hastie 0.2.0

data/lib/hastie/report_updater.rb

@@ -0,0 +1,40 @@
+require 'fileutils'
+require 'hastie/config_file'
+require 'hastie/constants'
+require 'hastie/server_reader'
+
+module Hastie
+  class ReportUpdater < ServerReader
+    def self.banner
+      "hastie update <REPORT_DIR> <OPTIONS>"
+    end
+
+    desc "Updates local files from remote server"
+    argument :name, :type => :string, :default => ".", :desc => "The name report directory"
+
+    def read_report_file
+      self.destination_root = name
+      report_config_file = File.join(self.destination_root, Hastie.report_config_name)
+      if !File.exists? report_config_file
+        say "Cannot locate #{Hastie.report_config_name}."
+        say "Report directory does not contain report"
+        say "#{File.expand_path(self.destination_root)}"
+        exit(1)
+      end
+      # we get the report filename from this config file
+      local_config = ConfigFile.load(report_config_file, :local)
+      self.options = local_config.merge(self.options)
+    end
+
+    def fetch_static_files
+      options[:server]["static"] ||= []
+      options[:server]["static"].each do |static_file|
+        static_path = File.join(options[:server_root], static_file)
+        if File.exists? static_path
+          say_status "copy", "#{static_path} to #{File.basename(destination_root)}"
+          FileUtils.cp_r static_path, self.destination_root
+        end
+      end
+    end
+  end
+end

data/lib/hastie/report_watcher.rb

@@ -0,0 +1,65 @@
+require 'fileutils'
+require 'hastie/constants'
+require 'hastie/config_file'
+require 'thor/group'
+
+module Hastie
+  class ReportWatcher < Thor::Group
+    include Thor::Actions
+
+    desc "Watches Directory Using Jekyll"
+    argument :path, :type => :string, :default => ".", :desc => "The path to the report directory"
+
+    attr_accessor :report_dir
+
+    # this is done just as a double check that we are in a report directory
+    def check_report_file
+      self.report_dir = File.expand_path(path)
+      report_config_file = File.join(report_dir, Hastie.report_config_name)
+      if !File.exists? report_config_file
+        say_status "error","Cannot locate #{Hastie.report_config_name}.", :red
+        say_status "error","Directory #{self.report_dir} is not a report.", :red
+        exit(1)
+      end
+    end
+
+    def set_root
+      self.destination_root = self.report_dir
+    end
+
+    def read_config_file
+      config_file = File.join(self.report_dir, Hastie.watch_config_file)
+      if !File.exists? config_file
+        say_status "error", "Cannot find #{config_file}", :red
+        say_status "error","Directory #{self.report_dir} is not a report.", :red
+        exit(1)
+      end
+      local_config = ConfigFile.load(config_file, :local)
+      self.options = local_config.merge(self.options)
+    end
+
+    def start_jekyll
+      port = self.options["local"]["server_port"] || "4000"
+      url = "http://0.0.0.0:#{port}"
+      say_status "open", url
+
+      in_root do
+        if !File.exist?("config.ru")
+          # use built in method
+          exec("jekyll --auto --server")
+        else
+          # use thin method
+          jekyllPid = Process.spawn("jekyll --auto")
+          thinPid = Process.spawn("thin -p #{port} -R config.ru start")
+          trap("INT") {
+            [jekyllPid, thinPid].each { |pid| Process.kill(9, pid) rescue Errno::ESRCH }
+            exit 0
+          }
+
+          [jekyllPid, thinPid].each { |pid| Process.wait(pid) }
+        end
+      end
+
+    end
+  end
+end

data/lib/hastie/server_generator.rb

@@ -0,0 +1,47 @@
+require 'fileutils'
+require 'hastie/constants'
+require 'hastie/config_file'
+require 'thor/group'
+require 'grit'
+
+module Hastie
+  class ServerGenerator < Thor::Group
+    include Thor::Actions
+
+    def self.banner
+      "hastie create_server [NAME]"
+    end
+
+    desc "Creates framework for new server"
+    argument :name, :type => :string, :desc => "The dir of the new server location. no spaces"
+
+    def self.source_root
+      File.dirname(__FILE__)
+    end
+
+    def set_destination
+      # hack to unfreeze the options hash
+      self.options = Thor::CoreExt::HashWithIndifferentAccess.new(options)
+
+      # want to allow for relative paths
+      options[:server_id] = File.basename(name)
+      self.destination_root = File.join(File.dirname(name), options[:server_id])
+      say_status "note", "root: #{self.destination_root}"
+    end
+
+    def create_server
+      directory("templates/server", self.destination_root)
+    end
+
+    def create_git_repo
+      in_root do
+        say_status "note", "creating git repository in #{self.destination_root}"
+        repo = Grit::Repo.init(".")
+        all_files = Dir.glob("./**")
+        #all_files.each {|f| say_status "note", "adding #{f}"}
+        repo.add(all_files)
+        repo.commit_all("initial commit of server scaffold. created from hastie")
+      end
+    end
+  end
+end

