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.
Recover PDF text extraction when readfile returns binary data by using pdftotext via shell
Install Pdftotext Fallback
$ npx skills add HKUDS/OpenSpace --skill pdftotext-fallback -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install HKUDS/OpenSpace pdftotext-fallback --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/pdftotext-fallback .claude/skills/pdftotext-fallback && 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 "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .claude/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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/pdftotext-fallbackType 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 pdftotext-fallback -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install HKUDS/OpenSpace pdftotext-fallback --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/pdftotext-fallback .agents/skills/pdftotext-fallback && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .agents/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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 pdftotext-fallback -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install HKUDS/OpenSpace pdftotext-fallback --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/pdftotext-fallback .cursor/skills/pdftotext-fallback && 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 "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .cursor/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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/pdftotext-fallback--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 pdftotext-fallback -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install HKUDS/OpenSpace pdftotext-fallback --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/pdftotext-fallback .gemini/skills/pdftotext-fallback && 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 "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .gemini/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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 pdftotext-fallbackInstalls 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 pdftotext-fallback -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/pdftotext-fallback .github/skills/pdftotext-fallback && 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 "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .github/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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 pdftotext-fallback -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 pdftotext-fallback --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/pdftotext-fallback .opencode/skills/pdftotext-fallback && 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 "pdftotext-fallback" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/pdftotext-fallback into .opencode/skills/pdftotext-fallback/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdftotext-fallback", 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
pdftotext-fallback- GitHub stars
- 7.7k
- Token cost
- ~782 tokens
- SKILL.md length
- 323 words
- Files
- 2
- Skills in repo
- 199
- Repo updated
- First seen
- Licence
- MIT
At a glance
Recover PDF text extraction when readfile returns binary data by using pdftotext via shell
- Works in 4 steps: Detect the Failure → Use pdftotext via run_shell → Handle Complex PDFs → …
- Tasks that involve PDF
- SKILL.md covers When to Use, Why This Works, Steps and Code Examples, plus 3 more sections
- Calls pdftotext and apt-get
What it does
Pdftotext Fallback is an agent skill from HKUDS/OpenSpace. Recover PDF text extraction when readfile returns binary data by using pdftotext via shell
Its SKILL.md is about 780 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
- “/pdftotext-fallback”
Requirements
- Python 3
Workflow steps
4 steps, taken from the step headings in SKILL.md.
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-get
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Pdftotext Fallback loads about 782 tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 323 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). 323 words, ~782 tokens.
Download SKILL.mdSave it as
.claude/skills/pdftotext-fallback/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- pdftotext-fallback
- description
- Recover PDF text extraction when read_file returns binary data by using pdftotext via shell
pdftotext Fallback for PDF Text Extraction
When to Use
Apply this pattern when:
read_fileon a PDF returns binary/image data instead of readable text- Python-based PDF extraction (PyMuPDF, pdfplumber, etc.) in
execute_code_sandboxfails or returns garbled content - You need reliable text extraction from PDF files as a recovery strategy
Why This Works
The pdftotext utility (from poppler-utils) is a mature, command-line tool that handles many PDF edge cases that confuse Python libraries or the read_file tool. It's pre-installed on most Linux systems and provides consistent, reliable text extraction.
Steps
Step 1: Detect the Failure
Recognize extraction failure when:
read_filereturns binary content, image data, or garbled text- Error messages indicate encoding issues or unsupported formats
- Python PDF libraries in sandbox fail with import errors or extraction failures
Step 2: Use pdftotext via run_shell
Extract to stdout (recommended for quick extraction):
pdftotext /path/to/file.pdf -The - argument outputs directly to stdout for easy capture in your tool response.
Example:
run_shell("pdftotext document.pdf -")Step 3: Handle Complex PDFs
Preserve layout (maintains original formatting):
pdftotext -layout /path/to/file.pdf -Extract to a file (for large PDFs):
pdftotext /path/to/file.pdf /path/to/output.txtThen read the output file with read_file.
Handle encoded text:
pdftotext -enc UTF-8 /path/to/file.pdf -Step 4: Verify and Continue
- Check the extracted text for completeness
- If text is still garbled, the PDF may be image-based (scanned) - consider OCR tools
- Proceed with your task using the extracted text
Code Examples
Basic extraction:
# Simple text extraction
text = run_shell("pdftotext document.pdf -")With error handling:
# Try extraction, check for success
result = run_shell("pdftotext document.pdf - && echo 'SUCCESS' || echo 'FAILED'")Multi-page PDF with layout:
# Preserve tables and formatting
text = run_shell("pdftotext -layout document.pdf -")Troubleshooting
| Issue | Solution |
|---|---|
pdftotext: command not found | Install poppler-utils: apt-get install poppler-utils |
| Garbled/special characters | Try -enc UTF-8 or -enc ASCII7 |
| Missing formatting | Use -layout flag |
| Scanned PDF (no text) | Requires OCR (e.g., tesseract), not text extraction |
| Large PDF timeout | Extract to file instead of stdout |
Limitations
- Does not work on image-only (scanned) PDFs without embedded text
- May lose complex formatting, tables, or embedded objects
- Requires poppler-utils to be installed (common on Linux, may need installation on other systems)
Related Tools
pdfinfo: Get PDF metadata (pages, size, etc.)pdftoppm: Convert PDF pages to imagestesseract: OCR for scanned PDFs
© 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/pdftotext-fallback of HKUDS/OpenSpace.
- SKILL.md
- .skill_id
Open the folder on GitHubat commit 3827781
Compare with similar skills
Pdftotext Fallback 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 |
|---|---|---|---|---|---|---|
| Pdftotext Fallback this skillHKUDS/OpenSpace | 7.7k | — | ~782 | 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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Questions about Pdftotext Fallback
What does Pdftotext Fallback do?
Recover PDF text extraction when readfile returns binary data by using pdftotext via shell. Pdftotext Fallback is an agent skill from HKUDS/OpenSpace.
When should I use Pdftotext Fallback?
Pdftotext Fallback fits situations like: tasks that involve PDF.
How do I install Pdftotext Fallback in Claude Code?
Run `npx skills add HKUDS/OpenSpace --skill pdftotext-fallback -a claude-code`. Or copy the skill folder (benchmarks/gdpval/skills/pdftotext-fallback in HKUDS/OpenSpace) into .claude/skills/pdftotext-fallback in your project. Claude Code loads it when a task matches its description.
How do I install Pdftotext Fallback in Codex?
Run `npx skills add HKUDS/OpenSpace --skill pdftotext-fallback -a codex`. Or copy the skill folder (benchmarks/gdpval/skills/pdftotext-fallback in HKUDS/OpenSpace) into .agents/skills/pdftotext-fallback in your project. Codex loads it when a task matches its description.
Can I use Pdftotext Fallback 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 pdftotext-fallback -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pdftotext-fallback, .gemini/skills/pdftotext-fallback, .github/skills/pdftotext-fallback and .opencode/skills/pdftotext-fallback in your project.
What does Pdftotext Fallback need to run?
Going by SKILL.md and its folder, Pdftotext Fallback needs the command-line tools its instructions call (pdftotext and apt-get). Our summary lists: Python 3.
Does Pdftotext Fallback access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Pdftotext Fallback 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 Pdftotext Fallback use?
Pdftotext Fallback 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 Pdftotext Fallback use?
About 782 tokens (SKILL.md is roughly 3.1k 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 Pdftotext Fallback?
Skills that share tags, products or a category with Pdftotext Fallback: 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 Pdftotext Fallback?
HKUDS (a GitHub organization) maintains it in HKUDS/OpenSpace, which has 7,749 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.