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

{%block title%}Data Upload{%endblock%}

{%block contents%}
<div class="row">
  <h1 class="heading">data upload</h1>

  <div class="explainer">
    <p>Each of the sections below gives you a different option for data upload.
      Please read the documentation for each section carefully to understand what
      each section is about.</p>
  </div>
</div>

<div class="row">
  <h2 class="heading">R/qtl2 Bundles</h2>

  <div class="explainer">
    <p>This feature combines and extends the two upload methods below. Instead of
      uploading one item at a time, the R/qtl2 bundle you upload can contain both
      the genotypes data (samples/individuals/cases and their data) and the
      expression data.</p>
    <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
      of the methods below can handle.</p>

    <a href={{url_for("upload.rqtl2.select_species")}}
       title="Upload a zip bundle of R/qtl2 files">
      <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
  </div>
</div>


<div class="row">
  <h2 class="heading">Expression Data</h2>

  <div class="explainer">
    <p>This feature enables you to upload expression data. It expects the data to
      be in <strong>tab-separated values (TSV)</strong> files. The data should be
      a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
      list of the <em>phenotypes</em> and the first row is a list of
      <em>samples/cases</em>.</p>

    <p>If you haven't done so please go to this page to learn the requirements for
      file formats and helpful suggestions to enter your data in a fast and easy
      way.</p>

    <ol>
      <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
        with our system requirements. (
        <a href="{{url_for('entry.data_review')}}#data-concerns"
	   title="Details for the data expectations.">Help</a>
        )</li>
      <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
        <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
        files (<a href="{{url_for('entry.data_review')}}#file-types"
	          title="Details for the data expectations.">Help</a>)</li>
    </ol>
  </div>

  <form action="{{url_for('entry.upload_file')}}"
        method="POST"
        enctype="multipart/form-data"
        id="frm-upload-expression-data">
    <legend class="heading">upload expression data</legend>
    {{flash_messages("error-expr-data")}}

    <div class="form-group">
      <label for="select_species01" class="form-label">Species</label>
      <select id="select_species01"
	      name="speciesid"
	      required="required"
              class="form-control">
        <option value="">Select species</option>
        {%for aspecies in species%}
        <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
        {%endfor%}
      </select>
    </div>

    <div class="form-group">
      <legend class="heading">file type</legend>

      <div class="form-check">
        <input type="radio" name="filetype" value="average" id="filetype_average"
	       required="required" class="form-check-input" />
        <label for="filetype_average" class="form-check-label">average</label>
      </div>

      <div class="form-check">
        <input type="radio" name="filetype" value="standard-error"
	       id="filetype_standard_error" required="required"
	       class="form-check-input" />
        <label for="filetype_standard_error" class="form-check-label">
          standard error
        </label>
      </div>
    </div>

    <div class="form-group">
      <span id="no-file-error" class="alert-danger" style="display: none;">
        No file selected
      </span>
      <label for="file_upload" class="form-label">select file</label>
      <input type="file" name="qc_text_file" id="file_upload"
	     accept="text/plain, text/tab-separated-values, application/zip"
	     class="form-control"/>
    </div>

    <button type="submit" class="btn btn-primary" />upload file</button>
</form>

{{upload_progress_indicator()}}
</div>

<div class="row">
  <h2 class="heading">samples/cases</h2>

  <div class="explainer">
    <p>For the expression data above, you need the samples/cases in your file to
      already exist in the GeneNetwork database. If there are any samples that do
      not already exist the upload of the expression data will fail.</p>
    <p>This section gives you the opportunity to upload any missing samples</p>
  </div>

  <a href={{url_for("samples.select_species")}}
     title="Upload samples/cases/individuals for your data"
     class="btn btn-primary">upload Samples/Cases</a>
</div>

{%endblock%}


{%block javascript%}
<script type="text/javascript" src="static/js/upload_progress.js"></script>
<script type="text/javascript">
  function setup_formdata(form) {
      var formdata = new FormData();
      formdata.append(
	  "speciesid",
	  form.querySelector("#select_species01").value)
      formdata.append(
	  "qc_text_file",
	  form.querySelector("input[type='file']").files[0]);
      formdata.append(
	  "filetype",
	  selected_filetype(
	      Array.from(form.querySelectorAll("input[type='radio']"))));
      return formdata;
  }

  setup_upload_handlers(
      "frm-upload-expression-data", make_data_uploader(setup_formdata));
</script>
{%endblock%}