# Galaxy Language Server
[](https://github.com/davelopez/galaxy-language-server/actions)
[](https://pypi.org/project/galaxy-language-server/)
[Language Server](https://microsoft.github.io/language-server-protocol/) implementation written in Python ([pygls](https://github.com/openlawlibrary/pygls)) to assist in the development of [Galaxy tool wrappers](https://docs.galaxyproject.org/en/latest/dev/schema.html).
#### Dependencies
- [pygls](https://github.com/openlawlibrary/pygls): generic implementation of the [Language Server Protocol](https://microsoft.github.io/language-server-protocol/specification) in Python.
- [lxml](https://lxml.de/index.html): Python library for processing XML files.
- [anytree](https://github.com/c0fec0de/anytree): Python library with an easy to use tree structure.
- [galaxy-tool-util](https://pypi.org/project/galaxy-tool-util/): the [Galaxy](https://galaxyproject.org/) tool utilities for Python.
# Getting Started
Check the [Getting Started](https://github.com/galaxyproject/galaxy-language-server/blob/main/docs/CONTRIBUTING.md#getting-started) section in the [contributing](https://github.com/galaxyproject/galaxy-language-server/blob/main/docs/CONTRIBUTING.md) docs.
# How to manually run the server
Usually, the [client](https://github.com/galaxyproject/galaxy-language-server/tree/main/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+`):
```sh
# Create a virtual environment and activate it
python -m venv myenv
source ./myenv/bin/activate
```
## Option 1: Installing from PyPi
```sh
# Install the language server and its dependencies
pip install galaxy-language-server
```
## Option 2: Building from source
```sh
# 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
```sh
# 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:
```sh
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
## [0.13.0] - 2024-09-30
### Added
- Add commands `Insert param reference` and `Insert param output filter` ([#264](https://github.com/galaxyproject/galaxy-language-server/pull/264)).
### Changed
- Update server dependencies + improve development experience ([#257](https://github.com/galaxyproject/galaxy-language-server/pull/257)).
## [0.12.1] - 2024-05-18
### Changed
- Update internal dependencies to support new Galaxy (24.0.2) XSD definitions.
## [0.12.0] - 2023-10-14
### Added
- Document Symbol provider ([#247](https://github.com/galaxyproject/galaxy-language-server/pull/247)).
## [0.11.0] - 2023-08-30
### Fixed
- Fix macros detection condition ([#239](https://github.com/galaxyproject/galaxy-language-server/pull/239)).
### Added
- Support for links to navigate to test-data files ([#231](https://github.com/galaxyproject/galaxy-language-server/pull/231)).
### Changed
- Improve attribute with enum auto-completion ([#241](https://github.com/galaxyproject/galaxy-language-server/pull/241)).
- Remove dead link ([#238](https://github.com/galaxyproject/galaxy-language-server/pull/238)).
## [0.10.2] - 2023-03-12
### Fixed
- Fix parameters and models conversion between client and server ([#224](https://github.com/galaxyproject/galaxy-language-server/pull/224)).
## [0.10.1] - 2023-03-04
### Fixed
- Config loading issue resulting in unhandled exception with new configuration models ([#220](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/216)).
## [0.9.0] - 2022-10-20
### Added
- New setting to silently install the language server ([#210](https://github.com/galaxyproject/galaxy-language-server/pull/210)).
### Changed
- Code quality: fix e2e tests for linting ([#211](https://github.com/galaxyproject/galaxy-language-server/pull/211)).
## [0.8.0] - 2022-10-02
### Added
- Full Galaxy tool linting integration ([#204](https://github.com/galaxyproject/galaxy-language-server/pull/204)).
### Changed
- Code quality: refactor validation system ([#205](https://github.com/galaxyproject/galaxy-language-server/pull/205)).
- Code quality: setup isort ([#203](https://github.com/galaxyproject/galaxy-language-server/pull/203)).
## [0.7.1] - 2022-01-31
### Fixed
- Check valid document extension before checking contents when validating documents ([#189](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/183)).
### Changed
- Update `pygls` dependency and fix how custom commands are registered ([#179](https://github.com/galaxyproject/galaxy-language-server/pull/179)).
### Fixed
- An error creating `Code Actions` to extract macros when selecting a text range in some situations ([#178](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/156)).
## [0.5.2] - 2021-06-08
### Fixed
- Line offset mismatch between diagnostic line and expanded document ([#150](https://github.com/galaxyproject/galaxy-language-server/pull/150)).
## [0.5.1] - 2021-06-03
### Fixed
- Clear diagnostics when the document is not valid ([#143](https://github.com/galaxyproject/galaxy-language-server/pull/143)).
- Fix empty document validation ([#144](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/127)).
- A custom command to generate the expanded version of a tool document ([#128](https://github.com/galaxyproject/galaxy-language-server/pull/128)).
