etna 0.1.12 → 0.1.18

data/etna_app.completion

@@ -0,0 +1,133 @@
+#!/usr/bin/env bash
+_etna_app_completions() {
+local all_completion_names=''
+if [ "${COMP_CWORD}" == "1" ]; then
+all_completion_names='add_model attribute_actions attribute_actions_template console create_project generate_completion_script help model_template project_template update_attributes_from_csv validate_attribute_actions validate_model validate_project'
+COMPREPLY=($(compgen -W "$all_completion_names" "${COMP_WORDS[COMP_CWORD]}"))
+else
+if [ "${COMP_WORDS[1]}" == 'add_model' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "4" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "5" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'attribute_actions' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "4" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'attribute_actions_template' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'console' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'create_project' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'generate_completion_script' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'help' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'model_template' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'project_template' ]; then
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'update_attributes_from_csv' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "4" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "5" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'validate_attribute_actions' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "4" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'validate_model' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "3" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "4" ]; then
+COMPREPLY=()
+return
+fi
+if [ "${COMP_CWORD}" == "5" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+if [ "${COMP_WORDS[1]}" == 'validate_project' ]; then
+if [ "${COMP_CWORD}" == "2" ]; then
+COMPREPLY=()
+return
+fi
+true
+fi
+fi
+}
+complete -o default -F _etna_app_completions etna_app

data/ext/completions/extconf.rb

@@ -0,0 +1,20 @@
+# Rubygem doesn't provide a great hook for executing completion or shared data on installing a gem by default,
+# but it does provide an extension installation hook in the form of extconf.rb.
+# We are 'hacking' this behavior to do a user installation of completion files on the system
+require 'mkmf'
+
+# Create a dummy extension file. Without this RubyGems would abort the
+# installation process
+FileUtils.touch(File.join(Dir.pwd, 'wat.' + RbConfig::CONFIG['DLEXT']))
+
+# Drop the completion file in the user's home directory so they can wire this based on their system.
+Dir.chdir(File.expand_path('..', __FILE__)) do
+  puts `cp ../../etna.completion ~/etna.completion`
+  puts "etna.completion has been copied to your home directory.  Source it from your bashrc file to add completions for the etna command."
+end
+
+# This is normally set by calling create_makefile() but we don't need that
+# method since we'll provide a dummy Makefile. Without setting this value
+# RubyGems will abort the installation.
+$makefile_created = true
+create_makefile('ext')

