https://github.com/broadinstitute/wdl-ide

Rich IDE support for Workflow Description Language

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
2 of 6 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary

Keywords

cromwell docker ide lsp theia vscode wdl wdl-devtools

Keywords from Contributors

bioinformatics labels application executor ga4gh workflow-description-language workflow-execution

Last synced: 5 months ago · JSON representation

Repository

Rich IDE support for Workflow Description Language

Basic Info

Host: GitHub
Owner: broadinstitute
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage:
Size: 604 KB

Statistics

Stars: 42
Watchers: 10
Forks: 9
Open Issues: 13
Releases: 0

Topics

cromwell docker ide lsp theia vscode wdl wdl-devtools

Created over 6 years ago · Last pushed 11 months ago

Metadata Files

Readme License Security

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: - [x] check the syntax of a workflow - [x] submit a workflow for execution to Cromwell API - [x] watch for completion/failure of each workflow (or cancel it) - [x] highlight task-specific failures - [ ] get feedback on runtime resource management - [x] 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.

Owner

Name: Broad Institute
Login: broadinstitute
Kind: organization
Location: Cambridge, MA

Website: http://www.broadinstitute.org/
Twitter: broadinstitute
Repositories: 1,083
Profile: https://github.com/broadinstitute

Broad Institute of MIT and Harvard

GitHub Events

Total

Watch event: 2
Pull request event: 1
Create event: 1

Last Year

Watch event: 2
Pull request event: 1
Create event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 223
Total Committers: 6
Avg Commits per committer: 37.167
Development Distribution Score (DDS): 0.063

Top Committers

Name	Email	Commits
Denis Loginov	d**s@b**g	209
dependabot[bot]	4**]@u**m	5
Denis Loginov	d**d@g**m	5
Michael Franklin	m**n@p**u	2
Vincent Selhorst-Jones	v**s@c**m	1
Phil Shapiro	p**o@b**g	1

Committer Domains (Top 20 + Academic)

broadinstitute.org: 2 chanzuckerberg.com: 1 populationgenomics.org.au: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 16
Total pull requests: 36
Average time to close issues: 12 months
Average time to close pull requests: 3 months
Total issue authors: 16
Total pull request authors: 5
Average comments per issue: 1.88
Average comments per pull request: 0.39
Merged pull requests: 27
Bot issues: 0
Bot pull requests: 13

Past Year

Issues: 1
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 1
Average comments per issue: 2.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

satwinderbanipal (1)
SHuang-Broad (1)
dinvlad (1)
lmtani (1)
cfriedline (1)
GregTD42 (1)
aofarrel (1)
vincent-czi (1)
JaylanLiu (1)
PriitPaluoja (1)
mmterpstra (1)
avilaHugo (1)
dformoso (1)
songmingl (1)
maribuon (1)

Pull Request Authors

dinvlad (30)
dependabot[bot] (20)
pshapiro4broad (2)
illusional (1)
vincent-czi (1)

Top Labels

Issue Labels

Pull Request Labels

dependencies (20) javascript (2)

Packages

Total packages: 1
Total downloads:
- pypi 131 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 58
Total maintainers: 2

pypi.org: wdl-lsp

Language Server Protocol (LSP) implementation for Workflow Definition Language (WDL)

Homepage: https://github.com/broadinstitute/wdl-ide
Documentation: https://wdl-lsp.readthedocs.io/
License: BSD 3-clause "New" or "Revised" License
Latest release: 0.0.90
published almost 2 years ago

Versions: 58
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 131 Last month

Rankings

Dependent packages count: 10.1%

Stargazers count: 10.4%

Downloads: 10.7%

Forks count: 11.9%

Average: 13.0%

Dependent repos count: 21.6%

Maintainers (2)

broadinst-pypi broad-wintergreen

Last synced: 6 months ago

Dependencies

client/intellij/build.gradle maven

com.github.ballerina-platform:lsp4intellij 0.93.4 implementation

client/theia/package.json npm

@theia/cli next development
@theia/editor-preview next
@theia/file-search next
@theia/git next
@theia/json next
@theia/keymaps next
@theia/markers next
@theia/merge-conflicts next
@theia/messages next
@theia/mini-browser next
@theia/navigator next
@theia/outline-view next
@theia/plugin-ext-vscode next
@theia/preferences next
@theia/preview next
@theia/search-in-workspace next
@theia/terminal next
@theia/textmate-grammars next
keytar latest
typescript latest

