Dockstore

Dockstore provides a place for users to share tools encapsulated in Docker and described with the Common Workflow Language (CWL), WDL (Workflow Description Language), Nextflow, or Galaxy. This enables scientists to share analytical workflows so that they are machine readable as well as runnable in a variety of environments. While the Dockstore is focused on serving researchers in the biosciences, the combination of Docker + workflow languages can be used by anyone to describe the tools and services in their Docker images in a standardized, machine-readable way.
Dockstore is also a leading implementor of the GA4GH API standard for container registries, TRS. The usage of this is to enumerate the docker containers (from quay.io and hopefully docker hub) and the workflows (from github/bitbucket) that are available to users of Dockstore.org.

For the live site see dockstore.org

This repo contains the web service component for Dockstore as well as collecting issues for the project as a whole.

For the related web UI see the dockstore-ui project. For the related CLI see the cli project.

For Dockstore Users

The following section is useful for users of Dockstore (e.g. those that want to browse, register, and launch tools).

After registering at dockstore.org, you will be able to download the Dockstore CLI at https://dockstore.org/onboarding

Configuration File

A basic Dockstore configuration file is available/should be created in ~/.dockstore/config and contains the following at minimum:

token = <your token generated by the dockstore site>
server-url = https://www.dockstore.org/api

File Provisioning

By default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems such as http, https, and ftp. Through a plug-in system, Dockstore also supports the Amazon S3 and Synapse via plugins.

Download the above set of default plugins via:

dockstore plugin download

Configuration for plugins can be placed inside the Dockstore configuration file in the following format

token = <your generated by the dockstore site>
server-url = https://www.dockstore.org/api

# options below this are optional

use-cache = false                           #set this to true to cache input files for rapid development
cache-dir = /home/<user>/.dockstore/cache   #set this to determine where input files are cached (should be the same filesystem as your tool working directories)

[dockstore-file-synapse-plugin]

[dockstore-file-s3-plugin]
endpoint = #set this to point at a non AWS S3 endpoint

[dockstore-file-icgc-storage-client-plugin]
client = /media/large_volume/icgc-storage-client-1.0.23/bin/icgc-storage-client

Additional plugins can be created by taking one of the repos in plugins as a model and using pf4j as a reference. See additional documentation for more details.

For Dockstore Developers

The following section is useful for Dockstore developers (e.g. those that want to improve or fix the Dockstore web service and UI)

Dependencies

The dependency environment for Dockstore is described by our CircleCI config or docker compose. In addition to the dependencies for Dockstore users, note the setup instructions for postgres. Specifically, you will need to have postgres installed and setup with the database user specified in .circleci/config.yml (ideally, postgres is needed only for integration tests but not unit tests).

Building

As an alternative to the following commands, if you do not have Maven installed you can use the maven wrapper as a substitute. For example:

./mvnw clean install
# instead of
mvn clean install

If you maven build in the root directory this will build all modules:

mvn clean install
# or
mvn clean install -Punit-tests

Consider the following if you need to build a specific version (such as in preparation for creating a tag for a release):

mvnw clean install  -Dchangelist=.0-beta.5 #or whatever version you need 

If you're running tests on CircleCI (or otherwise have access to the confidential data bundle) Run them via:

mvn clean install -Pintegration-tests

There are also certain categories for tests that they can be added to when writing new tests. Categories include:

1. ToilCompatibleTest are tests that can be run with our default cwltool and with Toil
2. ConfidentialTest are tests that require access to our confidential testing bundle (ask a member of the development team if you're on the team)

Running Locally

You can also run it on your local computer but will need to setup postgres separately.

1. Fill in the template dockstore.yml and stash it somewhere outside the git repo (like ~/.dockstore)
2. The dockstore.yml is mostly a standard Dropwizard configuration file. Refer to the linked document to setup httpClient and database.
3. Start with java -jar dockstore-webservice/target/dockstore-webservice-*.jar server ~/.dockstore/dockstore.yml
4. If you need integration with GitHub.com, Quay.io. or Bitbucket for your work, you will need to follow the appropriate sections below and then fill out the corresponding fields in your dockstore.yml.

One alternative if you prefer running things in containers would be using docker-compose

View Swagger UI

The Swagger UI is reachable while the Dockstore webservice is running. This allows you to explore available web resources.

