v7.0.0

cBioPortal v7 Release Notes

cBioPortal v7 is a major release centered on our move away from MySQL and toward ClickHouse as the primary database. This transition includes substantial backend and frontend refactoring to support the new architecture, while also delivering a broad set of improvements, bug fixes, and infrastructure upgrades across the cBioPortal platform.

For existing deployments, migrating to v7 does not require changes to your current data files. Our refactored importers remain fully backward-compatible, which helps reduce migration overhead while enabling the new ClickHouse-based architecture (cbioportal-core#156).

For migration details and upgrade guidance, see the v6 to v7 migration guide

Highlights

• Completed the foundation for the v7 ClickHouse transition, replacing the legacy MySQL-centered architecture with a refactored ClickHouse-based direction across backend and frontend components.
• Kept the upgrade path practical for existing installations: current data files do not need to change, because the new importers are backward-compatible (cbioportal-core#156).
• Expanded ClickHouse-backed platform support across backend and frontend (cbioportal#12036, cbioportal#12058, cbioportal#12165, frontend#5420, frontend#5430, frontend#5482, frontend#5496, frontend#5577).
• Added features and improvements, including area selection in Plots, Variant Allele Frequency heatmap in Oncoprint, optional Study View chart settings persistence, alternative TMB attribute support, versioned Ensembl transcript IDs, CCF/Clonality updates, and the Gene Specific Chart Comparison page (frontend#5339, frontend#5237, frontend#5524, frontend#5531, frontend#5506, frontend#5492, frontend#5415, frontend#5378).
• Delivered broad UX and correctness fixes across Clinical Data, OncoPrint, patient view, plots, structural variants, pathology report viewing, and study/session flows (cbioportal#12098, cbioportal#12067, cbioportal#12065, cbioportal#12077, frontend#5380, frontend#5435, frontend#5532, frontend#5408, frontend#5457, frontend#5505, frontend#5391, frontend#5365, frontend#5477, frontend#5520, frontend#5499, frontend#5474, frontend#5475, frontend#5383, frontend#5377, frontend#5372, frontend#5571).
• Modernized the frontend build, test, and deployment stack with Playwright migration, pnpm/rspack adoption, Node 22, improved CI caching, flake analysis, and more reliable Netlify/preview behavior (frontend#5550, frontend#5572, frontend#5564, frontend#5561, frontend#5508, frontend#5549, frontend#5354, frontend#5551, frontend#5556, frontend#5566, frontend#5567, frontend#5581, frontend#5588, frontend#5541).

Backend

ClickHouse, API, and release work

• Advanced the backend ClickHouse migration by moving clinical-data-enrichments to clean architecture with ClickHouse support, adding numeric-aware ordering for generic assay metadata, and disabling the legacy co-expression endpoint by default (cbioportal#12036, cbioportal#12058, cbioportal#12165).
• Prepared the release candidate and version alignment for the v7 cycle (cbioportal#12139, cbioportal#12121).

Bug fixes and backend correctness

• Fixed OncoPrint clinical gap save-track requests, required entrezGeneId in the GET mutations swagger spec, corrected the study-specific cache invalidation URL to include /api, prevented server errors for empty generic assay selector filters, validated virtual study request payloads, and fixed random CNA table ordering on patient view (cbioportal#12098, cbioportal#12069, cbioportal#11999, cbioportal#12065, cbioportal#12077, cbioportal#12067).

Documentation and release content

• Updated FAQs, OQL docs, chat interface docs, internal documentation links, news content, and release-facing content for the new clonality work (cbioportal#12149, cbioportal#12147, cbioportal#12056, cbioportal#12019, cbioportal#12089, cbioportal#12117).

Frontend

User-facing features and enhancements

• Added area-based point selection in the Plots tab and a Variant Allele Frequency heatmap in Oncoprint (frontend#5339, frontend#5237).
• Added an option to hide the Clinical Data tab, opt-in Study View settings persistence, and broader Study View URL/filter handling improvements (frontend#5273, frontend#5524, frontend#5312).
• Expanded patient- and plot-level data support with alternative TMB attributes, versioned Ensembl transcript IDs, Cancer Cell Fraction and Clonality support, and clearer single-sample CCF/Clonality presentation (frontend#5531, frontend#5506, frontend#5492, frontend#5415).
• Added the Gene Specific Chart Comparison page frontend, improved the resources feature, made the right sidebar responsive on small screens, and added roadmap/navigation polish across the portal (frontend#5378, frontend#5552, frontend#5397, frontend#5330).
• Refined smaller UI details including the coexpression loading state, news feed spacing, header email truncation, icon cleanup, and switching the Twitter icon to X (frontend#5429, frontend#5385, frontend#5409, frontend#5381, frontend#5344).

