cBioPortal / cbioportal

Коли додано кожну зірку й форк — зібрано з GitHub і згруповано за днями. Кумулятивне зростання розміщено просто над денними додаваннями, з яких воно складається, тож їх видно одне проти одного: рівномірне органічне накопичення виглядає зовсім інакше, ніж різкий короткочасний сплеск. Там, де цю різницю можна виміряти, її подано як автентичність росту.

Кожна точка охоплює 11 днів.

Повний розв'язаний набір залежностей із графа залежностей GitHub: 56 прямих і 355 непрямих (транзитивних) пакетів. Транзитивне замикання є повним, коли в репозиторії закомічено lockfile.

Встановлення maven:io.github.cbioportal:cbioportal@15f1a72410c5d8a8c19936baee9c4f9aea77af60 тягне 204 пакетів, прямих і транзитивних: 30 мають відомі сповіщення, з них 3 — прямі залежності.

Сповіщення означає, що версія, записана в графі залежностей, потрапляє в уражений діапазон. Досяжність не аналізується, а граф містить піниї розробки й тестування — знахідка може стосуватися інструментів, а не поставленого коду.

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          "is_bot": false,
          "headline": "Document Spring datasource migration properties (#12177)",
          "author_name": "Asish Kumar",
          "author_login": "officialasishkumar",
          "committed_at": "2026-07-06T17:53:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cbfeeb4b89d3ad699f31a86260254349365a9792",
          "body": null,
          "is_bot": false,
          "headline": "docs: clarify clinical data dictionary link (#12217)",
          "author_name": "Ren yiwei",
          "author_login": "SSDWGG",
          "committed_at": "2026-07-06T17:27:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c881286e3ad8cdc5ac053e2a1f55b91bace4eda3",
          "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",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "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",
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          "headline": "Fix sidebar nesting in SUMMARY.md: promote ClickHouse to sibling",
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          "headline": "Add numeric-aware ORDER BY to ClickHouse generic assay meta queries (…",
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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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          "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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          "is_bot": false,
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          "oid": "717536b2c79f521f6fa63bf62ddc1c3b0b6da24b",
          "body": "* Rename clinical_event_derived table to clinical_event_data_derived\n\nUpdate all ClickHouse mapper XML files and schema definition to\nreference the renamed table.\n\nCo-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>\n\nMigrate legacy mybatis mappers from clinical_event to clinical_event_derived\n\nL\n[…]\nt clinical_event_data_derived.\nThe table has always used patient_unique_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": "Migrate legacy mappers to clinical_event_derived (#12039)",
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          "headline": "Add AGENTS.md with endpoint authorization rules (#12033)",
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          "headline": "Fix Spotless import ordering and trailing newline violations (#12045)",
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          "author_login": "VarshiniGunti",
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          "body": "…tionHandler (#12024)\n\nTwo bugs found in GlobalExceptionHandler:\n\nBug 1 - Type mismatch in handleCacheOperationException:\n  The @ExceptionHandler is registered for CacheOperationException, but the\n  method signature accepts CacheNotFoundException. This means Spring cannot\n  inject the correct except\n[…]\nogging infrastructure and outputs at the correct level.\n\nAlso added the SLF4J Logger field required for the fix.\n\nCloses #11987\n\nCo-authored-by: Saurabh Kumar Bajpai <saurabhkumarbajpai7890@gmail.com>",
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          "headline": "fix: resolve type mismatch and replace printStackTrace in GlobalExcep…",
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          "oid": "2c5fc9ad0860911270717ea24473e5471b5e2de3",
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          "headline": "docs: fix spelling mistakes across documentation pages (#12020)",
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          "oid": "ff2e13b59c551f6635d4b2187470ef248308f50e",
          "body": "…rviceImpl (#12025)\n\n* fix: guard against IndexOutOfBoundsException in UuidDataAccessTokenServiceImpl\n\nIf a user has no data access tokens, the list is empty and calling\nget(size - 1) throws IndexOutOfBoundsException. Added an isEmpty() guard\nthat throws TokenNotFoundException with a descriptive mes\n[…]\ne.\n\nCloses #11905\n\n* Simplify exception message for token not found\n\n---------\n\nCo-authored-by: Saurabh Kumar Bajpai <saurabhkumarbajpai7890@gmail.com>\nCo-authored-by: alisman <lisman.aaron@gmail.com>",
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          "headline": "fix: guard against IndexOutOfBoundsException in UuidDataAccessTokenSe…",
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          "oid": "26f03b620e627c2ead8e7172caa934243cdef7b3",
          "body": "…#11979)\n\n* perf: optimize generic-assay-meta with ClickHouse derived tables and DDD architecture\n\nReplace N+1 loop + 3-step SQL chain with pre-computed ClickHouse derived\ntables and a single query. Reduces O(N) SQL queries to 1 (0 on cache hit)\nfor multi-profile requests. Introduces column-store DD\n[…]\nr\n  deterministic property ordering in JSON output\n\n---------\n\nCo-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>\nCo-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>",
          "is_bot": false,
          "headline": "Optimize generic-assay-meta endpoints with ClickHouse derived table (…",
          "author_name": "Gaofei Zhao",
