NameFilter component for improved entity search functionality feat: Create DataDownloader component for exporting association data in various formats feat: Develop DataUploader component for uploading and validating entity lists feat: Introduce NestedItem component for displaying validation results in a nested format feat: Add ValidationQuery GraphQL query for entity validation refactor: Update AssociationsToolkit index to include new components and improve structure style: Remove unused CSS styles related to Associations Toolkit header and legend * feat: Enhance Associations Toolkit with sorting and URL state management features * refactor: Remove unused facet filter logic and streamline state management in Associations context * docs: Update README to clarify context provider responsibilities and URL parameter details * feat: Implement Novelty Trend visualization and associated components - Added NoveltySparkline component for displaying novelty trends using a time series plot. - Introduced NoveltyDrawer for detailed novelty trend analysis with overall and data source breakdowns. - Created NoveltyInlinePanel for inline display of novelty trends within table rows. - Updated TableAssociations to integrate novelty trend visualizations and handle state management for novelty panels. - Enhanced AssociationsFocusContext to manage novelty panel state. - Modified GraphQL queries to fetch novelty time series data for targets and diseases. - Refactored row metrics to include novelty trend information. - Improved loading states and error handling for novelty data fetching. * feat: Enhance NoveltyInlinePanel with icon and improve focus context handling * feat: Refactor novelty charts and queries to include pagination and remove unused xDomain prop * feat: Refactor GeneEnrichmentAnalysis to use context hooks and update state handling; add key prop to AssociationsView in DiseaseAssociations and TargetAssociations * feat(tests):adjust locator due to PR changes * chore(cleanups):delete gsea file. * feat: solo app * feat: enhance access control for analysis page and update metrics visibility --------- Co-authored-by: polrus <polina@ebi.ac.uk> Co-authored-by: david oluwasusi <daviddamilola20@gmail.com>
Merges 222 upstream commits (v0.12.11 → v0.16.2) while preserving all E2G custom components (IGV browser, E2G predictions, LD section, ingestion page). Adapts E2G/LD sections to upstream's new widget-based architecture (SummaryRenderer/SectionsRenderer) and ports NavBar customizations to TypeScript. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…l backend Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Multi-stage build: yarn build -> nginx, no SSL (for compose/local use). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…gnore Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Only keep E2GPredictions and LinkageDisequilibrium sections that our backend serves. Remove ShouldAccessPPP component from HomePage. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Schema stitching in backend now proxies all OT fields, so upstream sections (VariantEffect, EVA, GWASCredibleSets, etc.) work again. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
merge: true on Query.meta so Apollo shallow-merges incoming Meta fields with existing ones instead of overwriting. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The old version tried to fetch genomes.json from igv.org which was blocked by CORS policy, breaking the IGV browser initialization. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The backend now fetches LD from Ensembl in the background and returns linkageDisequilibriumStatus (pending|complete|failed|not_available) instead of blocking the request. Update the LD section accordingly: - request linkageDisequilibriumStatus in LDQuery + LDSummaryFragment - hasData keeps the section/summary avatar visible while pending/failed (count is 0 on a variant's first view), not only when data exists - Body polls every 5s while pending (auto-stops on resolve/unmount) and renders spinner (pending) / error (failed) / table (complete) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Add a parallel Enhancer2Gene downloads page (pages/E2GDownloadsPage) and point the /downloads route at it; OT's DownloadsPage is left untouched to avoid upstream merge conflicts. The page mirrors OT's downloads UX (bordered dataset cards with Schema + Access Data dialogs) but lists only our supported datasets (enhancer–gene predictions, enhancers, cell types) and links out to the Open Targets downloads for everything else. - Access Data shows requester-pays instructions for gs://e2g: a billing-project memo plus `gcloud storage cp --billing-project=...` / `gsutil -u ...` commands (no anonymous HTTPS, since the bucket is requester-pays). - Hide "Documentation" and "Community" from the nav (mainMenuItems). - Dockerfile.compose: copy dependency manifests and run `yarn install` BEFORE copying source, so install is cached and only re-runs on dependency changes (source-only edits skip it). Adds a yarn cache mount. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Fold TLS termination and the API reverse-proxy into the frontend nginx (backend stays plain HTTP, no certs). VITE_API_URL is now relative (/graphql) so the SPA calls the API same-origin — no mixed content over HTTPS, and dev needs only one forwarded port. - nginx.app.conf: shared server body (proxy /graphql + /api -> backend:4000 via docker-DNS resolver; SPA try_files fallback), included by both configs - nginx.compose.conf: HTTP/dev config (port 3000), includes app.conf - nginx.tls.conf: cutover config (80->443 redirect + 443 ssl), includes app.conf - Dockerfile.compose: COPY the snippet, EXPOSE 80 443 - remove dead files: nginx.conf, .htpasswd, old standalone Dockerfile Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The async-LD section now shows a live spinner while the background fetch is pending, so the static description caveat is redundant. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
At narrow widths the button label wrapped to two lines and overflowed the button height. Add whiteSpace:nowrap + flexShrink:0 so the button always sizes to fit its text on a single line. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The custom E2G brand colors came in via an upstream merge with single quotes, failing the biome format + lint CI checks on every push. Apply biome formatting (single -> double quotes); no behavior change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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