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.

---
 uploader/templates/expression-data/index.html | 82 ++++-----------------------
 1 file changed, 10 insertions(+), 72 deletions(-)

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

diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html
index ed5d8dd..9ba3582 100644
--- a/uploader/templates/expression-data/index.html
+++ b/uploader/templates/expression-data/index.html
@@ -1,5 +1,6 @@
-{%extends "base.html"%}
+{%extends "expression-data/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
 
 {%block title%}Expression Data{%endblock%}
 
@@ -10,86 +11,23 @@
   <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>
+  <a href="{{url_for('species.populations.expression-data.index')}}"
+     title="Upload expression data.">
+    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>
+  {{flash_all_messages()}}
 
-  <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>
+  <p>This section allows you to enter the expression data for your experiment.
+    You will need to select the species that your data concerns below.</p>
 </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>
+  {{select_species_form(url_for("species.populations.expression-data.index"),
+  species)}}
 </div>
-
 {%endblock%}
-- 
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