- Existing macro names are now suggested when manually invoking IntelliSense with `Ctrl+Space` ([#132](https://github.com/galaxyproject/galaxy-language-server/pull/132)).
- Support for dynamic token parameter attributes in `<expand>` elements ([#133](https://github.com/galaxyproject/galaxy-language-server/pull/133)).
### Changed
- Updated main dependencies to latests versions, specially `pygls=0.10.3` which introduced some backward incompatible changes ([#126](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/129)).
- Auto-closing tags when writing `/` or `>` was broken in previous versions ([#137](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/110)).
- A custom command to reorder `<param>` attributes according to the IUC Style Guidelines ([#104](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/113)).
- Elements inside macros were not correctly associated with their XSD definition ([#111](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/109)).
## [0.3.2] - 2021-01-24
### Fixed
- The server was ignoring tool wrappers with syntax errors instead of reporting those syntax errors ([#100](https://github.com/galaxyproject/galaxy-language-server/pull/100)).
## [0.3.1] - 2021-01-09
### Fixed
- The autocompletion of tags and attributes was leaking into the `CDATA` sections ([#86](https://github.com/galaxyproject/galaxy-language-server/pull/86)).
- Weird behavior of the autoclosing tag feature ([#86](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/77)).
- A custom command to auto-generate `<test>` cases based on the current `inputs` and `outputs` defined in the tool ([#73](https://github.com/galaxyproject/galaxy-language-server/pull/73)).
### Fixed
- Avoid processing unknown XML documents (aka _not_ tool wrappers) ([#75](https://github.com/galaxyproject/galaxy-language-server/pull/75)).
- Broken XML parsing when more than one comment block was present in the document ([#70](https://github.com/galaxyproject/galaxy-language-server/pull/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](https://github.com/galaxyproject/galaxy-language-server/pull/64)).
## [0.2.0] - 2020-11-13
### Added
- Client settings to control completion features ([#56](https://github.com/galaxyproject/galaxy-language-server/pull/56)).
### Changed
- The XML parser has been replaced with a better implementation ([#55](https://github.com/galaxyproject/galaxy-language-server/pull/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.
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"description": "# Galaxy Language Server\n\n[](https://github.com/davelopez/galaxy-language-server/actions)\n\n[](https://pypi.org/project/galaxy-language-server/)\n\n[Language Server](https://microsoft.github.io/language-server-protocol/) implementation written in Python ([pygls](https://github.com/openlawlibrary/pygls)) to assist in the development of [Galaxy tool wrappers](https://docs.galaxyproject.org/en/latest/dev/schema.html).\n\n#### Dependencies\n\n- [pygls](https://github.com/openlawlibrary/pygls): generic implementation of the [Language Server Protocol](https://microsoft.github.io/language-server-protocol/specification) in Python.\n- [lxml](https://lxml.de/index.html): Python library for processing XML files.\n- [anytree](https://github.com/c0fec0de/anytree): Python library with an easy to use tree structure.\n- [galaxy-tool-util](https://pypi.org/project/galaxy-tool-util/): the [Galaxy](https://galaxyproject.org/) tool utilities for Python.\n\n# Getting Started\n\nCheck the [Getting Started](https://github.com/galaxyproject/galaxy-language-server/blob/main/docs/CONTRIBUTING.md#getting-started) section in the [contributing](https://github.com/galaxyproject/galaxy-language-server/blob/main/docs/CONTRIBUTING.md) docs.\n\n# How to manually run the server\n\nUsually, the [client](https://github.com/galaxyproject/galaxy-language-server/tree/main/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:\n\nIn any case, it is recommended to create a Python virtual environment first (assuming you are using `Python3.8+`):\n\n```sh\n# Create a virtual environment and activate it\npython -m venv myenv\nsource ./myenv/bin/activate\n```\n\n## Option 1: Installing from PyPi\n\n```sh\n# Install the language server and its dependencies\npip install galaxy-language-server\n```\n\n## Option 2: Building from source\n\n```sh\n# Clone the repo\ngit clone https://github.com/galaxyproject/galaxy-language-server.git\n\n# Go to the server directory\ncd galaxy-language-server/server\n\n# Install the dependencies\npython -m pip install -r ./requirements.txt\n```\n\n## Run the server\n\n```sh\n# Run the server with the default parameters\npython -m galaxyls\n```\n\nBy default, the server uses IO pipes to communicate with the client. If you want to use TCP, you can pass additional parameters, for example:\n\n```sh\npython -m galaxyls --tcp --host=127.0.0.1 --port=2087\n```\n\nTo 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:\n\n```\nINFO:pygls.server:Starting server on 127.0.0.1:2087\nINFO:pygls.server:Shutting down the server\nINFO:pygls.server:Closing the event loop.