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.
Execute Python scripts for spreadsheet operations with mandatory source data validation and fallback protocols
$ npx skills add HKUDS/OpenSpace --skill spreadsheet-source-validated -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install HKUDS/OpenSpace spreadsheet-source-validated --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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .claude/skills/spreadsheet-source-validated && 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 "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .claude/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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/spreadsheet-direct-python-enhanced-enhanced-2e6773Type 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 spreadsheet-source-validated -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install HKUDS/OpenSpace spreadsheet-source-validated --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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .agents/skills/spreadsheet-source-validated && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .agents/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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 spreadsheet-source-validated -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install HKUDS/OpenSpace spreadsheet-source-validated --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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .cursor/skills/spreadsheet-source-validated && 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 "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .cursor/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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/spreadsheet-direct-python-enhanced-enhanced-2e6773--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 spreadsheet-source-validated -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install HKUDS/OpenSpace spreadsheet-source-validated --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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .gemini/skills/spreadsheet-source-validated && 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 "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .gemini/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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 spreadsheet-source-validatedInstalls 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 spreadsheet-source-validated -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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .github/skills/spreadsheet-source-validated && 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 "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .github/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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 spreadsheet-source-validated -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 spreadsheet-source-validated --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/spreadsheet-direct-python-enhanced-enhanced-2e6773 .opencode/skills/spreadsheet-source-validated && 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 "spreadsheet-source-validated" agent skill from https://github.com/HKUDS/OpenSpace/tree/main/benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 into .opencode/skills/spreadsheet-source-validated/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-source-validated", 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.
spreadsheet-source-validatedExecute Python scripts for spreadsheet operations with mandatory source data validation and fallback protocols
Spreadsheet Source Validated is an agent skill from HKUDS/OpenSpace. Execute Python scripts for spreadsheet operations with mandatory source data validation and fallback protocols
Its SKILL.md is about 3.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file.
It sits in Documents & Office, covering Excel spreadsheets. 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.
3 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:
python3From the folder's file list and the shell code blocks in SKILL.md.
Hosts in commands or code, which the agent is likely to contact:
dataservices.epa.illinois.govepa.govwaterdata.usgs.govFrom 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.
Spreadsheet Source Validated loads about 3.2k tokens when it runs. Until then it costs about 35 tokens; SKILL.md has 700 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). 700 words, ~3,163 tokens.
.claude/skills/spreadsheet-source-validated/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.CRITICAL: Before attempting any spreadsheet operations, validate that your source data is accessible and complete.
import os
import sys
from pathlib import Path
def validate_source_data(source_paths):
"""Validate all required data sources before processing."""
missing = []
inaccessible = []
for path in source_paths:
p = Path(path)
if not p.exists():
missing.append(str(path))
elif not os.access(path, os.R_OK):
inaccessible.append(str(path))
if missing:
print(f"ERROR: Missing data sources: {', '.join(missing)}", file=sys.stderr)
return False
if inaccessible:
print(f"ERROR: Inaccessible data sources: {', '.join(inaccessible)}", file=sys.stderr)
return False
print(f"VALIDATED: {len(source_paths)} source(s) available")
return True
# Usage
sources = ['input.xlsx', 'reference_data.csv']
if not validate_source_data(sources):
sys.exit(1)import pandas as pd
from openpyxl import load_workbook
def validate_spreadsheet_integrity(file_path, required_sheets=None, required_columns=None):
"""Check spreadsheet structure before processing."""
try:
# Check file is readable
wb = load_workbook(file_path, read_only=True)
# Verify required sheets exist
if required_sheets:
missing_sheets = [s for s in required_sheets if s not in wb.sheetnames]
if missing_sheets:
print(f"ERROR: Missing sheets: {missing_sheets}", file=sys.stderr)
wb.close()
return False
# Verify required columns (sample first sheet)
if required_columns:
ws = wb.active
headers = [cell.value for cell in ws[1]]
missing_cols = [c for c in required_columns if c not in headers]
if missing_cols:
print(f"ERROR: Missing columns: {missing_cols}", file=sys.stderr)
wb.close()
return False
wb.close()
print(f"VALIDATED: Spreadsheet structure OK")
return True
except Exception as e:
print(f"ERROR: Cannot validate spreadsheet: {str(e)}", file=sys.stderr)
return FalseFor data retrieved from APIs, websites, or external services:
import requests
from urllib3.exceptions import SSLError, MaxRetryError
def validate_external_source(url, timeout=30, max_retries=2):
"""Verify external data source is accessible."""
