BioDSL 1.0.0

data/test/helper.rb

@@ -0,0 +1,82 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program is distributed in the hope that it will be useful,                #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
+# GNU General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of the BioDSL framework (www.BioDSL.org).          #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'simplecov'
+
+if ENV['SIMPLECOV']
+  SimpleCov.start do
+    add_filter "/test/"
+  end
+
+  SimpleCov.command_name 'test:units'
+end
+
+require 'pp'
+require 'tempfile'
+require 'fileutils'
+require 'BioDSL'
+require 'test/unit'
+require 'mocha/test_unit'
+
+ENV['BP_TEST'] = "true"
+
+module Kernel
+  def capture_stdout
+    out = StringIO.new
+    $stdout = out
+    yield
+    return out.string
+  ensure
+    $stdout = STDOUT
+  end
+
+  def capture_stderr
+    out = StringIO.new
+    $stderr = out
+    yield
+    return out.string
+  ensure
+    $stderr = STDERR
+  end
+end
+
+class Test::Unit::TestCase
+  # Ruby 2.2 have omit, < 2.2 have skip
+  alias :omit :skip if ! self.instance_methods.include? :omit
+
+  def self.test(desc, &impl)
+    define_method("test #{desc}", &impl)
+  end
+
+  def collect_result
+    @input2.each_with_object('') { |e, a| a << "#{e}#{$/}" }
+  end
+
+  def collect_sorted_result
+    @input2.sort_by { |a| a.to_s }.
+      each_with_object('') { |e, a| a << "#{e}#{$/}" }
+  end
+end

data/www/command.html.haml

@@ -0,0 +1,14 @@
+.section
+  %a{:name => "#{command.name}#{index}"}
+  %h2
+    Command: #{command.name}
+    %a{:href => help_url(command.name), :title => "Click for help on #{command.name}", :target => "_blank"} ?
+  %p.command #{command.to_s}
+  = render_status command
+  = render_time command.status
+  - if input? command.options
+    = render_input_files command.options
+  - if output? command.options
+    = render_output_files command.options
+  - if png? command.options
+    = render_png command.options

data/www/css.html.haml

@@ -0,0 +1,55 @@
+:css
+  .center {
+    text-align: center;
+  }
+
+  .right {
+    text-align: right;
+  }
+
+  .left {
+    text-align: left;
+  }
+
+  .bold {
+    font-weight: bold;
+  }
+
+  img {
+    display: block;
+    margin-left: auto;
+    margin-right: auto;
+  }
+
+  table {
+    border-collapse: collapse;
+  }
+
+  th {
+    padding-left: 10px;
+    padding-right: 10px;
+  }
+
+  td {
+    padding-left: 10px;
+    padding-right: 10px;
+  }
+
+  body {
+    font-family: Arial, Helvetica, Verdana, sans-serif;
+    min-width: 1000px;
+    margin-left: 10%;
+    margin-right: 10%;
+  }
+
+  .section {
+    padding-bottom: 1em;
+    border-bottom: 2px solid #ccc;
+  }
+
+  .command {
+    font-family: Courier, monospace, sans-serif;
+    border: 1px solid black;
+    padding: 1em;
+    white-space: pre;
+  }

data/www/input_files.html.haml

@@ -0,0 +1,3 @@
+%h3 Input
+- files.each do |file|
+  %p #{file}

data/www/layout.html.haml

@@ -0,0 +1,12 @@
+!!!
+%head
+  %title BioDSL report
+  = render_css
+%body
+  %h1.center BioDSL report
+  %p.center.bold Version #{BioDSL::VERSION}
+  %p.center.bold Generated #{Time.now}
+  = render_pipeline pipeline
+  = render_overview commands
+  - commands.each_with_index do |command, i|
+    = render_command command, i

data/www/output_files.html.haml

@@ -0,0 +1,3 @@
+%h3 Output
+%p
+  %a{:href => options[:output].split('/').last} #{options[:output].split('/').last}

data/www/overview.html.haml

@@ -0,0 +1,15 @@
+.section
+  %h2 Overview
+  %table
+    %tr.left
+      %th.bold Command
+      %th.bold Records in
+      %th.bold Records out
+      %th.bold Time elapsed
+    - commands.each_with_index do |command, i|
+      %tr
+        %td
+          %a{:href => "##{command.name}#{i}"} #{command.name}
+        %td.right #{command.status[:records_in].commify}
+        %td.right #{command.status[:records_out].commify}
+        %td.right #{command.status[:time_elapsed]}

data/www/pipeline.html.haml

@@ -0,0 +1,4 @@
+.section
+  %h2 Pipeline
+  .command
+    = pipeline

data/www/png.html.haml

@@ -0,0 +1,2 @@
+%p
+  %img{:src => png_data}/

data/www/status.html.haml

@@ -0,0 +1,9 @@
+%h3 Status: #{exit_status}
+%table
+  - statsus.each do |key, val|
+    %tr
+      %td.bold #{key}
+      - if val.is_a? Numeric
+        %td.right #{val.commify}
+      - else
+        %td.right #{val}

data/www/time.html.haml

@@ -0,0 +1,11 @@
+%h3 Time
+%table
+  %tr
+    %td.bold Time start
+    %td.right #{status[:time_start]}
+  %tr
+    %td.bold Time stop
+    %td.right #{status[:time_stop]}
+  %tr
+    %td.bold Time elapsed:
+    %td.right #{status[:time_elapsed]}