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.
Extract text from PDFs using shell tools when readfile fails
Install PDF Text Extraction
$ npx skills add HKUDS/OpenSpace --skill pdf-text-extraction -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install HKUDS/OpenSpace pdf-text-extraction --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-text-extraction .claude/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .claude/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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-text-extractionType 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-text-extraction -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install HKUDS/OpenSpace pdf-text-extraction --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-text-extraction .agents/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .agents/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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-text-extraction -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install HKUDS/OpenSpace pdf-text-extraction --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-text-extraction .cursor/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .cursor/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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-text-extraction--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-text-extraction -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install HKUDS/OpenSpace pdf-text-extraction --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-text-extraction .gemini/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .gemini/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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-text-extractionInstalls 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-text-extraction -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-text-extraction .github/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .github/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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-text-extraction -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-text-extraction --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-text-extraction .opencode/skills/pdf-text-extraction && 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-text-extraction" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdf-text-extraction into .opencode/skills/pdf-text-extraction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdf-text-extraction", 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.
Facts
- Skill name
pdf-text-extraction- GitHub stars
- 7.8k
- Token cost
- ~817 tokens
- SKILL.md length
- 175 words
- Files
- 2
- Skills in repo
- 199
- Repo updated
- First seen
- Licence
- MIT
At a glance
Extract text from PDFs using shell tools when readfile fails
- Works in 4 steps: Try pdftotext first - Fastest and most… → If pdftotext unavailable, check for… → For table/structured data, use pdfplumber → …
- Tasks that involve PDF
- SKILL.md covers When to Use This Skill, Available Methods, Workflow and Installation Notes, plus 2 more sections
- Calls pdftotext, apt-get and pip
What it does
PDF Text Extraction is an agent skill from HKUDS/OpenSpace. Extract text from PDFs using shell tools when readfile fails
Its SKILL.md is about 820 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.
When your agent uses it
- Tasks that involve PDF
Example prompts
- “/pdf-text-extraction”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Try pdftotext first - Fastest and most reliable for plain text
- If pdftotext unavailable, check for Python libraries
- For table/structured data, use pdfplumber
- Verify extraction succeeded - Check output contains readable text, not binary data
What it can do on your machine
Read from SKILL.md and the folder at commit 3827781. It shows what the files ask for, not the result of running them.
Tool permissions
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.
Runs code
Shell commands in SKILL.md call:
pdftotextapt-getpippython3
From the folder's file list and the shell code blocks in SKILL.md.
Network
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.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
PDF Text Extraction loads about 817 tokens when it runs. Until then it costs about 20 tokens; SKILL.md has 175 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.
Safety
Auto-check passed
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.
SKILL.md
The full file from HKUDS/OpenSpace at commit 3827781, republished under its MIT licence (© HKUDS). 175 words, ~817 tokens.
Download SKILL.mdSave it as
.claude/skills/pdf-text-extraction/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- pdf-text-extraction
- description
- Extract text from PDFs using shell tools when read_file fails
PDF Text Extraction (Fallback Method)
When to Use This Skill
Use this skill when read_file with filetype='pdf':
- Returns binary image data instead of text
- Produces errors or incomplete content
- Fails to extract structured data reliably
The built-in PDF handler is unreliable for structured text extraction. Shell-based tools provide more robust alternatives.
Available Methods
Method 1: pdftotext (Recommended)
# Extract text from PDF to stdout
pdftotext /path/to/file.pdf -
# Extract text to a file
pdftotext /path/to/file.pdf output.txt
# Preserve layout (maintains spacing/structure)
pdftotext -layout /path/to/file.pdf output.txtUsage in agent:
run_shell command="pdftotext -layout /path/to/document.pdf -"Method 2: pdfinfo (Metadata)
