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

{%block title%}Upload R/qtl2 Bundle{%endblock%}

{%block contents%}
<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>

<div class="explainer">
  <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
    file(s). This data needs to be organised under a dataset.</p>
  <p>This page gives you the ability to do that.</p>
</div>

{{flash_all_messages()}}

{%if datasets | length > 0%}
<form method="POST"
      action="{{url_for('upload.rqtl2.select_probeset_dataset',
	      species_id=species.SpeciesId, population_id=population.Id)}}"
      id="frm:select-probeset-dataset">
  <legend class="heading">Select from existing ProbeSet datasets</legend>

  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
  <input type="hidden" name="population_id"
	 value="{{population.InbredSetId}}" />
  <input type="hidden" name="rqtl2_bundle_file"
	 value="{{rqtl2_bundle_file}}" />
  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
  <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />

  <fieldset>
    <label for="select:probe-dataset">Dataset</label>
    <select id="select:probe-dataset"
	    name="probe-dataset-id"
	    required="required"
	    {%if datasets | length == 0%}disabled="disabled"{%endif%}>
      <option value="">Select a dataset</option>
      {%for dataset in datasets%}
      <option value={{dataset.Id}}>
	{{dataset.Name}}
	{%if dataset.FullName%}
	 -- ({{dataset.FullName}})
	{%endif%}
      </option>
      {%endfor%}
    </select>

    <span class="form-col-2">Select from existing ProbeSet datasets.</span>
  </fieldset>

  <fieldset>
    <input type="submit"
	   value="select dataset"
	   class="btn btn-main form-col-2" />
  </fieldset>
</form>

<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
{%endif%}

<div class="explainer">
  <p>Create an entirely new ProbeSet dataset for your data.</p>
</div>

<form method="POST"
      action="{{url_for('upload.rqtl2.create_probeset_dataset',
	      species_id=species.SpeciesId, population_id=population.Id)}}"
      id="frm:create-probeset-dataset">
  <legend class="heading">Create a new ProbeSet dataset</legend>

  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
  <input type="hidden" name="population_id"
	 value="{{population.InbredSetId}}" />
  <input type="hidden" name="rqtl2_bundle_file"
	 value="{{rqtl2_bundle_file}}" />
  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
  <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />

  <fieldset>
    <label for="select:average">averaging method</label>
    <select id="select:average"
	    name="averageid"
	    required="required">
      <option value="">Select averaging method</option>
      {%for avgmethod in avgmethods%}
      <option value="{{avgmethod.Id}}">
	{{avgmethod.Name}}
	{%if avgmethod.Normalization%}
	({{avgmethod.Normalization}})
	{%endif%}
      </option>
      {%endfor%}
    </select>

    <span class="form-col-2">
      Select the averaging method used for your data.
    </span>
  </fieldset>

  <fieldset>
    <label for="txt:datasetname">Name</label>
    <input type="text" id="txt:datasetname" name="datasetname"
	   required="required"
	   title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" />

    <span class="form-col-2">
      Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
      is mandatory <strong>MUST</strong> be provided.
    </span>
  </fieldset>

  <fieldset>
    <label for="txt:datasetfullname">Full Name</label>
    <input type="text" id="txt:datasetfullname" name="datasetfullname"
	   required="required"
	   title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" />

    <span class="form-col-2">
      Provide a longer, more descriptive name for the dataset e.g.
      "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
      <strong>MUST</strong> be provided.
    </span>
  </fieldset>

  <fieldset>
    <label for="txt:datasetshortname">Short Name</label>
    <input type="text" id="txt:datasetshortname" name="datasetshortname"
	   title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" />

    <span class="form-col-2">
      Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
      This is optional.
    </span>
  </fieldset>

  <fieldset>
    <input type="checkbox" id="chk:public" name="datasetpublic"
	   checked="checked"
	   title="Whether or not the dataset is accessible by the general public." />
    <label for="chk:datasetpublic">Public?</label>

    <span class="form-col-2">
      Check to specify that the dataset will be publicly available. Uncheck to
      limit access to the dataset.
    </span>
  </fieldset>

  <fieldset>
    <label for="select:datasetdatascale">Data Scale</label>
    <select id="select:datasetdatascale"
	    name="datasetdatascale"
	    required="required">
      <option value="log2" selected="selected">log2</option>
      <option value="z_score">z_score</option>
      <option value="log2_ratio">log2_ratio</option>
      <option value="linear">linear</option>
      <option value="linear_positive">linear_positive</option>
    </select>

    <span class="form-col-2">
      Select from a list of scaling methods.
    </span>
  </fieldset>

  <fieldset>
    <input type="submit"
	   value="create dataset"
	   class="btn btn-main form-col-2" />
  </fieldset>
</form>

{%endblock%}