<%= @user.name %>'s page
- <%if @user.fitbit_profile != nil%>
- <%=link_to(image_tag("fitbit-icon.png"), {:controller => "fitbit_profiles", :action => "show", :id => @user.fitbit_profile.id}, :data => {toggle:"tooltip", placement:"bottom"}, :title => "See Fitbit data")%>
- <%end%>
<%if @user.open_humans_profile != nil%>
<%=link_to(image_tag("open_humans_logo.png",size: '32x32'), {:controller => "open_humans_profiles", :action => "index"}, :data => {toggle:"tooltip", placement:"bottom"}, :title => "Linked to an Open Humans Account")%>
<%end%>
diff --git a/app/views/users/_user_is_user.html.erb b/app/views/users/_user_is_user.html.erb
index 6133614..ed3340f 100644
--- a/app/views/users/_user_is_user.html.erb
+++ b/app/views/users/_user_is_user.html.erb
@@ -2,9 +2,6 @@
<%= image_tag @user.avatar.url(:thumb), class: "hidden-xs pull-left userpage__profile-picture"%>
Hello, <%= @first_name %>
- <%if @user.fitbit_profile != nil%>
- <%=link_to(image_tag("fitbit-icon.png"), {:controller => "fitbit_profiles", :action => "show", :id => @user.fitbit_profile.id}, :data => {toggle:"tooltip", placement:"bottom"}, :title => "See your Fitbit data")%>
- <%end%>
<%if @user.open_humans_profile != nil%>
<%=link_to(image_tag("open_humans_logo.png", size: '32x32'), {:controller => "open_humans_profiles", :action => "index"}, :data => {toggle:"tooltip", placement:"bottom"}, :title => "Linked to an Open Humans Account")%>
<%end%>
diff --git a/app/workers/fitbit_dump.rb b/app/workers/fitbit_dump.rb
deleted file mode 100644
index c77d6c4..0000000
--- a/app/workers/fitbit_dump.rb
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
-# frozen_string_literal: true
-class FitbitDump
- include Sidekiq::Worker
- sidekiq_options queue: :fitbit, retry: 5, unique: true
-
- def perform(fitbit_profile_id,user_id)
- fp = FitbitProfile.find_by_id(fitbit_profile_id)
- # open handle
-
- @time = Time.now.utc
- @time_str = @time.strftime("%Y%m%d%H%M")
- @time = @time.to_s.gsub(":","_")
-
- @fitbit_handle = File.new(::Rails.root.to_s+"/public/data/fitbit/user"+fp.user.id.to_s+"_fitbit_data_"+@time_str.to_s+".csv","w")
- @fitbit_handle.puts("date;steps;floors;weight;bmi;minutes asleep;minutes awake; times awaken; minutes until fell asleep")
-
- # get all dates which have to be included in the csv
- @time_array = []
- fp.fitbit_bodies.each do |fb|
- @time_array << fb.date_logged
- end
- fp.fitbit_sleeps.each do |fs|
- @time_array << fs.date_logged
- end
- fp.fitbit_activities.each do |fa|
- @time_array << fa.date_logged
- end
-
- @time_array = @time_array.uniq.sort
-
- @time_array.each do |d|
- @line = d.to_s + ";"
- @activity = fp.fitbit_activities.find_by_date_logged(d)
- if @activity == nil
- @line = @line + "-;-;"
- else
- @line = @line + @activity.steps.to_s + ";" + @activity.floors.to_s+ ";"
- end
-
- @body = fp.fitbit_bodies.find_by_date_logged(d)
- if @body == nil
- @line = @line + "-;-;"
- else
- @line = @line + @body.weight.to_s + ";" + @body.bmi.to_s + ";"
- end
-
- @sleep = fp.fitbit_sleeps.find_by_date_logged(d)
- if @sleep == nil
- @line = @line + "-;-;-;-;"
- else
- @line = @line + @sleep.minutes_asleep.to_s+";"+@sleep.minutes_awake.to_s+";"+@sleep.number_awakenings.to_s+";"+@sleep.minutes_to_sleep.to_s+";"
- end
- @fitbit_handle.puts(@line)
- end
- @fitbit_handle.close
- puts "Saved fibit-date for "
- system("chmod 777 "+::Rails.root.to_s+"/public/data/fitbit/user"+fp.user.id.to_s+"_fitbit_data_"+@time_str.to_s+".csv")
- UserMailer.fitbit_dump("/data/fitbit/user#{fp.user.id.to_s}_fitbit_data_#{@time_str.to_s}.csv",user_id).deliver_later
- end
-end
diff --git a/app/workers/zipfulldata.rb b/app/workers/zipfulldata.rb
index 5377a15..c92f6e1 100644
--- a/app/workers/zipfulldata.rb
+++ b/app/workers/zipfulldata.rb
@@ -47,7 +47,6 @@ class Zipfulldata
logger.info("Starting zipfile #{zip_fs_path}")
Zip::File.open(zip_fs_path, Zip::File::CREATE) do |zipfile|
create_user_csv(genotypes, zipfile)
- create_fitbit_csv(zipfile)
list_of_pics = create_picture_phenotype_csv(zipfile)
create_picture_zip(list_of_pics, zipfile)
create_readme(zipfile)
@@ -100,64 +99,6 @@ class Zipfulldata
zipfile.add("phenotypes_#{time_str}.csv", csv_file_name)
end
- def create_fitbit_csv(zipfile)
- # Create a file of fitbit-data for each user with fitbit-data
- fitbit_profiles = FitbitProfile.
