Rename template

Rename original template to indicate it uses the R/qtl2 bundle format.

1 files changed, 0 insertions, 231 deletions

diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html
deleted file mode 100644
index 2bd5fab..0000000
--- a/uploader/templates/phenotypes/add-phenotypes.html
+++ /dev/null
@@ -1,231 +0,0 @@
-{%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%}