Instrument Data To Allotrope
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
Generate structured PDF documents with tables, sections, and scoring using Python libraries in executecodesandbox
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflow --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .claude/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .claude/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflowType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflow --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .agents/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .agents/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .agents/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflow --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .cursor/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .cursor/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/HKUDS/OpenSpace.git --path benchmarks/gdpval/skills/pdf-checklist-workflow--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflow --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .gemini/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .gemini/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflowInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .github/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .github/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .github/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install HKUDS/OpenSpace pdf-checklist-workflow --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/HKUDS/OpenSpace.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/benchmarks/gdpval/skills/pdf-checklist-workflow .opencode/skills/pdf-checklist-workflow && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "pdf-checklist-workflow" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-checklist-workflow into .opencode/skills/pdf-checklist-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-checklist-workflow", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
pdf-checklist-workflowGenerate structured PDF documents with tables, sections, and scoring using Python libraries in executecodesandbox
PDF Checklist Workflow is an agent skill from HKUDS/OpenSpace. Generate structured PDF documents with tables, sections, and scoring using Python libraries in executecodesandbox
Its SKILL.md is about 2.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file.
It sits in Documents & Office, covering PDF. It works with Python. The repository describes itself as: "OpenSpace: The Skill Management Layer for AI Agents" -- https://open-space.cloud/. The licence is MIT.
5 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 3827781. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
pippythonFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
PDF Checklist Workflow loads about 2.3k tokens when it runs. Until then it costs about 35 tokens; SKILL.md has 542 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from HKUDS/OpenSpace at commit 3827781, republished under its MIT licence (© HKUDS). 542 words, ~2,321 tokens.
.claude/skills/pdf-checklist-workflow/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.This skill provides a reusable pattern for creating structured PDF documents such as checklists, reports, or assessments using Python in a sandboxed environment.
Use this workflow when you need to:
Primary method: Use execute_code_sandbox for Python PDF generation
Fallback method: If execute_code_sandbox fails, create and run Python scripts via shell commands
Select a Python library based on your needs:
| Library | Best For | Complexity |
|---|---|---|
reportlab | Professional reports, complex layouts | Medium |
fpdf / fpdf2 | Simple documents, quick generation | Low |
matplotlib | Charts, graphs, visual elements | Medium |
Use the execute_code_sandbox tool with Python code that:
/workspace/output.pdfARTIFACT_PATH: prefix for downloadDetermine workspace directory dynamically: Before generating PDFs, identify the correct output path:
# Option 1: Use current directory
WORKDIR=$(pwd)
# Option 2: Check common workspace locations
if [ -d "/workspace" ]; then WORKDIR="/workspace"
elif [ -d "$HOME/workspace" ]; then WORKDIR="$HOME/workspace"
else WORKDIR=$(pwd); fiIn Python code, use environment variables or dynamic path detection:
import os
workspace = os.environ.get('WORKSPACE', os.getcwd())
output_path = os.path.join(workspace, 'output.pdf')Example using fpdf2:
from fpdf import FPDF
class PDFChecklist(FPDF):
def header(self):
self.set_font('Arial', 'B', 16)
self.cell(0, 10, 'Assessment Checklist', 0, 1, 'C')
self.ln(10)
def section_title(self, title):
self.set_font('Arial', 'B', 12)
self.cell(0, 10, title, 0, 1, 'L')
self.ln(5)
def add_checklist_item(self, item, criteria, score):
self.set_font('Arial', '', 10)
self.cell(100, 8, item, 1)
self.cell(60, 8, criteria, 1)
self.cell(30, 8, str(score), 1)
self.ln()
# Create PDF
pdf = PDFChecklist()
pdf.add_page()
pdf.set_auto_page_break(auto=True, margin=15)
# Add sections
pdf.section_title('Evaluation Criteria')
