From 0b37b9b3fa4fead86787a705713645fa14530a54 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 23 Sep 2024 14:28:49 -0500
Subject: Initialise the "Expression Data" section.

---
 .../templates/expression-data/select-file.html     | 115 +++++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 uploader/templates/expression-data/select-file.html

(limited to 'uploader/templates/expression-data/select-file.html')

diff --git a/uploader/templates/expression-data/select-file.html b/uploader/templates/expression-data/select-file.html
new file mode 100644
index 0000000..4ca461e
--- /dev/null
+++ b/uploader/templates/expression-data/select-file.html
@@ -0,0 +1,115 @@
+{%extends "expression-data/base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+{%from "upload_progress_indicator.html" import upload_progress_indicator%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Expression Data — Upload Data{%endblock%}
+
+{%block pagetitle%}Expression Data — Upload Data{%endblock%}
+
+{%block contents%}
+{{upload_progress_indicator()}}
+
+<div class="row">
+  <h2 class="heading">Upload Expression Data</h2>
+
+  <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('species.populations.expression-data.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('species.populations.expression-data.data_review')}}#file-types"
+	        title="Details for the data expectations.">Help</a>)</li>
+  </ol>
+</div>
+
+<div class="row">
+  <form action="{{url_for(
+                'species.populations.expression-data.upload_file',
+                species_id=species.SpeciesId,
+                population_id=population.Id)}}"
+        method="POST"
+        enctype="multipart/form-data"
+        id="frm-upload-expression-data">
+    {{flash_messages("error-expr-data")}}
+
+    <div class="form-group">
+      <legend class="heading">File Type</legend>
+
+      <div class="radio">
+        <label for="filetype_average" class="form-check-label">
+          <input type="radio" name="filetype" value="average" id="filetype_average"
+	         required="required" class="form-check-input" />
+          Average</label>
+        <p class="form-text text-muted">
+          <small>The averages data …</small></p>
+      </div>
+
+      <div class="radio">
+        <label for="filetype_standard_error" class="form-check-label">
+          <input type="radio" name="filetype" value="standard-error"
+	         id="filetype_standard_error" required="required"
+	         class="form-check-input" />
+          Standard Error
+        </label>
+        <p class="form-text text-muted">
+          <small>The standard errors computed from the averages …</small></p>
+      </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"/>
+      <p class="form-text text-muted">
+        <small>Select the file to upload.</small></p>
+    </div>
+
+    <button type="submit"
+            class="btn btn-primary"
+            data-toggle="modal"
+            data-target="#upload-progress-indicator">upload file</button>
+  </form>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/upload_progress.js"></script>
+<script type="text/javascript">
+  function setup_formdata(form) {
+      var formdata = new FormData();
+      formdata.append(
+	  "qc_text_file",
+	  form.querySelector("input[type='file']").files[0]);
+      formdata.append(
+	  "filetype",
+	  selected_filetype(
+	      Array.from(form.querySelectorAll("input[type='radio']"))));
+      return formdata;
+  }
+
+  setup_upload_handlers(
+      "frm-upload-expression-data", make_data_uploader(setup_formdata));
+</script>
+{%endblock%}
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