data/lib/hastie/server_reader.rb

@@ -0,0 +1,81 @@
+require 'yaml'
+require 'fileutils'
+require 'thor/group'
+require 'hastie/config_file'
+require 'hastie/constants'
+
+module Hastie
+  class ServerReader < Thor::Group
+    include Thor::Actions
+    class_option :server_root, :aliases => "-s", :desc => "Root directory of the server to read / publish to"
+    class_option :config_file, :aliases => "-c", :desc => "Path to .hastie config file", :default => Hastie.config_file
+
+    no_tasks do
+      def config_file
+        @config_file ||= if options[:config_file]
+                           File.expand_path(options[:config_file]) 
+                           else
+                             Hastie.config_file
+                           end
+        @config_file
+      end
+    end
+
+    def self.source_root
+      File.dirname(__FILE__)
+    end
+
+    # Tries to access users config file
+    # loads contents into the options hash
+    def read_config_file
+      say_status "note", "config file: #{self.config_file}"
+      if !File.exists? self.config_file
+        say "No config file found. Please create #{self.config_file}"
+        exit(1)
+      end
+      config = ConfigFile.load(self.config_file)
+      self.options = config.merge(self.options)
+    end
+
+    # Tries to access the servers
+    def get_server_config
+      say_status "note", "server root: #{options[:server_root]}"
+      # First check if the server directory exists
+      if !File.directory? options[:server_root]
+        say_status "error", "Cannot find server directory:", :red
+        say options[:server_root]
+        say "Please modify \'server_root\' to point to server root directory"
+        exit(1)
+      end
+
+      # Check for config file inside server_root
+      server_config_file = File.join(options[:server_root], SERVER_CONFIG_FILE)
+      if !File.exists? server_config_file
+        say_status "error", "Cannot find #{SERVER_CONFIG_FILE} file in server directory:", :red
+        say server_config_file
+        say ""
+        say "Are you sure #{options[:server_root]} is a valid server directory?"
+        exit(1)
+      end
+
+      # Check for reports file inside server_root
+      server_report_file = File.join(options[:server_root], SERVER_REPORTS_FILE)
+      if !File.exists? server_report_file
+        say_status "error", "Cannot find #{SERVER_REPORTS_FILE} file in server directory:", :red
+        say server_report_file
+        say ""
+        say "Are you sure #{options[:server_root]} is a valid server directory?"
+        exit(1)
+      end
+
+      # merge the server config and report file
+      # put them in their own 'namespace' to avoid
+      # collisions with existing configs
+      server_config = ConfigFile.load(server_config_file, :server)
+      self.options = server_config.merge(self.options)
+
+      server_reports = ConfigFile.load(server_report_file, :published_reports)
+      self.options = server_reports.merge(self.options)
+    end
+  end
+end

data/lib/hastie/templates/hastie_config.tt

@@ -0,0 +1,6 @@
+server_root: <%= server_root %>
+type: <%= options[:type] %>
+<% if options[:analyst] %>
+analyst: <%= options[:analyst] %>
+<% end %>
+

data/lib/hastie/templates/report.markdown.tt

@@ -0,0 +1,19 @@
+---
+layout: report
+title: <%= title %>
+analyst: <%= options[:analyst] %>
+researcher: <%= options[:researcher] %> 
+pi: <%= options[:pi] %>
+data:
+- <%= options[:data_dir] %>/
+categories: 
+- open
+---
+
+## Objective
+
+## Data
+
+## Methods
+
+## Results

data/lib/hastie/templates/report.textile.tt

@@ -0,0 +1,19 @@
+---
+layout: report
+title: <%= title %>
+analyst: <%= options[:analyst] %>
+researcher: <%= options[:researcher] %> 
+pi: <%= options[:pi] %>
+data:
+- <%= options[:data_dir] %>/
+categories: 
+- open
+---
+
+h2. Objective
+
+h2. Data
+
+h2. Methods
+
+h2. Results

data/lib/hastie/templates/report_index.html.tt

@@ -0,0 +1,8 @@
+<html>
+<head>
+<meta http-equiv="Refresh" content="0;url=<%= options[:report_file_generated] %>" />
+</head>
+<body>
+<a id="report_link" href="<%= options[:report_file_generated] %>"><%= options[:title] %></a>
+</body>
+</html>