for attempt in range(max_retries + 1):
try:
response = requests.head(url, timeout=timeout, allow_redirects=True)
if response.status_code == 200:
print(f"VALIDATED: External source accessible ({url})")
return True
else:
print(f"WARNING: External source returned {response.status_code}", file=sys.stderr)
except (SSLError, MaxRetryError, requests.ConnectionError) as e:
if attempt == max_retries:
print(f"ERROR: External source inaccessible after {max_retries + 1} attempts: {url}", file=sys.stderr)
return False
print(f"RETRY {attempt + 1}/{max_retries}: {str(e)}", file=sys.stderr)
return FalseUse validated Python execution for spreadsheet operations when:
openpyxl, pandas, or similar librariesWhen primary data sources are inaccessible:
ALTERNATIVE_SOURCES = {
'epa_water_data': [
'https://dataservices.epa.illinois.gov/swap', # Primary
'https://www.epa.gov/safewater/data-and-reports', # Federal fallback
'https://waterdata.usgs.gov/nwis', # USGS fallback
],
'financial_data': [
'internal_database.xlsx', # Primary
'backup_financial_data.csv', # Local backup
'request_from_stakeholder', # Manual acquisition
]
}
def try_alternative_sources(source_key):
"""Iterate through alternative sources until one succeeds."""
alternatives = ALTERNATIVE_SOURCES.get(source_key, [])
for i, source in enumerate(alternatives):
print(f"Attempting alternative {i + 1}/{len(alternatives)}: {source}")
if source.startswith('http'):
if validate_external_source(source):
return source
else:
if Path(source).exists():
print(f"SUCCESS: Alternative source found: {source}")
return source
print(f"ERROR: All alternatives exhausted for {source_key}", file=sys.stderr)
return Nonedef report_data_access_failure(source, error_type, alternatives_tried=0):
"""Standardized error reporting for data access failures."""
error_report = {
'timestamp': datetime.now().isoformat(),
'source': source,
'error_type': error_type,
'alternatives_tried': alternatives_tried,
'action_required': 'Manual data acquisition or source configuration update'
}
print("=" * 60, file=sys.stderr)
print("DATA ACCESS FAILURE REPORT", file=sys.stderr)
print("=" * 60, file=sys.stderr)
for key, value in error_report.items():
print(f"{key}: {value}", file=sys.stderr)
print("=" * 60, file=sys.stderr)
return error_reportThe shell_agent tool can:
Direct run_shell with Python is more reliable because it:
.py files first avoids shell_agent parsing issues with heredocs# Step 1: Write validation script
cat > validate_sources.py << 'EOF'
import sys
from pathlib import Path
sources = ['input.xlsx', 'config.json']
missing = [s for s in sources if not Path(s).exists()]
if missing:
print(f"BLOCKED: Missing sources: {missing}", file=sys.stderr)
sys.exit(1)
print("VALIDATED: All sources available")
EOF
# Step 2: Run validation
python3 validate_sources.py || exit 1
# Step 3: Write processing script
cat > process_spreadsheet.py << 'EOF'
import openpyxl
# Your spreadsheet code here
EOF
# Step 4: Execute processing
python3 process_spreadsheet.py
# Step 5: Clean up (optional)
rm validate_sources.py#!/usr/bin/env python3
"""
Complete workflow: Validate -> Process -> Report
"""
import sys
from pathlib import Path
from datetime import datetime
from openpyxl import load_workbook
def main():
# PHASE 1: Validation
print(f"[{datetime.now().isoformat()}] Starting validation...")
source_file = 'input_data.xlsx'
if not Path(source_file).exists():
print(f"ERROR: Source file not found: {source_file}", file=sys.stderr)
# Check for alternatives
for alt in ['backup_input.xlsx', 'data_backup.csv']:
if Path(alt).exists():
print(f"FALLBACK: Using alternative: {alt}")
source_file = alt
break
else:
print("ERROR: No alternative sources available", file=sys.stderr)
sys.exit(1)
# PHASE 2: Processing
print(f"[{datetime.now().isoformat()}] Processing {source_file}...")
