[WIP] OH integration

app/controllers/open_humans_profiles_controller.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+class OpenHumansProfilesController < ApplicationController
+  before_filter :require_user, except: [:index]
+
+  def start_auth
+    # there's little to do for the start. Just read the .env for our client_id
+    # then lead ppl to OH.org to give us a key
+    client_id = ENV.fetch('OH_client_id')
+    redirect_to "https://www.openhumans.org/direct-sharing/projects/oauth2/authorize/?client_id=#{client_id}&response_type=code"
+  end
+
+  def authorize
+    # let's get the current user and their code
+    @user = current_user
+    @code = params[:code]
+    oh_service = OpenHumansService.new()
+
+    # does the user have an OH profile on openSNP? if not, create one
+    if @user.open_humans_profile == nil
+      @user.open_humans_profile = OpenHumansProfile.new
+      @user.save
+    end
+    # lets convert
+    oh_service.get_access_tokens(@user,@code)
+    oh_service.set_open_humans_ids(@user.open_humans_profile)
+    # delete old files if there are any
+    begin
+      oh_service.delete_opensnp_id(@user)
+    end
+    oh_service.upload_opensnp_id(@user)
+  end
+end

app/models/open_humans_profile.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+class OpenHumansProfile < ActiveRecord::Base
+  belongs_to :user
+end

app/models/user.rb

@@ -13,7 +13,7 @@ class User < ActiveRecord::Base
     content_type: %r(\Aimage/.*\Z)
 
   # call on authlogic
-  acts_as_authentic do |c| 
+  acts_as_authentic do |c|
     # replace SHA512 by bcrypt
     c.transition_from_crypto_providers = Authlogic::CryptoProviders::Sha512
     c.crypto_provider = Authlogic::CryptoProviders::BCrypt
@@ -36,6 +36,7 @@ class User < ActiveRecord::Base
   has_many :phenotype_comments, dependent: :destroy
   has_many :picture_phenotype_comments, dependent: :destroy
   has_one :fitbit_profile, dependent: :destroy
+  has_one :open_humans_profile, dependent: :destroy
 
   # needed to edit several user_phenotypes at once, add and delete, and not empty
   accepts_nested_attributes_for :homepages, allow_destroy: true