data/lib/hastie/templates/server/.gitignore

@@ -0,0 +1 @@
+_site/*

data/lib/hastie/templates/server/_config.yml

@@ -0,0 +1,25 @@
+source:      .
+destination: ./_site
+includes:    ./_includes
+
+pygments:    true
+markdown:    rdiscount
+permalink:   /:year-:month-:day_:title.html
+
+baseurl: /
+
+rdiscount:
+  extensions: []
+
+exclude: []
+
+static:
+- css
+- js
+- _layouts
+- _includes
+- _plugins
+- _config.yml
+
+reports_dir: _posts
+

data/lib/hastie/templates/server/_server_config.yml

@@ -0,0 +1,15 @@
+source:      .
+destination: ./_site
+includes:    ./_includes
+
+pygments:    true
+markdown:    rdiscount
+permalink:   /:year-:month-:day_:title.html
+
+baseurl: /
+
+rdiscount:
+  extensions: []
+
+exclude: []
+

data/lib/hastie/version.rb

@@ -0,0 +1,3 @@
+module Hastie
+  VERSION = "0.2.0".freeze
+end

data/lib/hastie.rb

@@ -0,0 +1,15 @@
+
+if RUBY_VERSION =~ /1.9/
+  Encoding.default_external = Encoding::UTF_8
+  Encoding.default_internal = Encoding::UTF_8
+end
+
+# Most of Hastie functionality is derived from Thor groups.
+# Each Thor group is maintained in a separate file.
+
+require 'hastie/report_generator'
+require 'hastie/report_publisher'
+require 'hastie/report_updater'
+require 'hastie/server_generator'
+require 'hastie/config_generator'
+require 'hastie/report_watcher'

data/spec/config_generator_spec.rb

@@ -0,0 +1,124 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require File.expand_path(File.dirname(__FILE__) + '/fakefs_helper')
+require 'hastie/config_generator'
+
+describe Hastie::ConfigGenerator do
+  def read_file file
+    if File.exists? file
+      File.open(file, 'r').read
+    else
+      ""
+    end
+  end
+
+  before :each do
+    @server_dir = File.expand_path(File.join(File.dirname(__FILE__), "fixtures", "server"))
+    @output_dir = File.expand_path(File.join(File.dirname(__FILE__), "sandbox"))
+    @name = "hastie_config_gen"
+    @config_file = File.join(@output_dir, @name)
+    @input = [@server_dir, "--path", @output_dir, "--name", @name]
+    FileUtils.mkdir_p @output_dir
+  end
+
+  after :each do
+    FileUtils.rm_r @output_dir if File.exists?(@output_dir)
+  end
+
+  it "should have server_root" do
+    content = capture(:stdout) do
+      lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+    end
+
+    content = read_file @config_file
+    content.should match /server_root: #{@server_dir}/
+
+  end
+
+  describe "config flags" do
+    it "--analyst" do
+      @input << "--analyst" << "dog"
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+
+      content = read_file @config_file
+      content.should match /analyst: dog/
+    end
+
+    it "--type" do
+      @input << "--type" << "textile"
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+
+      content = read_file @config_file
+      content.should match /type: textile/
+    end
+  end
+end
+
+describe Hastie::ConfigGenerator, fakefs: true do
+  before :each do
+    @server_root = "/tmp/server/root"
+    @input = [@server_root]
+  end
+
+  describe "invalid server_root" do
+    it "should error if server_root does not exist" do
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should raise_error SystemExit
+      end
+      content.should match /not a directory/
+    end
+  end
+
+  describe "valid server_root" do
+    before :each do
+      FileUtils.mkdir_p @server_root
+      #
+      # CLONE: copies files from real fs to fakefs.
+      # TODO: use clone in other specs to copy the templates directory
+      #
+      FakeFS::FileSystem.clone(File.expand_path(File.join(File.dirname(__FILE__), "..", "lib", "hastie", "templates")))
+    end
+
+    it "should not error if server_root does not exist" do
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+    end
+
+    it "should create hastie config file" do
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+      File.exists?(File.expand_path("~/.hastie")).should == true
+    end
+
+    it "--path" do
+      path = "/alt/file/location"
+      @input << "--path" << path
+      # Hastie::ConfigGenerator.start @input
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+
+      File.exists?("#{path}/.hastie").should == true
+    end
+
+    it "--name" do
+      path = "/alt/file/location"
+      name = "hastier"
+      @input << "--path" << path << "--name" << name
+      # Hastie::ConfigGenerator.start @input
+      content = capture(:stdout) do
+        lambda { Hastie::ConfigGenerator.start @input }.should_not raise_error SystemExit
+      end
+
+      File.exists?("#{path}/#{name}").should == true
+    end
+  end
+
+
+end
+