\n```\n# Galaxy Language Server Changelog\n\n## [0.13.0] - 2024-09-30\n\n### Added\n\n- Add commands `Insert param reference` and `Insert param output filter` ([#264](https://github.com/galaxyproject/galaxy-language-server/pull/264)).\n\n### Changed\n\n- Update server dependencies + improve development experience ([#257](https://github.com/galaxyproject/galaxy-language-server/pull/257)).\n\n## [0.12.1] - 2024-05-18\n\n### Changed\n\n- Update internal dependencies to support new Galaxy (24.0.2) XSD definitions.\n\n## [0.12.0] - 2023-10-14\n\n### Added\n\n- Document Symbol provider ([#247](https://github.com/galaxyproject/galaxy-language-server/pull/247)).\n\n## [0.11.0] - 2023-08-30\n\n### Fixed\n\n- Fix macros detection condition ([#239](https://github.com/galaxyproject/galaxy-language-server/pull/239)).\n\n### Added\n\n- Support for links to navigate to test-data files ([#231](https://github.com/galaxyproject/galaxy-language-server/pull/231)).\n\n### Changed\n\n- Improve attribute with enum auto-completion ([#241](https://github.com/galaxyproject/galaxy-language-server/pull/241)).\n- Remove dead link ([#238](https://github.com/galaxyproject/galaxy-language-server/pull/238)).\n\n## [0.10.2] - 2023-03-12\n\n### Fixed\n\n- Fix parameters and models conversion between client and server ([#224](https://github.com/galaxyproject/galaxy-language-server/pull/224)).\n\n## [0.10.1] - 2023-03-04\n\n### Fixed\n\n- Config loading issue resulting in unhandled exception with new configuration models ([#220](https://github.com/galaxyproject/galaxy-language-server/pull/220)).\n\n## [0.10.0] - 2023-02-25\n\n### Changed\n\n- Update pygls to version 1.0.1. This enables Python 3.11 support and other features ([#216](https://github.com/galaxyproject/galaxy-language-server/pull/216)).\n\n## [0.9.0] - 2022-10-20\n\n### Added\n\n- New setting to silently install the language server ([#210](https://github.com/galaxyproject/galaxy-language-server/pull/210)).\n\n### Changed\n\n- Code quality: fix e2e tests for linting ([#211](https://github.com/galaxyproject/galaxy-language-server/pull/211)).\n\n## [0.8.0] - 2022-10-02\n\n### Added\n\n- Full Galaxy tool linting integration ([#204](https://github.com/galaxyproject/galaxy-language-server/pull/204)).\n\n### Changed\n\n- Code quality: refactor validation system ([#205](https://github.com/galaxyproject/galaxy-language-server/pull/205)).\n\n- Code quality: setup isort ([#203](https://github.com/galaxyproject/galaxy-language-server/pull/203)).\n\n## [0.7.1] - 2022-01-31\n\n### Fixed\n\n- Check valid document extension before checking contents when validating documents ([#189](https://github.com/galaxyproject/galaxy-language-server/pull/189)).\n\n## [0.7.0] - 2022-01-29\n\n### Added\n\n- New custom command to discover tests in a single tool file to support the new Testing API in the client ([#183](https://github.com/galaxyproject/galaxy-language-server/pull/183)).\n\n### Changed\n\n- Update `pygls` dependency and fix how custom commands are registered ([#179](https://github.com/galaxyproject/galaxy-language-server/pull/179)).\n\n### Fixed\n\n- An error creating `Code Actions` to extract macros when selecting a text range in some situations ([#178](https://github.com/galaxyproject/galaxy-language-server/pull/178)).\n\n## [0.6.1] - 2021-09-26\n\n### Changed\n\n- Revert `pygls` version to `0.11.1`. This should temporarily fix an issue that prevents using any custom command in the language server ([#172](https://github.com/galaxyproject/galaxy-language-server/pull/172)).\n\n## [0.6.0] - 2021-09-12\n\n### Added\n\n- Code Action language feature to be able to extract macros out of valid blocks of XML ([#165](https://github.com/galaxyproject/galaxy-language-server/pull/165)).\n\n## [0.5.3] - 2021-07-09\n\n### Fixed\n\n- An error when generating tests from inputs that contained boolean values different than `true` or `false` like `True` or `False` ([#156](https://github.com/galaxyproject/galaxy-language-server/pull/156)).\n\n## [0.5.2] - 2021-06-08\n\n### Fixed\n\n- Line offset mismatch between diagnostic line and expanded document ([#150](https://github.com/galaxyproject/galaxy-language-server/pull/150)).\n\n## [0.5.1] - 2021-06-03\n\n### Fixed\n\n- Clear diagnostics when the document is not valid ([#143](https://github.com/galaxyproject/galaxy-language-server/pull/143)).\n\n- Fix empty document validation ([#144](https://github.com/galaxyproject/galaxy-language-server/pull/144)).