spout 0.10.0.beta4 → 0.10.0.beta6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 67c77820069e95591293bb933da5eb2c3b51be5d
+  metadata.gz: d2c5a33171e6f9d0ed9ea65595d6fa2cc846c522
+  data.tar.gz: b83e43ccf34a70eac9d4485861a40f4a0f2269dc
 SHA512:
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+  metadata.gz: 8c6f37201645cd745c38d14ad5599ee702d313e41dc6f27cea28883d9a21c7cdf616287f7340df1e2fd1588c621fdb43f3a0c52b584e5744d60a8fcf277d3ade
+  data.tar.gz: e5d504aa8ab9bf0acdb71e0d0ad5a17fbecf4889b5d577fb1f8ecbca10d21446af6dd0e17ad925db8950af1ea5783a8b8c83b15955f85aeb41c9f19469b4be3a

data/CHANGELOG.md

@@ -1,11 +1,14 @@
 ## 0.10.0
 
 ### Enhancements
+- **Deploy Command**
+  - `spout deploy` command added that allows a data dictionary to be deployed to a web URL
+  - The webserver that is specified must respond to the web requests in a similar manner to nsrr/www.sleepdata.org
 - **Import Command**
   - `spout import` now changes variables with all caps `display_name` to use title case instead
     - Display names that use mixed case are unaffected
   - `spout import --domains` now marks options as `"missing": true` if the option value starts with a dot `.` or a dash `-`
-    - Display names for values are also changed to title case if they are all caps
+    - Display names for domain options are also changed to title case if they are all caps
 - **Testing Changes**
   - Tests now include checks to assure that variable display_name fields don't exceed 255 length requirement
     - `include Spout::Tests::VariableDisplayNameLength`

data/README.md

@@ -327,3 +327,56 @@ This will generate charts and tables for each variable in the dataset plotted ag
 }
 ```
 
+### Deploy your data dictionary to a staging or production webserver
+
+```
+spout deploy NAME
+```
+
+This command pushes a tagged version of the data dictionary to a webserver specified in the `.spout.yml` file.
+
+```
+webservers:
+  - name: production
+    url: https://sleepdata.org
+  - name: staging
+    url: https://staging.sleepdata.org
+```
+
+Shorthand
+
+**Deploy to Production**
+```
+spout d p
+```
+
+**Deploy to Staging**
+```
+spout d s
+```
+
+The following steps are run:
+
+- **User Authorization**
+  - User authenticates via token, the user must be a dataset editor
+- **Version Check**
+  - "v#{VERSION}" matches HEAD git tag annotation
+  - `CHANGELOG.md` top line should include version, ex: `## 0.1.0`
+  - Git Repo should have zero uncommitted changes
+- **Tests Pass**
+  - `spout t` passes for RC and FINAL versions (Include .rc, does not include .beta)
+  - `spout c` passes for RC and FINAL versions (Include .rc, does not include .beta)
+- **Graph Generation**
+  - `spout g` is run
+  - Graphs are pushed to server
+- **Image Generation**
+  - `spout p` is run
+  - `optipng` is run on image then uploaded to server
+  - Images are pushed to server
+- **Dataset Uploads**
+  - Dataset CSV data dictionary is generated (variables, domains, forms)
+  - Dataset and data dictionary CSVs uploaded to files section of dataset
+- **Server-Side Updates**
+  - Server checks out branch of specified tag
+  - Server runs `load_data_dictionary!` for specified dataset slug
+  - Server refreshes dataset folder to reflect new dataset and data dictionaries

data/lib/spout/commands/deploy.rb

@@ -0,0 +1,207 @@
+require 'colorize'
+require 'net/http'
+
+require 'spout/helpers/config_reader'
+require 'spout/helpers/quietly'
+
+# - **User Authorization**
+#   - User authenticates via token, the user must be a dataset editor
+# - **Version Check**
+#   - "v#{VERSION}" matches HEAD git tag annotation
+#   - `CHANGELOG.md` top line should include version, ex: `## 0.1.0`
+#   - Git Repo should have zero uncommitted changes
+# - **Tests Pass**
+#   - `spout t` passes for RC and FINAL versions (Include .rc, does not include .beta)
