path: root/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html

{%extends "phenotypes/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "macro-table-pagination.html" import table_pagination%}
{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}

{%block title%}Phenotypes{%endblock%}

{%block pagetitle%}Phenotypes{%endblock%}

{%block lvl4_breadcrumbs%}
<li {%if activelink=="add-phenotypes"%}
    class="breadcrumb-item active"
    {%else%}
    class="breadcrumb-item"
    {%endif%}>
  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
           species_id=species.SpeciesId,
           population_id=population.Id,
           dataset_id=dataset.Id)}}">Add Phenotypes</a>
</li>
{%endblock%}

{%block contents%}
{{flash_all_messages()}}

<div class="row">
  <form id="frm-add-phenotypes"
        method="POST"
        enctype="multipart/form-data"
        action="{{url_for('species.populations.phenotypes.add_phenotypes',
                species_id=species.SpeciesId,
                population_id=population.Id,
                dataset_id=dataset.Id)}}">
    <legend>Add New Phenotypes</legend>

    <div class="form-text help-block">
      <p>Select the zip file bundle containing information on the phenotypes you
        wish to upload, then click the "Upload Phenotypes" button below to
        upload the data.</p>
      <p>See the <a href="#section-file-formats">File Formats</a> section below
        to get an understanding of what is expected of the bundle files you
        upload.</p>
      <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p>
    </div>

    <div class="form-group">
      <label for="finput-phenotypes-bundle" class="form-label">
        Phenotypes Bundle</label>
      <input type="file"
             id="finput-phenotypes-bundle"
             name="phenotypes-bundle"
             accept="application/zip, .zip"
	     required="required"
             class="form-control" />
    </div>

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

<div class="row">
  <h2 class="heading" id="section-file-formats">File Formats</h2>
  <p>We accept an extended form of the
    <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files"
       title="R/qtl2 software input file format documentation">
      input files' format used with the R/qtl2 software</a> as a single ZIP
    file</p>
  <p>The files that are used for this feature are:
    <ul>
      <li>the <em>control</em> file</li>
      <li><em>pheno</em> file(s)</li>
      <li><em>phenocovar</em> file(s)</li>
      <li><em>phenose</em> files(s)</li>
    </ul>
  </p>
  <p>Other files within the bundle will be ignored, for this feature.</p>
  <p>The following section will detail the expectations for each of the
    different file types within the uploaded ZIP file bundle for phenotypes:</p>

  <h3 class="subheading">Control File</h3>
  <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts
    as the control file. This file can be:
    <ul>
      <li>a <em>JSON</em> file, or</li>
      <li>a <em>YAML</em> file.</li>
    </ul>
  </p>

  <p>The control file is useful for defining things about the bundle such as:</p>
  <ul>
    <li>The field separator value (default: <code>sep: ','</code>). There can
      only ever be one field separator and it <strong>MUST</strong> be the same
      one for <strong>ALL</strong> files in the bundle.</li>
    <li>The comment character (default: <code>comment.char: '#'</code>). Any
      line that starts with this character will be considered a comment line and
      be ignored in its entirety.</li>
    <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You
      can specify more than one code to indicate missing values, e.g.
      <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li>
  </ul>

  <h3 class="subheading"><em>pheno</em> File(s)</h3>
  <p>These files are the main data files. You must have at least one of these
    files in your bundle for it to be valid for this step.</p>
  <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as
    below:<br />
    <code>
      id,10001,10002,10003,10004,…<br />
      BXD1,61.400002,54.099998,483,49.799999,…<br />
      BXD2,49,50.099998,403,45.5,…<br />
      BXD5,62.5,53.299999,501,62.900002,…<br />
      BXD6,53.099998,55.099998,403,NA,…<br />
      ⋮<br /></code>
  </p>
  <p>If the <code>pheno_transposed</code> value is set to <code>True</code>,
    then the data will be a <em>phenotypes × individuals</em> matrix as in the
    example below:<br />
    <code>
      id,BXD1,BXD2,BXD5,BXD6,…<br />
      10001,61.400002,49,62.5,53.099998,…<br />
      10002,54.099998,50.099998,53.299999,55.099998,…<br />
      10003,483,403,501,403,…<br />
      10004,49.799999,45.5,62.900002,NA,…<br />
      ⋮
    </code>
  </p>