\n\n## [0.5.0] - 2021-05-13\n\n### Added\n\n- 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](https://github.com/galaxyproject/galaxy-language-server/pull/127)).\n\n- A custom command to generate the expanded version of a tool document ([#128](https://github.com/galaxyproject/galaxy-language-server/pull/128)).\n\n- Existing macro names are now suggested when manually invoking IntelliSense with `Ctrl+Space` ([#132](https://github.com/galaxyproject/galaxy-language-server/pull/132)).\n\n- Support for dynamic token parameter attributes in `<expand>` elements ([#133](https://github.com/galaxyproject/galaxy-language-server/pull/133)).\n\n### Changed\n\n- Updated main dependencies to latests versions, specially `pygls=0.10.3` which introduced some backward incompatible changes ([#126](https://github.com/galaxyproject/galaxy-language-server/pull/126)).\n\n### Fixed\n\n- When manually invoking IntelliSense with `Ctrl+Space` in the middle of a tag or attribute the auto-completion was suggesting wrong values ([#129](https://github.com/galaxyproject/galaxy-language-server/pull/129)).\n\n- Auto-closing tags when writing `/` or `>` was broken in previous versions ([#137](https://github.com/galaxyproject/galaxy-language-server/pull/137)).\n\n## [0.4.0] - 2021-02-15\n\n### Added\n\n- A custom command for tests discovery that provides information about the test definitions of all the opened tool documents in the virtual workspace ([#110](https://github.com/galaxyproject/galaxy-language-server/pull/110)).\n\n- A custom command to reorder `<param>` attributes according to the IUC Style Guidelines ([#104](https://github.com/galaxyproject/galaxy-language-server/pull/104)).\n\n### Fixed\n\n- 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](https://github.com/galaxyproject/galaxy-language-server/pull/113)).\n\n- Elements inside macros were not correctly associated with their XSD definition ([#111](https://github.com/galaxyproject/galaxy-language-server/pull/111)).\n\n- 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](https://github.com/galaxyproject/galaxy-language-server/pull/109)).\n\n## [0.3.2] - 2021-01-24\n\n### Fixed\n\n- The server was ignoring tool wrappers with syntax errors instead of reporting those syntax errors ([#100](https://github.com/galaxyproject/galaxy-language-server/pull/100)).\n\n## [0.3.1] - 2021-01-09\n\n### Fixed\n\n- The autocompletion of tags and attributes was leaking into the `CDATA` sections ([#86](https://github.com/galaxyproject/galaxy-language-server/pull/86)).\n\n- Weird behavior of the autoclosing tag feature ([#86](https://github.com/galaxyproject/galaxy-language-server/pull/86)).\n\n- 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](https://github.com/galaxyproject/galaxy-language-server/pull/83)).\n\n## [0.3.0] - 2021-01-01\n\n### Added\n\n- 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](https://github.com/galaxyproject/galaxy-language-server/pull/77)).\n- A custom command to auto-generate `<test>` cases based on the current `inputs` and `outputs` defined in the tool ([#73](https://github.com/galaxyproject/galaxy-language-server/pull/73)).\n\n### Fixed\n\n- Avoid processing unknown XML documents (aka _not_ tool wrappers) ([#75](https://github.com/galaxyproject/galaxy-language-server/pull/75)).\n- Broken XML parsing when more than one comment block was present in the document ([#70](https://github.com/galaxyproject/galaxy-language-server/pull/70)).\n\n## [0.2.1] - 2020-11-22\n\n### Fixed\n\n- The documentation displayed when hovering an element now shows the correct documentation instead of `No documentation available` ([#64](https://github.com/galaxyproject/galaxy-language-server/pull/64)).\n\n## [0.2.0] - 2020-11-13\n\n### Added\n\n- Client settings to control completion features ([#56](https://github.com/galaxyproject/galaxy-language-server/pull/56)).\n\n### Changed\n\n- The XML parser has been replaced with a better implementation ([#55](https://github.com/galaxyproject/galaxy-language-server/pull/55)).\n\n## [0.1.2] - 2020-10-25\n\n### Removed\n\n- Removed unused function `XsdTree.find_node_by_name()`.\n\n## [0.1.1] - 2020-10-24\n\n### Added\n\n- Support autocompletion for `<expand>` element.\n\n### Changed\n\n- Updated dependencies to latest versions.\n\n### Fixed\n\n- Fix error when hovering `<expand>` elements or it's atributes (#41).\n\n## [0.1.0] - 2020-10-14\n\n### Added\n\n- Basic tag and attribute auto-completion.\n- Auto-close tags feature.\n- XML tool validation when opening and saving file.\n- Basic validation of macros.\n- Auto-formatting document when saving file.\n- Display tag and attribute documentation when hovering.\n\n\n",
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