+#   - `spout c` passes for RC and FINAL versions (Include .rc, does not include .beta)
+# - **Graph Generation**
+#   - `spout g` is run
+#   - Graphs are pushed to server
+# - **Image Generation**
+#   - `spout p` is run
+#   - `optipng` is run on image then uploaded to server
+#   - Images are pushed to server
+# - **Dataset Uploads**
+#   - Dataset CSV data dictionary is generated (variables, domains, forms)
+#   - Dataset and data dictionary CSVs uploaded to files section of dataset
+# - **Server-Side Updates**
+#   - Server checks out branch of specified tag
+#   - Server runs `load_data_dictionary!` for specified dataset slug
+#   - Server refreshes dataset folder to reflect new dataset and data dictionaries
+
+class DeployError < StandardError
+end
+
+module Spout
+  module Commands
+    class Deploy
+
+      include Spout::Helpers::Quietly
+
+      INDENT_LENGTH = 23
+      INDENT = " "*INDENT_LENGTH
+
+      attr_accessor :token, :version, :slug, :url, :config, :environment
+
+      def initialize(argv, version)
+        # puts "CODE GREEN INITIALIZED...".colorize(:green)
+        # puts "Deploying to server...".colorize(:red)
+        @environment = argv[1].to_s
+        @version = version
+        @skip_checks = false
+        run_all
+      end
+
+      def run_all
+        begin
+          config_file_load
+          version_check unless @skip_checks
+          test_check unless @skip_checks
+          user_authorization
+          graph_generation
+          image_generation
+          dataset_uploads
+          trigger_server_updates
+        rescue DeployError
+        end
+      end
+
+      def config_file_load
+        print "   `.spout.yml` Check: "
+        @config = Spout::Helpers::ConfigReader.new
+
+        @slug = @config.slug
+
+        if @slug == ''
+          message = "#{INDENT}Please specify a dataset slug in your `.spout.yml` file!".colorize(:red) + " Ex:\n---\nslug: mydataset\n".colorize(:orange)
+          failure(message)
+        end
+
+        if @config.webservers.empty?
+          message = "#{INDENT}Please specify a webserver in your `.spout.yml` file!".colorize(:red) + " Ex:\n---\nwebservers:\n  - name: production\n    url: https://sleepdata.org\n  - name: staging\n    url: https://staging.sleepdata.org\n".colorize(:orange)
+          failure(message)
+        end
+
+        matching_webservers = @config.webservers.select{|wh| /^#{@environment}/i =~ wh['name'].to_s.downcase}
+        if matching_webservers.count == 0
+          message = "#{INDENT}0 webservers match '#{@environment}'.".colorize(:red) + " The following webservers exist in your `.spout.yml` file:\n" + "#{INDENT}#{@config.webservers.collect{|wh| wh['name'].to_s.downcase}.join(', ')}".colorize(:white)
+          failure(message)
+        elsif matching_webservers.count > 1
+          message = "#{INDENT}#{matching_webservers.count} webservers match '#{@environment}'.".colorize(:red) + " Did you mean one of the following?\n" + "#{INDENT}#{matching_webservers.collect{|wh| wh['name'].to_s.downcase}.join(', ')}".colorize(:white)
+          failure(message)
+        end
+
+        @url = URI.parse(matching_webservers.first['url'].to_s.strip) rescue @url = nil
+
+        if @url.to_s == ''
+          message = "#{INDENT}Invalid URL format for #{matching_webservers.first['name'].to_s.strip.downcase} webserver: ".colorize(:red) + "'#{matching_webservers.first['url'].to_s.strip}'".colorize(:white)
+          failure(message)
+        end
+
+        puts "PASS".colorize(:green)
+        puts "        Target Server: " + "#{@url}".colorize(:white)
+        puts "       Target Dataset: " + "#{@slug}".colorize(:white)
+      end
+
+      # - **Version Check**
+      #   - Git Repo should have zero uncommitted changes
+      #   - `CHANGELOG.md` top line should include version, ex: `## 0.1.0`