- includes(:fitbit_activities, :fitbit_bodies, :fitbit_sleeps)
- fitbit_profiles.each do |fp|
- csv_file_name =
- "#{tmp_dir}/dump_user#{fp.user.id}_fitbit_data_#{time_str}.csv"
- csv_header = ['date', 'steps', 'floors', 'weight', 'bmi',
- 'minutes asleep', 'minutes awake', 'times awaken',
- 'minutes until fell asleep']
- CSV.open(csv_file_name, "w", csv_options) do |csv|
- csv << csv_header
- bodies = fp.fitbit_bodies.group_by(&:date_logged)
- sleeps = fp.fitbit_sleeps.group_by(&:date_logged)
- activities = fp.fitbit_activities.group_by(&:date_logged)
-
- # get all dates which have to be included in the csv
- time_array = []
- time_array.concat(bodies.keys)
- time_array.concat(sleeps.keys)
- time_array.concat(activities.keys)
- time_array = time_array.uniq.sort
-
- time_array.each do |d|
- row = [d]
-
- activity = activities[d]
- if activity.present?
- activity = activity.first
- row.concat([activity.steps, activity.floors])
- else
- row.concat(%w(- -))
- end
-
- body = bodies[d]
- if body.present?
- body = body.first
- row.concat([body.weight, body.bmi])
- else
- row.concat(%w(- -))
- end
-
- sleep = sleeps[d]
- if sleep.present?
- sleep = sleep.first
- row.concat([sleep.minutes_asleep, sleep.minutes_awake,
- sleep.number_awakenings, sleep.minutes_to_sleep])
- else
- row.concat(%w(- - - -))
- end
- csv << row
- end
- end
- zipfile.add("user#{fp.user.id}_fitbit_data_#{time_str}.csv", csv_file_name)
- logger.info('Saved fibit-date for ')
- end
- end
-
# make a CSV describing all of them - which filename is for which user's phenotype
def create_picture_phenotype_csv(zipfile)
file_name = "#{tmp_dir}/picture_dump#{time_str}.csv"
diff --git a/bin/docker-run b/bin/docker-run
index a01f70d..e00ac76 100755
--- a/bin/docker-run
+++ b/bin/docker-run
@@ -33,8 +33,6 @@ docker run -d \
-e POSTGRES_URL='postgres://postgres@postgres/postgres' \
-e SECRET_KEY_BASE=foo \
-e SECRET_TOKEN=bar \
- -e FITBIT_CONSUMER_KEY=foo \
- -e FITBIT_CONSUMER_SECRET=bar \
-e PLOS_API_KEY=foo \
-e RECAPTCHA_PRIVATE_KEY=foo \
-e RECAPTCHA_PUBLIC_KEY=bar \
diff --git a/config/routes.rb b/config/routes.rb
index ed8bfb4..1149f5f 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -39,9 +39,6 @@ Snpr::Application.routes.draw do
get '/openhumans/new', to: 'open_humans_profiles#start_auth'
get '/openhumans/authorize', to: 'open_humans_profiles#authorize', as: :openhumans_authorize
get '/openhumans/destroy/:id', to: 'open_humans_profiles#destroy'
- get '/fitbit/show/:id', to: 'fitbit_profiles#show', as: :fitbit_show
- get '/fitbit/dump/:id', to: 'fitbit_profiles#dump', as: :fitbit_dump
- get '/fitbit/', to: 'fitbit_profiles#index', as: :fitbit_index
get '/phenotypesets/enter/:id', to: 'phenotype_sets#enter_userphenotypes'
get '/phenotypesets/user_phenotypes/save', to: 'phenotype_sets#save_user_phenotypes'
get '/users/:id/changepassword', to: 'users#changepassword'
diff --git a/config/sidekiq.yml b/config/sidekiq.yml
index 8b18ad1..71f11ab 100644
--- a/config/sidekiq.yml
+++ b/config/sidekiq.yml
@@ -10,7 +10,6 @@
- [zipgenotyping,5]
- [zipfulldata,5]
- [recommend,5]
- - [fitbit,3]
- [frequency,1]
- [fixphenotypes,1]
- [default, 1]
@@ -29,7 +28,6 @@
recommend: 1
zipgenotyping: 1
zipfulldata: 1
- fitbit: 3
frequency: 1
fixphenotypes: 1
mailnewgenotype: 1
diff --git a/db/migrate/20180118100003_remove_fitbit.rb b/db/migrate/20180118100003_remove_fitbit.rb
new file mode 100644