pdf.add_checklist_item('Requirement 1', 'Must meet standard', 5)
pdf.add_checklist_item('Requirement 2', 'Should be complete', 4)
# Save
output_path = '/workspace/checklist.pdf'
pdf.output(output_path)
print(f'ARTIFACT_PATH:{output_path}')Example using reportlab (more professional):
from reportlab.lib import colors
from reportlab.lib.pagesizes import letter
from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.units import inch
def create_pdf_report(output_path):
doc = SimpleDocTemplate(output_path, pagesize=letter)
styles = getSampleStyleSheet()
story = []
# Title
title_style = ParagraphStyle('CustomTitle', parent=styles['Heading1'],
fontSize=18, spaceAfter=30, alignment=1)
story.append(Paragraph("Assessment Report", title_style))
story.append(Spacer(1, 0.3*inch))
# Section header
story.append(Paragraph("Evaluation Summary", styles['Heading2']))
story.append(Spacer(1, 0.2*inch))
# Data table
data = [
['Criteria', 'Description', 'Score'],
['Completeness', 'All sections filled', '8/10'],
['Accuracy', 'Information verified', '9/10'],
['Clarity', 'Easy to understand', '7/10']
]
table = Table(data, colWidths=[2*inch, 2.5*inch, 1*inch])
table.setStyle(TableStyle([
('BACKGROUND', (0, 0), (-1, 0), colors.grey),
('TEXTCOLOR', (0, 0), (-1, 0), colors.whitesmoke),
('ALIGN', (0, 0), (-1, -1), 'CENTER'),
('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
('BOTTOMPADDING', (0, 0), (-1, 0), 12),
('BACKGROUND', (0, 1), (-1, -1), colors.beige),
('GRID', (0, 0), (-1, -1), 1, colors.black)
]))
story.append(table)
doc.build(story)
print(f'ARTIFACT_PATH:{output_path}')
create_pdf_report('/workspace/report.pdf')Call the tool:
execute_code_sandbox
code: <your PDF generation code from Step 2>
language: python If execute_code_sandbox fails repeatedly (e.g., "unknown error", timeouts), use this fallback:
1. Create the Python script via heredoc:
cat > /tmp/generate_pdf.py << 'EOF'
# Your PDF generation code here
from fpdf import FPDF
import os
workspace = os.environ.get('WORKSPACE', os.getcwd())
output_path = os.path.join(workspace, 'checklist.pdf')
pdf = FPDF()
pdf.add_page()
pdf.set_font('Arial', 'B', 16)
pdf.cell(0, 10, 'Checklist', 0, 1, 'C')
pdf.output(output_path)
print(f'ARTIFACT_PATH:{output_path}')
EOF2. Install required library if needed:
pip install fpdf2 --quiet 2>/dev/null || pip install fpdf23. Execute the script:
python /tmp/generate_pdf.py4. Verify the output file was created:
ls -lh $(pwd)/*.pdf 2>/dev/null || ls -lh /workspace/*.pdf 2>/dev/nullImportant for fallback: When using shell execution, ensure the script outputs the ARTIFACT_PATH so the file can be downloaded. Adjust the path based on where the file was actually created.
After execution, verify the PDF was created:
Option A - Use read_file:
read_file
filetype: pdf
file_path: /workspace/output.pdfOption B - Use shell inspection:
run_shell
command: ls -lh /workspace/*.pdfCheck that:
If using fallback execution, check multiple possible locations:
run_shell
command: find . -name "*.pdf" -type f -exec ls -lh {} \; 2>/dev/null| Issue | Solution |
|---|---|
| Library not installed | Add !pip install fpdf2 or !pip install reportlab at code start |
| Font errors | Use standard fonts (Arial, Helvetica, Courier) |
| File not found | Ensure path is /workspace/filename.pdf |
| Empty PDF | Check that pdf.output() or doc.build() is called |
| Encoding issues | Use ASCII text or handle unicode properly |
execute_code_sandbox fails | Switch to shell-based fallback (Step 3b): create script with heredoc, run with python |
| Wrong workspace path | Use dynamic detection: os.getcwd() or $(pwd) instead of hardcoded /workspace/ |
| Permission errors | Write to current directory or /tmp/ then move file |
execute_code_sandbox fails after 2-3 attempts, switch to shell-based execution immediately/workspace/; use os.getcwd() or environment variables# Install library if needed
# !pip install fpdf2
from fpdf import FPDF
import os
pdf = FPDF()
pdf.add_page()
pdf.set_font('Arial', 'B', 16)
pdf.cell(0, 10, 'Your Title Here', 0, 1, 'C')
pdf.ln(10)
pdf.set_font('Arial', '', 12)
pdf.multi_cell(0, 8, 'Your content here...')
workspace = os.environ.get('WORKSPACE', os.getcwd())
output_path = os.path.join(workspace, 'output.pdf')
pdf.output(output_path)
print(f'ARTIFACT_PATH:{output_path}')Shell fallback template:
# Create script
cat > /tmp/pdf_gen.py << 'PYEOF'
from fpdf import FPDF
import os
pdf = FPDF()
pdf.add_page()
pdf.set_font('Arial', 'B', 16)
pdf.cell(0, 10, 'Title', 0, 1, 'C')
workspace = os.environ.get('WORKSPACE', os.getcwd())
pdf.output(os.path.join(workspace, 'output.pdf'))
print(f'ARTIFACT_PATH:{workspace}/output.pdf')
PYEOF
# Run it
pip install fpdf2 -q 2>/dev/null; python /tmp/pdf_gen.pyexecute_code_sandbox - Run Python code for PDF generationread_file - Verify PDF content (type: pdf)run_shell - Check file existence and sizecreate_file - Alternative for simple text files if PDF not required© HKUDS, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 1 other file in benchmarks/gdpval/skills/pdf-checklist-workflow of HKUDS/OpenSpace.
