mumuki-r-runner 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 16dac79ec3a5bf8a0f39be4ea303b2a2ce76c6e880740ce6506b0f7d34900cd8
+  data.tar.gz: 61edafb16a21bbf9f4e8c205dd12aa563512c0a1d1006f710f6c19d50d1595ac
+SHA512:
+  metadata.gz: b3994020d6d9e97170d7735d7d79c135f32527d2b77d10113a5026d531dd35f5087d7eff923717d85598a46d688e6c73a4468a957428954316f8beaa7730fda5
+  data.tar.gz: 6dddb828be0def8f2f9d65a3c152d4be2c6f8cc2e26526b894dbffd4eab117d216514e39b27a4e555b54eba4b67125f9b39d032423006f78ede02a611f2a5987

data/lib/metadata_hook.rb

@@ -0,0 +1,24 @@
+class RMetadataHook < Mumukit::Hook
+  def metadata
+    {language: {
+        name: 'r',
+        icon: {type: 'devicon', name: 'r'},
+        version: '3.6.1',
+        extension: 'R',
+        ace_mode: 'R'
+    },
+     test_framework: {
+         name: 'testthat',
+         version: '2.3.1', # FIXME fix version using devtools
+         test_extension: '.R',
+         template: <<R
+test_that("{{ test_template_sample_description }}", {
+  expect_true( TRUE )
+})
+R
+     }}
+  end
+end
+
+
+

data/lib/query_hook.rb

@@ -0,0 +1,48 @@
+class RQueryHook < Mumukit::Templates::FileHook
+  with_error_patterns
+  isolated true
+
+  def tempfile_extension
+    '.R'
+  end
+
+  def compile_file_content(r)
+    "#{compile_file_header(r)}\n#{compile_query(r.query)}"
+  end
+
+  def compile_file_header(r)
+<<R
+#{r.extra}
+
+#{r.content}
+
+#{compile_cookie(r.cookie)}
+R
+  end
+
+  def compile_query(query)
+    query
+  end
+
+  def compile_cookie(cookie)
+    return if cookie.blank?
+
+    compile_statements(cookie).join "\n"
+  end
+
+  def command_line(filename)
+    "Rscript #{filename}"
+  end
+
+  private
+
+  def compile_statements(cookie)
+    cookie.map { |query| "invisible(tryCatch({ #{query} }, error = function(e) {}))" }
+  end
+
+  def error_patterns
+    [
+      Mumukit::ErrorPattern::Errored.new(/(?=Execution halted\n$)/)
+    ]
+  end
+end

data/lib/r_runner.rb

@@ -0,0 +1,15 @@
+require 'mumukit'
+require 'nokogiri'
+
+Mumukit.runner_name = 'r'
+Mumukit.configure do |config|
+  config.docker_image = 'mumuki/mumuki-r-worker:0.1'
+  config.structured = true
+  config.stateful = true
+end
+
+require_relative './version'
+require_relative './metadata_hook'
+require_relative './test_hook'
+require_relative './query_hook'
+require_relative './try_hook'

data/lib/test_hook.rb

@@ -0,0 +1,48 @@
+class RTestHook < Mumukit::Templates::FileHook
+  isolated true
+  structured true
+
+  def compile_file_content(request)
+<<R
+#{request.extra}
+#{request.content}
+#{request.test}
+R
+  end
+
+  def tempfile_extension
+    '.R'
+  end
+
+  def command_line(filename)
+    %Q{R -q -e testthat::test_file('#{filename}',reporter='junit')} #TODO use
+  end
+
+  def post_process_file(file, result, status)
+    if status.failed?
+      [result, :errored]
+    else
+      super
+    end
+  end
+
+  def to_structured_result(result)
+    clean_xml = result.gsub(/^>.+$/, '')
+    transform(Nokogiri::XML(clean_xml).xpath('//testcase'))
+  end
+
+  def transform(examples)
+    examples.map do |it|
+      failure = it.at('failure', 'error')
+      if failure
+        [it['name'].gsub('_', ' '), :failed, failure.content]
+      else
+        [it['name'].gsub('_', ' '), :passed, '']
+      end
+    end
+  end
+
+  def cleanup_raw_result(result)
+    super(result.gsub 'tmpmumuki', '/tmp/mumuki')
+  end
+end

data/lib/try_hook.rb

@@ -0,0 +1,47 @@
+class RTryHook < Mumukit::Templates::TryHook
+  isolated true
+  attr_reader :query_hook
+
+  def initialize(config = nil)
+    super config
+    @query_hook = RQueryHook.new
+  end
+
+  def compile_file_content(r)
+    <<R
+#{@query_hook.compile_file_header(r)}
+cat("#{query_separator}", fill = TRUE);
+#{@query_hook.compile_query(r.query)}
+cat("#{goal_separator}", fill = TRUE);
+#{@query_hook.compile_query(r.goal.with_indifferent_access[:query] || 'NULL')}
+R
+  end
+
+  delegate :tempfile_extension, to: :query_hook
+  delegate :command_line, to: :query_hook
+
+  def query_separator
+    '!!!MUMUKI-QUERY-START!!!'
+  end
+
+  def goal_separator
+    '!!!MUMUKI-GOAL-START!!!'
+  end
+
+  def to_structured_results(_file, result, status)
+    /#{query_separator}
+?(.*)
+#{goal_separator}
+?(.*)
+/m =~ result
+    {
+        query: to_query_result($1, status),
+        goal: $2,
+        status: status
+    }
+  end
+
+  def to_query_result(result, status)
+    { result: result, status: status }
+  end
+end

data/lib/version.rb

@@ -0,0 +1,3 @@
+module RVersionHook
+  VERSION = '0.1.0'
+end

metadata

@@ -0,0 +1,133 @@
+--- !ruby/object:Gem::Specification
+name: mumuki-r-runner
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Franco Leonardo Bulgarelli
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-02-06 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mumukit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.30'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.30'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.4'
+- !ruby/object:Gem::Dependency
+  name: codeclimate-test-reporter
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: mumukit-bridge
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+description: 
+email:
+- franco@mumuki.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/metadata_hook.rb
+- lib/query_hook.rb
+- lib/r_runner.rb
+- lib/test_hook.rb
+- lib/try_hook.rb
+- lib/version.rb
+homepage: http://github.com/mumuki/mumuki-r-runner
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.3
+signing_key: 
+specification_version: 4
+summary: R Runner for Mumuki
+test_files: []