sanger/sequencescape

<%# NOTE[xxx]: Kind of a hack because we need 'sample[sample_metadata_attributes][X]' -%>
<%= fields_for(sample) do |form| %>
  <%= form.fields_for(:sample_metadata, builder: Metadata::FormBuilder) do |metadata_fields| %>

    <%= metadata_fields.select(:consent_withdrawn, [['Yes', true], ['No', false]]) %>

    <%# Fields for 'Microarray genotyping' %>
    <%= metadata_fields.text_field(:cohort) %>
    <%= metadata_fields.select(:gender, Sample::GENDERS,include_blank: true) %>
    <%= metadata_fields.select(:country_of_origin, Insdc::Country.options) %>
    <%= metadata_fields.text_field(:geographical_region) %>
    <%= metadata_fields.text_field(:ethnicity) %>
    <%= metadata_fields.select(:dna_source, Sample::DNA_SOURCES,include_blank: true) %>
    <%= metadata_fields.text_field(:volume) %>
    <%= metadata_fields.text_field(:mother) %>
    <%= metadata_fields.text_field(:father) %>
    <%= metadata_fields.text_field(:replicate) %>

    <%# Fields for 'Next-gen sequencing' %>
    <%= metadata_fields.text_field(:organism) %>
    <%= metadata_fields.select(:gc_content, Sample::GC_CONTENTS,include_blank: true) %>

    <%# Fields for the SLF pipeline, by the looks of it %>
    <%= metadata_fields.text_field(:sibling) %>
    <%= metadata_fields.text_field(:is_resubmitted) %>
    <%= metadata_fields.text_field(:date_of_sample_collection) %>
    <%= metadata_fields.text_field(:date_of_sample_extraction) %>
    <%= metadata_fields.text_field(:sample_extraction_method) %>
    <%= metadata_fields.text_field(:sample_purified) %>
    <%= metadata_fields.text_field(:purification_method) %>
    <%= metadata_fields.text_field(:concentration) %>
    <%= metadata_fields.text_field(:concentration_determined_by) %>
    <%= metadata_fields.text_field(:sample_type) %>

    <!-- SRA -->
    <% metadata_fields.with_options(grouping: 'SRA') do |group| %>
      <%= group.text_field(:sample_public_name) %>
    <% end %>

    <!-- ENA requirement -->
    <% metadata_fields.with_options(grouping: 'ENA requirement') do |group| %>
      <%= group.select(:sample_sra_hold, Sample::SRA_HOLD_VALUES,include_blank: true) %>
      <%= group.text_field(:sample_common_name, 'data-organism' => 'common_name') %>
      <input class='btn btn-default validate_organism' type='button' value='Lookup'/>
      <%= group.text_field(:sample_taxon_id,    'data-organism' => 'taxon_id') %>
    <% end %>

    <!-- SRA attributes -->
    <% metadata_fields.with_options(grouping: 'SRA attributes') do |group| %>
      <%= group.text_field(:sample_strain_att) %>
      <%= group.text_field(:sample_description) %>
    <% end %>

    <!-- SRA Sample AN -->
    <% metadata_fields.with_options(grouping: 'SRA Sample AN') do |group| %>
      <%= group.text_field(:sample_ebi_accession_number) %>
    <% end %>

    <%= metadata_fields.select_by_association(:reference_genome)%>

    <!-- array express field -->
    <%= metadata_fields.text_field(:genotype) %>
    <%= metadata_fields.text_field(:phenotype) %>
    <%= metadata_fields.text_field(:age) %>
    <%= metadata_fields.text_field(:developmental_stage) %>
    <%= metadata_fields.text_field(:cell_type) %>
    <%= metadata_fields.text_field(:disease_state) %>
    <%= metadata_fields.text_field(:compound) %>
    <%= metadata_fields.text_field(:dose) %>
    <%= metadata_fields.text_field(:immunoprecipitate) %>
    <%= metadata_fields.text_field(:growth_condition) %>
    <%= metadata_fields.text_field(:rnai) %>
    <%= metadata_fields.text_field(:organism_part) %>
    <%= metadata_fields.text_field(:time_point) %>

    <!-- EGA field -->
    <%= metadata_fields.text_field(:subject) %>
    <%= metadata_fields.text_field(:donor_id) %>
    <%= metadata_fields.text_field(:disease) %>
    <%= metadata_fields.text_field(:treatment)%>

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

<%= organism_validation_javascript %>