Galaxy Utilities

26.0.0 · active · verified Fri Apr 17

The `galaxy-util` package provides common utility functions and helper classes used across the larger Galaxy bioinformatics platform. It is an integral part of the Galaxy ecosystem, supporting various functionalities within the main application. Currently at version 26.0.0, it follows the rapid release cadence of the main Galaxy project, often tied to its major releases. While available on PyPI, its primary use case is within the Galaxy project itself.

Common errors

```
ModuleNotFoundError: No module named 'galaxy.util'
```
cause The `galaxy-util` package has not been installed, or your Python environment's path does not include the installation location.

fix Ensure the package is installed: `pip install galaxy-util`. If using a virtual environment, ensure it's activated.
```
AttributeError: module 'galaxy.util.path' has no attribute 'some_function_name'
```
cause The specific utility function or class you are trying to import/use (`some_function_name`) was removed, renamed, or refactored in the version of `galaxy-util` you have installed. This is common due to its internal utility nature.

fix Check the `galaxy.util` source code in the Galaxy project's GitHub repository (`lib/galaxy/util` for your specific version) to find the current API or an alternative. Update your code to reflect the new API.
```
ImportError: cannot import name 'SomeSpecificClass' from 'galaxy.util.tool_shed'
```
cause A class or function previously available in a submodule of `galaxy.util` has been moved to a different module, or it has been removed entirely during a refactoring.

fix Consult the Galaxy project's official documentation or examine the source code for the exact `galaxy-util` version you are using to determine the correct import path or if the functionality has been replaced.

Warnings

breaking APIs within `galaxy.util` can change significantly between major Galaxy releases (e.g., v25 to v26). As an internal utility package, modules, functions, or their signatures might be refactored, moved, or removed without explicit deprecation warnings targeted at external users.
Fix: Refer to the Galaxy project's official release notes and source code (`lib/galaxy/util` directory in the main Galaxy repository) for the specific version you are using to confirm API stability and correct usage.
gotcha The `galaxy-util` package is primarily designed for internal use within the Galaxy project. Its APIs are tightly coupled with the larger Galaxy application's internal structure and evolution, and may not always be suitable or stable for standalone, general-purpose use outside of the Galaxy ecosystem.
Fix: Consider if a more general-purpose Python library exists for your specific utility need before integrating `galaxy-util` into non-Galaxy applications. Be prepared for potential API instability if you do use it externally.
gotcha Version mismatches between `galaxy-util` and the main `galaxy` package (if you are developing for Galaxy) can lead to unexpected behavior, `AttributeError`s, or runtime failures, as they are developed and released in tandem.
Fix: Ensure that your `galaxy-util` version is compatible with your `galaxy` core version. Ideally, manage dependencies through the main Galaxy project's recommended setup or requirements.txt.

Install

pip install galaxy-util Install latest version

Imports

safe_path
wrong:
```
from galaxy_util.path import safe_path
```
correct:
```
from galaxy.util.path import safe_path
```
The PyPI package `galaxy-util` exposes its modules under the `galaxy.util` namespace, not `galaxy_util`.

parse_json_string

from galaxy.util.json import parse_json_string

sanitize_text

from galaxy.util.sanitize_text import sanitize_text

Quickstart

This quickstart demonstrates basic usage of two common utility functions: `safe_path` for sanitizing path components and `sanitize_text` for removing potentially dangerous HTML/script tags from strings. These are representative of the type of general-purpose helpers found in `galaxy-util`.

from galaxy.util.path import safe_path
from galaxy.util.sanitize_text import sanitize_text

# Example 1: Safely resolve a path component
unsafe_path_component = '../etc/passwd'
safe_component = safe_path(unsafe_path_component)
print(f"Unsafe: {unsafe_path_component}, Safe: {safe_component}")

# Example 2: Sanitize text input
raw_text = '<script>alert("XSS")</script>Hello & World!'
sanitized_text = sanitize_text(raw_text)
print(f"Raw: {raw_text}\nSanitized: {sanitized_text}")

view raw JSON →