miga-base 0.7.9.0 → 0.7.12.1

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: ec59a539424db91f6744799ea022c1aa56c39123b4c43e19f1ce20b01954c16c90e481a4e062d3ed01d912f57eda4c29123047399041889ba1997a4eb839f94d

data/README.md

@@ -41,6 +41,7 @@ Developed and maintained by [Luis M. Rodriguez-R][lrr]. MiGA is the result of a
 collaboration between [Kostas Lab][kostas] at the Georgia Institute of
 Technology and [RDP][rdp] at Michigan State University.
 
+See also the [complete list of contributors](manual/part1/contributors.md).
 
 # License
 

data/lib/miga/cli/action/browse.rb

@@ -0,0 +1,213 @@
+# frozen_string_literal: true
+
+require 'miga/cli/action'
+
+# Action: miga browse
+class MiGA::Cli::Action::Browse < MiGA::Cli::Action
+  def parse_cli
+    cli.parse do |opt|
+      cli.defaults = { open: true }
+      cli.opt_object(opt, [:project])
+    end
+  end
+
+  def perform
+    p = cli.load_project
+    create_empty_page(p)
+    generate_project_page(p)
+    say 'Creating dataset pages'
+    cli.load_project.each_dataset do |d|
+      generate_dataset_page(p, d)
+    end
+    generate_datasets_index(p)
+    say "Open in your browser: #{File.join(p.path, 'index.html')}"
+  end
+
+  private
+
+  ##
+  # Create an empty page with necessary assets for project +p+
+  def create_empty_page(p)
+    say 'Creating project page'
+    FileUtils.mkdir_p(browse_file(p, '.'))
+    %w[favicon-32.png style.css].each do |i|
+      FileUtils.cp(template_file(i), browse_file(p, i))
+    end
+    write_file(p, 'about.html') do
+      build_from_template('about.html', citation: MiGA::MiGA.CITATION)
+    end
+  end
+
+  ##
+  # Create landing page for project +p+
+  def generate_project_page(p)
+    # Redirect page
+    write_file(p, '../index.html') { build_from_template('redirect.html') }
+
+    # Summaries
+    summaries = Dir["#{p.path}/*.tsv"].map do |i|
+      "<li><a href='file://#{i}'>#{File.basename(i)}</a></li>"
+    end.join('')
+
+    # Project index page
+    data = {
+      project_active: 'active',
+      information: format_metadata(p),
+      summaries: summaries.empty? ? 'None' : "<ul>#{summaries}</ul>",
+      results: format_results(p)
+    }
+    write_file(p, 'index.html') { build_from_template('index.html', data) }
+  end
+
+  ##
+  # Create page for dataset +d+ within project +p+
+  def generate_dataset_page(p, d)
+    data = {
+      unmiga_name: d.name.unmiga_name,
+      information: format_metadata(d),
+      results: format_results(d)
+    }
+    write_file(p, "d_#{d.name}.html") do
+      build_from_template('dataset.html', data)
+    end
+  end
+
+  ##
+  # Create pages for reference and query dataset indexes
+  def generate_datasets_index(p)
+    say 'Creating index pages'
+    data = format_dataset_index(p)
+    data.each do |k, v|
+      write_file(p, "#{k}_datasets.html") do
+        v[:list] = 'None' if v[:list] == ''
+        build_from_template(
+          'datasets.html',
+          v.merge(:"#{k}_datasets_active" => 'active')
+        )
+      end
+    end
+  end
+
+  def format_dataset_index(p)
+    data = {
+      ref: { type_name: 'Reference', list: '' },
+      qry: { type_name: 'Query', list: '' }
+    }
+    p.each_dataset do |d|
+      data[d.ref? ? :ref : :qry][:list] +=
+        "<li><a href='d_#{d.name}.html'>#{d.name.unmiga_name}</a></li>"
+    end
+    data
+  end
+
+  ##
+  # Format +obj+ metadata as a table
+  def format_metadata(obj)
+    '<table class="table table-sm table-responsive">' +
+      obj.metadata.data.map do |k, v|
+        case k
+        when /^run_/, :plugins, :user
+          next
+        when :web_assembly_gz
+          v = "<a href='#{v}'>#{v[0..50]}...</a>"
+        when :datasets
+          v = v.size
+        end
+        "<tr><td class='text-right pr-4'><b>#{format_name(k)}</b></td>" \
+             "<td>#{v}</td></tr>"
+      end.compact.join('') +
+      '</table>'
+  end
+
+  ##
+  # Format +obj+ results as cards
+  def format_results(obj)
+    o = ''
+    obj.each_result do |key, res|
+      links = format_result_links(res)
+      stats = format_result_stats(res)
+      next unless links || stats
+      name = format_name(key)
+      url_doc =
+        'http://manual.microbial-genomes.org/part5/workflow#' +
+        key.to_s.tr('_', '-')
+      o += <<~CARD
+        <div class="col-md-6 mb-4">
+          <h3>#{name}</h3>
+          <div class='border-left p-3'>
+            #{stats}
+            #{links}
+          </div>
+          <div class='border-top p-2 bg-light'>
+            <a target=_blank href="#{url_doc}" class='p-2'>Learn more</a>
+          </div>
+        </div>
+      CARD
+    end
+    "<div class='row'>#{o}</div>"
+  end
+
+  def format_name(str)
+    str
+      .to_s.unmiga_name
+      .sub(/^./, &:upcase)
+      .gsub(/(Aai|Ani|Ogs|Cds|Ssu| db$| ssu )/, &:upcase)
+      .sub(/Haai/, 'hAAI')
+      .sub(/Mytaxa/, 'MyTaxa')
+      .sub(/ pvalue$/, ' p-value')
+      .sub(/contigs$/, 'Contigs')
+  end
+
+  def format_result_links(res)
+    links = []
+    res.each_file do |key, _|
+      name = format_name(key)
+      links << "<a href='file://#{res.file_path(key)}'>#{name}</a><br/>"
+    end
+    links.empty? ? nil : links.join('')
+  end
+
+  def format_result_stats(res)
+    res.stats.map do |k, v|
+      v = [v, ''] unless v.is_a? Array
+      v[0] = ('%.3g' % v[0]) if v[0].is_a? Float
+      "<b>#{format_name(k)}:</b> #{v[0]}#{v[1]}<br/>"
+    end.join('') + '<br/>' unless res.stats.empty?
+  end
+
+  ##
+  # Write +file+ within the browse folder of project +p+ using the passed
+  # block output as content
+  def write_file(p, file)
+    File.open(browse_file(p, file), 'w') { |fh| fh.print yield }
+  end
+
+  ##
+  # Use a +template+ file to generate content with a hash of +data+ over the
+  # layout page if +layout+ is true
+  def build_from_template(template, data = {}, layout = true)
+    cont = File.read(template_file(template)).miga_variables(data)
+    return cont unless layout
+
+    build_from_template(
+      'layout.html',
+      data.merge(content: cont, project_name: cli.load_project.name),
+      false
+    )
+  end
+
+  ##
+  # Path to the template browse file
+  def template_file(file)
+    File.join(
+      MiGA::MiGA.root_path,
+      'lib', 'miga', 'cli', 'action', 'browse', file
+    )
+  end
+
+  ##
+  # Path to the browse file in the project
+  def browse_file(p, file)
+    File.join(p.path, 'browse', file)
+  end
+end