1. Browse to http://localhost:8080/static/swagger-ui/index.html

Development

Coding Standards

codestyle.xml defines the coding style for Dockstore as an IntelliJ Code Style XML file that should be imported into IntelliJ IDE. We also have a matching checkstyle.xml that can be imported into other IDEs and is run during the build.

For users of Intellij or comparable IDEs, we also suggest loading the checkstyle.xml with a plugin in order to display warnings and errors while coding live rather than encountering them later when running a build.

Installing git-secrets

Dockstore uses git-secrets to help make sure that keys and private data stay out of the source tree. For information on installing it on your platform check https://github.com/awslabs/git-secrets#id6 .

If you're on mac with homebrew use brew install git-secrets.

Dockstore Command Line

The dockstore command line should be installed in a location in your path.

/dockstore-client/bin/dockstore

You then need to setup a ~/.dockstore/config file with the following contents:

token: <dockstore_token_from_web_app>
server-url: http://www.dockstore.org:8080

If you are working with a custom-built or updated dockstore client you will need to update the jar in: ~/.dockstore/config/self-installs.

Swagger Client Generation

We use the swagger-codegen-maven-plugin to generate several sections of code which are not checked in. These include

1. All of swagger-java-client (talks to our webservice for the CLI via Swagger 2.0)
2. All of openapi-java-client (talks to our webservice for the CLI, but in OpenAPI 3.0)
3. The Tool Registry Server components (serves up the TRS endpoints)

To update these, you will need to point at a new version of the swagger.yaml provided by a service. For example, update the equivalent of inputSpec in your branch.

Encrypted Documents for CircleCI

Encrypted documents necessary for confidential testing are decrypted via decrypt.sh with access being granted to developers at UCSC and OICR.

A convenience script is provided as encrypt.sh which will compress confidential files, encrypt them, and then update an encrypted archive on GitHub. Confidential files should also be added to .gitignore to prevent accidental check-in. The unencrypted secrets.tar should be privately distributed among members of the team that need to work with confidential data. When using this script you will likely want to alter the CUSTOM_DIR_NAME. This is necessary since running the script will overwrite the existing encryption keys, instantly breaking existing builds using that key. Our current workaround is to use a new directory when providing a new bundle.

Adding Copyright header to all files with IntelliJ

To add copyright headers to all files with IntelliJ

1. Ensure the Copyright plugin is installed (Settings -> Plugins)
2. Create a new copyright profile matching existing copyright header found on all files, name it Dockstore (Settings -> Copyright -> Copyright Profiles -> Add New)
3. Set the default project copyright to Dockstore (Settings -> Copyright)

Setting up a Mac for Dockstore development

Install Docker (Be sure to click on 'Mac with Apple chip' if you have Apple silicon) https://docs.docker.com/desktop/mac/install/

Install Brew https://brew.sh/

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Run 'git' to trigger the install of Xcode or the Command Line Tools which will install and or update git https://developer.apple.com/forums/thread/672087?answerId=659036022#659036022

git

(If that doesn't work install git manually https://git-scm.com/download/mac)

Setup git user information

git config --global user.email "[email protected]"
git config --global user.name "Your Name"

Read about git token requirements

Setup personal access token for git CLI

It's helpful to cache your git personal access token

Install Hubflow https://datasift.github.io/gitflow/TheHubFlowTools.html

git clone https://github.com/datasift/gitflow
cd gitflow
sudo ./install.sh

Install JDK 17 https://formulae.brew.sh/formula/openjdk@17

brew install openjdk@17

Download and install node.js https://github.com/nvm-sh/nvm

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh | bash

Install git secrets https://github.com/awslabs/git-secrets

brew install git-secrets

Install wget

brew install wget

Install jq

brew install jq

Build the webservice

(cd to where you cloned the dockstore/dockstore repo)

./mvnw clean install

Build the UI

(cd to where you cloned the dockstore/dockstore-ui2 repo)

Set up UI requirements NOTE: You must use the --legacy-peer-deps switch due to using npm version 8.11.0 (> npm 6) for reasons mentioned in this post

npm ci --legacy-peer-deps

Run build

npm run build

Optional

Install IntelliJ (if on Apple Silicon, select the .dmg (Apple Silicon), otherwise select .dmg(Intel)

https://www.jetbrains.com/idea/download/#section=mac

Add the Scala plugin to IntelliJ https://www.jetbrains.com/help/idea/managing-plugins.html

Legacy Material

Additional documentation on developing Dockstore is available at legacy.md