bio-miga/miga-web

<% @reference ||= false %>
<% form_opts = { html: { multipart: true}, method: :post } %>
<% form_opts[:url] = project_create_reference_url(@project) if @reference %>
<%= form_for(@query_dataset, form_opts) do |f| %>
  <% if (@bad_objects || []).empty? %>
    <%= render 'shared/error_messages', object: f.object %>
  <% else %>
    <div class="alert alert-danger">
      <%= pluralize(@bad_objects.size, 'datasets') %> couldn't be saved:
      <ul>
        <% @bad_objects.each do |i| %>
          <li>
            <b><%= i.name %></b>:
            <%= i.errors.full_messages.to_sentence %>
          </li>
        <% end %>
      </ul>
    </div>
  <% end %>

  <% if current_user.nil? %>
    <div class="alert alert-info">
      You're currently not logged in, your analyses will be anonymous.
      Remember to store or bookmark the URL of the results page for your
      new dataset.
    </div>
    <%= f.hidden_field :user_id, value: 0 %>
  <% else %>
    <%= f.hidden_field :user_id, value: current_user.id %>
  <% end %>
  <%= f.hidden_field :project_id, value: @project.id %>

  <%= label_tag :type, 'Type of dataset' %>
  <%= select_tag(:type,
    options_for_select(
      MiGA::Dataset.KNOWN_TYPES.
        map{ |k,t|
          [
            k.to_s.capitalize + ': ' + t[:description].sub(/\.$/,''), k
          ] if @project.miga.is_multi? or !t[:multi]
        }.compact ), class: 'form-control') %>

  <%= f.label :input_type, 'Type of input' %>
  <%= f.collection_select(:input_type,
    { assembly: 'Assembly in FastA format',
      raw_reads: 'Raw reads in FastQ format',
      trimmed_fasta: 'Trimmed reads in FastA format' },
    :first, :last, {}, class: 'form-control') %>

  <div id='asm_files_fields'>
    <%= label_tag :asm_file, 'Assemblies (contigs or scaffolds)' %>
    <%= file_field_tag :asm_file, class: 'form-control',
      multiple: !current_user.nil?, name: 'asm_file[]' %>
    <p class=help-block>
      <%= current_user.nil? ?
        'Anonymous uploads only support 1 file at a time' :
        'Multiple selection allowed' %><br/>
      GZ compression supported (with .gz extension)
    </p>

    <ul class='list-group' id='asm_files_well'>
    </ul>
  </div>

  <div id='reads_files_fields'>
    <%= f.label :input_file, 'Forward or unpaired reads' %>
    <%= f.file_field :input_file, class: 'form-control' %>
    <p class=help-block>GZ compression supported (with .gz extension)</p>

    <%= f.label :input_file, 'Reverse reads (optional)' %>
    <%= f.file_field :input_file_2, class: 'form-control' %>
    <p class=help-block>GZ compression supported (with .gz extension)</p>

    <%= f.label :name %>
    <%= f.text_field :name, class: "form-control" %>
    <p class=help-block>Dataset names can only contain alphanumerics and
      underscores</p>

    <hr/>
    <h1>Optional information</h1>
    <%= label_tag :description, "Description" %>
    <%= text_field_tag :description, "", class: "form-control" %>

    <%= label_tag :comments, "Comments" %>
    <%= text_area_tag :comments, "", class: "form-control" %>
  </div>

  <hr/>
  <div class='alert alert-info'>
    <h3>Data privacy</h3>
    We intend to keep your data private, but your data may be subject to
    public disclosure due to security issues, programming error, human
    error, or other reasons. Please keep an up-to-date offline backup of
    your data at all times.
  </div>

  <%= f.submit 'Upload new dataset', class: "btn btn-primary" %>
<% end %>

<script>
  var max_upload_files = <%= current_user.nil? ? 1 : Settings.max_user_upload %>;
  function set_form_fields(speed){
    var input_type = $('#query_dataset_input_type').find(':selected').val();
    $('#query_dataset_input_file').val(null)
    $('#query_dataset_input_file_2').val(null)
    $('#asm_file').val(null)
    if(input_type == 'assembly'){
      $('#query_dataset_name').val(null);
      $('input[name=commit]').attr('disabled', true);
      $('#reads_files_fields').hide(speed);
      $('#asm_files_fields').show(speed);
    } else {
      $('input[name=commit]').removeAttr('disabled');
      $('#reads_files_fields').show(speed);
      $('#asm_files_fields').hide(speed);
    }
  }
  $('#query_dataset_input_type').change(function(){set_form_fields('medium');});
  set_form_fields(0);

  function asm_file_processing(){
    var files = $('#asm_file')[0].files;
    var well = $('#asm_files_well');
    var valid_ext = /\.(fa|fas|fasta|fna|txt)(\.gz)?$/
    var has_errors = false;
    well.html('');
    if(files.length > max_upload_files){
      alert('The maximum number of files allowed is ' + max_upload_files);
      return;
    }
    for(var i = 0; i < files.length; ++i){
      var file = files[i].name;
      if(file.match(valid_ext)){
        var size = files[i].size;
        if(size > 1024 * 1024){
          size = '' + Math.round(size/1024/1024) + ' Mb';
        }else if(size > 1024){
          size = '' + Math.round(size/1024) + ' Kb';
        }else{
          size = '' + size + ' b'
        }
        var miga_name = file.replace(valid_ext,'').replace(/[^A-Z0-9]/gi, '_').
          replace(/_(All|Large)?Contigs$/, '');
        well.append(
          '<li class="list-group-item">' +
            '<h2>' + file + ' (' + size + ')</h2> ' +
            '<label for="asm_name_' + i + '">Name</label> ' +
            '<input class="form-control" type="text" ' +
              'value="' + miga_name + '" name="asm_name[]" ' +
              'id="asm_name_' + i + '" />' +
            '<p class=help-block>Dataset names can only contain ' +
              'alphanumerics and underscores</p>' +
            '<label for="asm_description_' + i +
              '">Description (optional)</label> ' +
            '<input class="form-control" type="text" value="" ' +
              'name="asm_description[]" id="asm_description_' + i + '" />' +
            '<label for="asm_comments_' + i + '">Comments (optional)</label> ' +
            '<textarea class="form-control" ' +
              'name="asm_comments[]" id="asm_comments_' + i + '"></textarea>' +
          '</li>');
      }else{
        has_errors = true;
        break;
      }
    }
    if(files.length == 0){
      // Do nothing
    }if(has_errors){
      well.html('<div class="alert alert-danger">Unrecognized file: ' + file +
        '<br/>Supported extensions: .fa, .fas, .fasta, .fna, .txt</div>');
    }else{
      $('input[name=commit]').removeAttr('disabled');
    }
  }
  $('#asm_file').change(asm_file_processing);
</script>