galaxy-language-server 0.10.1

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

[0.10.1] - 2023-03-04

Fixed

• Config loading issue resulting in unhandled exception with new configuration models (#220).

[0.10.0] - 2023-02-25

Changed

• Update pygls to version 1.0.1. This enables Python 3.11 support and other features (#216).

[0.9.0] - 2022-10-20

Added

• New setting to silently install the language server (#210).

Changed

• Code quality: fix e2e tests for linting (#211).

[0.8.0] - 2022-10-02

Added

• Full Galaxy tool linting integration (#204).

Changed

• Code quality: refactor validation system (#205).

• Code quality: setup isort (#203).

[0.7.1] - 2022-01-31

Fixed

• Check valid document extension before checking contents when validating documents (#189).

[0.7.0] - 2022-01-29

Added

• New custom command to discover tests in a single tool file to support the new Testing API in the client (#183).

Changed

• Update pygls dependency and fix how custom commands are registered (#179).

Fixed

• An error creating Code Actions to extract macros when selecting a text range in some situations (#178).

[0.6.1] - 2021-09-26

Changed

• Revert pygls version to 0.11.1. This should temporarily fix an issue that prevents using any custom command in the language server (#172).

[0.6.0] - 2021-09-12

Added

• Code Action language feature to be able to extract macros out of valid blocks of XML (#165).

[0.5.3] - 2021-07-09

Fixed

• An error when generating tests from inputs that contained boolean values different than true or false like True or False (#156).

[0.5.2] - 2021-06-08

Fixed

• Line offset mismatch between diagnostic line and expanded document (#150).

[0.5.1] - 2021-06-03

Fixed

• Clear diagnostics when the document is not valid (#143).

• Fix empty document validation (#144).

[0.5.0] - 2021-05-13

Added

• New feature to navigate to (or peek) macro and token definitions, open referenced macro files directly from the <import> tag and preview token values on hover (#127).

• A custom command to generate the expanded version of a tool document (#128).

• Existing macro names are now suggested when manually invoking IntelliSense with Ctrl+Space (#132).

• Support for dynamic token parameter attributes in <expand> elements (#133).

Changed

• Updated main dependencies to latests versions, specially pygls=0.10.3 which introduced some backward incompatible changes (#126).

Fixed

• When manually invoking IntelliSense with Ctrl+Space in the middle of a tag or attribute the auto-completion was suggesting wrong values (#129).

• Auto-closing tags when writing / or > was broken in previous versions (#137).

[0.4.0] - 2021-02-15

Added

• A custom command for tests discovery that provides information about the test definitions of all the opened tool documents in the virtual workspace (#110).

• A custom command to reorder <param> attributes according to the IUC Style Guidelines (#104).

Fixed

• Unexpected errors when generating code were failing silently without providing feedback to the user. Now an error notification will be displayed to the user (#113).

• Elements inside macros were not correctly associated with their XSD definition (#111).

• An bug in the search algorithm when analyzing the tool input trees with nested conditional sharing the same 'when' value. This was causing the code generation commands to fail (#109).

[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.