omniauth-dnanexus 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 5bc7db96376c80561844bf3b28ba26985c23a6bdff6eca6180e2e089e7e8683b
+  data.tar.gz: ccbfc0ba353080882aa6be789e998782c7368b62cb3b3fbc2ec7ca1fa48139f3
+SHA512:
+  metadata.gz: 57c8795f54b75c185834464f6cd286a35fb78b474b157ccad8c054acd924ae08e6d619b07a8770b01ec3b9d543d277a56b370f17375dcafcb75465323c26538b
+  data.tar.gz: ad63b5a4311fd9b533f3fe1193c9481cfc809ba61d56a0dcd5bfaf1821b693399d9f25dbc074e1315634284847bdc6bda2a4d41abf07132c0080f377d472c24d

data/.github/workflows/changelog.yml

@@ -0,0 +1,36 @@
+# From: https://github.com/hopsoft/stimulus_reflex/blob/master/.github/workflows/changelog.yml
+name: Changelog
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 4
+    if: "!contains(github.event.head_commit.message, '[nodoc]')"
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.0
+        bundler-cache: true
+    - name: Create local changes
+      run: |
+        bundle exec github_changelog_generator -u ${{ github.repository_owner }} -p ${{ github.event.repository.name }} --token ${{ secrets.GITHUB_TOKEN }} --exclude-labels duplicate,question,invalid,wontfix,nodoc
+    - name: Commit files
+      run: |
+        git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        git config --local user.name "github-actions[bot]"
+        git commit -am "[nodoc] Update Changelog" || echo "No changes to commit"
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}

data/.github/workflows/ci.yml

@@ -0,0 +1,48 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  GIT_COMMIT_SHA: ${{ github.sha }}
+  GIT_BRANCH: ${{ github.ref }}
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Set up Ruby 2.7
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.7
+          bundler-cache: true
+
+      - name: Standard
+        run: |
+          bundle exec standardrb
+  build:
+    needs: [linting]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby: ['2.5', '2.6', '2.7', '3.0']
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby }}
+          bundler-cache: true
+
+      - name: Test
+        run: |
+          bundle exec rake

data/.github/workflows/publish.yml

@@ -0,0 +1,29 @@
+name: Publish
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Publish to Rubygems
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@master
+
+      - name: Set up Ruby
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: 2.7.x
+
+      - name: Publish to RubyGems
+        run: |
+          mkdir -p $HOME/.gem
+          touch $HOME/.gem/credentials
+          chmod 0600 $HOME/.gem/credentials
+          printf -- "---\n:rubygems_api_key: ${GEM_HOST_API_KEY}\n" > $HOME/.gem/credentials
+          gem build omniauth-dnanexus.gemspec
+          gem push omniauth-dnanexus-*.gem
+        env:
+          GEM_HOST_API_KEY: ${{ secrets.RUBYGEMS_AUTH_TOKEN }}

data/.gitignore

@@ -0,0 +1,19 @@
+.idea/
+.bundle/
+.yardoc
+_yardoc/
+coverage/
+doc/
+pkg/
+spec/reports/
+tmp/
+
+*.gem
+gemfile.lock
+
+.rvmrc
+.ruby-version
+
+.rspec_status
+
+/coverage/

data/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+
+## [Unreleased](https://github.com/MikeRogers0/omniauth-dnanexus/tree/HEAD)
+
+[Full Changelog](https://github.com/MikeRogers0/omniauth-dnanexus/compare/c419477e02461b4bc41b754f0daeaa997fb7ad1f...HEAD)
+
+**Merged pull requests:**
+
+- feat: Automate the changelog [\#3](https://github.com/MikeRogers0/omniauth-dnanexus/pull/3) ([MikeRogers0](https://github.com/MikeRogers0))
+- fix: Correcting gem name in GH Action [\#2](https://github.com/MikeRogers0/omniauth-dnanexus/pull/2) ([MikeRogers0](https://github.com/MikeRogers0))
+- refactor: Consistent capitalisation for DNAnexus [\#1](https://github.com/MikeRogers0/omniauth-dnanexus/pull/1) ([MikeRogers0](https://github.com/MikeRogers0))
+
+
+
+\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*

data/Gemfile

@@ -0,0 +1,3 @@
+source "https://rubygems.org"
+
+gemspec

data/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Mike Rogers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

@@ -0,0 +1,44 @@
+# OmniAuth::DNAnexus
+
+OmniAuth strategy for [DNAnexus](https://documentation.dnanexus.com/developer/api/authentication).
+
+## Installation
+
+```bash
+$ bundle add omniauth-dnanexus
+```
+## Usage
+
+```ruby
+Rails.application.config.middleware.use OmniAuth::Builder do
+  provider :dnanexus, ENV["DNANEXUS_CLIENT_ID"], ENV["DNANEXUS_CLIENT_SECRET"], {
+    dnanexus_api_endpoint: "https://api.dnanexus.com",
+    client_options: {
+      site: "https://auth.dnanexus.com",
+      authorize_url: "/oauth2/authorize",
+      token_url: "/oauth2/token"
+    }
+  }
+end
+```
+
+### DNAnexus Staging
+
+```ruby
+Rails.application.config.middleware.use OmniAuth::Builder do
+  provider :dnanexus, ENV["DNANEXUS_CLIENT_ID"], ENV["DNANEXUS_CLIENT_SECRET"], {
+    dnanexus_api_endpoint: "https://stagingapi.dnanexus.com",
+    client_options: {
+      site: "https://stagingauth.dnanexus.com"
+    }
+  }
+end
+```
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/MikeRogers0/omniauth-dnanexus
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new
+
+task default: :spec

