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cBioPortal/cbioportal

https://github.com/cBioPortal/cbioportal · scanned 2026-06-17 01:45 UTC (1 month, 1 week ago)

79 raw signals (0 security + 79 graph)

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Complete repo analysis

Last scanned 1 month, 1 week ago · v2 · last Δ -24.5 (diff) · 36 actionable findings from 1 signal source. 43 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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88.9% cov · 36 findings

Severity distribution — click a segment to filter

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Severity: Critical 3 High 1 Medium 10 Low 20 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 36 Crowd 0 Layer: Frontend 4 Hardware 6 Security 9 Cicd 3 Quality 14

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Bug-class explainers. Each card groups findings of the same shape — these are the patterns most likely to ship to prod and reappear in future scans unless you systematically fix the cause, not just the instance.

Legacy markers 8 findings

What it is: TODO, FIXME, XXX, HACK comments. Often indicate a known-broken path the author meant to fix.

Why it matters: Each marker is an unfinished thought. Production code shouldn't ship with debt that's documented but not tracked.

How AI causes it: AI mirrors the style of the codebase, so existing TODOs propagate into new code.

Fix approach: Convert each into a ticket. Delete the comment when the ticket lands. Use a pre-commit hook to block new TODOs without an issue link.

8 matching findings on this repo

low Very large file: src/main/java/org/cbioportal/legacy/web/StudyViewController.ja…
low Very large file: src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStu…
low Very large file: src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterAp…
low Very large file: src/test/java/org/cbioportal/legacy/persistence/mybatis/Altera…
low Very large file: src/test/java/org/cbioportal/legacy/web/StudyViewControllerTes…
low Very large file: src/test/java/org/cbioportal/legacy/web/MutationControllerTest…
low Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.…
low Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.ja…

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Commented-out code 2 findings

What it is: Lines of source that were intentionally disabled but never deleted.

Why it matters: Git already remembers history — commented code rots, becomes wrong, and adds noise to diffs.

How AI causes it: AI sometimes comments out broken code instead of fixing it. Reviewers approve out of inertia.

Fix approach: Delete. Trust `git log`. If you really need to remember, save it in a notes file under `docs/`.

2 matching findings on this repo

info Commented-code block (12 lines) in src/e2e/js/test/ColumnStoreClinicalDataCount…
info Commented-code block (9 lines) in src/e2e/js/test/ColumnStoreClinicalDataEnrich…

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Config drift 1 finding

What it is: Settings duplicated across env files, Docker compose, K8s, and code defaults, all with slightly different values.

Why it matters: Production behaviour depends on whichever copy your loader reads first. Subtle bugs in staging that don't reproduce in dev.

How AI causes it: AI writes new config from memory rather than reading the existing source.

Fix approach: Pick one source of truth (env vars + a settings module). Have every other place import from there. Lint for duplicates in CI.

1 matching finding on this repo

critical Possible secret in .circleci/config.yml .circleci/config.yml:651

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