From 3c8ec9af68d593e7e5eef52aca3d001e22c8e0f7 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 9 Sep 2024 16:39:50 -0500
Subject: Enable samples uploads.

---
 uploader/templates/samples/upload-samples.html | 155 +++++++++++++++++++++++++
 1 file changed, 155 insertions(+)
 create mode 100644 uploader/templates/samples/upload-samples.html

(limited to 'uploader/templates/samples/upload-samples.html')

diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
new file mode 100644
index 0000000..b101b2e
--- /dev/null
+++ b/uploader/templates/samples/upload-samples.html
@@ -0,0 +1,155 @@
+{%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 a character-separated value (CSV) 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="&#x0009;">TAB</option>
+        <option value="&#x0020;">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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