sanger/sequencescape

<%# NOTE[xxx]: Kind of a hack because we need 'study[study_metadata_attributes][X]' -%>

<%= fields_for(study) do |form| %>
  <%= form.fields_for(:study_metadata, builder: Metadata::FormBuilder) do |metadata_fields| %>
    <%= metadata_fields.select_by_association(:faculty_sponsor)%>
    <%= metadata_fields.select_by_association(:program)%>
    <%= metadata_fields.text_field(:number_of_gigabases_per_sample) %>
    <%= metadata_fields.text_field(:prelim_id) %>

    <%= metadata_fields.select_by_association(:reference_genome, {}, { class: 'select2' }) %>

    <% metadata_fields.with_options(grouping: 'ENA requirement') do |group| %>
      <%= group.text_field(:study_study_title) %>
      <%= group.select_by_association(:study_type)%>
      <%= group.text_area(:study_description) %>
      <%= group.text_area(:study_abstract) %>
      <%= group.radio_select(:study_sra_hold, Study::STUDY_SRA_HOLDS) %>
    <% end %>

    <%= metadata_fields.radio_select(:contains_human_dna, Study::YES_OR_NO) %>
    <%= metadata_fields.radio_select(:contaminated_human_dna, Study::YES_OR_NO) %>
    <%= metadata_fields.radio_select(:commercially_available, Study::YES_OR_NO) %>
    <%= metadata_fields.radio_select(:remove_x_and_autosomes, Study::YES_OR_NO) %>
    <%= metadata_fields.check_box(:separate_y_chromosome_data) %>

    <%= metadata_fields.text_field(:study_project_id, grouping: 'SRA') %>
    <%= metadata_fields.text_field(:study_ebi_accession_number, grouping: 'SRA AN') %>
    <%= metadata_fields.text_field(:study_name_abbreviation) %>

    <%= metadata_fields.check_box(:bam) %>

    <% metadata_fields.with_options(grouping: 'Data Release') do |group| %>
      <%= metadata_fields.text_field(:data_access_group) %>
      <%= group.select_by_association(:data_release_study_type)%>
      <%= help_link 'Introduction to Accessioning', 'Accessioing', class: 'offset-md-2' %>
      <% strategies = Study::DATA_RELEASE_STRATEGIES.map { |s| [t(s.downcase.gsub(' ','_'),scope:'metadata.study.metadata.data_release_strategy.values'),s ] } %>
      <%= group.radio_select(:data_release_strategy, strategies) %>
      <% metadata_fields.related_fields(to: :data_release_strategy, when: Study::DATA_RELEASE_STRATEGY_MANAGED) do %>
        <%= group.radio_select(:data_release_standard_agreement, Study::YES_OR_NO) %>
        <% metadata_fields.related_fields(to: :data_release_standard_agreement, when: Study::NO) do %>
          <%= group.document_field(:data_release_non_standard_agreement) %>
        <% end %>
        <%= metadata_fields.text_field(:dac_policy_title) %>
        <%= metadata_fields.text_field(:dac_policy) %>
        <%= metadata_fields.text_field(:ega_dac_accession_number) %>
        <%= metadata_fields.text_field(:ega_policy_accession_number) %>
        <%= metadata_fields.text_field(:array_express_accession_number) if study.for_array_express? %>
      <% end %>

      <%= metadata_fields.text_field :hmdmc_approval_number %>

      <%= metadata_fields.select(:data_release_timing, Study::DATA_RELEASE_TIMINGS + [ Study::DATA_RELEASE_TIMING_NEVER ]) %>
      <%
        metadata_fields.change_select_options_for(:data_release_timing, when: :data_release_strategy, values: {
          Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE                                    => Study::DATA_RELEASE_TIMING_NEVER,
          (Study::DATA_RELEASE_STRATEGIES-[Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE]) => Study::DATA_RELEASE_TIMINGS
        })
      %>

      <% metadata_fields.related_fields(to: :data_release_strategy, when: Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE) do %>
        <%= group.select(:data_release_prevention_reason, Study::DATA_RELEASE_PREVENTION_REASONS) %>
        <%= group.radio_select(:data_release_prevention_approval, Study::YES_OR_NO) %>
        <%= group.text_area(:data_release_prevention_reason_comment) %>
      <% end %>
      <% metadata_fields.related_fields(to: :data_release_strategy, in: Study::DATA_RELEASE_STRATEGIES, not: Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE) do %>
        <% metadata_fields.related_fields(to: :data_release_timing, when: Study::DATA_RELEASE_TIMING_DELAYED) do %>
          <%= group.select(:data_release_delay_reason, Study::DATA_RELEASE_DELAY_REASONS_STANDARD) %>
          <%
            group.change_select_options_for(:data_release_delay_reason, when: :data_release_study_type_id, values: {
              DataReleaseStudyType.assay_types.map(&:id)     => [ '' ] + Study::DATA_RELEASE_DELAY_REASONS_ASSAY,
              DataReleaseStudyType.non_assay_types.map(&:id) => [ '' ] + Study::DATA_RELEASE_DELAY_REASONS_STANDARD
            })
          %>

          <%= group.select(:data_release_delay_period, Study::DATA_RELEASE_DELAY_PERIODS) %>
          <% metadata_fields.related_fields(to: :data_release_delay_period, in: Study::DATA_RELEASE_DELAY_PERIODS) do %>
              <%= group.radio_select(:data_release_delay_approval, Study::YES_OR_NO) %>
            <% end %>
          <% metadata_fields.related_fields(to: :data_release_delay_reason, when: Study::DATA_RELEASE_DELAY_FOR_OTHER) do %>
            <%= group.text_area(:data_release_delay_other_comment) %>
            <% metadata_fields.related_fields(to: :data_release_delay_period, in: Study::DATA_RELEASE_DELAY_PERIODS) do %>
              <%= group.text_area(:data_release_delay_reason_comment) %>
            <% end %>
          <% end %>
        <% end %>
      <% end %>
    <% end %>

    <%= metadata_fields.text_field(:s3_email_list) %>
    <%= metadata_fields.select(:data_deletion_period, ['','3 months']) %>
    <%= metadata_fields.text_field(:contaminated_human_data_access_group) %>

    <% metadata_fields.finalize_related_fields %>
  <% end %>
<% end %>