index 0000000..6e7d5a5
--- /dev/null
+++ b/db/migrate/20180118100003_remove_fitbit.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+class RemoveFitbit < ActiveRecord::Migration
+ def self.up
+ drop_table :fitbit_activities
+ drop_table :fitbit_sleeps
+ drop_table :fitbit_bodies
+ drop_table :fitbit_profiles
+ end
+
+ def self.down
+ raise ActiveRecord::IrreversibleMigration
+ end
+end
diff --git a/db/structure.sql b/db/structure.sql
index 2308146..635960c 100644
--- a/db/structure.sql
+++ b/db/structure.sql
@@ -272,150 +272,6 @@ CREATE SEQUENCE file_links_id_seq
ALTER SEQUENCE file_links_id_seq OWNED BY file_links.id;
---
--- Name: fitbit_activities; Type: TABLE; Schema: public; Owner: -
---
-
-CREATE TABLE fitbit_activities (
- id integer NOT NULL,
- fitbit_profile_id integer,
- steps integer,
- floors integer,
- date_logged date,
- created_at timestamp without time zone,
- updated_at timestamp without time zone
-);
-
-
---
--- Name: fitbit_activities_id_seq; Type: SEQUENCE; Schema: public; Owner: -
---
-
-CREATE SEQUENCE fitbit_activities_id_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-
---
--- Name: fitbit_activities_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
---
-
-ALTER SEQUENCE fitbit_activities_id_seq OWNED BY fitbit_activities.id;
-
-
---
--- Name: fitbit_bodies; Type: TABLE; Schema: public; Owner: -
---
-
-CREATE TABLE fitbit_bodies (
- id integer NOT NULL,
- fitbit_profile_id integer,
- date_logged date,
- weight double precision,
- bmi double precision,
- created_at timestamp without time zone,
- updated_at timestamp without time zone
-);
-
-
---
--- Name: fitbit_bodies_id_seq; Type: SEQUENCE; Schema: public; Owner: -
---
-
-CREATE SEQUENCE fitbit_bodies_id_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-
---
--- Name: fitbit_bodies_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
---
-
-ALTER SEQUENCE fitbit_bodies_id_seq OWNED BY fitbit_bodies.id;
-
-
---
--- Name: fitbit_profiles; Type: TABLE; Schema: public; Owner: -
---
-
-CREATE TABLE fitbit_profiles (
- id integer NOT NULL,
- fitbit_user_id character varying(255),
- user_id integer,
- request_token character varying(255),
- request_secret character varying(255),
- access_token character varying(255),
- access_secret character varying(255),
- verifier character varying(255),
- body boolean DEFAULT true,
- activities boolean DEFAULT true,
- sleep boolean DEFAULT true,
- created_at timestamp without time zone,
- updated_at timestamp without time zone
-);
-
-
---
--- Name: fitbit_profiles_id_seq; Type: SEQUENCE; Schema: public; Owner: -
---
-
-CREATE SEQUENCE fitbit_profiles_id_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-
---
--- Name: fitbit_profiles_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
---
-
-ALTER SEQUENCE fitbit_profiles_id_seq OWNED BY fitbit_profiles.id;
-
-
---
--- Name: fitbit_sleeps; Type: TABLE; Schema: public; Owner: -
---
-
-CREATE TABLE fitbit_sleeps (
- id integer NOT NULL,
- fitbit_profile_id integer,
- minutes_asleep integer,
- minutes_awake integer,
- number_awakenings integer,
- minutes_to_sleep integer,
- date_logged date,
- created_at timestamp without time zone,
- updated_at timestamp without time zone
-);
-
-
---
--- Name: fitbit_sleeps_id_seq; Type: SEQUENCE; Schema: public; Owner: -
---
-
-CREATE SEQUENCE fitbit_sleeps_id_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-
---