app/services/open_humans_service.rb

@@ -0,0 +1,116 @@
+class OpenHumansService
+  # used to do the interfacing w/ Open Humans
+
+  def get_access_tokens(user,code)
+    # authenticate w/ our client id/secret against API
+    # post with the key the user provided us with.
+    url = URI.parse('https://www.openhumans.org/oauth2/token/')
+    req = Net::HTTP::Post.new(url.request_uri)
+    req.basic_auth ENV.fetch('OH_client_id'), ENV.fetch('OH_client_secret')
+    req.set_form_data({'grant_type' => 'authorization_code',
+                       'code' => code,
+                       'redirect_uri' => "http://localhost:3000/openhumans/authorize"
+                       })
+    # set up request to use https
+    http = Net::HTTP.new(url.host, url.port)
+    http.use_ssl = (url.scheme == 'https')
+    # do actual request, get the json it returns
+    response = http.request(req)
+    response_json = JSON.parse(response.body)
+    update_tokens(user.open_humans_profile,response_json)
+  end
+
+  def refresh_token(user)
+    oh_profile = user.open_humans_profile
+    url = URI.parse('https://www.openhumans.org/oauth2/token/')
+    req = Net::HTTP::Post.new(url.request_uri)
+    req.set_form_data({'grant_type' => 'refresh_token',
+                       'refresh_token' => oh_profile.refresh_token
+                       })
+    http = Net::HTTP.new(url.host, url.port)
+    http.use_ssl = (url.scheme == 'https')
+    response = http.request(req)
+    response_json = JSON.parse(response.body)
+    update_tokens(oh_profile,response_json)
+  end
+
+
+  def set_open_humans_ids(oh_profile)
+    uri = URI.parse('https://www.openhumans.org/api/direct-sharing/project/exchange-member/')
+    uri_params = {:access_token => oh_profile.access_token}
+    uri.query = URI.encode_www_form(uri_params)
+    res = Net::HTTP.get_response(uri)
+    res_json = JSON.parse(res.body)
+    oh_profile.project_member_id = res_json["project_member_id"]
+    oh_profile.open_humans_user_id = res_json["username"]
+    oh_profile.save
+  end
+
+  def upload_opensnp_id(user)
+    uri = URI.parse("https://www.openhumans.org/api/direct-sharing/project/files/upload/?access_token=#{user.open_humans_profile.access_token}")
+    boundary = '0P3NSNPH34RT50PENHUM4N5'
+    http = Net::HTTP.new(uri.host, uri.port)
+    http.use_ssl = (uri.scheme == 'https')
+    upload = Net::HTTP::Post.new(uri.request_uri)
+    upload.content_type = "multipart/form-data; boundary=#{boundary}"
+    post_body = generate_form_body(user,boundary)
+    upload.body = post_body.join
+    puts post_body.join
+    http.request(upload)
+  end
+
+  def delete_opensnp_id(user)
+    url = URI.parse("https://www.openhumans.org/api/direct-sharing/project/files/delete/?access_token=#{user.open_humans_profile.access_token}")
+    req = Net::HTTP::Post.new(url.request_uri)
+    oh_profile = user.open_humans_profile
+    req.set_form_data({
+                project_member_id: oh_profile.project_member_id,
+                all_files: true
+                })
+    http = Net::HTTP.new(url.host, url.port)
+    http.use_ssl = (url.scheme == 'https')
+    http.set_debug_output($stdout)
+    http.request(req)
+  end
+
+  private
+
+  def update_tokens(oh_profile,tokens)
+    oh_profile.expires_in = Time.now + tokens["expires_in"]
+    oh_profile.access_token = tokens["access_token"]
+    oh_profile.refresh_token = tokens["refresh_token"]
+    oh_profile.save
+  end
+
+  def generate_json(user)
+    json = {
+            user_name: user.name,
+            user_id: user.id,
+            has_sequence: user.has_sequence,
+            user_uri: "https://opensnp.org/users/#{user.id}"
+           }
+  end
+
+  def generate_metadata(user)
+    metadata = generate_json(user)
+    metadata['tags'] = ['opensnp']
+    metadata['description'] = "links to openSNP user #{user.id}"
+    return metadata
+  end
+
+  def generate_form_body(user,boundary)
+    metadata = generate_metadata(user)
+    file_content = generate_json(user)
+    post_body = []
+    post_body << "--#{boundary}\r\n"
+    post_body << "Content-Disposition: form-data; name=\"project_member_id\"\r\n\r\n"
+    post_body << user.open_humans_profile.project_member_id
+    post_body << "\r\n--#{boundary}\r\n"
+    post_body << "Content-Disposition: form-data; name=\"metadata\"\r\n\r\n"
+    post_body << metadata.to_json
+    post_body << "\r\n--#{boundary}\r\n"
+    post_body << "Content-Disposition: form-data; name=\"data_file\"; filename=\"#{user.id}.json\"\r\n\r\n"
+    post_body << file_content.to_json
+    post_body << "\r\n\r\n--#{boundary}--\r\n"
+  end
+end

app/views/open_humans_profiles/authorize.html.erb

@@ -0,0 +1,7 @@
+<div class="general__container container">
+  <div class="row">
+    <div class="col-md-6">
+      <h3>Authorize</h3>
+    </div>
+  </div>
+</div>

config/routes.rb

@@ -35,6 +35,8 @@
   resources :user_achievements
   resources :index
 
+  get '/openhumans/new', to: 'open_humans_profiles#start_auth'
+  get '/openhumans/authorize', to: 'open_humans_profiles#authorize'
   post '/fitbit/notification/', to: 'fitbit_profiles#new_notification'
   get '/fitbit/start_auth', to: 'fitbit_profiles#start_auth'
   get '/fitbit/verify', to: 'fitbit_profiles#verify_auth'

db/migrate/20171113104813_create_open_humans_profiles.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+class CreateOpenHumansProfiles < ActiveRecord::Migration
+  def self.up
+    create_table :open_humans_profiles do |t|
+      t.string :open_humans_user_id
+      t.string :project_member_id
+      t.belongs_to :user
+      t.string :access_token
+      t.string :refresh_token
+      t.timestamp :expires_in
+      t.timestamps
+    end
+  end
+
+  def self.down
+    drop_table :open_humans_profiles
+  end
+
+end