galaxy-language-server 0.3.2

A language server for Galaxy (https://galaxyproject.org) tool wrappers

Galaxy Language Server

Language Server implementation written in Python (pygls) to assist in the development of Galaxy tool wrappers.

Dependencies

• pygls: generic implementation of the Language Server Protocol in Python.
• lxml: Python library for processing XML files.
• anytree: Python library with an easy to use tree structure.
• galaxy-tool-util: the Galaxy tool utilities for Python.

Getting Started

Check the Getting Started section in the contributing docs.

How to manually run the server

Usually, the client will be in charge of running the server when it is needed, but, in case you want to run it manually for some reason, you can use the following commands:

In any case, it is recommended to create a Python virtual environment first (assuming you are using Python3.8+):

# Create a virtual environment and activate it
python -m venv myenv
source ./myenv/bin/activate

Option 1: Installing from PyPi

# Install the language server and its dependencies
pip install galaxy-language-server

Option 2: Building from source

# Clone the repo
git clone https://github.com/galaxyproject/galaxy-language-server.git

# Go to the server directory
cd galaxy-language-server/server

# Install the dependencies
python -m pip install -r ./requirements.txt

Run the server

# Run the server with the default parameters
python -m galaxyls

By default, the server uses IO pipes to communicate with the client. If you want to use TCP, you can pass additional parameters, for example:

python -m galaxyls --tcp --host=127.0.0.1 --port=2087

To check if everything went ok, you can look at the content of the server log file (galaxy-language-server.log) that should contain the following lines:

INFO:pygls.server:Starting server on 127.0.0.1:2087
INFO:pygls.server:Shutting down the server
INFO:pygls.server:Closing the event loop.

Galaxy Language Server Changelog

[0.3.2] - 2021-01-24

Fixed

• The server was ignoring tool wrappers with syntax errors instead of reporting those syntax errors (#100)

[0.3.1] - 2021-01-09

Fixed

• The autocompletion of tags and attributes was leaking into the CDATA sections (#86).

• Weird behavior of the autoclosing tag feature (#86).

• When using a custom command to auto-generate the <command> or the <tests> sections (with a tool document containing macros), the insert position inside the document for the code snippets was offset (#83).

[0.3.0] - 2021-01-01

Added

• A custom command to auto-generate the <command> section with boilerplate Cheetah template based on the current inputs and outputs defined in the tool (#77).
• A custom command to auto-generate <test> cases based on the current inputs and outputs defined in the tool (#73).

Fixed

• Avoid processing unknown XML documents (aka not tool wrappers) (#75).
• Broken XML parsing when more than one comment block was present in the document (#70).

[0.2.1] - 2020-11-22

Fixed

• The documentation displayed when hovering an element now shows the correct documentation instead of No documentation available (#64).

[0.2.0] - 2020-11-13

Added

• Client settings to control completion features (#56).

Changed

• The XML parser has been replaced with a better implementation (#55).

[0.1.2] - 2020-10-25

Removed

• Removed unused function XsdTree.find_node_by_name().

[0.1.1] - 2020-10-24

Added

• Support autocompletion for <expand> element.

Changed

• Updated dependencies to latest versions.

Fixed

• Fix error when hovering <expand> elements or it's atributes (#41).

[0.1.0] - 2020-10-14

Added

• Basic tag and attribute auto-completion.
• Auto-close tags feature.
• XML tool validation when opening and saving file.
• Basic validation of macros.
• Auto-formatting document when saving file.
• Display tag and attribute documentation when hovering.