{"version": "2.1.0", "$schema": "https://json.schemastore.org/sarif-2.1.0.json", "runs": [{"tool": {"driver": {"name": "Repobility", "informationUri": "https://repobility.com", "rules": [{"id": "scanner-c3ce86fc70432917", "name": "Stray `console.log` in TS/JS \u2014 src/main/resources/js/load-frontend.js:66", "shortDescription": {"text": "Stray `console.log` in TS/JS \u2014 src/main/resources/js/load-frontend.js:66"}, "fullDescription": {"text": "Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable.\n\nWhy: Hygiene \u2014 easy to leak debug output.\nRule id: fq.console-leak"}, "properties": {"scanner": "scanner-primary", "layer": "frontend", "severity": "low", "confidence": 1.0}}, {"id": "scanner-276f4d485c8ba91e", "name": "Stray `console.log` in TS/JS \u2014 src/main/resources/webapp/js/src/load-frontend.js:66", "shortDescription": {"text": "Stray `console.log` in TS/JS \u2014 src/main/resources/webapp/js/src/load-frontend.js:66"}, "fullDescription": {"text": "Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable.\n\nWhy: Hygiene \u2014 easy to leak debug output.\nRule id: fq.console-leak"}, "properties": {"scanner": "scanner-primary", "layer": "frontend", "severity": "low", "confidence": 1.0}}, {"id": "scanner-b3ab2387db890233", "name": "Stray `console.log` in TS/JS \u2014 test/api-e2e/mergeJson.js:15", "shortDescription": {"text": "Stray `console.log` in TS/JS \u2014 test/api-e2e/mergeJson.js:15"}, "fullDescription": {"text": "Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable.\n\nWhy: Hygiene \u2014 easy to leak debug output.\nRule id: fq.console-leak"}, "properties": {"scanner": "scanner-primary", "layer": "frontend", "severity": "low", "confidence": 1.0}}, {"id": "scanner-2f64900c3d493825", "name": "Stray `console.log` in TS/JS \u2014 test/api-e2e/watch.js:8", "shortDescription": {"text": "Stray `console.log` in TS/JS \u2014 test/api-e2e/watch.js:8"}, "fullDescription": {"text": "Replace with the toast helper, an error boundary, or remove. `console.warn` / `console.error` are acceptable.\n\nWhy: Hygiene \u2014 easy to leak debug output.\nRule id: fq.console-leak"}, "properties": {"scanner": "scanner-primary", "layer": "frontend", "severity": "low", "confidence": 1.0}}, {"id": "scanner-bdcf5d93732cf877", "name": "Dockerfile runs as root: docker/web-and-data/Dockerfile", "shortDescription": {"text": "Dockerfile runs as root: docker/web-and-data/Dockerfile"}, "fullDescription": {"text": "No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-ecc92a8bdd86e972", "name": "Docker base image is tag-pinned but not digest-pinned: maven:3-eclipse-temurin-21", "shortDescription": {"text": "Docker base image is tag-pinned but not digest-pinned: maven:3-eclipse-temurin-21"}, "fullDescription": {"text": "Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "low", "confidence": 1.0}}, {"id": "scanner-b34e3d8d5eebb204", "name": "Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre", "shortDescription": {"text": "Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre"}, "fullDescription": {"text": "Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "low", "confidence": 1.0}}, {"id": "scanner-b602ac094b22f23f", "name": "Dockerfile ADD downloads remote content without checksum", "shortDescription": {"text": "Dockerfile ADD downloads remote content without checksum"}, "fullDescription": {"text": "Remote build inputs can change or be replaced upstream. Use Dockerfile ADD --checksum or download with an explicit digest/signature verification step."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-b89489c3b1c531bc", "name": "Dockerfile runs as root: docker/web/Dockerfile", "shortDescription": {"text": "Dockerfile runs as root: docker/web/Dockerfile"}, "fullDescription": {"text": "No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-31775539adf3ae26", "name": "Docker base image is tag-pinned but not digest-pinned: maven:3-eclipse-temurin-21", "shortDescription": {"text": "Docker base image is tag-pinned but not digest-pinned: maven:3-eclipse-temurin-21"}, "fullDescription": {"text": "Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "low", "confidence": 1.0}}, {"id": "scanner-f1dfeaa84c21722a", "name": "Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre", "shortDescription": {"text": "Docker base image is tag-pinned but not digest-pinned: eclipse-temurin:21-jre"}, "fullDescription": {"text": "Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "low", "confidence": 1.0}}, {"id": "scanner-0642a1fffb0cade0", "name": "Runtime dotenv file present in repo: dev/.env", "shortDescription": {"text": "Runtime dotenv file present in repo: dev/.env"}, "fullDescription": {"text": "`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."