data/lib/commands.rb

@@ -0,0 +1,368 @@
+require 'date'
+require 'logger'
+require 'rollbar'
+require 'tempfile'
+require_relative 'helpers'
+require 'yaml'
+
+# /bin/etna will confirm execution before running any command that includes this module.
+module RequireConfirmation
+end
+
+class EtnaApp
+  def self.config_file_path
+    File.join(Dir.home, 'etna.yml')
+  end
+
+  string_flags << '--environment'
+
+  def dispatch_to_subcommand(cmd = 'help', *args, environment: nil, **kwds)
+    set_environment(environment)
+    super(cmd, *args, **kwds)
+  end
+
+  def environment
+    if @environment
+      @environment
+    elsif @config && @config.is_a?(Hash) && @config.keys.length == 1
+      @config.keys.last.to_sym
+    elsif @config && @config.is_a?(Hash) && @config.keys.length > 1
+      raise "You have multiple environments configured, please specify your environment by adding --environment #{@config.keys.join("|")}"
+    else
+      raise "You do not have a successfully configured environment, please run #{program_name} config set https://polyphemus.ucsf.edu"
+    end
+  end
+
+  def set_environment(env)
+    @environment = env.nil? ? nil : env.to_sym
+  end
+
+  class Config
+    include Etna::CommandExecutor
+
+    class Show < Etna::Command
+
+      boolean_flags << '--all'
+
+      def execute(all: false)
+        if all
+          File.open(EtnaApp.config_file_path, 'r') { |f| puts f.read }
+        else
+          puts "Current environment: #{EtnaApp.instance.environment}"
+          pp EtnaApp.instance.env_config
+        end
+      end
+    end
+
+    class Set < Etna::Command
+      include WithEtnaClients
+      include WithLogger
+
+      boolean_flags << '--ignore-ssl'
+
+      def execute(host, ignore_ssl: false)
+        polyphemus_client ||= Etna::Clients::Polyphemus.new(
+            host: host,
+            token: token,
+            ignore_ssl: ignore_ssl)
+        workflow = Etna::Clients::Polyphemus::SetConfigurationWorkflow.new(
+            polyphemus_client: polyphemus_client,
+            config_file: EtnaApp.config_file_path)
+        config = workflow.update_configuration_file(ignore_ssl: ignore_ssl)
+        logger.info("Updated #{config.environment} configuration from #{host}.")
+      end
+
+      def setup(config)
+        super
+        EtnaApp.instance.setup_logger
+      end
+    end
+  end
+
+  class CreateTemplate
+    include Etna::CommandExecutor
+
+    # TODO: Refactor and replace with a command workflow similar to AddProjectModels
+    class AttributeActions < Etna::Command
+      def execute
+        spec = Gem::Specification.find_by_name("etna")
+        gem_root = spec.gem_dir
+        FileUtils.cp(
+            "#{gem_root}/lib/etna/templates/attribute_actions_template.json",
+            'attribute_actions_template.json')
+        puts "A sample attribute actions JSON template has been provided in the current directory as `attribute_actions_template.json`."
+      end
+    end
+  end
+
+  class Administrate
+    include Etna::CommandExecutor
+
+    class Project
+      include Etna::CommandExecutor
+
+      class Create < Etna::Command
+        include WithEtnaClients
+        include WithLogger
+
+        def execute(project_name, project_name_full)
+          create_args = {project_name: project_name, project_name_full: project_name_full}
+          Etna::Clients::Magma::ProjectValidator.new(**create_args).validate!("#{program_name} args invalid!")
+
+          create_project_workflow = Etna::Clients::Magma::CreateProjectWorkflow.new(
+              magma_client: magma_client,
+              janus_client: janus_client,
+              **create_args
+          )
+          create_project_workflow.create!
+        end
+      end
+    end
+
+    class Models
+      include Etna::CommandExecutor
+
+      class CopyTemplate < Etna::Command
+        include WithEtnaClients
+        include WithLogger
+        include StrongConfirmation
+
+        string_flags << '--file'
+        string_flags << '--target-model'
+
+        def execute(project_name, target_model: 'project', file: "#{project_name}_models_#{target_model}_tree.csv")
+          unless File.exists?(file)
+            puts "File #{file} is being prepared from the #{project_name} project."
+            puts "Copying models descending from #{target_model}..."
+            prepare_template(file, project_name, target_model)
+            puts
+            puts "Done!  You can start editing the file #{file} now"
+          else
+            puts "File #{file} already exists!  Please remove or specify a different file name before running again."
+          end
+        end
+
+        def workflow
+          @workflow ||= Etna::Clients::Magma::AddProjectModelsWorkflow.new(magma_client: magma_client)
+        end
+
+        def prepare_template(file, project_name, target_model)
+          tf = Tempfile.new
+
+          begin
+            File.open(tf.path, 'wb') { |f| workflow.write_models_template_csv(f, project_name, target_model) }
+            FileUtils.cp(tf.path, file)
+          ensure
+            tf.close!
+          end
+        end
+      end
+
+      class ApplyTemplate < Etna::Command
+        include WithEtnaClients
+        include StrongConfirmation
+        include WithLogger
+
+        string_flags << '--file'
+        string_flags << '--target-model'
+
+        def execute(project_name, target_model: 'project', file: "#{project_name}_models_#{target_model}_tree.csv")
+          reset
+
+          unless File.exists?(file)
+            puts "Could not find file #{file}"
+            return
