Discover uc-cdis/userdatamodel Open Source project

Windmill: data portal for metadata submission and query

data-portal

indexd

Index service server

Deploy Gen3 using Docker compose

compose-services

The Metadata Service provides API for retrieving JSON metadata of GUIDs.

metadata-service

GraphQL search API service

peregrine

gen3sdk-python

arborist

gen3.org

The website for gen3.org

The Gen3 Workflow Execution Service

mariner

sheepdog

API for herding data submissions

Helm charts for Gen3 Deployments

gen3-helm

Smarty

pypfb

Python library & CLI to create, view and edit PFB files

an S3 file system built on jacobsa/fuse that uses the workspace-token-service

gen3-fuse

cdis-data-client

data access client

hatchery

guppy

Server that supports GraphQL queries on data from Elasticsearch

Little groovy helper for Jenkins pipelines

cdis-jenkins-lib

Groovy

ndh-demo

Jupyter notebook and shinyR apps for NIAID Data Hub demo

dcfdictionary

audit-service

Manifests tracking service versions to release to each environment

cdis-manifest

data-simulator

gitops-dev

A data dictionary for the Medical Imaging Resource Data Commons (MIDRC).

midrc_dictionary

python wrapper and metaschema for datadictionary

dictionaryutils

Integration Tests for Gen3

gen3-qa

Prototype index service client.

indexclient

API to manage access requests

requestor

Python CLI to generate release notes by scanning a repo's pull requests descriptions

release-helper

Collection of helpful scripts for mapping, ETL, automation and others related to PlanX bioinformatics team. It includes tools for data model and data dictionary creation as well as data submission.

planx-bioinfo-tools

acronym-bot

Expand CTDS acronyms

Cloud Management Library (Wrapping Cloud APIs)

cirrus

Create Gen3 apps without configuration.

create-gen3-app

Job dispatcher for Kubernetes

sower

commons-frontend-app

Gen3 Data Commons template repository for gen3 frontend framework

covid19-tools

tube

gen3_dictionary_tools

A collection of python functions for converting data dictionaries between YAML and TSV formats.

gitops-qa

Base UI component in gen3

gen3-ui-component

Wrapping Argo into nice API for VADC GWAS app

argo-wrapper

Data dictionary for NIAID Commons project

ndhdictionary

Information gathered by the Gen3 User Service Team for Documentation

gen3-userservices-info

gtex-dictionary

Data dictionary to collect GTEx dataset

workspace-token-service

Sower jobs for PFB export & import

pelican

key value metadata service

ssjdispatcher

SQS S3 Job Dispatcher

pidgin

covid19_datadictionary

Extract sample data from NCBI's dbGaP site

dbgap-extract

A Frontend Framework for Gen3 data portals

gen3-frontend-framework

TypeScript

gen3utils

Utils for Gen3 commons management

This is the client library for making requests to the GA4GH DRS compatible services and returning an Indexd compatible document.

drsclient

A light-weight Gen3 data dictionary for representing TCGA/PCAWG/ICGC studies.

tcga_dictionary

GenoMEL pipelines in Bionimbus

genomel_pipelines

Gen3 release process automation tools

gen3-release-utils

Demonstrations for the IBDGC Commons

IBDGC_demos

gen3-user-doc

utilities to ease python code development

cdis-python-utils

gen3authz

Artifacts for SC19 paper about PFB

sc19-pfb-artifacts

genomel-dictionary

Data dictionary for GenoMEL project

New NDE Microbiome data dictionary

Microbiome_datadictionary

This is cwl pipeline for alignment potentially used for TopMed data analysis

topmed-cwl

Common Workflow Language

dcp-demo

Jupyter notebook for GTEx and TOPMed projects at Data Commons Pilot (DCP) project

Data dictionary for VA Precision Oncology project

gen3-terraform

HCL

vadictionary

forked from https://github.com/otiai10/cwl.go/

cwl.go

cdislogging

JCOIN_datadictionary

JCOIN Data Dictionary

server side user session for flask app with postgres as backend

bc-jupyterNotebook

Jupyter Notebook

gen3-spark

Dockerfile

bc-cwl

Common Workflow Language

flask-postgres-session