From 66e7970c3ff5305f8a7d6d60d34b974389f8fe78 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 18 Sep 2024 17:10:50 -0500
Subject: Separate genetic markers from encodings and datasets

---
 uploader/genotypes/views.py                      |  27 ++++--
 uploader/templates/genotypes/list-genotypes.html |  87 +++++--------------
 uploader/templates/genotypes/list-markers.html   | 102 +++++++++++++++++++++++
 3 files changed, 146 insertions(+), 70 deletions(-)
 create mode 100644 uploader/templates/genotypes/list-markers.html

diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0618949..2ff9965 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -90,6 +90,26 @@ def list_genotypes(species_id: int, population_id: int):
                 "species.populations.genotypes.select_population",
                 species_id=species_id))
 
+        return render_template("genotypes/list-genotypes.html",
+                               species=species,
+                               population=population,
+                               genocode=genocode_by_population(
+                                   conn, population_id),
+                               total_markers=genotype_markers_count(
+                                   conn, species_id),
+                               activelink="list-genotypes")
+
+
+@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
+@require_login
+def list_markers(species_id: int):
+    """List a species' genetic markers."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("Invalid species provided!", "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+
         start_from = safe_int(request.args.get("start_from") or 0)
         if start_from < 0:
             start_from = 0
@@ -97,14 +117,11 @@ def list_genotypes(species_id: int, population_id: int):
         markers = enumerate_sequence(
             genotype_markers(conn, species_id, offset=start_from, limit=count),
             start=start_from+1)
-        return render_template("genotypes/list-genotypes.html",
+        return render_template("genotypes/list-markers.html",
                                species=species,
-                               population=population,
-                               genocode=genocode_by_population(
-                                   conn, population_id),
                                total_markers=genotype_markers_count(
                                    conn, species_id),
                                start_from=start_from,
                                count=count,
                                markers=markers,
-                               activelink="list-genotypes")
+                               activelink="list-markers")
diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html
index 9b27540..0efc693 100644
--- a/uploader/templates/genotypes/list-genotypes.html
+++ b/uploader/templates/genotypes/list-genotypes.html
@@ -22,12 +22,24 @@
 {{flash_all_messages()}}
 
 <div class="row">
+  <h2>Genetic Markers</h2>
+  <p>There are a total of {{total_markers}} currently registered genetic markers
+    for the "{{species.FullName}}" species. You can click
+    <a href="{{url_for('species.populations.genotypes.list_markers',
+             species_id=species.SpeciesId)}}"
+       title="View genetic markers for species '{{species.FullName}}">
+      this link to view the genetic markers
+    </a>.
+  </p>
+</div>
+
+<div class="row">
+  <h2>Genotype Encoding</h2>
   <p>
     The genotype encoding used for the "{{population.FullName}}" population from
     the "{{species.FullName}}" species is as shown in the table below.
   </p>
   <table class="table">
-    <legend>Genotype Encoding</legend>
 
     <thead>
       <tr>
@@ -54,6 +66,14 @@
       {%endfor%}
     </tbody>
   </table>
+
+  {%if genocode | length < 1%}
+  <a href="#add-genotype-encoding"
+     title="Add a genotype encoding system for this population"
+     class="btn btn-primary">
+    add genotype encoding
+    </a>
+  {%endif%}
 </div>
 
 <div class="row text-danger">
@@ -65,75 +85,12 @@
   <h3>Possible references</h3>
   <ul>
     <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li>
+    <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li>
   </ul>
 </div>
 