data/lib/miga/cli/action/browse/about.html

@@ -0,0 +1,31 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">About MiGA</h1>
+<p>
+MiGA is developed and maintained by
+<a href='https://rodriguez-r.com/'>Luis M. Rodriguez-R</a>.
+
+The MiGA codebase is
+<a href='http://code.microbial-genomes.org/miga'>freely available</a> under the
+terms of the terms of the
+<a href='http://code.microbial-genomes.org/miga/blob/master/LICENSE'>Artistic License 2.0</a>.
+</p>
+
+<p>
+MiGA is the result of a collaboration between the
+<a href='http://enve-omics.gatech.edu/'>Kostas Lab</a>
+(<a href='http://www.gatech.edu/'>Georgia Institute of Technology</a>) and the
+<a href='http://rdp.cme.msu.edu/'>RDP team</a>
+(<a href='http://cme.msu.edu/'>Center for Microbial Ecology</a>,
+<a href='https://msu.edu/'>Michigan State University</a>).
+The MiGA project is funded by the
+<a href='http://nsf.gov/'>US National Science Foundation</a>
+(Awards <a href='http://nsf.gov/awardsearch/showAward?AWD_ID=1356288'>#1356288</a> &amp;
+<a href='https://xras.xsede.org/public/requests/31162-XSEDE-MCB190042-1190572'>#MCB190042</a>).
+</p>
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Citation</h1>
+If you use MiGA in your work, consider citing:
+<blockquote class='border-left p-3'>
+{{citation}}
+</blockquote>
+
+

data/lib/miga/cli/action/browse/dataset.html

@@ -0,0 +1,5 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">{{unmiga_name}}</h1>
+{{information}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Results</h1>
+{{results}}

data/lib/miga/cli/action/browse/dataset_menu_item.html

@@ -0,0 +1,3 @@
+<li class="nav-item">
+  <a class="nav-link" href="ds_{{name}}.html">{{unmiga_name}}</a>
+</li>

data/lib/miga/cli/action/browse/datasets.html

@@ -0,0 +1,4 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">{{type_name}} Datasets</h1>
+<ul>
+  {{list}}
+</ul>

data/lib/miga/cli/action/browse/index.html

@@ -0,0 +1,8 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Project Information</h1>
+{{information}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Summaries</h1>
+{{summaries}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Project Results</h1>
+{{results}}

