IDE for WDL

This project aims to provide a "batteries-included" environment for developing WDL workflows.

Please note: it is currently under active development, and is not yet feature-complete.

Editor-agnostic WDL support

We will provide a WDL Language Server plugin, based on Language Server Protocol (LSP), cromwell-tools, pygls, and miniwdl.

This protocol is supported by many code editors, and enables universal support for language features.

More specifically, our plugin will enable you to:

check the syntax of a workflow
submit a workflow for execution to Cromwell API
watch for completion/failure of each workflow (or cancel it)
highlight task-specific failures
get feedback on runtime resource management
enjoy rich editor support (jump to definition etc.)

You can find the following published extensions based on this plugin:

WDL DevTools for VS Code
WDL DevTools for IntelliJ

Other editors are supported via their respective LSP plugins. Examples on how to connect them are in the client directory.

Browser IDE

Additionally, we provide an Integrated Development Environment (IDE), which runs in a web browser and is based on Theia.

It bundles WDL extensions for Visual Studio Code - WDL DevTools and WDL Syntax Highlighter - along with a "local" instance of Cromwell.

The bundle consists of Docker containers, which you can set up with a single Docker Compose command.

This approach is used to

develop workflows locally, with an ultra-fast feedback loop
run workflows in the cloud from developer machine - no need for a Cromwell server
create reproducible setup - it works on any OS with Docker Compose
run the same setup on a remote server - think Notebooks, but for WDL!
simplify local development - it just works™

Deployment

To deploy the IDE:

clone or download this repo into a local folder
install Docker Compose
for local-only development, run this command in the cloned folder:
```
docker-compose pull && docker-compose up
```
for local and Google Cloud development, do the following instead [*]:
- create a project on Google Cloud Platform
- create a service account with project-wide Genomics Pipelines Runner role, and download its key in JSON format
- grant it Service Account User permission on Compute Engine default service account in that project
- create a bucket for Cromwell executions
- grant Storage Object Admin permission on the Cromwell executions bucket
- run this command, replacing <...> with your values:
```
docker-compose pull && \
GOOGLE_APPLICATION_CREDENTIALS=./<your-service-account-key>.json \
GOOGLE_AUTH_MODE=service-account \
GOOGLE_CLOUD_PROJECT=<your-project-name> \
GOOGLE_EXECUTIONS_BUCKET=<executions-bucket-name> \
docker-compose up
```
[*] In the future, we may provide a simplified script to do most of the above. Additionally, we may add settings for other cloud providers (PRs are welcome!).

The first time you run the Docker compose command, it will take ~5 minutes to compile the IDE from sources and bring up the environment. Later on, we will provide a Docker image to speed that up.

When you no longer see the log messages, the IDE is running and you can navigate to it in a browser at this address: localhost:3000.

Metadata

Release files for wdl-lsp 0.0.90

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Source distribution for wdl-lsp 0.0.90
File	Size	Uploaded	Provenance
wdl-lsp-0.0.90.tar.gz	12.6 kB	Apr 23, 2024	Without provenance	Details

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File	Interpreter	ABI	Platform	Reset
wdl_lsp-0.0.90-py3-none-any.whl 12.9 kB Apr 23, 2024 Without provenance	Python 3	none	any	Details

Total release size: 25.5 kB

Release files / wdl-lsp-0.0.90.tar.gz

Download URL	wdl-lsp-0.0.90.tar.gz
Size	12.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`d50a0a4231443d2822bda65945d7f0e9748d0d1f8b1a1c1cdbe9aa86366b769d`
BLAKE2b-256 checksum How to use checksums	`bc754840a538cf4969608ffd6452de50b7fb0ce4ed4a9859970b2e4d5277b188`
Upload date	Apr 23, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/5.0.0 CPython/3.12.3`

Release files / wdl_lsp-0.0.90-py3-none-any.whl

Download URL	wdl_lsp-0.0.90-py3-none-any.whl
Size	12.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`3f3d44228b4b091db4bd29cd3fa20219b51ac0a8e70a0bb4df01b1e9ad8ac3dd`
BLAKE2b-256 checksum How to use checksums	`308d1dce0ba622b65b3d0a1c53fefb9039a8d8887384615c36d0a3df0d0a3c6c`
Upload date	Apr 23, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/5.0.0 CPython/3.12.3`

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