cBioPortal / cbioportal

Cuándo se añadió cada estrella y fork, recopilado de GitHub y agrupado por día. El crecimiento acumulado se sitúa justo encima de las adiciones diarias que lo componen, de modo que ambos se leen en conjunto: la acumulación orgánica sostenida no se parece en nada a un pico abrupto y efímero. Cuando esa diferencia es medible, se informa como autenticidad del crecimiento.

Cada punto abarca 11 días.

Conjunto completo de dependencias resueltas según el grafo de dependencias de GitHub: 56 paquetes directos y 355 indirectos (transitivos). El cierre transitivo es completo cuando el repositorio incluye un lockfile.

Instalar maven:io.github.cbioportal:cbioportal@15f1a72410c5d8a8c19936baee9c4f9aea77af60 arrastra 204 paquetes, directos y transitivos: 30 tienen avisos conocidos, de los cuales 3 son dependencias directas.

Un aviso significa que la versión registrada en el grafo de dependencias cae dentro del rango afectado de un aviso. No se analiza la alcanzabilidad, y el grafo incluye fijaciones de desarrollo y prueba: un hallazgo puede referirse al utillaje y no al software distribuido.

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          "committed_at": "2026-07-06T17:27:15Z",
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          "body": "Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Fix release drafter prerelease base (#12260)",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-07-02T17:48:15Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "7d77b68b75375286907724d3c312bbf2340ab7e3",
          "body": null,
          "is_bot": false,
          "headline": "Update version to v7.0.5-SNAPSHOT in pom.xml",
          "author_name": "Zain Nasir",
          "author_login": "zainasir",
          "committed_at": "2026-07-01T02:40:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c75eeef3f4be1663e3a0451be10784b09eec8245",
          "body": null,
          "is_bot": false,
          "headline": "Frontend v7.0.4",
          "author_name": "github-actions",
          "author_login": null,
          "committed_at": "2026-07-01T02:21:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0e5f245eab807f878bd8e28be796b162ac798865",
          "body": "* Document mutational signature frontend conventions\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n* Clarify mutational signature stable_id docs\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n* Simplify mutational signature doc wording\n\nCo-authored-by\n[…]\n>\n\n* Use plainer mutational signature doc wording\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Docs/mutational signature frontend conventions (#12249)",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-25T22:11:52Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "fa7a8a11d4e55114052826bb924f0724b3a38163",
          "body": null,
          "is_bot": false,
          "headline": "Update SessionServiceController.java to use Hashset",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-24T20:23:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "175821c83624ddd70f8fa828e3380c7d657c5f1d",
          "body": "…… (#12235)\n\n* fix: sanitize owner and users fields for anonymous virtual study sessions\n\n* fix: extend session sanitization to custom_data type (same anonymous injection gap)\n\n* chore: use anonymous instead of null for default owner\n\n* Potential fix for pull request finding\n\nCo-authored-by: Copilot\n[…]\n AI <175728472+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: alisman <lisman.aaron@gmail.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "fix: sanitize owner and users fields for anonymous virtual study sess…",
          "author_name": "DevPradyumansh.",
          "author_login": "Pradyuman-aviator",
          "committed_at": "2026-06-24T20:19:21Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "9f65f8fca3c00e6d1adbcf3cc5734d953546b5bc",
          "body": "…egacy classes (#12243)\n\n- BasicDataBinner: remove redundant @Autowired on single constructor\n  (Spring 4.3+ auto-detects injection when there is exactly one constructor)\n- ClinicalDataBinner: same redundant @Autowired removal\n- ProxyController: convert @Autowired field injection of Monkifier to\n  constructor injection; make field final for immutability",
          "is_bot": false,
          "headline": "refactor: replace field injection with constructor injection in non-l…",
          "author_name": "DevPradyumansh.",
          "author_login": "Pradyuman-aviator",
          "committed_at": "2026-06-24T20:05:51Z",
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        },
        {
          "oid": "979a4ea28e2e760ce7f9d2209a9ee334e99afe7f",
          "body": "…ency) (#12238)\n\n* Add dev/qc-harness: replay real traffic to QC a PR (parity/memory/latency)\n\nA reusable harness that replays real captured requests\n(cbioportal_qc.logged_requests) against two builds of cBioPortal to verify a\nchange returns identical responses and to measure its effect on memory an\n[…]\nroot .mcp.json so credentials can't be committed.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add dev/qc-harness: replay real traffic to QC a PR (parity/memory/lat…",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-24T20:03:39Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "4d08ec9b9bade58e86d1409fe9ddc57a71ef4fe3",
