From dea29486883b5b13369a6d2c5392ec01a24555ee Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 13 Dec 2024 15:30:29 -0600
Subject: Refactor template to extend common base

Extend the common base template in order to reuse the common parts for
uploading phenotypes.
---
 .../add-phenotypes-with-rqtl2-bundle.html          | 82 +++++++---------------
 1 file changed, 24 insertions(+), 58 deletions(-)

(limited to 'uploader')

diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
index a1953df..8f67baa 100644
--- a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
+++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
@@ -1,4 +1,4 @@
-{%extends "phenotypes/base.html"%}
+{%extends "phenotypes/add-phenotypes-base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
 {%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
@@ -20,54 +20,35 @@
 </li>
 {%endblock%}
 
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <form id="frm-add-phenotypes"
-        method="POST"
-        enctype="multipart/form-data"
-        action="{{url_for('species.populations.phenotypes.add_phenotypes',
-                species_id=species.SpeciesId,
-                population_id=population.Id,
-                dataset_id=dataset.Id)}}">
-    <legend>Add New Phenotypes</legend>
-
-    <div class="form-text help-block">
-      <p>Select the zip file bundle containing information on the phenotypes you
-        wish to upload, then click the "Upload Phenotypes" button below to
-        upload the data.</p>
-      <p>If you wish to upload the files individually instead,
-        <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
+{%block frm_add_phenotypes_documentation%}
+<p>Select the zip file bundle containing information on the phenotypes you
+  wish to upload, then click the "Upload Phenotypes" button below to
+  upload the data.</p>
+<p>If you wish to upload the files individually instead,
+  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
            species_id=species.SpeciesId,
            population_id=population.Id,
            dataset_id=dataset.Id)}}"
-           title="">click here</a>.</p>
-      <p>See the <a href="#section-file-formats">File Formats</a> section below
-        to get an understanding of what is expected of the bundle files you
-        upload.</p>
-      <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p>
-    </div>
-
-    <div class="form-group">
-      <label for="finput-phenotypes-bundle" class="form-label">
-        Phenotypes Bundle</label>
-      <input type="file"
-             id="finput-phenotypes-bundle"
-             name="phenotypes-bundle"
-             accept="application/zip, .zip"
-	     required="required"
-             class="form-control" />
-    </div>
+     title="">click here</a>.</p>
+<p>See the <a href="#section-file-formats">File Formats</a> section below
+  to get an understanding of what is expected of the bundle files you
+  upload.</p>
+{%endblock%}
 
-    <div class="form-group">
-      <input type="submit"
-             value="upload phenotypes"
-             class="btn btn-primary" />
-    </div>
-  </form>
+{%block frm_add_phenotypes_elements%}
+<div class="form-group">
+  <label for="finput-phenotypes-bundle" class="form-label">
+    Phenotypes Bundle</label>
+  <input type="file"
+         id="finput-phenotypes-bundle"
+         name="phenotypes-bundle"
+         accept="application/zip, .zip"
+	 required="required"
+         class="form-control" />
 </div>
+{%endblock%}
 
+{%block page_documentation%}
 <div class="row">
   <h2 class="heading" id="section-file-formats">File Formats</h2>
   <p>We accept an extended form of the
@@ -219,19 +200,4 @@
     <code>pheno_transposed: True</code>, then the file will be a matrix of
     <em>phenotypes × individuals</em>.</p>
 </div>
-
-<div class="row text-warning">
-  <h3 class="subheading">Notes for Devs (well… Fred, really.)</h3>
-  <p>Use the following resources for automated retrieval of certain data</p>
-  <ul>
-    <li><a href="https://www.ncbi.nlm.nih.gov/pmc/tools/developers/"
-           title="NCBI APIs: Retrieve articles' metadata etc.">
-        NCBI APIS</a></li>
-  </ul>
-</div>
-
-{%endblock%}
-
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
 {%endblock%}
-- 
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