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TheAxonLab/hcph-sops

https://github.com/TheAxonLab/hcph-sops · scanned 2026-06-16 00:34 UTC (2 months, 2 weeks ago)

39 raw signals (0 security + 39 graph)

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Complete repo analysis

Last scanned 2 months, 2 weeks ago · v1 · 34 actionable findings from 1 signal source. 5 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

JSON
Combined
85.8
/100
Security checks
86
0 findings
System graph
86
77.8% cov · 34 findings
Critical
0
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 0 High 0 Medium 7 Low 23 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 34 Crowd 0 Layer: Software 19 Network 1 Frontend 1 Security 2 Cicd 2 Quality 9
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Scan summary Repository scanned at 85.8/100 with 77.8% coverage. It contains 290 nodes across 0 cross-layer flows, written primarily in mixed languages. Engine surfaced 39 findings — concentrated in software (19), quality (13), cicd (3). Risk profile is low: 0 critical, 0 high, 7 medium. Recommended next step: open the software layer findings first — that's where the highest-impact wins live.

Showing 29 of 34 actionable findings. 39 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.

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 security security conf 1.00 Insecure pattern 'subprocess_shell_true' in code/bugfixes/fix_pe_fieldmaps.py:80
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
code/bugfixes/fix_pe_fieldmaps.py:80 Subprocess shell true
medium System graph quality Integrity conf 1.00 Network/subprocess call without timeout or try/except — code/confounds/parse_mood_quest.py:216
`requests.get(...)` here lacks both a `timeout=` arg and an enclosing try/except. This is exactly the class of bug that took down our git-clone earlier (HTTP/2 stream cancel surfaced as a fatal). Add a `timeout=` and wrap in try/except, or use a wrapper that retries.
runtime safetyRobustness
medium System graph security Coverage conf 1.00 No auth library detected
The scanner did not find any standard auth library (JWT, OAuth, NextAuth, Auth0, etc.). The repo has auth/admin/session surface indicators, so auth may live in custom code, in a separate service, or be missing.
auth
medium System graph network Security conf 1.00 Privileged port 20 in use
Port 20 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer.
code/fmriprep/ss-fmriprep.sh Ports
medium System graph quality Tests conf 1.00 Very low test-to-source ratio
3 test file(s) for 38 source file(s) (ratio 0.08). Consider adding integration or unit tests for critical paths.
Coverage
low System graph quality Debug conf 1.00 Debug logging residue appears in source files
Found 91 console/debugger/print-style debug statements in non-test source. This is a common fast-generation residue before production cleanup.
CleanupRepo hardeningGenerated repo pattern
low System graph cicd CI/CD security conf 1.00 2 occurrences GitHub Action is tag-pinned rather than SHA-pinned
actions/setup-python@v5 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
2 files, 2 locations
.github/workflows/deploy.yml:17
.github/workflows/tests.yml:12
CI/CD securitySupply chainGithub actions
low System graph quality Integrity conf 1.00 5 occurrences Near-duplicate function bodies in 2 places
Functions with the same first-5-line body hash: code/fmri/reports.py:group_reportlet_censoring, code/fmri/reports.py:group_report This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hygiene). Consolidate or document why they're separate.
5 occurrences
repo-level (5 hits)
duplicatesduplication
low System graph software Dead code conf 1.00 Possibly dead Python function: decode_string
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/qc/from_mongodb_to_dataframe.py:71
low System graph software Dead code conf 1.00 Possibly dead Python function: define_env
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
main.py:26
low System graph software Dead code conf 1.00 Possibly dead Python function: filter_dicom
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/heudiconv/reproin.py:196
low System graph software Dead code conf 1.00 Possibly dead Python function: filter_files
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/heudiconv/reproin.py:201
low System graph software Dead code conf 1.00 Possibly dead Python function: fit_edge
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/analysis/run_bayesian_sc.py:39
low System graph software Dead code conf 1.00 Possibly dead Python function: infotodict
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/heudiconv/reproin.py:284
low System graph software Dead code conf 1.00 Possibly dead Python function: init_save_layout
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/data_loader/load_save.py:583
low System graph software Dead code conf 1.00 Possibly dead Python function: iterencode
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/eyetracking/ppjson.py:104
low System graph software Dead code conf 1.00 Possibly dead Python function: load_matrices
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/data_loader/load_save.py:618
low System graph software Dead code conf 1.00 Possibly dead Python function: parse_session
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/physioconv/splitruns.py:210
low System graph software Dead code conf 1.00 Possibly dead Python function: plot_heatmap_coordinate
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/eyetracking/plot.py:39
low System graph software Dead code conf 1.00 Possibly dead Python function: plot_timeseries_carpet
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/fmri/reports.py:68
low System graph software Dead code conf 1.00 Possibly dead Python function: save_caption
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/data_loader/load_save.py:600
low System graph software Dead code conf 1.00 Possibly dead Python function: simulate_sc_fns
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/dmri/simulate_sc.py:408
low System graph software Dead code conf 1.00 Possibly dead Python function: simulate_sc_fps
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/dmri/simulate_sc.py:339
low System graph software Dead code conf 1.00 Possibly dead Python function: simulate_sc_length_bias
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/dmri/simulate_sc.py:172
low System graph software Dead code conf 1.00 Possibly dead Python function: simulate_sc_no_bias
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/dmri/simulate_sc.py:299
low System graph software Dead code conf 1.00 Possibly dead Python function: simulate_sc_noisy_copies
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/dmri/simulate_sc.py:249
low System graph software Dead code conf 1.00 Possibly dead Python function: transform
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
code/fmri/nilearn_patcher.py:250
low System graph quality Provenance conf 1.00 Shallow git history limits provenance confidence
The repository is a shallow clone. Origin/evolution analysis cannot distinguish fresh generation, imported legacy code, or long-lived human code with high confidence.
Git historyGenerated repo pattern
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