          "body": "* Compute co-expression in a single ClickHouse scan\n\nThe getCoExpressions query scanned genetic_alteration_derived for profile B\nthree times: once for the non_constant_genes CTE, once for the\nvalid-correlation branch, and once more for the NULL-correlation branch of the\nUNION ALL.\n\nCollect each gene\n[…]\not@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Compute co-expression in a single ClickHouse scan (#12187)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-22T21:48:26Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "e35795a6f14bf0d244e3fba60a050af973a7ebee",
          "body": "…/fetch (#12210) (#12230)\n\n* perf(api): cut memory on gene-panel-data/fetch and generic_assay_meta/fetch\n\nTwo memory-footprint reductions for known memory-hog fetch endpoints,\nverified against a ClickHouse Cloud clone.\n\ngene-panel-data/fetch (sampleMolecularIdentifiers path):\nPreviously fetched gene\n[…]\nction\nfiltered to NAME/DESCRIPTION/URL).\n\n\n\n---------\n\nCo-authored-by: Claude Fable 5 <noreply@anthropic.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "perf(api): cut memory on gene-panel-data/fetch and generic_assay_meta…",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-22T18:57:14Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "7e5b34ee599b36e6f403f3cabdd835faf28b5250",
          "body": "…add breaking API label (#12233)\n\n* Fix stale release-drafter action namespace and cl-skip-changelog label check\n\n- Update release-management.yml from toolmantim/release-drafter@v5.2.0 to\n  release-drafter/release-drafter@v7.4.0 (action moved orgs, was 3+ years stale)\n- Fix label-check.yml to also a\n[…]\nby the check until after merge. Read from the checked-out file instead.\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Improve release-drafter: update action, fix cl-skip-changelog check, …",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-19T22:54:30Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "c0ce35c9587e171b2a81d666dc58c4bfbc9a4bd0",
          "body": "* Stable-order fetchSamples queries (clickhouse + legacy)\n\nClickHouse MergeTree returns rows in arbitrary order when ORDER BY is\nomitted, which makes /api/samples/fetch responses non-deterministic\nacross runs. That non-determinism propagates through the results view\ndownload tab and shows up as flak\n[…]\not@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Stable-order fetchSamples queries (clickhouse + legacy) (#12167)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-18T16:31:49Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "51f887a9bd56d525391ee3dbab502597290ca7ed",
          "body": null,
          "is_bot": false,
          "headline": "Prepare for v7.0.4",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-18T15:56:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "aef808023426740e798849a6af0ae4551ae0915b",
          "body": null,
          "is_bot": false,
          "headline": "Frontend v7.0.3",
          "author_name": "github-actions",
          "author_login": null,
          "committed_at": "2026-06-18T15:29:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "47cdb38ce0bf002903ce2edd64d18b6aec3cffe8",
          "body": "* Add profile-level generic assay aggregation\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n* Format generic assay mapper SQL\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n* Apply Spotless formatting\n\nCo-authored-by: Copilot <223556219+Copilot@users.\n[…]\ngithub.com>\n\n* Clean up study view sonar warnings\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Add profile-level generic assay aggregation (#12181)",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-17T21:11:09Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "7d2f4aeffebe40ff73a9ba0b671b221b8c687a2a",
          "body": "…(#12227)\n\n* update cancer study query to conditionally join type_of_cancer\n\n* refactor CancerStudyMapper and CancerStudyMetadata to remove type_of_cancer fields",
          "is_bot": false,
          "headline": "Remove TypeOfCancer field in studies endpoint for SUMMARY projection …",
          "author_name": "Onur Sumer",
          "author_login": "onursumer",
          "committed_at": "2026-06-17T19:47:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0f9e42f570f2e0d2e5420464bac10322d823b60e",
          "body": "* Add MongoDB HTTP request logging for endpoint QC\n\nCapture every matching HTTP request (method, url, headers, body) and\nupsert it into MongoDB, deduplicated by a SHA-256 of method+path+query+\nbody so the collection stays bounded by the number of distinct requests\nrather than by traffic. Each docume\n[…]\nthored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Ubuntu <ubuntu@vps-870e202d.vps.ovh.us>\nCo-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add ClickHouse HTTP request logging for endpoint QC (#12226)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-17T17:03:10Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "30831bfb21da115cd05395752bc1bbffd2c2ce0e",
