prefixmaps

library0.2.6pypypi✓ verified 86d ago

The `prefixmaps` library, currently at version 0.2.6, is a Python tool for managing and resolving semantic prefix maps, particularly for CURIEs (Compact URIs). It simplifies the expansion of short-form identifiers into full IRIs and vice versa, primarily by leveraging community-maintained prefix registries like those from OBO Foundry. Releases occur periodically to update prefix data and improve functionality.

data serialization

pip install prefixmaps

github ↗package ↗

INSTALL

IMPORT

SIG · PREFIXMAPS

prefixmaps

datapythonv0.2.6

Install

3.7s avg

Import

—

Disk

38MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.2.6 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

installs and imports cleanly · install 0.0s · import 0.000s · 40MB

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 3.7s · import 0.000s · 40MB

38MB installed

● package 38MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Context

✓ from prefixmaps import Context

✗ from prefixmaps import PrefixMap

PrefixExpansion

✓ from prefixmaps import PrefixExpansion

load_context

✓ from prefixmaps import load_context

Demonstrates initializing a PrefixMap, expanding a CURIE, compressing an IRI, and checking for prefix existence.

from prefixmaps import PrefixMap # Initialize with the default OBO Foundry prefix map (loaded from the web) pm = PrefixMap() # Expand a CURIE (Compact URI) to a full IRI curie = "GO:0008150" iri = pm.expand(curie) print(f"Expanded {curie} to: {iri}") # Compress a full IRI to a CURIE (if a matching prefix is found) full_iri = "http://purl.obolibrary.org/obo/BFO_0000001" compressed_curie = pm.compress(full_iri) print(f"Compressed {full_iri} to: {compressed_curie}") # Check if a prefix exists in the map print(f"Has prefix 'GO': {pm.has_prefix('GO')}") print(f"Has prefix 'UNKNOWN': {pm.has_prefix('UNKNOWN')}")

prefixmaps --version

Debug

Known issues

breakingThe method for loading the default registry has changed across minor versions. Directly calling `prefixmaps.io.get_and_parse_default_registry()` is now deprecated or removed.

fix

Use `pm = PrefixMap()` for the default registry or `PrefixMap.load_default_registry()` for explicit loading.

affects: <0.2.0

gotchaInitializing `PrefixMap()` without arguments attempts to load the default prefix registry from a remote web source (e.g., OBO Foundry). This operation will fail without an internet connection or if the remote source is temporarily unavailable.

fix

For offline or controlled environments, consider using `PrefixMap.load_from_json(filepath)` or `PrefixMap.load_from_shacl(filepath)` with a locally cached registry file. The library also allows specifying a custom URL for the registry.

affects: >=0.1.0

gotchaThe `expand()` method returns `None` if a given CURIE's prefix is not found in the loaded `PrefixMap`, rather than raising an error. This requires explicit `None` checking in application code.

fix

Always check the return value of `pm.expand(curie)`: `iri = pm.expand(curie); if iri is None: print(f"Unknown prefix for {curie}")`.

affects: >=0.1.0

deprecatedDirect access to `prefixmaps.io.get_and_parse_default_registry()` is deprecated. This function was an internal detail that has been superseded by the `PrefixMap` constructor and class methods.

fix

Use `pm = PrefixMap()` to load the default registry or `PrefixMap.load_default_registry()` if you need to load it explicitly without creating a new `PrefixMap` instance immediately.

affects: >=0.2.0

Upgrade

Version history

0.2.6latest on PyPI · released Oct 17, 2024

Audit

Dependencies

pydanticrequiredUsed for data validation and parsing of prefix map schemas.

Agent activity

4 hits · last 30 days

node

Resources

githubhttps://github.com/linkml/prefixmaps ↗

packagehttps://pypi.org/project/prefixmaps/ ↗