+      #   - "v#{VERSION}" matches HEAD git tag annotation
+      def version_check
+        stdout = quietly do
+          `git status --porcelain`
+        end
+
+        print "     Git Status Check: "
+        if stdout.to_s.strip == ''
+          puts "PASS".colorize(:green) + " " + "nothing to commit, working directory clean".colorize(:white)
+        else
+          message = "#{INDENT}working directory contains uncomitted changes".colorize(:red)
+          failure message
+        end
+
+        changelog = File.open('CHANGELOG.md', &:readline).strip rescue changelog = ''
+        if changelog.match(/^## #{@version.split('.')[0..2].join('.')}/)
+          puts "         CHANGELOG.md: " + "PASS".colorize(:green) + " " + changelog.colorize(:white)
+        else
+          print "         CHANGELOG.md: "
+          message = "#{INDENT}Expected: ".colorize(:red) + "## #{@version}".colorize(:white) +
+                  "\n#{INDENT}  Actual: ".colorize(:red) + changelog.colorize(:white)
+          failure message
+        end
+
+        stdout = quietly do
+          `git describe --exact-match HEAD`
+        end
+
+        print "        Version Check: "
+        tag = stdout.to_s.strip
+        if "v#{@version}" != tag
+          message = "#{INDENT}Version specified in `VERSION` file ".colorize(:red) + "'v#{@version}'".colorize(:white) + " does not match git tag on HEAD commit ".colorize(:red) + "'#{tag}'".colorize(:white)
+          failure message
+        else
+          puts   "PASS".colorize(:green) + " VERSION " + "'v#{@version}'".colorize(:white) + " matches git tag " + "'#{tag}'".colorize(:white)
+        end
+
+      end
+
+      def test_check
+        print "          Spout Tests: "
+
+        stdout = quietly do
+          `spout t`
+        end
+
+        if stdout.match(/[^\d]0 failures, 0 errors,/)
+          puts "PASS".colorize(:green)
+        else
+          message = "#{INDENT}spout t".colorize(:white) + " had errors or failures".colorize(:red) + "\n#{INDENT}Please fix all errors and failures and then run spout deploy again."
+          failure message
+        end
+
+        puts "       Spout Coverage: " + "SKIP".colorize(:blue)
+      end
+
+      def user_authorization
+        puts  "  Get your token here: " + "#{@url}/token".colorize(:blue).on_white.underline
+        print "     Enter your token: "
+        @token =  STDIN.gets.chomp
+        # failure ''
+        # puts "PASS".colorize(:green)
+      end
+
+      def graph_generation
+        # failure ''
+        require 'spout/commands/graphs'
+        Spout::Commands::Graphs.new([], @version, true, @url, @slug, @token)
+        puts "\r     Graph Generation: " + "DONE          ".colorize(:green)
+      end
+
+      def image_generation
+        # failure ''
+        require 'spout/commands/images'
+        Spout::Commands::Images.new([], [], [], @version, [], true, @url, @slug, @token)
+        puts "\r     Image Generation: " + "DONE          ".colorize(:green)
+      end
+
+      def dataset_uploads
+        print "      Dataset Uploads: "
+        # failure ''
+        # puts "PASS".colorize(:green)
+        puts "SKIP".colorize(:blue)
+      end
+
+      def trigger_server_updates
+        print "Launch Server Scripts: "
+        # failure ''
+        # puts "PASS".colorize(:green)
+        puts "SKIP".colorize(:blue)
+      end
+
+      def failure(message)
+        puts "FAIL".colorize(:red)
+        puts message
+        raise DeployError
+      end
+    end
+  end
+end

data/lib/spout/commands/graphs.rb

@@ -3,16 +3,22 @@ require 'fileutils'
 require 'rubygems'
 require 'json'
 require 'yaml'
+require 'colorize'
 
 require 'spout/helpers/subject_loader'
 require 'spout/helpers/chart_types'
 require 'spout/helpers/config_reader'
+require 'spout/helpers/send_file'
 
 module Spout
   module Commands
     class Graphs
