From 06c6a7f7f42e8ff2d33a934ff695efde24d26d65 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 28 Aug 2024 17:12:26 -0500
Subject: Move code handling expression data upload into new module.

---
 uploader/templates/expression-data/index.html | 95 +++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 uploader/templates/expression-data/index.html

(limited to 'uploader/templates/expression-data')

diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html
new file mode 100644
index 0000000..ed5d8dd
--- /dev/null
+++ b/uploader/templates/expression-data/index.html
@@ -0,0 +1,95 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Expression Data{%endblock%}
+
+{%block pagetitle%}Expression Data{%endblock%}
+
+{%block breadcrumb%}
+<li class="breadcrumb-item">
+  <a href="{{url_for('base.index')}}">Home</a>
+</li>
+<li class="breadcrumb-item active">
+  <a href="{{url_for('expression-data.index.index')}}">Expression Data</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+  {{flash_all_messages()}}
+
+  <h1 class="heading">data upload</h1>
+
+  <div class="explainer">
+    <p>Each of the sections below gives you a different option for data expression-data.
+      Please read the documentation for each section carefully to understand what
+      each section is about.</p>
+  </div>
+</div>
+
+<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('expression-data.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>
+
+
+<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('expression-data.index.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('expression-data.index.data_review')}}#file-types"
+	          title="Details for the data expectations.">Help</a>)</li>
+    </ol>
+  </div>
+
+  <a href="{{url_for('expression-data.index.upload_file')}}"
+     title="Upload your expression data"
+     class="btn btn-primary">upload expression data</a>
+</div>
+
+<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>
+
+  <a href="{{url_for('expression-data.samples.select_species')}}"
+     title="Upload samples/cases/individuals for your data"
+     class="btn btn-primary">upload Samples/Cases</a>
+</div>
+
+{%endblock%}
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