allotrope-tier1-native-parsing-preferred

Sub-skill of instrument-data-allotrope: Tier 1: Native allotropy parsing (PREFERRED) (+2).

5 stars

Best use case

allotrope-tier1-native-parsing-preferred is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Sub-skill of instrument-data-allotrope: Tier 1: Native allotropy parsing (PREFERRED) (+2).

Teams using allotrope-tier1-native-parsing-preferred should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/tier-1-native-allotropy-parsing-preferred/SKILL.md --create-dirs "https://raw.githubusercontent.com/vamseeachanta/workspace-hub/main/.agents/skills/_archive/science/bio-research/instrument-data-allotrope/tier-1-native-allotropy-parsing-preferred/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/tier-1-native-allotropy-parsing-preferred/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How allotrope-tier1-native-parsing-preferred Compares

Feature / Agent	allotrope-tier1-native-parsing-preferred	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Sub-skill of instrument-data-allotrope: Tier 1: Native allotropy parsing (PREFERRED) (+2).

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# Tier 1: Native allotropy parsing (PREFERRED) (+2)

## Tier 1: Native allotropy parsing (PREFERRED)

**Always try allotropy first.** Check available vendors directly:

```python
from allotropy.parser_factory import Vendor

# List all supported vendors
for v in Vendor:
    print(f"{v.name}")

# Common vendors:
# AGILENT_TAPESTATION_ANALYSIS  (for TapeStation XML)
# BECKMAN_VI_CELL_BLU
# THERMO_FISHER_NANODROP_EIGHT
# MOLDEV_SOFTMAX_PRO
# APPBIO_QUANTSTUDIO
# ... many more
```

**When the user provides a file, check if allotropy supports it before falling back to manual parsing.** The `scripts/convert_to_asm.py` auto-detection only covers a subset of allotropy vendors.


## Tier 2: Flexible fallback parsing

**Only use if allotropy doesn't support the instrument.** This fallback:
- Does NOT generate `calculated-data-aggregate-document`
- Does NOT include full traceability
- Produces simplified ASM structure

Use flexible parser with:
- Column name fuzzy matching
- Unit extraction from headers
- Metadata extraction from file structure


## Tier 3: PDF extraction

For PDF-only files, extract tables using pdfplumber, then apply Tier 2 parsing.

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