-      def initialize(variables, standard_version)
+      def initialize(variables, standard_version, deploy_mode = false, url = '', slug = '', token = '')
+        @deploy_mode = deploy_mode
+        @url = url
         @standard_version = standard_version
+        @slug = slug
+        @token = token
 
         @config = Spout::Helpers::ConfigReader.new
 
@@ -54,7 +60,7 @@ module Spout
         @subjects = @subject_loader.subjects
         compute_tables_and_charts
 
-        puts "Took #{Time.now - t} seconds." if @subjects.size > 0
+        puts "Took #{Time.now - t} seconds." if @subjects.size > 0 and not @deploy_mode
       end
 
       def compute_tables_and_charts
@@ -67,7 +73,12 @@ module Spout
           variable_name  = json['id'].to_s.downcase
           next unless Spout::Models::Subject.method_defined?(variable_name)
 
-          puts "#{file_index+1} of #{variable_files_count}: #{variable_file.gsub(/(^variables\/|\.json$)/, '').gsub('/', ' / ')}"
+          if @deploy_mode
+            print "\r     Graph Generation: " + "#{"% 3d" % ((file_index+1)*100/variable_files_count)}% Uploaded".colorize(:white)
+          else
+            puts "#{file_index+1} of #{variable_files_count}: #{variable_file.gsub(/(^variables\/|\.json$)/, '').gsub('/', ' / ')}"
+          end
+
 
 
           stats = {
@@ -101,9 +112,17 @@ module Spout
           chart_json_file = File.join('graphs', @standard_version, "#{json['id']}.json")
           File.open(chart_json_file, 'w') { |file| file.write( JSON.pretty_generate(stats) + "\n" ) }
 
+          if @deploy_mode
+            send_to_server(chart_json_file)
+          end
+
         end
       end
 
+      def send_to_server(chart_json_file)
+        response = Spout::Helpers::SendFile.post("#{@url}/datasets/#{@slug}/upload_graph.json", chart_json_file, @standard_version, @token)
+      end
+
       # [["Visit 1", "1"], ["Visit 2", "2"], ["CVD Outcomes", "3"]]
       def visits
         @visits ||= begin

data/lib/spout/commands/images.rb

@@ -7,12 +7,20 @@ require 'yaml'
 require 'spout/helpers/subject_loader'
 require 'spout/helpers/chart_types'
 require 'spout/helpers/config_reader'
+require 'spout/helpers/send_file'
 
 module Spout
   module Commands
     class Images
 
-      def initialize(types, variable_ids, sizes, standard_version, argv)
+      def initialize(types, variable_ids, sizes, standard_version, argv, deploy_mode = false, url = '', slug = '', token = '')
+        @deploy_mode = deploy_mode
+        @url = url
+        @standard_version = standard_version
+        @slug = slug
+        @token = token
+
+
         @variable_files = Dir.glob('variables/**/*.json')
         @standard_version = standard_version
         @pretend = (argv.delete('--pretend') != nil)
@@ -34,7 +42,7 @@ module Spout
         @subjects = @subject_loader.subjects
 
         compute_images
-        puts "Took #{Time.now - t} seconds." if @subjects.size > 0
+        puts "Took #{Time.now - t} seconds." if @subjects.size > 0 and not @deploy_mode
       end
 
       def compute_images
@@ -53,7 +61,11 @@ module Spout
           variable_name  = json['id'].to_s.downcase
           next unless Spout::Models::Subject.method_defined?(variable_name)
 
-          puts "#{file_index+1} of #{variable_files_count}: #{variable_file.gsub(/(^variables\/|\.json$)/, '').gsub('/', ' / ')}"
+          if @deploy_mode
+            print "\r     Image Generation: " + "#{"% 3d" % ((file_index+1)*100/variable_files_count)}% Uploaded".colorize(:white)
+          else
+            puts "#{file_index+1} of #{variable_files_count}: #{variable_file.gsub(/(^variables\/|\.json$)/, '').gsub('/', ' / ')}"
+          end
 
           filtered_subjects = @subjects.select{ |s| s.send(@config.visit) != nil }
 
@@ -115,8 +127,13 @@ module Spout
           puts phantomjs_command
         else