client/vscode/package-lock.json npm

@babel/code-frame 7.12.13 development
@babel/helper-validator-identifier 7.14.0 development
@babel/highlight 7.14.0 development
@types/node 8.10.66 development
@types/vscode 1.56.0 development
ansi-styles 3.2.1 development
argparse 1.0.10 development
azure-devops-node-api 10.2.2 development
balanced-match 1.0.0 development
boolbase 1.0.0 development
brace-expansion 1.1.11 development
buffer-crc32 0.2.13 development
builtin-modules 1.1.1 development
call-bind 1.0.2 development
chalk 2.4.2 development
cheerio 1.0.0-rc.9 development
cheerio-select 1.4.0 development
color-convert 1.9.3 development
color-name 1.1.3 development
commander 6.2.1 development
commander 2.20.3 development
concat-map 0.0.1 development
css-select 4.1.2 development
css-what 5.0.1 development
denodeify 1.2.1 development
diff 4.0.2 development
dom-serializer 1.3.2 development
domelementtype 2.2.0 development
domhandler 4.2.0 development
domutils 2.6.0 development
entities 2.2.0 development
entities 2.0.3 development
escape-string-regexp 1.0.5 development
esprima 4.0.1 development
fd-slicer 1.1.0 development
fs.realpath 1.0.0 development
function-bind 1.1.1 development
get-intrinsic 1.1.1 development
glob 7.1.4 development
has 1.0.3 development
has-flag 3.0.0 development
has-symbols 1.0.2 development
htmlparser2 6.1.0 development
inflight 1.0.6 development
inherits 2.0.3 development
is-core-module 2.4.0 development
js-tokens 4.0.0 development
js-yaml 3.14.1 development
leven 3.1.0 development
linkify-it 2.2.0 development
lodash 4.17.21 development
markdown-it 10.0.0 development
mdurl 1.0.1 development
mime 1.6.0 development
minimatch 3.0.4 development
minimist 1.2.5 development
mkdirp 0.5.5 development
mute-stream 0.0.8 development
nth-check 2.0.1 development
object-inspect 1.10.3 development
once 1.4.0 development
os-homedir 1.0.2 development
os-tmpdir 1.0.2 development
osenv 0.1.5 development
parse-semver 1.1.1 development
parse5 6.0.1 development
parse5-htmlparser2-tree-adapter 6.0.1 development
path-is-absolute 1.0.1 development
path-parse 1.0.7 development
pend 1.2.0 development
qs 6.10.1 development
read 1.0.7 development
resolve 1.20.0 development
semver 5.7.0 development
side-channel 1.0.4 development
sprintf-js 1.0.3 development
supports-color 5.5.0 development
tmp 0.0.29 development
tslib 2.2.0 development
tslib 1.10.0 development
tslint 5.20.1 development
tslint-microsoft-contrib 6.2.0 development
tsutils 2.29.0 development
tsutils 3.21.0 development
tsutils 2.28.0 development
tunnel 0.0.6 development
typed-rest-client 1.8.4 development
typescript 3.9.9 development
uc.micro 1.0.6 development
underscore 1.13.1 development
url-join 1.1.0 development
vsce 1.88.0 development
wrappy 1.0.2 development
yauzl 2.10.0 development
yazl 2.5.1 development
semver 6.3.0
vscode-jsonrpc 5.0.1
vscode-languageclient 6.1.4
vscode-languageserver-protocol 3.15.3
vscode-languageserver-types 3.15.1

client/vscode/package.json npm

@types/node ^8.10.66 development
@types/vscode ^1.56.0 development
tslint ^5.20.1 development
tslint-microsoft-contrib ^6.2.0 development
tsutils ^3.21.0 development
typescript ^3.9.9 development
vsce ^1.64.0 development
vscode-languageclient ^6.1.4

server/setup.py pypi

cromwell-tools *
miniwdl *
pygls *

client/theia/Dockerfile docker

alpine latest build
base latest build

.github/workflows/publish-pypi.yml actions

actions/checkout v4 composite
actions/setup-python v5 composite
pypa/cibuildwheel v2.17 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/publish-jetbrains.yml actions

actions/checkout v4 composite
actions/setup-java v4 composite

.github/workflows/publish-vscode.yml actions

actions/checkout v4 composite
actions/setup-node v4 composite

https://github.com/broadinstitute/wdl-ide

Science Score: 23.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

IDE for WDL

Editor-agnostic WDL support

Browser IDE

Deployment

Owner

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: wdl-lsp

Rankings

Maintainers (2)

Dependencies