  <h3 class="subheading"><em>phenocovar</em> File(s)</h3>
  <p>At least one phenotypes metadata file with the metadata values such as
    descriptions, PubMed Identifier, publication titles (if present), etc.</p>
  <p>The data in this/these file(s) is a matrix of
    <em>phenotypes × phenotypes-covariates</em>. The first column is always the
    phenotype names/identifiers — same as in the R/qtl2 format.</p>
  <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p>
  <p>This file <strong>MUST</strong> be present in the bundle, and have data for
    the bundle to be considered valid by our system for this step.<br />
    In addition to that, the following are the fields that <strong>must be
      present</strong>, and
    have values, in the file before the file is considered valid:
    <ul>
      <li><em>description</em>: A description for each phenotype. Useful
        for users to know what the phenotype is about.</li>
      <li><em>units</em>: The units of measurement for the phenotype,
        e.g. milligrams for brain weight, centimetres/millimetres for
        tail-length, etc.</li>
  </ul></p>

  <p>The following <em>optional</em> fields can also be provided:
    <ul>
      <li><em>pubmedid</em>: A PubMed Identifier for the publication where
        the phenotype is published. If this field is not provided, the system will
        assume your phenotype is not published.</li>
    </ul>
  </p>
  <p>These files will be marked up in the control file with the
    <code>phenocovar</code> key, as in the examples below:
    <ol>
      <li>JSON: single file<br />
        <code>{<br />
          &nbsp;&nbsp;⋮,<br />
          &nbsp;&nbsp;"phenocovar": "your_covariates_file.csv",<br />
          &nbsp;&nbsp;⋮<br />
          }
        </code>
      </li>
      <li>JSON: multiple files<br />
        <code>{<br />
          &nbsp;&nbsp;⋮,<br />
          &nbsp;&nbsp;"phenocovar": [<br />
          &nbsp;&nbsp;&nbsp;&nbsp;"covariates_file_01.csv",<br />
          &nbsp;&nbsp;&nbsp;&nbsp;"covariates_file_01.csv",<br />
          &nbsp;&nbsp;&nbsp;&nbsp;⋮<br />
          &nbsp;&nbsp;],<br />
          &nbsp;&nbsp;⋮<br />
          }
        </code>
      </li>
      <li>YAML: single file or<br />
        <code>
          ⋮<br />
          phenocovar: your_covariates_file.csv<br />
          ⋮
        </code>
      </li>
      <li>YAML: multiple files<br />
        <code>
          ⋮<br />
          phenocovar:<br />
          - covariates_file_01.csv<br />
          - covariates_file_02.csv<br />
          - covariates_file_03.csv<br />
          …<br />
          ⋮
        </code>
      </li>
    </ol>
  </p>

  <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3>
  <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are
    not supported by the original R/qtl2 file format</p>
  <p>We use these files to upload the standard errors (<em>phenose</em>) when
    the data file (<em>pheno</em>) is average data. In that case, the
    <em>phenonum</em> file(s) contains the number of individuals that were
    involved when computing the averages.</p>
  <p>Both types of files are matrices of <em>individuals × phenotypes</em> by
    default. Like the related <em>pheno</em> files, if
    <code>pheno_transposed: True</code>, then the file will be a matrix of
    <em>phenotypes × individuals</em>.</p>
</div>

<div class="row text-warning">
  <h3 class="subheading">Notes for Devs (well… Fred, really.)</h3>
  <p>Use the following resources for automated retrieval of certain data</p>
  <ul>
    <li><a href="https://www.ncbi.nlm.nih.gov/pmc/tools/developers/"
           title="NCBI APIs: Retrieve articles' metadata etc.">
        NCBI APIS</a></li>
  </ul>
</div>

{%endblock%}

{%block sidebarcontents%}
{{display_pheno_dataset_card(species, population, dataset)}}
{%endblock%}