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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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UNIFIED Repobility · multi-layer engine · AI coders

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.

JSON
Combined
52.2
/100
Security checks
52
0 findings
System graph
52
88.9% cov · 36 findings
Critical
3
click to filter
Agents
10
0 votes
Crowd
0
reported
Severity distribution — click a segment to filter
Active filters: excluding tests × Reset all
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
Scan summary Repository scanned at 52.2/100 with 88.9% coverage. It contains 2031 nodes across 0 cross-layer flows, written primarily in mixed languages. Engine surfaced 79 findings — concentrated in cicd (44), quality (14), security (9). Risk profile is high: 3 critical, 3 high, 27 medium. Recommended next step: open the cicd layer findings first — that's where the highest-impact wins live.

Showing 33 of 36 actionable findings. 79 raw detector signals were grouped into reader-sized issues. Click TP / FP to vote on a finding's accuracy — votes adjust the confidence weighting and improve detection across the platform.

critical System graph security Secrets conf 1.00 Possible secret in .circleci/config.yml
Detected pattern matching password_literal. Rotate the credential and move to a secret manager.
.circleci/config.yml:651
critical System graph security Secrets conf 1.00 Runtime dotenv file present in repo: dev/.env
`dev/.env` looks like a runtime dotenv file. It contains secret-looking assignments for DOCKER_IMAGE_KEYCLOAK. Move real values to a secret manager and keep only `.env.example` style templates in source control.
dev/.env ConfigEnv fileRuntime env
high System graph cicd CI/CD security conf 1.00 3 occurrences GitHub Action tracks a moving branch
ad-m/github-push-action@master can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
lines 288, 295, 302
.github/workflows/dockerimage.yml:288, 295, 302 (3 hits)
CI/CD securitySupply chainGithub actions
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: AGENTS.md
This agent instruction grants code or shell authority but does not state the verification gate that decides promotion. The recurring safe pattern is: LLM proposes; deterministic tests/build/security checks verify; only verified code promotes.
AGENTS.md VerificationAgents md
medium System graph quality Placeholder conf 1.00 Critical user flow still appears backed by mock or placeholder data
A payment/auth/admin/order/billing-style flow contains mock, fake, TODO, dummy, or placeholder markers in runtime source. In the Fable corpus this is a high-leverage completeness smell: the app can look finished while the money, identity, or tenant flow is still scaffolded.
Mock dataCritical flowGenerated repo pattern
medium System graph hardware Supply chain conf 1.00 Dockerfile ADD downloads remote content without checksum
Remote build inputs can change or be replaced upstream. Use Dockerfile ADD --checksum or download with an explicit digest/signature verification step.
docker/web-and-data/Dockerfile:47 containersChecksum
medium System graph hardware Security conf 1.00 Dockerfile runs as root: docker/web-and-data/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph hardware Security conf 1.00 Dockerfile runs as root: docker/web/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph cicd CI/CD security conf 1.00 18 occurrences GitHub Action is tag-pinned rather than SHA-pinned
whoan/docker-build-with-cache-action@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
3 files, 18 locations
.github/workflows/dockerimage.yml:43, 48, 51, 88, 97, 102, 134, 139, +6 more (14 hits)
.github/workflows/cbioportal-performance-test.yml:21, 31, 37 (3 hits)
.github/workflows/core-test.yml:34
CI/CD securitySupply chainGithub actions
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/js/load-frontend.js:15
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/main/resources/js/load-frontend.js:15 Direct innerhtml assignment
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/webapp/js/src/load-frontend.js:15
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/main/resources/webapp/js/src/load-frontend.js:15 Direct innerhtml assignment
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/webapp/swf/src/cytoscapeweb.js:1688
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/main/resources/webapp/swf/src/cytoscapeweb.js:1688 Direct innerhtml assignment
medium System graph security security conf 1.00 Insecure pattern 'weak_hash' in docs/deployment/standalone/README.md:287
Found a known-risky pattern (weak_hash). Review and replace if possible.
docs/deployment/standalone/README.md:287 Weak hash
low System graph quality Maintenance conf 1.00 70 TODO/FIXME markers
High count of TODO/FIXME/HACK markers — track them as issues so they're not forgotten.
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
docker/web-and-data/Dockerfile:57 containersPinned dependencies
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
docker/web/Dockerfile:35 containersPinned dependencies
low System graph hardware Supply chain conf 1.00 3 occurrences Docker base image is tag-pinned but not digest-pinned: maven:3-eclipse-temurin-21
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
2 files, 3 locations
docker/web-and-data/Dockerfile:15, 43 (2 hits)
docker/web/Dockerfile:14
containersPinned dependencies
low System graph cicd CI/CD security conf 1.00 23 occurrences GitHub Action is tag-pinned rather than SHA-pinned
actions/github-script@v6 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
10 files, 23 locations
.github/workflows/dockerimage.yml:37, 67, 81, 128, 156, 170 (6 hits)
.github/workflows/sonarcloud.yml:35, 63, 67, 73 (4 hits)
.github/workflows/maven-package-build.yml:28, 34, 41 (3 hits)
.github/workflows/spotless-check.yml:19, 22, 28 (3 hits)
.github/workflows/core-test.yml:30, 39 (2 hits)
.github/workflows/auto-label.yml:12
.github/workflows/cbioportal-performance-test.yml:12
.github/workflows/label-check.yml:20
CI/CD securitySupply chainGithub actions
low System graph security security conf 1.00 Insecure pattern 'document_write' in src/main/resources/js/load-frontend.js:72
Found a known-risky pattern (document_write). Review and replace if possible.
src/main/resources/js/load-frontend.js:72 Document write
low System graph security security conf 1.00 Insecure pattern 'document_write' in src/main/resources/webapp/js/src/load-frontend.js:72
Found a known-risky pattern (document_write). Review and replace if possible.
src/main/resources/webapp/js/src/load-frontend.js:72 Document write
low System graph frontend Frontend quality conf 1.00 Stray `console.log` in TS/JS — src/main/resources/js/load-frontend.js:66
Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable. Why: Hygiene — easy to leak debug output. Rule id: fq.console-leak
Fq console leak
low System graph frontend Frontend quality conf 1.00 Stray `console.log` in TS/JS — src/main/resources/webapp/js/src/load-frontend.js:66
Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable. Why: Hygiene — easy to leak debug output. Rule id: fq.console-leak
Fq console leak
low System graph frontend Frontend quality conf 1.00 Stray `console.log` in TS/JS — test/api-e2e/mergeJson.js:15
Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable. Why: Hygiene — easy to leak debug output. Rule id: fq.console-leak
Fq console leak
low System graph frontend Frontend quality conf 1.00 Stray `console.log` in TS/JS — test/api-e2e/watch.js:8
Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable. Why: Hygiene — easy to leak debug output. Rule id: fq.console-leak
Fq console leak
low System graph quality Complexity conf 1.00 Very large file: src/main/java/org/cbioportal/legacy/web/StudyViewController.java (1731 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java (1147 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java (1712 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/main/resources/webapp/swf/src/cytoscapeweb.js (3078 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java (1328 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java (1257 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java (1519 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java (5027 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java (1389 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
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