Claude Code, Skill
Biomedical Paper Reader
为单篇生物医学研究论文生成中文精读报告：逐图解释实验为什么这样设计、方法与结果如何支持结论、证据边界在哪里，并提炼可借鉴的研究设计；支持速读筛选与指定图／方法专题解析，英文或中英双语按需提供。输入可为 PDF、DOI、链接或正文。Deep-read, figure-by-figure analysis, quick screening, or focused figure/method analysis of one biomedical paper (PDF, DOI, link, or full text).
Compatibility: Not stated.
Grade B
Minor issues only, no Medium or High. Worth a quick look at the findings below before installing.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
PERMISSION_DELETE_FILES NETWORK_NO_FIXED_HOST SECRETS_PATH_DOTENV
Why this grade
- PERMISSION_DELETE_FILES Low
Contains a call that can delete files.
app/backend/main.py, line 215
shutil.rmtree(figures_dir, ignore_errors=True) - NETWORK_NO_FIXED_HOST Low
Makes a network call whose host is not written as a fixed address.
app/frontend/app.js, line 25
const resp = await fetch(url, opts); - SECRETS_PATH_DOTENV Low
Mentions a .env file.
.gitignore, line 10
.env
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Concern
can delete files.
PERMISSION_DELETE_FILES
app/backend/main.py, line 215
shutil.rmtree(figures_dir, ignore_errors=True)
app/backend/main.py, line 396
shutil.rmtree(d, ignore_errors=True)
app/backend/main.py, line 465
shutil.rmtree(paper_dir(paper_id))
Show more
evals/test_prepare_release.py, line 92
completed = subprocess.run(command, capture_output=True, text=True)
evals/test_prepare_release.py, line 97
completed = subprocess.run(command, capture_output=True, text=True)
evals/test_reading_record.py, line 210
ok = subprocess.run([sys.executable, str(SCRIPT), str(src), '--events', str(events)], capture_output=True, text=True)
evals/test_reading_record.py, line 214
bad = subprocess.run([sys.executable, str(SCRIPT), str(src), '--events', str(events)], capture_output=True, text=True)
evals/test_reading_record.py, line 218
duplicate = subprocess.run([sys.executable, str(SCRIPT), str(src)], capture_output=True, text=True)
evals/test_reading_record.py, line 223
malformed = subprocess.run([sys.executable, str(SCRIPT), str(src), '--events', str(events)], capture_output=True, text=True)
Install and update
Pass
No install-time script found, and dependencies are pinned or absent.
Network
Concern
can reach a host that is not written as a fixed address.
NETWORK_NO_FIXED_HOST
app/frontend/app.js, line 25
const resp = await fetch(url, opts);
app/frontend/app.js, line 773
const resp = await fetch(paperPath(paper.id, '/read?mode=' + encodeURIComponent(mode)), { method: 'POST', signal: ctrl.signal });
app/frontend/app.js, line 860
const resp = await fetch(api.figUrl(state.current.id, fid));
Show more
app/frontend/app.js, line 969
const resp = await fetch(api.figUrl(state.current.id, fid));
app/frontend/app.js, line 1167
const resp = await fetch(paperPath(state.current.id, '/figures/read') + (force ? '?force=1' : ''), { method: 'POST' });
app/frontend/app.js, line 1264
const resp = await fetch(paperPath(paper.id, '/file'));
Secrets
Concern
reads a credential or environment file.
SECRETS_PATH_DOTENV
.gitignore, line 9
# Credentials and local runtime artifacts
.gitignore, line 10
.env
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Pass
No encoded or minified payload found.
Licence
Pass
A licence file is present (LICENSE).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit adb7e1ed7284. can delete files. can reach a host that is not written as a fixed address. reads a credential or environment file.
Date and source
Date checked:
github.com
Commit graded: adb7e1ed72844d98ac68c1953afe5ac868689ee0
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