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{%extends "samples/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "populations/macro-select-population.html" import select_population_form%}
{%from "populations/macro-display-population-card.html" import display_population_card%}
{%block title%}Samples — Upload Samples{%endblock%}
{%block pagetitle%}Samples — Upload Samples{%endblock%}
{%block lvl4_breadcrumbs%}
<li {%if activelink=="uploade-samples"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
<a href="{{url_for('species.populations.samples.upload_samples',
species_id=species.SpeciesId,
population_id=population.Id)}}">List</a>
</li>
{%endblock%}
{%block contents%}
{{flash_all_messages()}}
<div class="row">
<p>
You can now upload the samples for the "{{population.FullName}}" population
from the "{{species.FullName}}" species here.
</p>
<p>
Upload a <strong>character-separated value (CSV)</strong> file that contains
details about your samples. The CSV file should have the following fields:
<dl>
<dt>Name</dt>
<dd>The primary name/identifier for the sample/individual.</dd>
<dt>Name2</dt>
<dd>A secondary name for the sample. This can simply be the same as
<strong>Name</strong> above. This field <strong>MUST</strong> contain a
value.</dd>
<dt>Symbol</dt>
<dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for
species that have strains. This field can be left empty for species like
Humans that do not have strains..</dd>
<dt>Alias</dt>
<dd>An alias for the sample. Can be an empty field, or take on the same
value as that of the Symbol.</dd>
</dl>
</p>
</div>
<div class="row">
<form id="form-samples"
method="POST"
action="{{url_for('species.populations.samples.upload_samples',
species_id=species.SpeciesId,
population_id=population.InbredSetId)}}"
enctype="multipart/form-data">
<legend class="heading">upload samples</legend>
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
<input type="hidden" name="population_id" value="{{population.Id}}" />
<div class="form-group">
<label for="file-samples" class="form-label">select file</label>
<input type="file" name="samples_file" id="file:samples"
accept="text/csv, text/tab-separated-values"
class="form-control" />
</div>
<div class="form-group">
<label for="select:separator" class="form-label">field separator</label>
<select id="select:separator"
name="separator"
required="required"
class="form-control">
<option value="">Select separator for your file: (default is comma)</option>
<option value="	">TAB</option>
<option value=" ">Space</option>
<option value=",">Comma</option>
<option value=";">Semicolon</option>
<option value="other">Other</option>
</select>
<input id="txt:separator"
type="text"
name="other_separator"
class="form-control" />
<small class="form-text text-muted">
If you select '<strong>Other</strong>' for the field separator value,
enter the character that separates the fields in your CSV file in the form
field below.
</small>
</div>
<div class="form-group form-check">
<input id="chk:heading"
type="checkbox"
name="first_line_heading"
class="form-check-input" />
<label for="chk:heading" class="form-check-label">
first line is a heading?</label>
<small class="form-text text-muted">
Select this if the first line in your file contains headings for the
columns.
</small>
</div>
<div class="form-group">
<label for="txt:delimiter" class="form-label">field delimiter</label>
<input id="txt:delimiter"
type="text"
name="field_delimiter"
maxlength="1"
class="form-control" />
<small class="form-text text-muted">
If there is a character delimiting the string texts within particular
fields in your CSV, provide the character here. This can be left blank if
no such delimiters exist in your file.
</small>
</div>
<button type="submit"
class="btn btn-primary">upload samples file</button>
</form>
</div>
<div class="row">
<h3>Preview File Content</h3>
<table id="tbl:samples-preview" class="table">
<caption class="heading">preview content</caption>
<thead>
<tr>
<th>Name</th>
<th>Name2</th>
<th>Symbol</th>
<th>Alias</th>
</tr>
</thead>
<tbody>
<tr id="default-row">
<td colspan="4">
Please make some selections in the form above to preview the data.</td>
</tr>
</tbody>
</table>
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_population_card(species, population)}}
{%endblock%}
{%block javascript%}
<script src="/static/js/upload_samples.js" type="text/javascript"></script>
{%endblock%}
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