+          end
+
+          load_models_from_csv(file)
+
+          while true
+            if @changeset && @errors.empty?
+              puts "File #{file} is well formatted.  Calculating expected changes..."
+              sync_workflow = workflow.plan_synchronization(@changeset, project_name, target_model)
+              models_and_action_types = sync_workflow.planned_actions.map { |a| Etna::Clients::Magma::ModelSynchronizationWorkflow.models_affected_by(a).map { |m| [m, a.action_name] }.flatten }
+              models_and_action_types.sort!
+              models_and_action_types = models_and_action_types.group_by(&:first)
+
+              models_and_action_types.each do |model, actions|
+                actions = actions.map { |a| a[1] }.sort
+                actions = actions.group_by { |v| v }
+                puts
+                puts "#{model} changes:"
+                actions.each do |type, actions|
+                  puts " * #{type}: #{actions.length}"
+                end
+              end
+
+              puts
+              puts "Would you like to execute?"
+              if confirm
+                sync_workflow.update_block = Proc.new do |action|
+                  puts "Executing #{action.action_name} on #{Etna::Clients::Magma::ModelSynchronizationWorkflow.models_affected_by(action)}..."
+                end
+
+                sync_workflow.execute_planned!
+                File.unlink(file)
+              end
+
+              return
+            end
+
+            # Poll for updates
+            puts "Watching for changes to #{file}..."
+            while File.stat(file).mtime == @last_load
+              sleep(1)
+            end
+
+            load_models_from_csv(file)
+          end
+        end
+
+        def workflow
+          @workflow ||= Etna::Clients::Magma::AddProjectModelsWorkflow.new(magma_client: magma_client)
+        end
+
+        def reset
+          @errors = []
+          @changeset = nil
+          @last_load = Time.at(0)
+        end
+
+        def load_models_from_csv(file)
+          reset
+
+          @last_load = File.stat(file).mtime
+          @changeset = File.open(file, 'r') do |f|
+            workflow.prepare_changeset_from_csv(f) do |err|
+              @errors << err
+            end
+          end
+
+          return if @errors.empty?
+
+          puts "Input file #{file} is invalid:"
+          @errors.each do |err|
+            puts "  * " + err.gsub("\n", "\n\t")
+          end
+        end
+      end
+
+      class Attributes
+        include Etna::CommandExecutor
+
+        class UpdateFromCsv < Etna::Command
+          include WithEtnaClients
+          include WithLogger
+          include RequireConfirmation
+
+          def magma_crud
+            @magma_crud ||= Etna::Clients::Magma::MagmaCrudWorkflow.new(
+                magma_client: magma_client,
+                project_name: @project_name)
+          end
+
+          def execute(project_name, model_name, filepath)
+            @project_name = project_name
+
+            update_attributes_workflow = Etna::Clients::Magma::UpdateAttributesFromCsvWorkflowSingleModel.new(
+                magma_crud: magma_crud,
+                project_name: project_name,
+                model_name: model_name,
+                filepath: filepath)
+            update_attributes_workflow.update_attributes
+          end
+        end
+      end
+    end
+  end
+
+  class Polyphemus < Etna::Command
+    include WithEtnaClients
+    string_flags << '--tag'
+    boolean_flags << '--local'
+
+    def execute(tag: nil, local: false)
+      @tag = tag || default_tag
+      @local = local
+      create_config_yml
+
+      unless @local
+        puts `docker pull #{image}`
+      end
+
+      puts run_cmd
+      exec(run_cmd)
+    end
+
+    def run_cmd
+      parts = ['docker run --rm -it']
+
+      unless Gem.win_platform?
+        uid = Etc.getpwnam(ENV['USER']).uid
+        gid = Etc.getgrnam('docker').gid
+        parts << "-u #{uid}:#{gid}"
+        parts << "-v /etc/passwd:/etc/passwd:ro"
+        parts << "-v /etc/group:/etc/group:ro"
+      end
+
+      parts << "-v #{temp_config_file.path}:/app/config.yml:ro"
+      parts << "-v #{Dir.pwd}:/app/workspace"
+      parts << "-e HOME=/root"
+
+      parts << image
+      parts << "bash -c 'cd /app/workspace && exec bash --rcfile /root/.bashrc'"
+
+      parts.join(' ')
+    end
+
+    def temp_config_file
+      @temp_config_file ||= Tempfile.new
+    end
+
+    def create_config_yml
+      host_config = [:metis, :magma, :janus, :timur].map do |host|
+        [host, (EtnaApp.instance.config(host) || {}).update(token: token)]
+      end.to_h
+
+      config = {
+          EtnaApp.instance.environment => {
+                                              log_file: '/dev/stdout',
+                                              log_level: 'info',
+                                          }.update(host_config)
+      }
+
+      File.open(temp_config_file.path, 'w') { |f| YAML.dump(config, f) }
+    end
+
+    def default_tag
+      docker = EtnaApp.instance.config(:docker)
+      if docker.nil?
+        nil
+      else
+        docker[:default_tag]
+      end || 'master'
+    end
+
+    def image
+      if @local
+        "polyphemus:#{@tag}"
+      else
+        "etnaagent/polyphemus:#{@tag}"
+      end
+    end
+  end
+
+  class Console < Etna::Command
+    usage 'Open a console with a connected Etna instance.'
+
+    def execute
+      require 'irb'
+      ARGV.clear
+      IRB.start
+    end
+
+    def setup(config)
+      super
+    end
+  end
+end