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          "body": "* Add single study endpoint to ColumnStore API\n\nAdd GET /studies/{studyId} endpoint that returns metadata for a single\ncancer study by its identifier, including resource counts.\n\nCo-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>\n\n* Add e2e tests for GET /api/column-store/studies/{studyId}\n\nCo-\n[…]\n in treatment CTE\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>\n\n---------\n\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>\nCo-authored-by: Ubuntu <ubuntu@vps-8193e9ef.vps.ovh.us>",
          "is_bot": false,
          "headline": "Add GET /api/column-store/studies/{studyId} endpoint (#12030)",
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          "oid": "26b690474d4d70d95d4373ea86ebc9f09ab58a3b",
          "body": "* Update News.md\n\n* Update News.md\n\n* Update News.md\n\n* Update News.md\n\n---------\n\nCo-authored-by: ritikakundra <kundrar@mskcc.org>",
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          "headline": "Update News.md (#12023)",
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          "headline": "Update frontend version to v7.0.0-rc.1 (#12038)",
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          "headline": "update frontend version to latest in pom.xml (#12017)",
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          "oid": "cd7f1916db394094edd2fdc31dc86c06adb69ef5",
          "body": "…Formats.md (#11994)\n\n* Initial plan\n\n* docs: clarify ASCN CCF and Clonal column UI display behavior in File-Formats.md\n\nCo-authored-by: inodb <1334004+inodb@users.noreply.github.com>\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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          "headline": "docs: clarify ASCN CCF and Clonal column UI display behavior in File-…",
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          "committed_at": "2026-03-13T20:07:11Z",
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          "oid": "11c4bee4e1164479337eb188fb54e1c3c4cd59c3",
          "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>",
          "is_bot": false,
          "headline": "Add ORDER BY for deterministic query results (#12014)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-03-06T19:20:22Z",
          "body_truncated": true,
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          "oid": "265b9ddaf3cf5e72ac958251b7db564d65b0a7ee",
          "body": "…results (#12009)\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\nwhere genes would appear in different positions across runs.\n\nAdds ORDER BY totalCount DESC, hugo_gene_symbol ASC to match the\nClickhouseAlterationMapper queries.\n\nCo-authored-by: Claude Opus 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add ORDER BY to StudyViewMapper ClickHouse queries for deterministic …",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-03-05T20:20:21Z",
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        },
        {
          "oid": "e7947c93f3db487fba3e74c3db83c5228db8526f",
          "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)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-03-04T19:28:23Z",
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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>",
          "is_bot": false,
          "headline": "Include null spearmansCorrelation and pValue in JSON response (#12002)",
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          "author_login": "alisman",
          "committed_at": "2026-03-02T15:44:11Z",
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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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          "headline": "Add ClickHouse-backed co-expression endpoint (#11991)",
          "author_name": "alisman",
          "author_login": "alisman",
          "committed_at": "2026-03-02T15:14:04Z",
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          "oid": "9cea6741fb38c8a6c95dd46bc44c8afa8ecdcf63",
          "body": "* For detailed projection sampleids are provided for the comparison page",
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          "headline": "Gene-specific charts include sample ids (#11904)",
          "author_name": "Leslie",
          "author_login": "i-am-leslie",
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          "oid": "87b88c24088c9eafedbfecb7c310b72daa1a405f",
          "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",
          "author_login": "Gautam-aman",
          "committed_at": "2026-02-19T15:50:57Z",
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          "oid": "3f2f00b9a18cdca52f924465104104bd185704b7",
          "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>",
          "is_bot": false,
          "headline": "Fix Clinical Attribute NA Filtering (#11822)",
          "author_name": "Zhaoyuan (Ryan) Fu",
          "author_login": "fuzhaoyuan",
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          "oid": "0960737bcdc83168385083195323ddeb770d0bf4",
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          "headline": "upgrade testcontainers to fix Docker compatibility (#11956)",
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          "oid": "ed898d394c385448aab875b5009c27545a9ebdcf",
          "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>",
          "is_bot": false,
          "headline": "Increment derived table db version number to 1.0.7 (#11952)",
          "author_name": "Robert Sheridan",
          "author_login": "sheridancbio",
          "committed_at": "2026-02-11T21:55:41Z",
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          "oid": "14a2170f7a168c050168dda5dc868d2647ac1634",
          "body": "…on (#11759)\n\nAdds configuration properties for the UptimeRobot status page integration\nthat automatically displays service status banners in the frontend.\n\nChanges:\n- Add uptime_robot_status_page_url and uptime_robot_api_key properties\n  to application.properties.EXAMPLE\n- Create comprehensive Upti\n[…]\nc\n- Banner styling based on severity\n- Troubleshooting common issues\n- Security considerations\n- Architecture overview\n\nRelated frontend PR: https://github.com/cBioPortal/cbioportal-frontend/pull/5282",
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          "headline": "Add UptimeRobot status page integration configuration and documentati…",
          "author_name": "Ino de Bruijn",
          "author_login": "inodb",
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        {
          "oid": "5def3f457b453046a53f36206bd7d6ae88a9b8da",