# Get PDF metadata (pages, author, creation date, etc.)
pdfinfo /path/to/file.pdfUsage in agent:
run_shell command="pdfinfo /path/to/document.pdf"Method 3: Python with PyMuPDF (fitz)
import fitz # PyMuPDF
doc = fitz.open("/path/to/file.pdf")
text = ""
for page in doc:
text += page.get_text()
doc.close()
print(text)Usage in agent:
run_shell command="python3 -c \"import fitz; doc=fitz.open('file.pdf'); print(''.join(p.get_text() for p in doc))\""Method 4: Python with pdfplumber (Tables)
import pdfplumber
with pdfplumber.open("/path/to/file.pdf") as pdf:
for page in pdf.pages:
text = page.extract_text()
tables = page.extract_tables() # For tabular dataUsage in agent:
run_shell command="python3 -c \"import pdfplumber; pdf=pdfplumber.open('file.pdf'); print(''.join(p.extract_text() or '' for p in pdf.pages))\""Workflow
Try pdftotext first - Fastest and most reliable for plain text
bash run_shell command="pdftotext -layout /path/to/file.pdf -"If pdftotext unavailable, check for Python libraries
bash run_shell command="python3 -c \"import fitz; print('PyMuPDF available')\""For table/structured data, use pdfplumber
bash run_shell command="python3 -c \"import pdfplumber; ...\""Verify extraction succeeded - Check output contains readable text, not binary data
Installation Notes
If tools are not available:
# Ubuntu/Debian
apt-get install poppler-utils # pdftotext, pdfinfo
# Install Python libraries
pip install pymupdf pdfplumberAnti-Patterns to Avoid
- Do NOT rely solely on
read_filewithfiletype='pdf'for critical text extraction - Do NOT assume PDF text is in any particular order - verify extracted content
- Do NOT use image-based extraction unless the PDF is scanned (use OCR instead)
Example: Complete Extraction Pattern
# Step 1: Try pdftotext
RESULT=$(pdftotext -layout /path/to/form.pdf - 2>/dev/null)
# Step 2: Verify we got text, not error
if [ -z "$RESULT" ]; then
# Fallback to Python
RESULT=$(python3 -c "import fitz; doc=fitz.open('/path/to/form.pdf'); print(''.join(p.get_text() for p in doc))")
fi
# Step 3: Use extracted text
echo "$RESULT"© HKUDS, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file in benchmarks/gdpval/skills/pdf-text-extraction of HKUDS/OpenSpace.
- SKILL.md
- .skill_id
Open the folder on GitHubat commit 3827781
Compare with similar skills
PDF Text Extraction 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 Text Extraction this skillHKUDS/OpenSpace | 7.8k | — | ~817 | 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 |
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Related
Works with
Categories
Questions about PDF Text Extraction
What does PDF Text Extraction do?
Extract text from PDFs using shell tools when readfile fails. PDF Text Extraction is an agent skill from HKUDS/OpenSpace.
When should I use PDF Text Extraction?
PDF Text Extraction fits situations like: tasks that involve PDF.
How do I install PDF Text Extraction in Claude Code?
Run `npx skills add HKUDS/OpenSpace --skill pdf-text-extraction -a claude-code`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-text-extraction in HKUDS/OpenSpace) into .claude/skills/pdf-text-extraction in your project. Claude Code loads it when a task matches its description.
How do I install PDF Text Extraction in Codex?
Run `npx skills add HKUDS/OpenSpace --skill pdf-text-extraction -a codex`. Or copy the skill folder (benchmarks/gdpval/skills/pdf-text-extraction in HKUDS/OpenSpace) into .agents/skills/pdf-text-extraction in your project. Codex loads it when a task matches its description.
Can I use PDF Text Extraction in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add HKUDS/OpenSpace --skill pdf-text-extraction -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-text-extraction, .gemini/skills/pdf-text-extraction, .github/skills/pdf-text-extraction and .opencode/skills/pdf-text-extraction in your project.
What does PDF Text Extraction need to run?
Going by SKILL.md and its folder, PDF Text Extraction needs the command-line tools its instructions call (pdftotext, apt-get, pip and python3). Our summary lists: Python 3.
Does PDF Text Extraction access the network?
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.
Is PDF Text Extraction safe to install?
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.
What licence does PDF Text Extraction use?
PDF Text Extraction is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does PDF Text Extraction use?
About 817 tokens (SKILL.md is roughly 3.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to PDF Text Extraction?
Skills that share tags, products or a category with PDF Text Extraction: 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.
Who maintains PDF Text Extraction?
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.