--- Name: fitbit_sleeps_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
---
-
-ALTER SEQUENCE fitbit_sleeps_id_seq OWNED BY fitbit_sleeps.id;
-
-
--
-- Name: friendly_id_slugs; Type: TABLE; Schema: public; Owner: -
--
@@ -1264,34 +1120,6 @@ ALTER TABLE ONLY admin_users ALTER COLUMN id SET DEFAULT nextval('admin_users_id
ALTER TABLE ONLY file_links ALTER COLUMN id SET DEFAULT nextval('file_links_id_seq'::regclass);
---
--- Name: fitbit_activities id; Type: DEFAULT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_activities ALTER COLUMN id SET DEFAULT nextval('fitbit_activities_id_seq'::regclass);
-
-
---
--- Name: fitbit_bodies id; Type: DEFAULT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_bodies ALTER COLUMN id SET DEFAULT nextval('fitbit_bodies_id_seq'::regclass);
-
-
---
--- Name: fitbit_profiles id; Type: DEFAULT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_profiles ALTER COLUMN id SET DEFAULT nextval('fitbit_profiles_id_seq'::regclass);
-
-
---
--- Name: fitbit_sleeps id; Type: DEFAULT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_sleeps ALTER COLUMN id SET DEFAULT nextval('fitbit_sleeps_id_seq'::regclass);
-
-
--
-- Name: friendly_id_slugs id; Type: DEFAULT; Schema: public; Owner: -
--
@@ -1471,38 +1299,6 @@ ALTER TABLE ONLY file_links
ADD CONSTRAINT file_links_pkey PRIMARY KEY (id);
---
--- Name: fitbit_activities fitbit_activities_pkey; Type: CONSTRAINT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_activities
- ADD CONSTRAINT fitbit_activities_pkey PRIMARY KEY (id);
-
-
---
--- Name: fitbit_bodies fitbit_bodies_pkey; Type: CONSTRAINT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_bodies
- ADD CONSTRAINT fitbit_bodies_pkey PRIMARY KEY (id);
-
-
---
--- Name: fitbit_profiles fitbit_profiles_pkey; Type: CONSTRAINT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_profiles
- ADD CONSTRAINT fitbit_profiles_pkey PRIMARY KEY (id);
-
-
---
--- Name: fitbit_sleeps fitbit_sleeps_pkey; Type: CONSTRAINT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_sleeps
- ADD CONSTRAINT fitbit_sleeps_pkey PRIMARY KEY (id);
-
-
--
-- Name: friendly_id_slugs friendly_id_slugs_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
@@ -1819,14 +1615,6 @@ CREATE UNIQUE INDEX index_users_on_persistence_token ON users USING btree (persi
CREATE INDEX snps_position_idx ON snps USING btree ("position");
---
--- Name: fitbit_profiles fitbit_profiles_user_id_fk; Type: FK CONSTRAINT; Schema: public; Owner: -
---
-
-ALTER TABLE ONLY fitbit_profiles
- ADD CONSTRAINT fitbit_profiles_user_id_fk FOREIGN KEY (user_id) REFERENCES users(id);
-
-
--
-- Name: genotypes genotypes_user_id_fk; Type: FK CONSTRAINT; Schema: public; Owner: -
--
@@ -2169,3 +1957,5 @@ INSERT INTO schema_migrations (version) VALUES ('20161226175703');
INSERT INTO schema_migrations (version) VALUES ('20171113104813');
+INSERT INTO schema_migrations (version) VALUES ('20180118100003');
+
diff --git a/spec/features/fitbit_spec.rb b/spec/features/fitbit_spec.rb
deleted file mode 100644
index 2562bf7..0000000
--- a/spec/features/fitbit_spec.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-# frozen_string_literal: true
-RSpec.feature 'Fitbit profiles' do
- let!(:user) { create(:user) }
- let!(:fitbit_profile) { create(:fitbit_profile, user: user) }
-
- scenario 'are shown' do
- visit '/fitbit'
-
- expect(page).to have_content('Listing all connected Fitbit accounts')
