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authorFrederick Muriuki Muriithi2024-08-28 17:12:26 -0500
committerFrederick Muriuki Muriithi2024-08-28 17:54:17 -0500
commit06c6a7f7f42e8ff2d33a934ff695efde24d26d65 (patch)
tree0ab6115fa7a8ee490cc6efc343c44549c1871281 /uploader/templates/expression-data/index.html
parent05191fa146fac31fd079c50bf6bcc4983f2f0792 (diff)
downloadgn-uploader-06c6a7f7f42e8ff2d33a934ff695efde24d26d65.tar.gz
Move code handling expression data upload into new module.
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+{%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%}