Open the folder on GitHubat commit 3827781
PDF Checklist Workflow next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| PDF Checklist Workflow this skillHKUDS/OpenSpace | 7.8k | — | ~2.3k | Automated safety check: Pass | MIT | |
| Instrument Data To Allotropeaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | 2 repos | ~2.7k | Automated safety check: Pass | Apache-2.0 | |
| Software Certificate SkillIvanCodesDev/software-certificate-skill | 156 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Doc Cleanernotoriouslab/doc-cleaner | 309 | — | ~712 | Automated safety check: Pass | MIT | |
| MineruNebutra/MinerU-Skill | 122 | — | ~504 | Automated safety check: Pass | MIT | |
| Office To Mdshuyu-labs/WebCode | 278 | — | ~1k | Automated safety check: Notes | Custom licence |
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
IvanCodesDev/software-certificate-skill
面向普通用户,从真实软件项目全自动生成中国软件著作权申请资料:一次收集登记事实,自动分析业务、选择可追溯源码、取得真实界面证据,生成申请表信息、规范黑白灰操作手册、代码前后30页或全部材料及真实 DOCX/PDF;内部验证、渲染、哈希与备份只进入系统临时运行区,项目最终仅保留正式资料。适配 Codex、Claude…
notoriouslab/doc-cleaner
Convert PDF, DOCX, XLSX, and text files to clean, structured Markdown.
Nebutra/MinerU-Skill
An AI-Native skill for parsing PDF / Office / image files into Markdown with MinerU — a fast, zero-config document parser for AI agents.
shuyu-labs/WebCode
Convert Office documents (Word, Excel, PowerPoint, PDF) to Markdown format.
doccker/cc-use-exp
当实现用户驱动的大文件导出或批量序列化(Excel/CSV/JSON/JSONL/PDF,数据量未知或超过 1 万行/10 MB)时触发;普通小文件下载、静态资源下载、非导出 Writer/Report 类不触发。防止 OOM、临时文件残留、同步导出阻塞 HTTP 线程和表格公式注入。
HKUDS/OpenSpace
Walks through producing a master audio track plus stems in Python, from checking a reference file and timing sections by BPM to effects, a zip archive and final verification.
HKUDS/OpenSpace
Handle cascading data retrieval tool failures by falling back to embedded knowledge generation
HKUDS/OpenSpace
Gives an agent a workaround when its code-execution sandbox keeps failing: save the Python script to a file and run it through the shell instead.
HKUDS/OpenSpace
A recovery routine for agents whose sandboxed code runner keeps failing: save the Python script to disk, then run it through the shell and read the output.
HKUDS/OpenSpace
Fallback ladder for failed sandboxed code runs, plus the habit of fixing the working directory first so generated files land in the right place.
HKUDS/OpenSpace
Fallback workflow for executing Python code when executecodesandbox fails repeatedly
Works with
Categories
Generate structured PDF documents with tables, sections, and scoring using Python libraries in executecodesandbox. PDF Checklist Workflow is an agent skill from HKUDS/OpenSpace.
PDF Checklist Workflow fits situations like: tasks that involve PDF.
Run `npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a claude-code`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-checklist-workflow in HKUDS/OpenSpace) into .claude/skills/pdf-checklist-workflow in your project. Claude Code loads it when a task matches its description.
Run `npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a codex`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-checklist-workflow in HKUDS/OpenSpace) into .agents/skills/pdf-checklist-workflow in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add HKUDS/OpenSpace --skill pdf-checklist-workflow -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pdf-checklist-workflow, .gemini/skills/pdf-checklist-workflow, .github/skills/pdf-checklist-workflow and .opencode/skills/pdf-checklist-workflow in your project.
Going by SKILL.md and its folder, PDF Checklist Workflow needs the command-line tools its instructions call (pip and python). Our summary lists: Python 3.
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
PDF Checklist Workflow is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.3k tokens (SKILL.md is roughly 9.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with PDF Checklist Workflow: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Software Certificate Skill (IvanCodesDev/software-certificate-skill, 156 stars), Doc Cleaner (notoriouslab/doc-cleaner, 309 stars) and Mineru (Nebutra/MinerU-Skill, 122 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
HKUDS (a GitHub organization) maintains it in HKUDS/OpenSpace, which has 7,750 GitHub stars. The repository holds 199 skills in this directory. The repository was last updated on August 12, 2026.
Source: HKUDS/OpenSpace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.