- end
-end
diff --git a/spec/requests/das_spec.rb b/spec/requests/das_spec.rb
new file mode 100644
index 0000000..97c7b75
--- /dev/null
+++ b/spec/requests/das_spec.rb
@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+RSpec.describe 'DAS-API', type: :request do
+ let!(:user) { create(:user, name: 'API-Hacker', id: 1) }
+ let!(:genotype) { create(:genotype,id: 1, user: user) }
+ let!(:snp) { create(:snp, name: 'rs2345', chromosome: 1, position: 10) }
+ let!(:snp_two) { create(:snp, name: 'rs1234', chromosome: 1, position: 12) }
+ let!(:user_snp) { create(:user_snp, user: user, snp: snp, genotype: genotype) }
+ let!(:user_snp_two) { create(:user_snp, user: user, snp: snp_two, genotype: genotype) }
+
+ it 'GET /das/:id/' do
+ get "/das/#{user.id}/features?segment=1:10,11",
+ nil,
+ 'SERVER_SOFTWARE' => 'faked for test'
+ assert_response :success
+ expect(response.body).to include('rs2345')
+ expect(response.body).not_to include('rs1234')
+ end
+end
diff --git a/spec/workers/zipfulldata_spec.rb b/spec/workers/zipfulldata_spec.rb
index 981f729..863084c 100644
--- a/spec/workers/zipfulldata_spec.rb
+++ b/spec/workers/zipfulldata_spec.rb
@@ -48,29 +48,6 @@ describe Zipfulldata do
expect(csv).to eq([exp_header, exp_row1, exp_row2])
end
- it "creates fitbit CSVs" do
- file_name =
- "#{job.tmp_dir}/dump_user#{user.id}_fitbit_data_#{job.time_str}.csv"
- fp = create(:fitbit_profile, user: user)
- expect(zipfile).to receive(:add).
- with("user#{fp.user.id}_fitbit_data_#{job.time_str}.csv", file_name)
- job.create_fitbit_csv(zipfile)
- csv = CSV.read(file_name, job.csv_options)
- exp_header = ["date", "steps", "floors", "weight", "bmi",
- "minutes asleep", "minutes awake", "times awaken",
- "minutes until fell asleep"]
- exp_row = [fp.fitbit_activities.first.date_logged.to_s,
- fp.fitbit_activities.first.steps.to_s,
- fp.fitbit_activities.first.floors.to_s,
- fp.fitbit_bodies.first.weight.to_s,
- fp.fitbit_bodies.first.bmi.to_s,
- fp.fitbit_sleeps.first.minutes_asleep.to_s,
- fp.fitbit_sleeps.first.minutes_awake.to_s,
- fp.fitbit_sleeps.first.number_awakenings.to_s,
- fp.fitbit_sleeps.first.minutes_to_sleep.to_s]
- expect(csv).to eq([exp_header, exp_row])
- end
-
it "creates picture phenotype CSVs" do
user2 = create(:user)
pp = create(:picture_phenotype)
@@ -122,7 +99,6 @@ Thanks for using openSNP!
expect(Zip::File).to receive(:open).with(job.zip_fs_path, Zip::File::CREATE).
and_yield(zipfile)
expect(job).to receive(:create_user_csv).with([genotype], zipfile)
- expect(job).to receive(:create_fitbit_csv).with(zipfile)
expect(job).to receive(:create_picture_phenotype_csv).with(zipfile).and_return([upp])
expect(job).to receive(:create_picture_zip).with([upp], zipfile)
expect(job).to receive(:create_readme).with(zipfile)
diff --git a/test/functional/fitbit_profiles_controller_test.rb b/test/functional/fitbit_profiles_controller_test.rb
deleted file mode 100644
index 016bbf2..0000000
--- a/test/functional/fitbit_profiles_controller_test.rb
+++ /dev/null
@@ -1,16 +0,0 @@
-# frozen_string_literal: true
-require_relative '../test_helper'
-
-class FitbitProfilesControllerTest < ActionController::TestCase
- context "Fitbit profiles" do
- setup do
- @user = FactoryGirl.create(:user)
- @fitbit_profile = FactoryGirl.create(:fitbit_profile, user: @user)
- end
-
- should "show up" do
- get 'show', id: @fitbit_profile.id
- assert_response :ok
- end
- end
-end