Idiomatic conversion between URIs and compact URIs (CURIEs)

0.13.3 · active · verified Thu Apr 16

The `curies` Python package provides efficient, faultless, and idiomatic utilities for converting between Uniform Resource Identifiers (URIs) and Compact URIs (CURIEs). It is a crucial low-level tool for linked data applications, enabling data scientists, curators, and software developers to handle prefix maps, expand CURIEs to URIs, and compress URIs to CURIEs. The library is actively developed, currently at version 0.13.3, with ongoing enhancements for robustness and usability.

Common errors

```
NameError: name 'curies' is not defined
```
cause The `curies` module was used without being imported first.

fix Add `import curies` at the top of your Python script or interactive session before using any functions or classes from the library.
```
AttributeError: 'NoneType' object has no attribute 'compress'
```
cause A converter object (e.g., returned by `curies.load_prefix_map()` or `curies.get_obo_converter()`) was `None`, indicating that it failed to initialize properly, and subsequently, a method like `compress()` was called on this `None` object.

fix Verify that your prefix map input is valid, or that the predefined converter could be loaded successfully. Always check that the `converter` object is not `None` before attempting to use its methods.

Warnings

breaking As a library in the 0.x.x version range, `curies` is not yet considered stable. Breaking changes to the API may occur between minor versions (e.g., from 0.12 to 0.13).
Fix: Always review the release notes and changelog when upgrading `curies` to a new minor version to identify any necessary code adjustments.
gotcha When loading prefix maps, especially with overlapping URI prefixes (e.g., 'http://purl.obolibrary.org/obo/' and 'http://purl.obolibrary.org/obo/CHEBI_'), `curies` prioritizes the first matching prefix encountered. This behavior ensures 'faultless' conversion but may differ from expectations if not explicitly considered.
Fix: Ensure that your custom prefix maps are ordered from most specific to least specific, or be aware that the first definition for a prefix/URI prefix pair will take precedence in resolution.

Install

pip install curies Install latest version

Imports

curies
```
import curies
```
Standard import for accessing all top-level functions and classes.
Converter
```
from curies import Converter
```
For direct instantiation of the Converter class, though often created via helper functions.

Quickstart

This quickstart demonstrates how to load a predefined CURIE converter and then use it to expand CURIEs to URIs and compress URIs back to CURIEs. Alternatively, you can define and load your own prefix map.

import curies

# Option 1: Load a predefined converter (e.g., OBO Foundry)
converter = curies.get_obo_converter()

# Option 2: Load a custom prefix map
# prefix_map = {"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_"}
# converter = curies.load_prefix_map(prefix_map)

# Expand a CURIE to a URI
curie_example = "CHEBI:1"
expanded_uri = converter.expand(curie_example)
print(f"Expanded '{curie_example}' to '{expanded_uri}'")
# Expected: Expanded 'CHEBI:1' to 'http://purl.obolibrary.org/obo/CHEBI_1'

# Compress a URI to a CURIE
uri_example = "http://purl.obolibrary.org/obo/CHEBI_2"
compressed_curie = converter.compress(uri_example)
print(f"Compressed '{uri_example}' to '{compressed_curie}'")
# Expected: Compressed 'http://purl.obolibrary.org/obo/CHEBI_2' to 'CHEBI:2'

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