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "omniauth/dnanexus"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/omniauth-dnanexus.rb

@@ -0,0 +1 @@
+require "omniauth/dnanexus"

data/lib/omniauth/dnanexus.rb

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+require "omniauth/dnanexus/version"
+require "omniauth/strategies/dnanexus"

data/lib/omniauth/dnanexus/version.rb

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+module OmniAuth
+  module DNAnexus
+    VERSION = "0.1.0"
+  end
+end

data/lib/omniauth/strategies/dnanexus.rb

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+require "omniauth-oauth2"
+
+module OmniAuth
+  module Strategies
+    class DNAnexus < OmniAuth::Strategies::OAuth2
+      option :name, "dnanexus"
+
+      # This is where you pass the options you would pass when
+      # initializing your consumer from the OAuth gem.
+      option :client_options, {
+        site: "https://auth.dnanexus.com",
+        authorize_url: "/oauth2/authorize",
+        token_url: "/oauth2/token"
+      }
+
+      option :dnanexus_api_endpoint, "https://api.dnanexus.com"
+
+      # These are called after authentication has succeeded. If
+      # possible, you should try to set the UID without making
+      # additional calls (if the user id is returned with the token
+      # or as a URI parameter). This may not be possible with all
+      # providers.
+      uid { raw_info["id"] }
+
+      info do
+        {
+          email: raw_info["email"],
+          handle: raw_info["handle"],
+          first: raw_info["first"],
+          middle: raw_info["middle"],
+          last: raw_info["last"]
+        }
+      end
+
+      extra do
+        {
+          "raw_info" => raw_info
+        }
+      end
+
+      def raw_info
+        @raw_info ||= access_token.post(
+          "#{options.dnanexus_api_endpoint}/#{access_token.params["user_id"]}/describe",
+          body: "{}",
+          headers: {
+            "Content-Type" => "application/json"
+          }
+        ).parsed
+      end
+    end
+  end
+end
+
+OmniAuth.config.add_camelization "dnanexus", "DNAnexus"

data/omniauth-dnanexus.gemspec

@@ -0,0 +1,32 @@
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "omniauth/dnanexus/version"
+
+Gem::Specification.new do |spec|
+  spec.name = "omniauth-dnanexus"
+  spec.version = OmniAuth::DNAnexus::VERSION
+  spec.authors = ["Mike Rogers"]
+  spec.email = ["me@mikerogers.io"]
+
+  spec.summary = "OmniAuth strategy for DNAnexus"
+  spec.description = "OmniAuth strategy for DNAnexus"
+  spec.homepage = "https://github.com/MikeRogers0/omniauth-dnanexus"
+  spec.license = "MIT"
+
+  spec.files = Dir.chdir(File.expand_path("..", __FILE__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir = "exe"
+  spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "omniauth-oauth2"
+  spec.add_dependency "jwt"
+  spec.add_development_dependency "bundler", "~> 2.0"
+  spec.add_development_dependency "rake", "~> 13.0"
+  spec.add_development_dependency "rspec", "~> 3.9"
+  spec.add_development_dependency "webmock", "~> 3.8"
+  spec.add_development_dependency "simplecov", "~> 0.18"
+  spec.add_development_dependency "standard", "~> 1.1"
+  spec.add_development_dependency "github_changelog_generator", "~> 1.15"
+end

metadata

@@ -0,0 +1,185 @@
+--- !ruby/object:Gem::Specification
+name: omniauth-dnanexus
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Mike Rogers
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2021-07-13 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: omniauth-oauth2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jwt
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.9'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.8'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.18'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.18'
+- !ruby/object:Gem::Dependency
+  name: standard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: github_changelog_generator
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+description: OmniAuth strategy for DNAnexus
+email:
+- me@mikerogers.io
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".github/workflows/changelog.yml"
+- ".github/workflows/ci.yml"
+- ".github/workflows/publish.yml"
+- ".gitignore"
+- CHANGELOG.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/omniauth-dnanexus.rb
+- lib/omniauth/dnanexus.rb
+- lib/omniauth/dnanexus/version.rb
+- lib/omniauth/strategies/dnanexus.rb
+- omniauth-dnanexus.gemspec
+homepage: https://github.com/MikeRogers0/omniauth-dnanexus
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.6
+signing_key: 
+specification_version: 4
+summary: OmniAuth strategy for DNAnexus
+test_files: []