data/spec/fakefs_helper.rb

@@ -0,0 +1,67 @@
+class FakeFsHelper
+  CONFIG_FILE = "/tmp/.hastie"
+  SERVER_DIR = "/sites/test_server"
+  REPORTS_FILE = "_reports.yml"
+  SERVER_CONFIG_FILE = "_config.yml"
+
+  def self.read_file file
+    if File.exists? file
+      File.open(file, 'r').read
+    else
+      ""
+    end
+  end
+
+  def self.stub_config_file config_file = CONFIG_FILE, server_dir = SERVER_DIR
+    FileUtils.mkdir(File.dirname(config_file))
+    File.open(config_file, 'w') do |file|
+      file.puts "server_root: #{server_dir}"
+    end
+  end
+
+  def self.stub_server_dir dir = SERVER_DIR
+    FileUtils.mkdir_p dir
+  end
+
+  def self.stub_server_config dir = SERVER_DIR
+    stub_server_dir dir
+    File.open(File.join(dir, SERVER_CONFIG_FILE), 'a') do |file|
+      file.puts ""
+    end
+  end
+
+  def self.add_reports_dir dir = SERVER_DIR
+    stub_server_config dir
+    File.open(File.join(dir, SERVER_CONFIG_FILE), 'a') do |file|
+      file.puts "reports_dir: _posts"
+    end
+  end
+
+  def self.add_static_files dir = SERVER_DIR
+    stub_server_config dir
+    static_dirs = ["css", "js", "_layouts", "_includes", "_plugins"]
+    static_files = ["_config.yml"]
+    File.open(File.join(dir, SERVER_CONFIG_FILE), 'a') do |file|
+      file.puts "static:"
+      static_dirs.each {|sdir| file.puts "- #{sdir}"}
+      static_files.each {|f| file.puts "- #{f}"}
+    end
+
+    static_dirs.each {|sdir| FileUtils.mkdir File.join(dir, sdir)}
+    static_files.each {|sfile| FileUtils.touch File.join(dir, sfile)}
+  end
+
+  def self.stub_reports_file dir = SERVER_DIR
+    stub_server_dir dir
+    File.open(File.join(dir, REPORTS_FILE), 'a') do |file|
+      file.puts ""
+    end
+  end
+
+  def self.add_published_report report_id, dir = SERVER_DIR
+    stub_reports_file dir
+    File.open(File.join(dir, REPORTS_FILE), 'a') do |file|
+      file.puts "- #{report_id}"
+    end
+  end
+end

data/spec/fixtures/config.ru

@@ -0,0 +1,29 @@
+require 'bundler/setup'
+require 'sinatra/base'
+
+# The project root directory
+$root = ::File.dirname(__FILE__)
+
+BUILD_DIR = '_site'
+
+class SinatraStaticServer < Sinatra::Base
+
+
+  get(/.+/) do
+    send_sinatra_file(request.path) {404}
+  end
+
+  not_found do
+    send_sinatra_file('404.html') {"Sorry, I cannot find #{request.path}"}
+  end
+
+  def send_sinatra_file(path, &missing_file_block)
+    file_path = File.join(File.dirname(__FILE__), BUILD_DIR,  path)
+    file_path = File.join(file_path, 'index.html') unless file_path =~ /\.[a-z]+$/i
+    File.exist?(file_path) ? send_file(file_path) : missing_file_block.call
+  end
+
+end
+
+run SinatraStaticServer
+

data/spec/fixtures/hastie_config

@@ -0,0 +1,2 @@
+analyst: jfv
+type: textile

data/spec/fixtures/report/2110-12-16-report.textile

@@ -0,0 +1,19 @@
+---
+layout: report
+title: Spec/fixtures/report
+analyst: jfv
+researcher: unknown 
+pi: unknown
+data:
+- data/report/
+---
+
+h2. Objective
+
+h2. Data
+
+h2. Analysis
+
+h3. Methods
+
+h3. Results

data/spec/fixtures/report/_config.yml

@@ -0,0 +1,9 @@
+static:
+- css
+- js
+- _layouts
+- _includes
+- _plugins
+- _config.yml
+
+reports_dir: _posts

data/spec/fixtures/report/report.yml

@@ -0,0 +1,23 @@
+---
+published_reports:
+- jfv_mak_snp_analysis
+server:
+  static:
+  - css
+  - js
+  - _layouts
+  - _includes
+  - _plugins
+  - _config.yml
+  reports_dir: _posts
+server_root: spec/fixtures/server/
+analyst: jfv
+type: textile
+config_file: /Users/jfv/.hastie
+name: report
+title: Spec/fixtures/report
+report_id: report
+researcher: unknown
+pi: unknown
+data_dir: data/report
+report_file: 2110-12-16-report.textile