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "critical", "confidence": 1.0}}, {"id": "scanner-0d7ca6f76b4972e1", "name": "Possible secret in .github/workflows/cbioportal-performance-test.yml", "shortDescription": {"text": "Possible secret in .github/workflows/cbioportal-performance-test.yml"}, "fullDescription": {"text": "Detected pattern matching password_literal. Rotate the credential and move to a secret manager."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "critical", "confidence": 1.0}}, {"id": "scanner-844b24d86e57feab", "name": "Possible secret in .circleci/config.yml", "shortDescription": {"text": "Possible secret in .circleci/config.yml"}, "fullDescription": {"text": "Detected pattern matching password_literal. Rotate the credential and move to a secret manager."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "critical", "confidence": 1.0}}, {"id": "scanner-dca93a99dc78f13f", "name": "Insecure pattern 'document_write' in src/main/resources/js/load-frontend.js:72", "shortDescription": {"text": "Insecure pattern 'document_write' in src/main/resources/js/load-frontend.js:72"}, "fullDescription": {"text": "Found a known-risky pattern (document_write). Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "low", "confidence": 1.0}}, {"id": "scanner-d8598f19355b20ae", "name": "Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/js/load-frontend.js:15", "shortDescription": {"text": "Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/js/load-frontend.js:15"}, "fullDescription": {"text": "Found a known-risky pattern (direct_innerhtml_assignment). 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Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-9304aa19ef4c72e6", "name": "Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/webapp/swf/src/cytoscapeweb.js:1688", "shortDescription": {"text": "Insecure pattern 'direct_innerhtml_assignment' in src/main/resources/webapp/swf/src/cytoscapeweb.js:1688"}, "fullDescription": {"text": "Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-183bb4c974961dcc", "name": "Insecure pattern 'weak_hash' in docs/deployment/standalone/README.md:287", "shortDescription": {"text": "Insecure pattern 'weak_hash' in docs/deployment/standalone/README.md:287"}, "fullDescription": {"text": "Found a known-risky pattern (weak_hash). Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-84dae8b4d9cfdd4c", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v2 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-1d36213800efc3de", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/github-script@v6 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-473c42defca39070", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v1 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-785e54217b53cf54", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v2 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-ec6a32b22a2719a1", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/download-artifact@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-c905722e116a8e50", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-e2dbf9de9eba8775", "name": "GitHub Action tracks a moving branch", "shortDescription": {"text": "GitHub Action tracks a moving branch"}, "fullDescription": {"text": "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."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "high", "confidence": 1.0}}, {"id": "scanner-b4a22866b7dc554d", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v2 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-26578443483ceeab", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-1c5d5a9dd1c80fb4", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-276e29d4e0ea0cbf", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/upload-artifact@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-5db3495f3ddc06fd", "name": "Very large file: src/main/resources/webapp/swf/src/cytoscapeweb.js (3078 lines)", "shortDescription": {"text": "Very large file: src/main/resources/webapp/swf/src/cytoscapeweb.js (3078 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-167fe49c769f03a3", "name": "Very large file: src/main/java/org/cbioportal/legacy/web/StudyViewController.java (1731 lines)", "shortDescription": {"text": "Very large file: src/main/java/org/cbioportal/legacy/web/StudyViewController.java (1731 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-3066957f602b5846", "name": "Very large file: src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java (1147 lines)", "shortDescription": {"text": "Very large file: src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java (1147 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-4ea1a529969d8c5a", "name": "Very large file: src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java (1712 lines)", "shortDescription": {"text": "Very large file: src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java (1712 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-b4c1605c75ec2377", "name": "Very large file: src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java (1328 line", "shortDescription": {"text": "Very large file: src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java (1328 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-11c8c68420fc62f9", "name": "Very large file: src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java (1519 lines)", "shortDescription": {"text": "Very large file: src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java (1519 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-fa1008e37c753186", "name": "Very large file: src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java (1257 lines)", "shortDescription": {"text": "Very large file: src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java (1257 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-f2402369bcfd0a55", "name": "Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java (5027 lines)", "shortDescription": {"text": "Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java (5027 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-c8a0d89d1b37f2f5", "name": "Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java (1389 lines)", "shortDescription": {"text": "Very large file: src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java (1389 lines)"}, "fullDescription": {"text": "Files with >800 lines often hide complexity hotspots and discourage tests."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-bbb9fd1f090c13a2", "name": "70 TODO/FIXME markers", "shortDescription": {"text": "70 TODO/FIXME markers"}, "fullDescription": {"text": "High count of TODO/FIXME/HACK markers \u2014 track them as issues so they're not forgotten."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-2d0c7b7ab8f8aacf", "name": "Critical user flow still appears backed by mock or placeholder data", "shortDescription": {"text": "Critical user flow still appears backed by mock or placeholder data"}, "fullDescription": {"text": "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."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-2679282aa1c484b5", "name": "Agent authority lacks a verifier contract: AGENTS.md", "shortDescription": {"text": "Agent authority lacks a verifier contract: AGENTS.md"}, "fullDescription": {"text": "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."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-71d028d279e8d947", "name": "Commented-code block (12 lines) in src/e2e/js/test/ColumnStoreClinicalDataCountsController/ColumnStoreClinicalDataCounts", "shortDescription": {"text": "Commented-code block (12 lines) in src/e2e/js/test/ColumnStoreClinicalDataCountsController/ColumnStoreClinicalDataCountsController.spec.ts:19"}, "fullDescription": {"text": "A long run of `//` or `#` lines usually means abandoned code. Delete or move to git history. Keeps the canvas + dead-code detection honest."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "info", "confidence": 1.0}}, {"id": "scanner-3d8181ee872e9605", "name": "Commented-code block (9 lines) in src/e2e/js/test/ColumnStoreClinicalDataEnrichmentController/ColumnStoreClinicalDataEnr", "shortDescription": {"text": "Commented-code block (9 lines) in src/e2e/js/test/ColumnStoreClinicalDataEnrichmentController/ColumnStoreClinicalDataEnrichmentController.spec.ts:26"}, "fullDescription": {"text": "A long run of `//` or `#` lines usually means abandoned code. Delete or move to git history. Keeps the canvas + dead-code detection honest."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "info", "confidence": 1.0}}]}}, "automationDetails": {"id": "repobility/24855"}, "properties": {"repository": "cBioPortal/cbioportal", "repoUrl": "https://github.com/cBioPortal/cbioportal", "branch": "main"}, "results": [{"ruleId": "scanner-c3ce86fc70432917", "level": "note", "message": {"text": "Stray `console.log` in TS/JS \u2014 src/main/resources/js/load-frontend.js:66"}, "properties": {"repobilityId": "804cc87406730a4f", "scanner": "scanner-primary", "fingerprint": "c3ce86fc70432917", "layer": "frontend", "severity": "low", "confidence": 1.0, "tags": ["frontend-quality", "fq.console-leak"]}}, {"ruleId": "scanner-276f4d485c8ba91e", "level": "note", "message": {"text": "Stray `console.log` in TS/JS \u2014 src/main/resources/webapp/js/src/load-frontend.js:66"}, "properties": {"repobilityId": "322632ec2cc909e4", "scanner": "scanner-primary", "fingerprint": 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