           `#{phantomjs_command}`
+
+          send_to_server(graph_path) if @deploy_mode
         end
+      end
 
+      def send_to_server(file)
+        response = Spout::Helpers::SendFile.post("#{@url}/datasets/#{@slug}/upload_graph.json", file, @standard_version, @token, 'images')
       end
 
     end

data/lib/spout/helpers/config_reader.rb

@@ -4,13 +4,13 @@ module Spout
   module Helpers
     class ConfigReader
 
-      attr_reader :slug, :visit, :charts
-
+      attr_reader :slug, :visit, :charts, :webservers
 
       def initialize
         @slug = ''
         @visit = ''
         @charts = []
+        @webservers = []
         parse_yaml_file
       end
 
@@ -26,6 +26,12 @@ module Spout
           else
             []
           end
+
+          @webservers = if spout_config['webservers'].kind_of?(Array)
+            spout_config['webservers'].select{|c| c.kind_of?(Hash)}
+          else
+            []
+          end
         else
           puts "The YAML file needs to be in the following format:"
           puts "---\nvisit: visit_variable_name\ncharts:\n- chart: age_variable_name\n  title: Age\n- chart: gender_variable_name\n  title: Gender\n- chart: race_variable_name\n  title: Race\n"

data/lib/spout/helpers/quietly.rb

@@ -0,0 +1,27 @@
+
+module Spout
+  module Helpers
+    module Quietly
+
+      # From Rails: http://apidock.com/rails/v3.2.13/Kernel/silence_stream
+      def silence_stream(stream)
+        old_stream = stream.dup
+        stream.reopen(RbConfig::CONFIG['host_os'] =~ /mswin|mingw/ ? 'NUL:' : '/dev/null')
+        stream.sync = true
+        yield
+      ensure
+        stream.reopen(old_stream)
+      end
+
+      # From Rails: http://apidock.com/rails/v3.2.13/Kernel/quietly
+      def quietly
+        silence_stream(STDOUT) do
+          silence_stream(STDERR) do
+            yield
+          end
+        end
+      end
+
+    end
+  end
+end

data/lib/spout/helpers/send_file.rb

@@ -0,0 +1,102 @@
+require 'openssl'
+require 'net/http'
+require 'json'
+
+module Spout
+  module Helpers
+    class SendFile
+      class << self
+        def post(*args)
+          new(*args).post
+        end
+      end
+
+      attr_reader :url
+
+      def initialize(url, filename, version, token, type = nil)
+
+        @params = {}
+        @params["version"] = version
+        @params["auth_token"] = token if token
+        @params["type"] = type if type
+        begin
+          file = File.open(filename, "rb")
+          @params["file"] = file
+
+          mp = Multipart::MultipartPost.new
+          @query, @headers = mp.prepare_query(@params)
+        ensure
+          file.close if file
+        end
+
+        begin
+          @url = URI.parse(url)
+
+          @http = Net::HTTP.new(@url.host, @url.port)
+          if @url.scheme == 'https'
+            @http.use_ssl = true
+            @http.verify_mode = OpenSSL::SSL::VERIFY_NONE
+          end
+        rescue
+        end
+      end
+
+      def post
+        begin
+          response = @http.start do |http|
+            http.post(@url.path, @query, @headers)
+          end
+          JSON.parse(response.body)
+        rescue
+          nil
+        end
+      end
+    end
+  end
+end
+
+
+module Multipart
+  class Param
+    attr_accessor :k, :v
+    def initialize( k, v )
+      @k = k
+      @v = v
+    end
+
+    def to_multipart
+      return "Content-Disposition: form-data; name=\"#{k}\"\r\n\r\n#{v}\r\n"
+    end
+  end
+
+  class FileParam
+    attr_accessor :k, :filename, :content
+    def initialize( k, filename, content )
+      @k = k
+      @filename = filename
+      @content = content
+    end
+
+    def to_multipart
+      mime_type = 'application/octet-stream'
+      return "Content-Disposition: form-data; name=\"#{k}\"; filename=\"#{filename}\"\r\n" + "Content-Transfer-Encoding: binary\r\n" + "Content-Type: #{mime_type}\r\n\r\n" + content + "\r\n"
