{%extends "populations/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}

{%block title%}Create Population{%endblock%}

{%block pagetitle%}Create Population{%endblock%}

{%block breadcrumbs%}
{{super()}}
<li class="breadcrumb-item">
  <a href="{{url_for('species.populations.create_population',
           species_id=species['SpeciesId'])}}">
    create population</a>
</li>
{%endblock%}


{%block contents%}
<div class="row">
  <p>The population is the next hierarchical node under Species. Data is grouped under a specific population, under a particular species.</p>
  <p>
    This page enables you to create a new population, in the case that you
    cannot find the population you want in the
    <a
      href="{{url_for('species.populations.list_species_populations',
            species_id=species.SpeciesId)}}"
      title="Population for species '{{species.FullName}}'.">
      list of species populations
    </a>
  </p>
</div>

<div class="row">
  <form method="POST"
        action="{{url_for('species.populations.create_population',
                species_id=species.SpeciesId,
                return_to=return_to)}}">

    <legend>Create Population</legend>

    {{flash_all_messages()}}

    <input type="hidden" name="return_to" value="{{return_to}}">

    <div {%if errors.population_fullname%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="txt-population-fullname" class="form-label">Full Name</label>
      {%if errors.population_fullname%}
      <small class="form-text text-danger">{{errors.population_fullname}}</small>
      {%endif%}
      <input type="text"
             id="txt-population-fullname"
             name="population_fullname"
             required="required"
             minLength="3"
             maxLength="100"
             value="{{error_values.population_fullname or ''}}"
             class="form-control" />
      <small class="form-text text-muted">
        <p>
          This is a descriptive name for your population &mdash; useful for
          humans.
        </p>
      </small>
    </div>

    <div {%if errors.population_name%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="txt-population-name" class="form-label">Name</label>
      {%if errors.population_name%}
      <small class="form-text text-danger">{{errors.population_name}}</small>
      {%endif%}
      <input type="text"
             id="txt-population-name"
             name="population_name"
             required="required"
             minLength="3"
             maxLength="30"
             value="{{error_values.population_name or ''}}"
             class="form-control" />
      <small class="form-text text-muted">
        <p>
          This is a short representative, but constrained name for your
          population.
          <br />
          The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens
          and underscores. Any other character will cause the name to be
          rejected.
        </p>
      </small>
    </div>

    <div class="form-group">
      <label for="txt-population-code" class="form-label">Population Code</label>
      <input type="text"
             id="txt-population-code"
             name="population_code"
             maxLength="5"
             minLength="3"
             value="{{error_values.population_code or ''}}"
             class="form-control" />
      <small class="form-text text-muted">
        <p class="form-text text-muted">
          This is a 3-character code for your population, that is prepended to
          the phenotype identifiers. e.g. For the "BXD Family" population, the
          code is "BXD" and therefore, the phenotype identifiers for the
          population look like the following examples: <em>BXD_10148</em>,
          <em>BXD_10180</em>, <em>BXD_10197</em>, etc.
        </p>
      </small>
    </div>

    <div {%if errors.population_description%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="txt-population-description" class="form-label">
        Description
      </label>
      {%if errors.population_description%}
      <small class="form-text text-danger">{{errors.population_description}}</small>
      {%endif%}
      <textarea
        id="txt-population-description"
        name="population_description"
        required="required"
        class="form-control"
        rows="5">{{error_values.population_description or ''}}</textarea>
      <small class="form-text text-muted">
        <p>
          This is a more detailed description for your population. This is
          useful to communicate with other researchers some details regarding
          your population, and what its about.
          <br />
          Put, here, anything that describes your population but does not go
          cleanly under metadata.
        </p>
      </small>
    </div>

    <div {%if errors.population_family%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="txt-population-family" class="form-label">Family</label>
      <input type="text"
             id="txt-population-family"
             name="population_family"
             class="form-control"
             list="families-list" />
      <datalist id="families-list">
        {%for family in families%}
        <option value="{{family}}">{{family}}</option>
        {%endfor%}
      </datalist>
      <small class="form-text text-muted">
        <p>
          This is <strong>optional</strong> metadata. It is used to group
          populations into "families" for presentation in the menus.
          {%if families | length > 0%}
          Examples of currently existing families are:
          <ul>
            {%for family in families[0:7]%}
            <li>{{family}}</li>
            {%endfor%}
            <li>etc.</li>
          </ul>
          {%endif%}

          You can
          {%if families|length>0%} select from existing families, or {%endif%}
          create a new family by typing in the input box above. You can also
          leave the family blank.</p>
      </small>
    </div>

    <div {%if errors.population_mapping_method_id%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="select-population-mapping-methods"
             class="form-label">Mapping Methods</label>

      <select id="select-population-mapping-methods"
              name="population_mapping_method_id"
              class="form-control"
              required="required">
        <option value="">Select appropriate mapping methods</option>
        {%for mmethod in mapping_methods%}
        <option value="{{mmethod.id}}"
                {%if error_values.population_mapping_method_id == mmethod.id%}
                selected="selected"
                {%endif%}>{{mmethod.value}}</option>
        {%endfor%}
      </select>

      <small class="form-text text-muted">
        <p>Select the mapping methods that your population will support.</p>
      </small>
    </div>

    <div {%if errors.population_genetic_type%}
         class="form-group has-error"
         {%else%}
         class="form-group"
         {%endif%}>
      <label for="select-population-genetic-type"
             class="form-label">Genetic Type</label>
      <select id="select-population-genetic-type"
              name="population_genetic_type"
              class="form-control">
        <option value="">Select proper genetic type</option>
        {%for gtype in genetic_types%}
        <option value="{{gtype}}"
                {%if error_values.population_genetic_type == gtype%}
                selected="selected"
                {%endif%}>{{gtype}}</option>
        {%endfor%}
      </select>
      <small class="form-text text-muted text-danger">
        <p>
          <span class="glyphicon glyphicon-exclamation-sign"></span>
          This might be a poorly named field.
        </p>
        <p>
          It probably has more to do with the mating crosses/crossings used to
          produce the individuals in the population. I am no biologist, however,
          and I'm leaving this here to remind myself to confirm this.
        </p>
        <p>
          I still don't know what riset is.<br />
          … probably something to do with Recombinant Inbred Strains
        </p>
        <p>
          Possible resources for this:
          <ul>
            <li>https://www.informatics.jax.org/silver/chapters/3-2.shtml</li>
            <li>https://www.informatics.jax.org/silver/chapters/9-2.shtml</li>
          </ul>
        </p>
      </small>
    </div>

    <div class="form-group">
      <input type="submit"
             value="create population"
             class="btn btn-primary"  />
    </div>

  </form>
</div>
{%endblock%}