try:
wb = load_workbook(source_file)
ws = wb.active
# Your operations here
for row in ws.iter_rows(min_row=2):
pass # Process data
wb.save('output.xlsx')
print(f"SUCCESS: Processed {ws.max_row - 1} rows")
except Exception as e:
print(f"ERROR: Processing failed: {str(e)}", file=sys.stderr)
sys.exit(1)
# PHASE 3: Cleanup
print(f"[{datetime.now().isoformat()}] Complete")
if __name__ == '__main__':
main().py file first, then execute via run_shell| Library | Best For |
|---|---|
openpyxl | Reading/writing .xlsx files, formatting, formulas |
pandas | Data manipulation, analysis, merging datasets |
xlrd | Reading older .xls files (read-only) |
xlsxwriter | Creating new .xlsx files with advanced formatting |
requests | Validating external API/data sources |
pathlib | Cross-platform file path validation |
Issue: Heredoc syntax fails with 'unknown error' when using shell_agent
.py file first, then execute it with python3 script.py. This pattern is significantly more reliable than inline heredoc execution when shell_agent is the executor.Issue: Source data validation fails
ls -laIssue: External data source inaccessible (SSL/proxy errors)
requests.get(url, verify=False)Issue: FileNotFoundError
Issue: PermissionError
Issue: MemoryError on large files
chunksize parameterIssue: Formatting not applying
.copy() for style objectsIssue: Data validation passes but processing fails
© 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/spreadsheet-direct-python-enhanced-enhanced-2e6773 of HKUDS/OpenSpace.
Open the folder on GitHubat commit 3827781
Spreadsheet Source Validated 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 |
|---|---|---|---|---|---|---|
| Spreadsheet Source Validated this skillHKUDS/OpenSpace | 7.7k | — | ~3.2k | 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 | |
| Doc Cleanernotoriouslab/doc-cleaner | 309 | — | ~712 | Automated safety check: Pass | MIT | |
| MineruNebutra/MinerU-Skill | 122 | — | ~504 | Automated safety check: Pass | MIT | |
| XLSXzzhonglei/GeoCode-Release | 186 | — | ~3.1k | Automated safety check: Pass | MIT | |
| Python Bridgetmustier/pi-for-excel | 434 | — | ~820 | Automated safety check: Pass | MIT |
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.
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.
zzhonglei/GeoCode-Release
Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) where the workbook file is the primary deliverable.
tmustier/pi-for-excel
Native Python execution via the local Python bridge. An agent skill from tmustier/pi-for-excel.
shuyu-labs/WebCode
Convert Office documents (Word, Excel, PowerPoint, PDF) to Markdown format.
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
Execute Python scripts for spreadsheet operations with mandatory source data validation and fallback protocols. Spreadsheet Source Validated is an agent skill from HKUDS/OpenSpace.
Spreadsheet Source Validated fits situations like: tasks that involve Excel spreadsheets.
Run `npx skills add HKUDS/OpenSpace --skill spreadsheet-source-validated -a claude-code`. Or copy the skill folder (benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 in HKUDS/OpenSpace) into .claude/skills/spreadsheet-source-validated in your project. Claude Code loads it when a task matches its description.
Run `npx skills add HKUDS/OpenSpace --skill spreadsheet-source-validated -a codex`. Or copy the skill folder (benchmarks/gdpval/skills/spreadsheet-direct-python-enhanced-enhanced-2e6773 in HKUDS/OpenSpace) into .agents/skills/spreadsheet-source-validated 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 spreadsheet-source-validated -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spreadsheet-source-validated, .gemini/skills/spreadsheet-source-validated, .github/skills/spreadsheet-source-validated and .opencode/skills/spreadsheet-source-validated in your project.
Going by SKILL.md and its folder, Spreadsheet Source Validated needs the command-line tools its instructions call (python3). Our summary lists: Python 3.
SKILL.md names 3 domains. In commands or code: dataservices.epa.illinois.gov, epa.gov and waterdata.usgs.gov; the agent is likely to contact these when it follows the instructions. 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.
Spreadsheet Source Validated is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 3.2k tokens (SKILL.md is roughly 13k 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 Spreadsheet Source Validated: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Doc Cleaner (notoriouslab/doc-cleaner, 309 stars), Mineru (Nebutra/MinerU-Skill, 122 stars) and XLSX (zzhonglei/GeoCode-Release, 186 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.