+    end
+  end
+  class MultipartPost
+    BOUNDARY = 'a#41-93r1-^&#213-rule0000'
+    HEADER = {"Content-type" => "multipart/form-data, boundary=" + BOUNDARY + " "}
+
+    def prepare_query (params)
+      fp = []
+      params.each {|k,v|
+        if v.respond_to?(:read)
+          fp.push(FileParam.new(k, v.path, v.read))
+        else
+          fp.push(Param.new(k,v))
+        end
+      }
+      query = fp.collect {|p| "--" + BOUNDARY + "\r\n" + p.to_multipart }.join("") + "--" + BOUNDARY + "--"
+      return query, HEADER
+    end
+  end
+end

data/lib/spout/helpers/subject_loader.rb

@@ -41,11 +41,11 @@ module Spout
         @csv_files = Dir.glob("csvs/#{@csv_directory}/*.csv")
         @csv_files.each_with_index do |csv_file, index|
           count = 0
-          puts "Parsing: #{csv_file}"
+          print "\nParsing #{csv_file}"
           CSV.parse( File.open(csv_file, 'r:iso-8859-1:utf-8'){|f| f.read}, headers: true, header_converters: lambda { |h| h.to_s.downcase } ) do |line|
             row = line.to_hash
             count += 1
-            print '.' if (count % 10 == 0)
+            print "\rParsing #{csv_file} - line ##{count}" if (count % 10 == 0)
             @subjects << Spout::Models::Subject.create do |t|
               t._visit = row[@visit]
 
@@ -68,7 +68,7 @@ module Spout
             # puts "Memory Used: " + (`ps -o rss -p #{$$}`.strip.split.last.to_i / 1024).to_s + " MB" if count % 1000 == 0
             break if @number_of_rows != nil and count >= @number_of_rows
           end
-          puts "\n\n"
+          puts "\n"
         end
 
         if @csv_directory != @standard_version

data/lib/spout/version.rb

@@ -3,7 +3,7 @@ module Spout
     MAJOR = 0
     MINOR = 10
     TINY = 0
-    BUILD = "beta4" # nil, "pre", "rc", "rc2"
+    BUILD = "beta6" # nil, "pre", "rc", "rc2"
 
     STRING = [MAJOR, MINOR, TINY, BUILD].compact.join('.')
   end

data/lib/spout.rb

@@ -11,7 +11,8 @@ Spout::COMMANDS = {
   'c' => :coverage_report,
   'p' => :generate_images,
   'g' => :generate_charts_and_tables,
-  'o' => :outliers_report
+  'o' => :outliers_report,
+  'd' => :deploy
 }
 
 module Spout
@@ -72,6 +73,8 @@ The most common spout commands are:
   [g]raphs          Generates JSON graphs for each variable
                     in a dataset and places them
                     in `<project_name>/graphs/<version>/`
+  [d]eploy NAME     Push dataset and data dictionary to a
+                    webserver specified in `.spout.yml`
   [v]ersion         Returns the version of Spout
 
 Commands can be referenced by the first letter:
@@ -80,6 +83,11 @@ Commands can be referenced by the first letter:
 EOT
   end
 
+  def self.deploy(argv)
+    require 'spout/commands/deploy'
+    Spout::Commands::Deploy.new(argv, standard_version)
+  end
+
   def self.importer(argv)
     require 'spout/commands/importer'
     Spout::Commands::Importer.new(argv)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: spout
 version: !ruby/object:Gem::Version
-  version: 0.10.0.beta4
+  version: 0.10.0.beta6
 platform: ruby
 authors:
 - Remo Mueller
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-15 00:00:00.000000000 Z
+date: 2014-10-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -110,6 +110,7 @@ files:
 - bin/spout
 - lib/spout.rb
 - lib/spout/commands/coverage.rb
+- lib/spout/commands/deploy.rb
 - lib/spout/commands/exporter.rb
 - lib/spout/commands/graphs.rb
 - lib/spout/commands/images.rb
@@ -122,7 +123,9 @@ files:
 - lib/spout/helpers/iterators.rb
 - lib/spout/helpers/json_loader.rb
 - lib/spout/helpers/number_helper.rb
+- lib/spout/helpers/quietly.rb
 - lib/spout/helpers/semantic.rb
+- lib/spout/helpers/send_file.rb
 - lib/spout/helpers/subject_loader.rb
 - lib/spout/helpers/table_formatting.rb
 - lib/spout/models/coverage_result.rb