 <div class="row">
-  <p>
-    There are a total of {{total_markers}} genotype markers for this species.
-  </p>
-  <div class="row">
-    <div class="col-md-2" style="text-align: start;">
-      {%if start_from > 0%}
-      <a href="{{url_for('species.populations.genotypes.list_genotypes',
-               species_id=species.SpeciesId,
-               population_id=population.Id,
-               start_from=start_from-count,
-               count=count)}}">
-        <span class="glyphicon glyphicon-backward"></span>
-        Previous
-      </a>
-      {%endif%}
-    </div>
-    <div class="col-md-8" style="text-align: center;">
-      Displaying markers {{start_from+1}} to {{start_from + count}} of
-      {{total_markers}}
-    </div>
-    <div class="col-md-2" style="text-align: end;">
-      {%if start_from + count < total_markers%}
-      <a href="{{url_for('species.populations.genotypes.list_genotypes',
-               species_id=species.SpeciesId,
-               population_id=population.Id,
-               start_from=start_from+count,
-               count=count)}}">
-        Next
-        <span class="glyphicon glyphicon-forward"></span>
-      </a>
-      {%endif%}
-    </div>
-  </div>
-  <table class="table">
-    <thead>
-      <tr>
-        <th title="">#</th>
-        <th title="">Marker Name</th>
-        <th title="Chromosome">Chr</th>
-        <th title="Physical location of the marker in megabasepairs">
-          Location (Mb)</th>
-        <th title="">Source</th>
-        <th title="">Source2</th>
-    </thead>
 
-    <tbody>
-      {%for marker in markers%}
-      <tr>
-        <td>{{marker.sequence_number}}</td>
-        <td>{{marker.Marker_Name}}</td>
-        <td>{{marker.Chr}}</td>
-        <td>{{marker.Mb}}</td>
-        <td>{{marker.Source}}</td>
-        <td>{{marker.Source2}}</td>
-      </tr>
-      {%else%}
-      <tr>
-        <td colspan="7" class="text-info">
-          <span class="glyphicon glyphicon-exclamation-sign"></span>
-          No markers to display!
-        </td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
 </div>
 {%endblock%}
 
diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html
new file mode 100644
index 0000000..9198b44
--- /dev/null
+++ b/uploader/templates/genotypes/list-markers.html
@@ -0,0 +1,102 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
+
+{%block title%}Genotypes: List Markers{%endblock%}
+
+{%block pagetitle%}Genotypes: List Markers{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="list-markers"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.genotypes.list_markers',
+           species_id=species.SpeciesId)}}">List markers</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+{%if markers | length > 0%}
+<div class="row">
+  <p>
+    There are a total of {{total_markers}} genotype markers for this species.
+  </p>
+  <div class="row">
+    <div class="col-md-2" style="text-align: start;">
+      {%if start_from > 0%}
+      <a href="{{url_for('species.populations.genotypes.list_markers',
+               species_id=species.SpeciesId,
+               start_from=start_from-count,
+               count=count)}}">
+        <span class="glyphicon glyphicon-backward"></span>
+        Previous
+      </a>
+      {%endif%}
+    </div>
+    <div class="col-md-8" style="text-align: center;">
+      Displaying markers {{start_from+1}} to {{start_from+count if start_from+count < total_markers else total_markers}} of
+      {{total_markers}}
+    </div>
+    <div class="col-md-2" style="text-align: end;">
+      {%if start_from + count < total_markers%}
+      <a href="{{url_for('species.populations.genotypes.list_markers',
+               species_id=species.SpeciesId,
+               start_from=start_from+count,
+               count=count)}}">
+        Next
+        <span class="glyphicon glyphicon-forward"></span>
+      </a>
+      {%endif%}
+    </div>
+  </div>
+  <table class="table">
+    <thead>
+      <tr>
+        <th title="">#</th>
+        <th title="">Marker Name</th>
+        <th title="Chromosome">Chr</th>
+        <th title="Physical location of the marker in megabasepairs">
+          Location (Mb)</th>
+        <th title="">Source</th>
+        <th title="">Source2</th>
+    </thead>
+
+    <tbody>
+      {%for marker in markers%}
+      <tr>
+        <td>{{marker.sequence_number}}</td>
+        <td>{{marker.Marker_Name}}</td>
+        <td>{{marker.Chr}}</td>
+        <td>{{marker.Mb}}</td>
+        <td>{{marker.Source}}</td>
+        <td>{{marker.Source2}}</td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+</div>
+{%else%}
+<div class="row">
+  <p class="text-warning">
+    <span class="glyphicon glyphicon-exclamation-sign"></span>
+    This species does not currently have any genetic markers uploaded, therefore,
+    there is nothing to display here.
+  </p>
+  <p>
+    <a href="#add-genetic-markers-for-species-{{species.SpeciesId}}"
+     title="Add genetic markers for this species"
+     class="btn btn-primary">
+    add genetic markers
+    </a>
+  </p>
+</div>
+{%endif%}
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}
-- 
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