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diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
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@@ -5,118 +5,130 @@
{%block title%}Data Upload{%endblock%}
{%block contents%}
-<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 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>
-<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 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>
-<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")}}
-
- <fieldset>
- <label for="select_species01">Species</label>
- <select id="select_species01"
- name="speciesid"
- required="required">
- <option value="">Select species</option>
- {%for aspecies in species%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </select>
- </fieldset>
-
- <fieldset>
- <legend>file type</legend>
-
- <input type="radio" name="filetype" value="average" id="filetype_average"
- required="required" class="form-col-1" />
- <label for="filetype_average" class="form-col-2">average</label>
-
- <input type="radio" name="filetype" value="standard-error"
- id="filetype_standard_error" required="required"
- class="form-col-1" />
- <label for="filetype_standard_error" class="form-col-2">
- standard error
- </label>
- </fieldset>
-
- <fieldset>
- <span id="no-file-error" class="alert-danger" style="display: none;">
- No file selected
- </span>
- <label for="file_upload" class="form-col-1">select file</label>
- <input type="file" name="qc_text_file" id="file_upload"
- accept="text/plain, text/tab-separated-values, application/zip"
- class="form-col-2"/>
- </fieldset>
-
- <fieldset>
- <input type="submit" value="upload file" class="btn btn-primary form-col-2" />
- </fieldset>
+<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>
-<h2 class="heading">samples/cases</h2>
+<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>
+ <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">
- upload Samples/Cases</a>
+ <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%}