{"id":19857121,"url":"https://github.com/griffithlab/civic-server","last_synced_at":"2025-10-08T22:01:47.053Z","repository":{"id":19417865,"uuid":"22660201","full_name":"griffithlab/civic-server","owner":"griffithlab","description":"Backend Server for CIViC Project","archived":false,"fork":false,"pushed_at":"2023-07-06T18:25:34.000Z","size":198910,"stargazers_count":39,"open_issues_count":65,"forks_count":32,"subscribers_count":27,"default_branch":"staging","last_synced_at":"2025-04-06T21:01:46.906Z","etag":null,"topics":["backend-server","cancer","cancer-genomics","civic","nci-itcr","ruby","variants"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-08-05T21:32:22.000Z","updated_at":"2022-07-08T15:40:40.000Z","dependencies_parsed_at":"2023-02-10T23:01:11.602Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/civic-server","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-server","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-server/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-server/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-server/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/civic-server/tar.gz/refs/heads/staging","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251972410,"owners_count":21673599,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["backend-server","cancer","cancer-genomics","civic","nci-itcr","ruby","variants"],"created_at":"2024-11-12T14:17:32.427Z","updated_at":"2025-10-08T22:01:47.047Z","avatar_url":"https://github.com/griffithlab.png","language":"HTML","readme":"# CIViC - Clinical Interpretations of Variants in Cancer\n\n[![Code Climate](https://codeclimate.com/github/griffithlab/civic-server/badges/gpa.svg)](https://codeclimate.com/github/griffithlab/civic-server)\n[![DOI](https://zenodo.org/badge/22660201.svg)](https://zenodo.org/badge/latestdoi/22660201)\n\n\n\nThis repository contains the server component of the CIViC. It is a Ruby on Rails application that serves JSON data to power the [frontend website](https://github.com/griffithlab/civic-client) and [API](https://griffithlab.github.io/civic-api-docs/).\n\n### Setup\n\nDeveloping for CIViC involves setting up a development environment.\n\nTo get started quickly, we recommend launching an AWS EC2 instance from our pre-configured and maintained AMI ([getting started wiki page](https://github.com/griffithlab/civic-server/wiki/Getting-Started-with-CIViC-Development-on-AWS)). Alternatively, you may set up your own local development environment using the following setup instructions.\n\n#### Prerequisites\n\nBefore attempting to install the CIViC server and client software, you should obtain the following applications and libraries:\n\n * A relatively modern Ruby (\u003e= 2.1)\n    * If your OS doesn't ship with a modern Ruby, you can use [rbenv](https://github.com/sstephenson/rbenv) and [ruby-build](https://github.com/sstephenson/ruby-build) to obtain it.\n * Postgres\n * NodeJS\n * npm\n * libxml2\n * libxslt\n * libpq-dev\n * openssl\n\nOn OSX with homebrew, this should install the needed library dependencies: \n\n    brew install libxml2 libxslt openssl postgres node\n\n#### Installation\nThe following will set up the server side application and load the database schema.\n\n    git clone https://github.com/griffithlab/civic-server.git\n    cd civic-server\n    gem install bundler\n    rbenv rehash\n    bundle install\n    rbenv rehash\n    rake db:create\n    rake db:migrate\n\nFor convenience, a sanitized version of a recent database backup is provided for your local development environment. You can load it with the following command:\n\n    rake civic:load[force]\n\nFinally, start the CIViC rails server\n\n    rails s\n\nIf you only intend to do server development, you can stop here. The server repository already contains the most recent production build of the frontend javascript. You can load CIViC in your browser at `http://127.0.0.1:3000`.\n\nIf you intend to develop front end features however, you'll need to set up the [client side application](https://github.com/griffithlab/civic-client) using the following:\n\n    git clone https://github.com/griffithlab/civic-client.git\n    cd civic-client\n    npm install -g bower gulp\n    npm install\n    bower install\n    gulp serve\n\nYou should now be able to access the backend server at `http://127.0.0.1:3000` and the frontend application at `http://127.0.0.1:3001`\n\nNote that certain tasks needed by a running instance of CIViC are accomplished by 'background workers'. This includes data release generation as well as notification delivery.\n\nYou can start the workers in the background with the following command:\n\n    bin/delayed_job start \n\nIf you would prefer the workers to run in the foreground you can start them in a console (`rails c`) with this command instead:\n\n    Delayed::Worker.new.start\n\nNote to make yourself an admin in a local install you can do the following from your civic-server repo.\nFirst log into the front end `http://127.0.0.1:3001` and sign in with your user.\nLog into a rails console, run a command that makes you an admin in the db, and exit.\n\n    rails c\n    User.find_by(email: 'your_email@example.com').make_admin!\n    exit\n\nNow log into the backend admin interface as follows:\nhttp://127.0.0.1:3000/admin\n\n### Git repositories related to the CIViC project\nThe CIViC source code and application are organized in a client-server model. The backend code is available in the [civic-server repository](https://github.com/griffithlab/civic-server) and frontend code is available in the [civic-client repository](https://github.com/griffithlab/civic-client). Issues relating to curation are tracked in the [civic-curation repository](https://github.com/griffithlab/civic-curation). An example of a Python client is available in the [civic-api-client repository](https://github.com/griffithlab/civic-api-client). Issues relating to public CIViC meetings are tracked in the [civic-meeting repository](https://github.com/griffithlab/civic-meeting).\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic-server","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fcivic-server","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic-server/lists"}