          "body": "- Add 6 Datadog RUM properties to FrontendPropertiesServiceImpl enum\n- Add example configuration to application.properties.EXAMPLE\n- All properties default to null (frontend handles defaults)\n- Properties: application_id, client_token, site, env, session_sample_rate, session_replay_sample_rate",
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          "headline": "Add Datadog RUM configuration properties (#11950)",
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          "body": "* Make the entrezGeneId param required",
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          "headline": "Make the entrezGeneId param required (#11946)",
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      "commits_last_year": 204,
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              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "16 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 16
                    }
                  }
                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 24,
                "status": "met",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 0,
                "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"
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                }
              },
              {
                "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)"
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                  },
                  {
                    "code": "advisories_affected_more",
                    "params": {
                      "count": 24
                    }
                  }
                ],
                "max_points": 25
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              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
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                "points": 7,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_stale",
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                      "count": 27,
                      "oldest": 1875
                    }
                  }
                ],
                "max_points": 40
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            ]
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            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
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              "packages": [],
              "red_flag": false,
              "assessed_packages": 204,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
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            "components": [
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                "name": "No dependency reported as a malicious package",
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                "points": 100,
                "status": "met",
                "details": [
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                  }
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                "max_points": 100
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          },
          {
            "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": [
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                "Iran",
                "North Korea"
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              "review_only_matches": 0,
              "assessed_self_published_locations": 22
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            "components": [
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                "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?"
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        "name": "AI Readiness",
        "value": 73,
        "weight": 0,
        "metrics": [
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            "band": "excellent",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
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              "legible_history_share": 0.85,
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            "components": [
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                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "AGENTS.md, src/e2e/js/CLAUDE.md",
                "points": 45,
                "status": "met",
                "details": [
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                    "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",
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                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
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                "max_points": 40
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          {
            "key": "ai_verify_loop",
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            "note": null,
            "notes": [],
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            "inputs": {
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              "lockfiles": [
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              "has_dockerfile": true,
              "typed_language": true,
              "bootstrap_files": [],
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              "toolchain_manifests": [
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              "dependency_bot_commit_share": 0
            },
            "components": [
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                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "pom.xml (toolchain convention, no task runner)",
                "points": 12.6,
                "status": "partial",
                "details": [
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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"
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                  }
                ],
                "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": {
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                      "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,
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                "details": [
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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"
}