metasalmonpy

Create, review, validate, and publish Salmon Data Packages from Python

Python implementation of the metasalmon workflows for portable, ontology-aware salmon data.

metasalmonpy provides the Python implementation of the metasalmon workflows: the core package lifecycle, semantic review, ontology term governance, validation, and Enterprise Data Hub (EDH) metadata behaviour. The version number is a parity claim naming the metasalmon release whose functionality this package actually delivers, and R and Python parity is where that number lives — this page deliberately does not carry a second copy of it, having read 0.1.6 for the three releases after 0.1.6.

import pandas as pd
from metasalmonpy import create_sdp, validate_salmon_datapackage

observations = pd.DataFrame(
    {
        "species": ["Coho", "Chinook"],
        "catch_count": [100, 200],
    }
)

package_path = create_sdp(
    observations,
    path="catch-sdp",
    dataset_id="catch-monitoring",
    table_id="observations",
    seed_semantics=False,
)

validate_salmon_datapackage(package_path)
Important

Generated metadata is review-ready, not publication-ready. Replace all MISSING values and every REVIEW: IRI, then run strict validation with require_iris=True.

Workflow

flowchart LR
    A["pandas DataFrame(s)"] --> B["create_sdp()"]
    B --> C["Review metadata and semantics"]
    C --> D["validate_salmon_datapackage()"]
    D --> E["Rebuild EDH XML"]
    E --> F["Publish complete package"]

Where to start

Goal Documentation Main functions
Create a package from raw tables Get started create_sdp()
Control inference and package assembly Package lifecycle infer_salmon_datapackage_artifacts(), write_salmon_datapackage()
Decide ontology IRIs and fill in metadata Semantic review review_semantics(), accept_suggestion(), apply_sdp_semantics(), review_metadata(), set_sdp_*()
Record missing ontology concepts Term requests detect_semantic_term_gaps(), render_ontology_term_request()
Validate and export EDH metadata EDH and validation validate_salmon_datapackage(), write_edh_xml_from_sdp()
Look up function signatures API reference All exported functions

LLM review is strictly opt-in. Supplying context files or context text does not enable a provider call; llm_assess=True is always required.

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