          "body": "…… (#12225)\n\n* Revert \"perf(api): cut memory on gene-panel-data/fetch and generic_assay_meta/fetch (#12210)\"\n\nThis reverts commit 3b00a2688a595246c713fd5c4ea20662345c7efd.\n\n* fix: address SonarCloud issues in GenePanelServiceImpl\n\nRename non-constant fields to camelCase (S116) and use Stream.toList(\n[…]\n\ninstead of collect(Collectors.toList()) (S6204).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Revert \"perf(api): cut memory on gene-panel-data/fetch and generic_as…",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-17T15:31:59Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "3b00a2688a595246c713fd5c4ea20662345c7efd",
          "body": "…/fetch (#12210)\n\n* perf(api): cut memory on gene-panel-data/fetch and generic_assay_meta/fetch\n\nTwo memory-footprint reductions for known memory-hog fetch endpoints,\nverified against a ClickHouse Cloud clone.\n\ngene-panel-data/fetch (sampleMolecularIdentifiers path):\nPreviously fetched gene panel da\n[…]\nBy: Claude Fable 5 <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Fable 5 <noreply@anthropic.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "perf(api): cut memory on gene-panel-data/fetch and generic_assay_meta…",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-15T18:51:31Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "77ab4ae638413bc82dfcead62b689450b5eec442",
          "body": "…(#12214)\n\nReplaces the WDIO run_e2e_localdb_tests job with the Playwright localdb\nsuite ported from cbioportal-frontend (e2e_localdb_shards + e2e_localdb_merge).\n12 parallel shards each boot the cbioportal + keycloak + clickhouse stack and\nrun tests/local; the merge job consolidates per-shard blob \n[…]\nrry picked from commit 4026902c78cda92ab67e2eb73c34b769f1af00fa)\n\nCo-authored-by: alisman <186521+alisman@users.noreply.github.com>\nCo-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "ci: port localdb e2e to Playwright, run against the PR backend image …",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-06-12T17:09:48Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "34eb131ce14bf4963163ead2596c68d8bf7f2864",
          "body": "…ated tests (#12206)",
          "is_bot": false,
          "headline": "refactor: remove deprecated and unused GeneMemoizerService and associ…",
          "author_name": "DevPradyumansh.",
          "author_login": "Pradyuman-aviator",
          "committed_at": "2026-06-11T17:38:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "434b5959b24b4030baf160bcf4b3404ba8fd4f8d",
          "body": null,
          "is_bot": false,
          "headline": "Update version to 7.0.3",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-10T15:18:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "de372d808227e5a64c5d7b5be042a9a3a04f7946",
          "body": null,
          "is_bot": false,
          "headline": "Prepare for v7.0.3",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-10T15:17:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "99e257b7ab705279ec8ae60472d66ba6c75152fd",
          "body": null,
          "is_bot": false,
          "headline": "Frontend v7.0.2",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-10T15:14:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7445e31c16dcc4463db1bae62e8bc133d8f8ff56",
          "body": null,
          "is_bot": false,
          "headline": "Documentation suggestions proposed by ClickHouse team (#12185)",
          "author_name": "James Ko",
          "author_login": "jamesqo",
          "committed_at": "2026-06-10T12:55:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "87ca43ed270d7defd2ef80ef5dee61459ba8d583",
          "body": "- Bump retypeapp/action-build to v4.6.0 (SHA: 511f266c5d)\n- Update actions/setup-dotnet from v1 (dotnet 7.x) to v4 (dotnet 10.x)\n- Update actions/checkout from v2 to v4\n- Retype v3.9.0 has expired and blocks documentation builds\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "ci: update Retype action from v3.9.0 (expired) to v4.6.0 (#12203)",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-09T15:40:29Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "6ff378ffb6c6a993dd017e4e65f34eb472686a92",
          "body": "… studies (#12196)\n\n* fix: deserialize GeneFilterQuery from legacy string format in virtual studies\n\nDynamic virtual studies saved before this fix stored gene queries as plain\nstrings (e.g. \"BRAF\", \"BRAF:AMP\") in the session service.  On read,\nVirtualStudy.setData() tried to deserialize those string\n[…]\nng a checked IOException in an unchecked context.\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "fix: deserialize GeneFilterQuery from legacy string format in virtual…",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-09T14:45:37Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "c7614bf4523e0c1f84a0ef56d3ca803a0ae7164d",
          "body": "* docs: unify chat-interface page (single cBioPortalChat agent)\n\nThrough 2026-Q2 the platform exposed two separate agents (cBioDBAgent\nand cBioNavigator) that the user had to choose between. These have\nbeen merged into a single cBioPortalChat agent with access to all of\nthe original tools.\n\n- Drop t\n[…]\not@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "docs: unify chat-interface page (single cBioPortalChat agent) (#12200)",
          "author_name": "Ino de Bruijn",
          "author_login": "inodb",
          "committed_at": "2026-06-08T20:42:37Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "00435026aaf01e65af7986e9a9d902da76b4260b",
          "body": "…… (#12197)\n\n* refactor: replace System.out.println and e.printStackTrace with SLF4J logging\n\nReplace raw System.out.println() and e.printStackTrace() calls with proper SLF4J logger calls across legacy files. No logic changes.\n\n- WebServletContextListener: replace 7 System.out.println calls with log\n[…]\nnding\n\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "refactor: replace System.out.println and e.printStackTrace with SLF4J…",
          "author_name": "DevPradyumansh.",
          "author_login": "Pradyuman-aviator",
          "committed_at": "2026-06-08T13:49:46Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "608e0b73eaff4cf5fdd92f27f4af19bea3dfa63e",
          "body": "* Fix typos in CONTRIBUTING.md and Versioning-and-Upgrades.md\n\n- Fix spelling: 'commmunity' -> 'community' in CONTRIBUTING.md\n\n- Fix grammar: 'your working on' -> 'you're working on' in CONTRIBUTING.md\n\n- Fix grammar: 'v7 released' -> 'v7 release' in Versioning-and-Upgrades.md\n\n* docs: fix additiona\n[…]\nnd\n\n- Importer-Tool.md: The page → This page, follow → following, clinicla → clinical\n\n- Testing.md: remove stray double-quote in SQL GRANT statement\n\n- Migration-Guide.md: be be → be (duplicate word)",
          "is_bot": false,
          "headline": "Fix typos in CONTRIBUTING.md and Versioning-and-Upgrades.md (#12194)",
          "author_name": "DevPradyumansh.",
          "author_login": "Pradyuman-aviator",
          "committed_at": "2026-06-06T14:48:05Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "29481a4cc27baf8715d892c0fc6276a80fcb8bf1",
          "body": null,
          "is_bot": false,
          "headline": "Prepare for v7.0.2",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-04T15:40:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7473844190f4a60a8557633a2656ff7f7d929868",
          "body": null,
          "is_bot": false,
          "headline": "Bump version from v7.0.0 to v7.0.1",
          "author_name": "Gaofei Zhao",
          "author_login": "dippindots",
          "committed_at": "2026-06-04T15:29:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "53aa13cb4f1fc5d3da2754d6a4bf24cebf25f578",
          "body": null,
          "is_bot": false,
          "headline": "Frontend v7.0.1",
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          "body": "- ClickHouse Setup was nested as a child of 'Deploy with Docker' but\n  should be a sibling — it lives at deployment/clickhouse/, same level\n  as deployment/docker/, standalone/, kubernetes/, etc.\n- Integration with Other Webservices used an empty link () and\n  now links to its existing deployment/integration-with-other-webservices/README.md\n\nCo-authored-by: James Ko <james@jamesko.org>",
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          "headline": "Fix sidebar nesting in SUMMARY.md: promote ClickHouse to sibling",
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          "headline": "This is a documentation update for newer Keycloak versions [issue#116…",
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          "headline": "refactor (v7 release) rfc100 : import to ClickHouse",
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          "body": "* Initial plan\n\n* Add news item for clonality feature\n\nAgent-Logs-Url: https://github.com/cBioPortal/cbioportal/sessions/25a45786-7530-411d-bb15-1d038ff5dfd1\n\nCo-authored-by: inodb <1334004+inodb@users.noreply.github.com>\n\n* Update News.md with new clonality features\n\nAdded new feature for visualizi\n[…]\n--------\n\nCo-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: inodb <1334004+inodb@users.noreply.github.com>\nCo-authored-by: Ino de Bruijn <ino@ino.bio>",
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          "body": "* Accept gapMode in saved results-view clinical track settings\n\n* fix: ignore unknown clinical track fields\n\nSigned-off-by: Asish Kumar <officialasishkumar@gmail.com>\n\n---------\n\nSigned-off-by: Asish Kumar <officialasishkumar@gmail.com>",
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          "headline": "Fix save-track requests for OncoPrint clinical gap settings (#12098)",
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          "headline": "[BUG] Fix generic_assay_data/fetch empty selector filters returning s…",
          "author_name": "Varshini",
          "author_login": "VarshiniGunti",
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          "body": "…endpoint (#11974) (#12069)",
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          "headline": "Fix: Mark entrezGeneId as required in swagger spec for GET mutations …",
          "author_name": "ZOHAIB",
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          "is_bot": false,
          "headline": "Add numeric-aware ORDER BY to ClickHouse generic assay meta queries (…",
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          "headline": "Add validation for virtual study request payloads (#12077)",
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          "body": "* Fix: Preserve CNA gene order by using LinkedHashMap in combineCopyNumberCountsWithConflictingHugoSymbols\n\nAgent-Logs-Url: https://github.com/cBioPortal/cbioportal/sessions/001ddb7c-1aa3-450f-8f17-ecd1c7fb6ebc\n\nCo-authored-by: dippindots <15748980+dippindots@users.noreply.github.com>\n\n* Fix spotles\n[…]\nagent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: dippindots <15748980+dippindots@users.noreply.github.com>\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>",
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          "body": "* docs: fix broken API client links in Downloads\n\n* docs: fix migration guide database settings link\n\n* docs: fix FAQ link in News\n\n* docs: fix authorization toc link in summary\n\n* docs: fix docker links in study curation guide\n\n* docs: fix incremental loading link in docker examples\n\n* docs: fix backend module dependency image path\n\n* docs: fix deployment procedure self link",
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          "body": "…th ClickHouse support (#12036)\n\n* Refactor clinical-data-enrichments with conflicting attribute handling\n\n- Refactor clinical-data-enrichments to use column-store architecture\n- Fix conflicting clinical attribute handling: add conflicting attributes\n  to sampleAttributeIds so data is fetched from b\n[…]\n-By: Claude Opus 4.6 <noreply@anthropic.com>\n\n* Address Copilot comments\n\n---------\n\nCo-authored-by: Zhaoyuan (Ryan) Fu <fuzhaoyuan@gmail.com>\nCo-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>",
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          "headline": "Migrate `clinical-data-enrichments` endpoint to clean architecture wi…",
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          "body": "* Initial plan\n\n* Fix GitHub Actions shell injection vulnerability with github.head_ref\n\nAgent-Logs-Url: https://github.com/cBioPortal/cbioportal/sessions/eaade6b7-733c-4405-8850-7237015191e6\n\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>\n\n* Use printf instead of echo to saf\n[…]\nursumer@users.noreply.github.com>\n\n---------\n\nCo-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>",
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          "oid": "c9400d026e629381e5bab74c1b74fe76a95f5ffa",
          "body": "…Cloud analysis for fork PRs (#12054)\n\n* Initial plan\n\n* fix: replace hard-coded SONAR_TOKEN with secrets reference in sonarcloud workflow\n\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>\nAgent-Logs-Url: https://github.com/cBioPortal/cbioportal/sessions/0b6494e1-eea9-4654-afe0\n[…]\nhored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>\nCo-authored-by: Onur Sumer <s.onur.sumer@gmail.com>",
          "is_bot": false,
          "headline": "fix: source SONAR_TOKEN from GitHub Actions secrets and support Sonar…",
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          "body": "* Enable run_api_tests job in CircleCI workflow\n\nUncomment the run_api_tests job in the CI workflow so that e2e API tests\nrun against a live portal instance on every PR.\n\nCo-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>\n\n* add context for api tests\n\n* Fix run_api_tests: add JUnit reporter and\n[…]\n-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: dippindots <15748980+dippindots@users.noreply.github.com>\nCo-authored-by: alisman <186521+alisman@users.noreply.github.com>",
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          "oid": "be69c705eb5a17cbb4a2cd7d7780332c53588fe7",
          "body": "…ase (#12057)\n\nCloses #11609\n\nThe cancer study group names were not being uppercased before comparison\nwith granted authorities (which are already uppercased), causing group-based\naccess to be denied even when the authority matched.\n\nRather than introducing a new caseInsensitiveDisjoint utility meth\n[…]\nd handles case\n(e.g. stableStudyID.toUpperCase(), ALL_CANCER_STUDIES_ID.toUpperCase()).\n\nCo-authored-by: Ubuntu <ubuntu@vps-8193e9ef.vps.ovh.us>\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Fix case-insensitive group auth check by normalizing groups to upperc…",
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          "committed_at": "2026-03-25T18:34:29Z",
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        },
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          "oid": "0de3f634dfec9d551e5f50788fc6194c2f19ad1f",
          "body": "* Initial plan\n\n* Consolidate duplicate Sonar analysis into a single CI step\n\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>\nAgent-Logs-Url: https://github.com/cBioPortal/cbioportal/sessions/8f983d97-008d-4f59-956e-62be46174ecd\n\n* Revert SONAR_TOKEN change (handled in separat\n[…]\nhored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>\nCo-authored-by: onursumer <3604198+onursumer@users.noreply.github.com>\nCo-authored-by: Onur Sumer <s.onur.sumer@gmail.com>",
          "is_bot": false,
          "headline": "Consolidate duplicate SonarCloud analysis into a single CI step (#12053)",
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        {
          "oid": "0ae2e6c3b374cb485de8ab04246d43878d165ecc",
          "body": "* Add configuration property to hide clinical data tab in study view\n\nImplements #11653 by adding a new configuration property\nskin.hide_clinical_data_tab_study_view that allows administrators\nto hide the clinical data tab in the study view.\n\n- Property defaults to 'false' (tab is shown by default)\n\n[…]\n - previous failure unrelated to changes\n\n---------\n\nCo-authored-by: W0474997SteveArmstrong <113034949+W0474997SteveArmstrong@users.noreply.github.com>\nCo-authored-by: alisman <lisman.aaron@gmail.com>",
          "is_bot": false,
          "headline": "Add configuration to hide clinical data tab in study view (#11825)",
          "author_name": "Steve Armstrong",
          "author_login": "stevearmstrong-dev",
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          "headline": "Migrate legacy mappers to clinical_event_derived (#12039)",
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          "headline": "docs: clarify ASCN CCF and Clonal column UI display behavior in File-…",
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          "body": "* Add ORDER BY to StudyViewMapper ClickHouse queries for deterministic results\n\nThe getMutatedGenes, getCnaGenes, and getStructuralVariantGenes queries\nin StudyViewMapper were missing ORDER BY clauses, causing non-deterministic\nresult ordering from ClickHouse. This led to flaky e2e screenshot diffs\n\n[…]\ndeterministic ordering by entrez_gene_id, alteration, and sample stable_id.\n\nCo-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>",
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          "headline": "Add ORDER BY for deterministic query results (#12014)",
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          "headline": "Add ORDER BY to StudyViewMapper ClickHouse queries for deterministic …",
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          "body": "* Prevent co-expression OOM on large studies with external group by\n\nThe rankCorr() aggregate function maintains one accumulator state per\ngene group (~20K simultaneous states), each holding all sample pairs.\nFor large studies like pancan_pdmr_2025 (6,273 samples × 20K genes),\nthis exceeds available\n[…]\nthored-by: Copilot <175728472+Copilot@users.noreply.github.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>\nCo-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Prevent co-expression OOM on large studies (#12005)",
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          "oid": "f82249925c870e22c32b777c48acddf613c05eff",
          "body": "The global Jackson NON_NULL setting was causing these fields to be\nomitted entirely when null. Add @JsonInclude(ALWAYS) to ensure they\nserialize as null for uncorrelatable genes, so the frontend can\ndisplay them as N/A.\n\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>",
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          "headline": "Include null spearmansCorrelation and pValue in JSON response (#12002)",
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          "oid": "5d68a9e1533b2d657aaa50b89ff3ca8ad92af3d7",
          "body": " Add ClickHouse-backed co-expression endpoint using rankCorr()                                                                                                                                                  \n                                                                                           \n[…]\nsage\n  - ~22-27% additional speedup from CTE JOIN removal optimization\n\n  The legacy co-expression endpoint remains untouched — both coexist.\n\n  Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>",
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          "author_name": "Leslie",
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          "body": "* Return 404 instead of 500 for missing reference genome gene\n\n* Improve 404 description to include missing reference genome",
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          "headline": "Return 404 instead of 500 for missing reference genome gene (#11910)",
          "author_name": "Aman Gautam",
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          "body": "* Fix Clinical Attribute NA Filtering\n\nSigned-off-by: Zhaoyuan (Ryan) Fu <fuzhaoyuan@gmail.com>\n\n* Clean up\n\nSigned-off-by: Zhaoyuan (Ryan) Fu <fuzhaoyuan@gmail.com>\n\n* Optimize to use meta tables\n\nSigned-off-by: Zhaoyuan (Ryan) Fu <fuzhaoyuan@gmail.com>\n\n* Add unit test coverage as suggested\n\n---------\n\nSigned-off-by: Zhaoyuan (Ryan) Fu <fuzhaoyuan@gmail.com>",
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          "headline": "Fix Clinical Attribute NA Filtering (#11822)",
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          "body": "This update is assigning a new schema number to the updated\nclickhouse.sql which was recently merged to the master branch\nin PR #11945\n\nCo-authored-by: alisman <lisman.aaron@gmail.com>",
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          "headline": "Increment derived table db version number to 1.0.7 (#11952)",
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                "status": "missed",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 9.6
              },
              {
                "key": "editorconfig",
                "name": ".editorconfig",
                "detail": null,
                "points": 6.4,
                "status": "met",
                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "22 out of 22 merged PRs checked by a CI test -- score normalized to 10",
                "points": 20,
                "status": "met",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "topics": [
                "cancer-genomics",
                "science",
                "visualization",
                "precision-medicine"
              ],
              "has_wiki": true,
              "homepage": "https://cbioportal.org",
              "has_readme": true,
              "has_docs_dir": true,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 25,
                "status": "met",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": "https://cbioportal.org",
                "points": 15,
                "status": "met",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "4 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 4
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "moderate",
        "name": "Security",
        "value": 54,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "moderate",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 64,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 17,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 1,
              "scorecard_aggregate": 6.4
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "branch_protection",
                "name": "Branch-Protection",
                "detail": "branch protection is not maximal on development and all release branches",
                "points": 6,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "22 out of 22 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 7/30 approved changesets -- score normalized to 2",
                "points": 1.5,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 28 contributing companies or organizations",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no dangerous workflow patterns detected",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "update tool detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "30 commit(s) and 16 issue activity found in the last 90 days -- score normalized to 10",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow detected",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool detected",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file detected",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "45 existing vulnerabilities detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "critical",
            "name": "Dependency advisories",
            "note": "Matched the maven:io.github.cbioportal:cbioportal@15f1a72410c5d8a8c19936baee9c4f9aea77af60 runtime dependency closure — what installing the published package pulls in — 204 packages. Reachability is not analyzed.",
            "notes": [
              {
                "code": "advisories_scope_published",
                "params": {
                  "package": "maven:io.github.cbioportal:cbioportal@15f1a72410c5d8a8c19936baee9c4f9aea77af60",
                  "assessed": 204
                }
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 15,
            "inputs": {
              "source": "osv",
              "advisories": 95,
              "affected_packages": 30,
              "assessed_packages": 204,
              "unassessed_packages": 0,
              "affected_by_severity": "critical 5, high 13, moderate 11, low 1",
              "direct_affected_packages": 3
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "3 affected: org.springframework.security:spring-security-core 6.4.2 (critical 9.1), org.springframework.security:spring-security-web 6.4.2 (critical 9.1), ch.qos.logback:logback-core 1.5.12 (moderate 4.8)",
                "points": 7.1,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_affected",
                    "params": {
                      "count": 3,
                      "packages": "org.springframework.security:spring-security-core 6.4.2 (critical 9.1), org.springframework.security:spring-security-web 6.4.2 (critical 9.1), ch.qos.logback:logback-core 1.5.12 (moderate 4.8)"
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "27 affected: org.apache.tomcat.embed:tomcat-embed-core 10.1.34 (critical 9.8), org.thymeleaf:thymeleaf 3.1.3.RELEASE (critical 9.0), org.thymeleaf:thymeleaf-spring6 3.1.3.RELEASE (critical 9.0), +24 more",
                "points": 1,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_affected",
                    "params": {
                      "count": 27,
                      "packages": "org.apache.tomcat.embed:tomcat-embed-core 10.1.34 (critical 9.8), org.thymeleaf:thymeleaf 3.1.3.RELEASE (critical 9.0), org.thymeleaf:thymeleaf-spring6 3.1.3.RELEASE (critical 9.0)"
                    }
                  },
                  {
                    "code": "advisories_affected_more",
                    "params": {
                      "count": 24
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "27 advisory-carrying package(s) unaddressed past 90 days; oldest published 1875 days ago",
                "points": 7,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_stale",
                    "params": {
                      "days": 90,
                      "count": 27,
                      "oldest": 1875
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
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              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 204,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
            },
            "components": [
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                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
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                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
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              "review_only_matches": 0,
              "assessed_self_published_locations": 22
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "good",
        "name": "AI Readiness",
        "value": 73,
        "weight": 0,
        "metrics": [
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            "key": "ai_agent_context",
            "band": "excellent",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
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              "legible_history_share": 0.85,
              "agent_instruction_files": [
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            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "AGENTS.md, src/e2e/js/CLAUDE.md",
                "points": 45,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
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                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "85 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
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                      "sampled": 100
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                "max_points": 40
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          },
          {
            "key": "ai_verify_loop",
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            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 66,
            "inputs": {
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              "has_tests": true,
              "lockfiles": [
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              "has_dockerfile": true,
              "typed_language": true,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [
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              "agent_commit_share": 0.47,
              "toolchain_manifests": [
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              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "pom.xml (toolchain convention, no task runner)",
                "points": 12.6,
                "status": "partial",
                "details": [
                  {
                    "code": "toolchain_convention",
                    "params": {
                      "files": "pom.xml"
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                  }
                ],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 22,
                "status": "met",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": "src/e2e/js/tsconfig.json",
                "points": 11,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "src/e2e/js/tsconfig.json"
                    }
                  }
                ],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "Dockerfile, lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile, lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "47 of the last 100 commits agent-authored or agent-credited",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "agent_authored_commits",
                    "params": {
                      "count": 47,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "excellent",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "primary_language": "Java",
              "largest_source_bytes": 169108,
              "source_files_sampled": 1249,
              "oversized_source_files": 8
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Java (statically typed)",
                "points": 45,
                "status": "met",
                "details": [
                  {
                    "code": "statically_typed_language",
                    "params": {
                      "language": "Java"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "8/1249 source files over 60KB",
                "points": 54.6,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 1249,
                      "oversized": 8
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          },
          {
            "key": "ai_interfaces",
            "band": "at_risk",
            "name": "Machine-readable interfaces",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "example_dirs": [
                "examples",
                "sample"
              ],
              "has_mcp_signal": false,
              "api_schema_files": []
            },
            "components": [
              {
                "key": "api_schema_openapi_graphql_proto",
                "name": "API schema (OpenAPI/GraphQL/proto)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 40
              },
              {
                "key": "mcp_server",
                "name": "MCP server",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "runnable_examples",
                "name": "Runnable examples",
                "detail": "examples, sample",
                "points": 40,
                "status": "met",
                "details": [
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                    "code": "file_list",
                    "params": {
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        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-23T02:38:23.840659Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/cBioPortal/cbioportal.svg",
  "full_name": "cBioPortal/cbioportal",
  "license_state": "standard",
  "license_spdx": "AGPL-3.0"
}