ClickHouse and API-related frontend updates

• Added column-store support for generic assay metadata endpoints, batched metadata requests by profile suffix, and aligned frontend API naming/documentation with the migration work (frontend#5420, frontend#5430, frontend#5482, frontend#5496).
• Updated co-expression handling with getInternalClient(), null-correlation handling, and refreshed screenshots to match the newer behavior (frontend#5425, frontend#5423, frontend#5426).
• Added "ClickHouse" footer badge (frontend#5577).

Bug fixes and UX improvements

• Fixed Clinical Data rendering and table behavior, including missing values, disappearing headers, and data availability edge cases (frontend#5380, frontend#5435, frontend#5571).
• Fixed results, plot, and study interactions including the "Open in Oncoprinter" action, + encoding in plot data merge, scatter plot drag-selection tooltip interference, the missing log-scale toggle handler, and a leftover debugger statement in StudyViewPage (frontend#5532, frontend#5408, frontend#5457, frontend#5499, frontend#5463).
• Fixed patient view, OncoPrint, and molecular-profile issues including CNA civic variant crashes, molecular profile misordering, random ordering-related UI problems, OncoKB wrapping, track removal, disappearing PDB/3D Structure tracks, and structural variant export behavior (frontend#5505, frontend#5365, frontend#5474, frontend#5477, frontend#5520, frontend#5372).
• Fixed pathology and structural-variant-specific issues, including pathology report retry/URL encoding, survival attribute rendering, structural variant sorting, and broken 3D structure visualization (frontend#5391, frontend#5383, frontend#5377, frontend#5475).

Build, deployment, and test modernization

• Completed the major migration from legacy frontend tooling to pnpm, rspack, SWC, and Node 22, with additional improvements to developer startup flow and repo automation/docs (frontend#5508, frontend#5561, frontend#5549, frontend#5354, frontend#5433, frontend#5516).
• Migrated remote and localdb e2e coverage to Playwright, replaced legacy nightly WDIO coverage, improved rerun behavior, and added cross-run flake analysis (frontend#5550, frontend#5572, frontend#5564, frontend#5559, frontend#5566, frontend#5567).
• Stabilized deploys and branch-aware environment handling for Netlify and preview flows, including restoring CBIOPORTAL_URL substitution and hardening production builds (frontend#5588, frontend#5581, frontend#5541, frontend#5384).
• Improved e2e stability, screenshots, and helper behavior across mutation, patient view, plots, group comparison, Oncoprint, gnomAD, URL/session-save, remote/localdb suites, and request logging (frontend#5574, frontend#5529, frontend#5540, frontend#5530, frontend#5514, frontend#5494, frontend#5487, frontend#5481, frontend#5479, frontend#5476, frontend#5461, frontend#5434, frontend#5428, frontend#5407, frontend#5390, frontend#5387, frontend#5376, frontend#5361).
• Added operational and monitoring support such as UptimeRobot incident reporting and Datadog RUM integration (frontend#5282, frontend#5389).

Release engineering and maintenance

• Simplified package publishing and release workflows, including combined version/publish flows, module publishing, Lerna upgrades, publish script fixes, serialized publishing, and tag-triggered package builds (frontend#5523, frontend#5511, frontend#5501, frontend#5491, frontend#5469, frontend#5445).
• Improved CI efficiency and repository hygiene with custom Playwright images, node_modules/turbo cache fixes, updated generated internal API clients and synced API definitions, oncoprintjs metadata fixes, removal of unused dependencies, removal of dead scripts, removal of the 2025 survey banner, and removal of the unused jspdf dependency (frontend#5556, frontend#5551, frontend#5431, frontend#5500, frontend#5512, frontend#5509, frontend#5400, frontend#5458).
• Included internal prototype work for the biobank timeline track structure (frontend#5478).

Dependency updates

• Updated frontend/runtime/build dependencies including brace-expansion, @babel/plugin-transform-modules-systemjs, fast-uri, axios, jquery, node-forge, handlebars, lodash, yaml, underscore, jsonpath, rollup, bn.js, and webpack (frontend#5582, frontend#5575, frontend#5576, frontend#5558, frontend#5504, frontend#5510, frontend#5471, frontend#5472, frontend#5486, frontend#5480, frontend#5465, frontend#5427, frontend#5392, frontend#5416, frontend#5410, frontend#5388, frontend#5362, frontend#5379, frontend#5382).
• Updated end-to-end test dependencies including basic-ftp, axios, ajv, and validator in /end-to-end-test (frontend#5503, frontend#5498, frontend#5495, frontend#5414, frontend#5404, frontend#5310).

Full Commit Logs

• Backend: v6.4.5...v7.0.0
• Frontend: cBioPortal/cbioportal-frontend@v6.4.4...v7.0.0

Notes on Versioning and Release Procedure

• https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning