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.
PDF text extraction with tool cascade prioritizing shell pdftotext before Python fallback
$ npx skills add HKUDS/OpenSpace --skill pdf-extract-shell-first -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install HKUDS/OpenSpace pdf-extract-shell-first --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-download-extract-fallback-enhanced-e27e0c .claude/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .claude/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-download-extract-fallback-enhanced-e27e0cType 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-extract-shell-first -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install HKUDS/OpenSpace pdf-extract-shell-first --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-download-extract-fallback-enhanced-e27e0c .agents/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .agents/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-extract-shell-first -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install HKUDS/OpenSpace pdf-extract-shell-first --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-download-extract-fallback-enhanced-e27e0c .cursor/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .cursor/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-download-extract-fallback-enhanced-e27e0c--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-extract-shell-first -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install HKUDS/OpenSpace pdf-extract-shell-first --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-download-extract-fallback-enhanced-e27e0c .gemini/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .gemini/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-extract-shell-firstInstalls 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-extract-shell-first -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-download-extract-fallback-enhanced-e27e0c .github/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .github/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-extract-shell-first -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-extract-shell-first --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-download-extract-fallback-enhanced-e27e0c .opencode/skills/pdf-extract-shell-first && 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-extract-shell-first" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c into .opencode/skills/pdf-extract-shell-first/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-extract-shell-first", 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-extract-shell-firstPDF text extraction with tool cascade prioritizing shell pdftotext before Python fallback
PDF Extract Shell First is an agent skill from HKUDS/OpenSpace. PDF text extraction with tool cascade prioritizing shell pdftotext before Python fallback
Its SKILL.md is about 2.6k 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:
curlapt-getpython3From the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use curl, 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 Extract Shell First loads about 2.6k tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 739 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). 739 words, ~2,634 tokens.
.claude/skills/pdf-extract-shell-first/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.This skill provides an optimized workflow for extracting text content from PDF documents (local files or downloaded URLs) using a prioritized tool cascade that favors shell-based extraction before falling back to Python libraries.
Analysis of execution patterns shows:
read_file on PDFs sometimes returns binary/image data instead of textrun_shell with pdftotext has higher success rate and fewer sandbox errorsexecute_code_sandbox can fail with "unknown error" in constrained environmentsBefore beginning, identify your scenario:
| Scenario | Start Here | Skip |
|---|---|---|
| PDF already on local disk | Step 1 (Try read_file) | Shell download steps |
| PDF at a web URL | Shell download, then Step 1 | None |
| Need maximum reliability | Full cascade (all 3 tools) | None |
If your PDF is at a web URL, download it first using browser user-agent:
curl -L -A "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36" -o target.pdf "URL_HERE"Key flags:
-L: Follow redirects-A: Set user-agent header to mimic a real browser-o: Specify output filenameIf you already have the PDF locally, skip to Step 1.
First, attempt to extract text using the read_file tool:
read_file(filetype="pdf", file_path="target.pdf")Evaluate the response:
| Response Type | Interpretation | Next Action |
|---|---|---|
| Clean readable text | Success | Proceed to content analysis |
| Binary data / PNG image / garbled | read_file returned raw data | Go to Step 2 immediately |
| Error / timeout | Tool failure | Go to Step 2 immediately |
Critical: If read_file returns binary image data or garbled content, do not retry read_file. Immediately proceed to Step 2.
When read_file fails or returns binary data, use run_shell with pdftotext:
run_shell(command="pdftotext target.pdf output.txt")Then read the extracted text:
read_file(filetype="txt", file_path="output.txt")If pdftotext is not found, install it first:
run_shell(command="apt-get update && apt-get install -y poppler-utils")
# Or for macOS:
run_shell(command="brew install poppler")Then retry:
run_shell(command="pdftotext target.pdf output.txt")Verify extraction quality:
output.txt exists and has contentIf pdftotext is unavailable or produces poor results, use Python's PyMuPDF via execute_code_sandbox:
import fitz # PyMuPDF
doc = fitz.open("target.pdf")
text = ""
for page in doc:
text += page.get_text()
doc.close()
with open("output.txt", "w") as f:
f.write(text)
print(f"Extracted {len(text)} characters from {len(doc)} pages")Execute via:
execute_code_sandbox(code="<python code above>")Then read the result:
read_file(filetype="txt", file_path="output.txt")Note: execute_code_sandbox may fail with "unknown error" in some environments. If this occurs, document the failure and proceed to Step 4.
If all extraction methods fail:
Example degradation documentation:
EXTRACTION FAILURE REPORT:
- Source: [URL or file path]
- read_file: Returned binary/image data (no text extraction)
- run_shell/pdftotext: [Tool not available / produced garbled output / succeeded]
- execute_code_sandbox/PyMuPDF: [Failed with unknown error / succeeded]
NOTE: Content below combines partial extraction with established domain
knowledge for [topic]. Verify against official sources when available. PDF to Extract
│
▼
┌───────────────┐
│ read_file │
│ (primary) │
└───────┬───────┘
│
┌─────────────┼─────────────┐
│ │ │
Returns text Returns binary Error/timeout
(✓) / image data │
│ │ │
▼ ▼ ▼
SUCCESS ┌───────────────┐
│ run_shell │
│ pdftotext │
└───────┬───────┘
│
┌───────┼───────┐
│ │ │
Succeeds Not Garbled
(✓) avail. output
│ │ │
▼ ▼ ▼
SUCCESS ┌───────────────┐
│ execute_code │
│ _sandbox │
│ PyMuPDF │
└───────┬───────┘
│
┌───────┼───────┐
│ │ │
Succeeds Fails Error
(✓) │ │
│ ▼ │
▼ Domain │
SUCCESS Knowledge │
│ │
└──────┘
FAILURE
DOCUMENTED#!/bin/bash
# pdf-extract-cascade.sh
# Implements the full tool cascade for PDF extraction
INPUT="$1"
OUTPUT_PDF="target.pdf"
OUTPUT_TXT="output.txt"
# Step 0: Handle URL vs local file
if [[ "$INPUT" =~ ^https?:// ]]; then
echo "Downloading PDF from URL..."
curl -L -A "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36" -o "$OUTPUT_PDF" "$INPUT"
else
if [ ! -f "$INPUT" ]; then
echo "ERROR: Local file not found: $INPUT"
exit 1
fi
OUTPUT_PDF="$INPUT"
fi
# Step 1: Verify file type
echo "Verifying file type..."
if ! file "$OUTPUT_PDF" | grep -q "PDF document"; then
echo "WARNING: File is not a valid PDF"
file "$OUTPUT_PDF"
fi
# Step 2: Try pdftotext (shell-first approach)
echo "Attempting pdftotext extraction..."
if command -v pdftotext &> /dev/null; then
if pdftotext "$OUTPUT_PDF" "$OUTPUT_TXT" 2>/dev/null; then
if [ -s "$OUTPUT_TXT" ]; then
echo "SUCCESS: Extraction completed with pdftotext"
wc -l "$OUTPUT_TXT"
exit 0
fi
fi
fi
# Step 3: Fallback to PyMuPDF
echo "Falling back to PyMuPDF..."
python3 << 'PYTHON_SCRIPT'
import fitz
import sys
try:
doc = fitz.open("target.pdf")
text = ""
for page in doc:
text += page.get_text()
doc.close()
with open("output.txt", "w") as f:
f.write(text)
print(f"SUCCESS: Extracted {len(text)} characters from {len(doc)} pages")
sys.exit(0)
except Exception as e:
print(f"PyMuPDF failed: {e}")
sys.exit(1)
PYTHON_SCRIPT
# Step 4: Handle complete failure
if [ $? -ne 0 ]; then
echo "FAILURE: All extraction methods failed"
echo "ACTION: Generate content from domain knowledge"
echo "Document each tool's failure mode for future reference"
exit 1
firead_file returns image/binary data, immediately switch to run_shellpdftotext before starting complex workflows| Symptom | Likely Cause | Recommended Action |
|---|---|---|
| read_file returns PNG/binary | PDF rendered as image, not parsed | Immediately use run_shell with pdftotext |
| pdftotext: command not found | poppler-utils not installed | Run apt-get install poppler-utils first |
| pdftotext produces empty file | Password-protected or scanned PDF | Try PyMuPDF, or use OCR tools |
| execute_code_sandbox "unknown error" | Sandbox execution issue | Document failure, use domain knowledge fallback |
| Garbled text output | Encoding issues | Try PyMuPDF with page.get_text("text") |
| All tools fail | Severely corrupted or encrypted PDF | Document limitation, use knowledge-based content |
read_file may return binary dataexecute_code_sandbox has shown instabilityThis skill (pdf-extract-shell-first) differs from the parent in these key ways:
read_file → run_shell → execute_code_sandboxpdftotext via run_shell as preferred over Python© 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-download-extract-fallback-enhanced-e27e0c of HKUDS/OpenSpace.
Open the folder on GitHubat commit 3827781
PDF Extract Shell First 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 Extract Shell First this skillHKUDS/OpenSpace | 7.7k | — | ~2.6k | 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
PDF text extraction with tool cascade prioritizing shell pdftotext before Python fallback. PDF Extract Shell First is an agent skill from HKUDS/OpenSpace.
PDF Extract Shell First fits situations like: tasks that involve PDF.
Run `npx skills add HKUDS/OpenSpace --skill pdf-extract-shell-first -a claude-code`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c in HKUDS/OpenSpace) into .claude/skills/pdf-extract-shell-first in your project. Claude Code loads it when a task matches its description.
Run `npx skills add HKUDS/OpenSpace --skill pdf-extract-shell-first -a codex`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-download-extract-fallback-enhanced-e27e0c in HKUDS/OpenSpace) into .agents/skills/pdf-extract-shell-first 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-extract-shell-first -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-extract-shell-first, .gemini/skills/pdf-extract-shell-first, .github/skills/pdf-extract-shell-first and .opencode/skills/pdf-extract-shell-first in your project.
Going by SKILL.md and its folder, PDF Extract Shell First needs the command-line tools its instructions call (curl, apt-get and python3). Our summary lists: Python 3.
SKILL.md contains no URLs. Its commands use curl, 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 Extract Shell First is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.6k tokens (SKILL.md is roughly 11k 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 Extract Shell First: 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 7,743 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.