data/lib/miga/cli/action/browse/layout.html

@@ -0,0 +1,57 @@
+<!doctype html>
+<head>
+  <meta charset="utf-8">
+  <title>MiGA | {{project_name}}</title>
+
+  <!-- Remote assets -->
+  <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css" integrity="sha384-9aIt2nRpC12Uk9gS9baDl411NQApFmC26EwAOH8WgZl5MYYxFfc+NcPb1dKGj7Sk" crossorigin="anonymous">
+  <script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
+  <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js" integrity="sha384-OgVRvuATP1z7JjHLkuOU7Xw704+h835Lr+6QL9UvYjZE3Ipu6Tp75j7Bh/kR0JKI" crossorigin="anonymous"></script>
+
+  <!-- Local assets -->
+  <link href="style.css" rel="stylesheet">
+  <link rel="icon" href="favicon-32.png" sizes="32x32" type="image/png">
+</head>
+<body>
+  <nav class="navbar navbar-dark sticky-top bg-dark flex-md-nowrap p-0 shadow">
+    <a class="navbar-brand col-md-12 col-lg-12 mr-0 px-3"
+          href="index.html">MiGA | {{project_name}}</a>
+    <button class="navbar-toggler position-absolute d-md-none collapsed"
+          type="button" data-toggle="collapse" data-target="#sidebarMenu"
+          aria-controls="sidebarMenu" aria-expanded="false"
+          aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+  </nav>
+  <div class="container-fluid">
+  <div class="row">
+    <nav id="sidebarMenu" class="col-md-3 col-lg-2 d-md-block bg-light sidebar collapse">
+      <div class="sidebar-sticky pt-3">
+        <ul class="nav flex-column">
+          <li class="nav-item">
+            <a class="nav-link {{project_active}}" href="index.html">Project</a>
+          </li>
+          <li class="nav-item">
+            <a class="nav-link {{ref_datasets_active}}"
+                  href="ref_datasets.html">Reference datasets</a>
+          </li>
+          <li class="nav-item">
+            <a class="nav-link {{qry_datasets_active}}"
+                  href="qry_datasets.html">Query datasets</a>
+          </li>
+          <li class="nav-item border-top mt-4">
+            <a class="nav-link {{about_miga_active}}"
+                  href="about.html">About MiGA</a>
+          </li>
+        </ul>
+      </div>
+    </nav>
+
+    <main role="main" class="col-md-9 ml-sm-auto col-lg-10 px-md-4">
+      {{content}}
+    </main>
+  </div>
+</div>
+</body>
+

data/lib/miga/cli/action/browse/redirect.html

@@ -0,0 +1,11 @@
+<!doctype html>
+<head>
+  <title>MiGA Project</title>
+  <meta http-equiv = "refresh" content = "1; url = browse/index.html" />
+</head>
+<body>
+  <div style='font-size:200%; margin-top: 5em; text-align: center;'>
+    Redirecting to <a href='browse/index.html'>Project page</a>...
+  </div>
+</body>
+

data/lib/miga/cli/action/browse/style.css

@@ -0,0 +1,97 @@
+body {
+  font-size: .875rem;
+}
+
+/*
+ * Sidebar
+ */
+
+.sidebar {
+  position: fixed;
+  top: 0;
+  bottom: 0;
+  left: 0;
+  z-index: 100; /* Behind the navbar */
+  padding: 48px 0 0; /* Height of navbar */
+  box-shadow: inset -1px 0 0 rgba(0, 0, 0, .1);
+}
+
+@media (max-width: 767.98px) {
+  .sidebar {
+    top: 3rem;
+  }
+}
+
+.sidebar-sticky {
+  position: relative;
+  top: 0;
+  height: calc(100vh - 48px);
+  padding-top: .5rem;
+  overflow-x: hidden;
+  overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
+}
+
+@supports ((position: -webkit-sticky) or (position: sticky)) {
+  .sidebar-sticky {
+    position: -webkit-sticky;
+    position: sticky;
+  }
+}
+
+.sidebar .nav-link {
+  font-weight: 500;
+  color: #333;
+}
+
+.sidebar .nav-link .feather {
+  margin-right: 4px;
+  color: #999;
+}
+
+.sidebar .nav-link.active {
+  color: #007bff;
+}
+
+.sidebar .nav-link:hover .feather,
+.sidebar .nav-link.active .feather {
+  color: inherit;
+}
+
+.sidebar-heading {
+  font-size: .75rem;
+  text-transform: uppercase;
+}
+
+/*
+ * Navbar
+ */
+
+.navbar-brand {
+  padding-top: .75rem;
+  padding-bottom: .75rem;
+  font-size: 1rem;
+  background-color: rgba(0, 0, 0, .25);
+  box-shadow: inset -1px 0 0 rgba(0, 0, 0, .25);
+}
+
+.navbar .navbar-toggler {
+  top: .25rem;
+  right: 1rem;
+}
+
+.navbar .form-control {
+  padding: .75rem 1rem;
+  border-width: 0;
+  border-radius: 0;
+}
+
+.form-control-dark {
+  color: #fff;
+  background-color: rgba(255, 255, 255, .1);
+  border-color: rgba(255, 255, 255, .1);
+}
+
+.form-control-dark:focus {
+  border-color: transparent;
+  box-shadow: 0 0 0 3px rgba(255, 255, 255, .25);
+}