From e49b4367f1dab1c3acb3cd5d71ba09359c5ab4ee Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 29 Aug 2024 15:21:27 -0500
Subject: Initialise package for dealing with Species.

---
 uploader/templates/base.html                   |  10 ++-
 uploader/templates/species/base.html           |  11 +++
 uploader/templates/species/create-species.html | 116 +++++++++++++++++++++++++
 uploader/templates/species/list-species.html   |  68 +++++++++++++++
 4 files changed, 204 insertions(+), 1 deletion(-)
 create mode 100644 uploader/templates/species/base.html
 create mode 100644 uploader/templates/species/create-species.html
 create mode 100644 uploader/templates/species/list-species.html

(limited to 'uploader/templates')

diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 58227f4..7431767 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -44,6 +44,7 @@
     <aside id="nav-sidebar" class="container-fluid">
       <ul class="nav flex-column">
         <li><a href="/" >Home</a></li>
+        <li><a href="{{url_for('species.list_species')}}" >Species</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}" >Expression Data</a></li>
       </ul>
     </aside>
@@ -54,7 +55,14 @@
         <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
         <nav>
           <ol class="breadcrumb">
-            {%block breadcrumb%}{%endblock%}
+            <li {%if activelink is not defined or activelink=="home"%}
+                class="breadcrumb-item active"
+                {%else%}
+                class="breadcrumb-item"
+                {%endif%}>
+              <a href="{{url_for('base.index')}}">Home</a>
+            </li>
+            {%block breadcrumbs%}{%endblock%}
           </ol>
         </nav>
       </div>
diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html
new file mode 100644
index 0000000..b77cc8b
--- /dev/null
+++ b/uploader/templates/species/base.html
@@ -0,0 +1,11 @@
+{%extends "base.html"%}
+
+{%block breadcrumbs%}
+<li {%if activelink=="species"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.list_species')}}">Species</a>
+</li>
+{%endblock%}
diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html
new file mode 100644
index 0000000..b96e2d3
--- /dev/null
+++ b/uploader/templates/species/create-species.html
@@ -0,0 +1,116 @@
+{%extends "species/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Create Species{%endblock%}
+
+{%block pagetitle%}Create Species{%endblock%}
+
+{%block breadcrumbs%}
+<li {%if activelink=="create-species"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.create_species')}}">Species</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+  <form id="frm-create-species"
+        method="POST"
+        action="{{url_for('species.create_species')}}">
+    <legend>Create Species</legend>
+
+    {{flash_all_messages()}}
+
+    <div class="form-group">
+      <label for="txt-taxonomy-id" class="form-label">
+        Taxonomy ID</label>
+      <div class="input-group">
+        <input id="txt-taxonomy-id"
+               name="species_taxonomy_id"
+               type="text"
+               class="form-control" />
+        <span class="input-group-btn">
+          <button id="btn-search-taxonid" class="btn btn-info">Search</button>
+        </span>
+      </div>
+      <small class="form-text text-small text-muted">Provide the taxonomy ID for
+        your species that can be used to link to external sites like NCBI. Enter
+        the taxonomy ID and click "Search" to auto-fill the form with data.
+        <br />
+        While it is recommended to provide a value for this field, doing so is
+        optional.
+      </small>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-species-name" class="form-label">Common Name</label>
+      <input id="txt-species-name"
+             name="common_name"
+             type="text"
+             class="form-control"
+             required="required" />
+      <small class="form-text text-muted">Provide the common, possibly
+        non-scientific name for the species here, e.g. Human, Mouse, etc.</small>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-species-scientific" class="form-label">
+        Scientific Name</label>
+      <input id="txt-species-scientific"
+             name="scientific_name"
+             type="text"
+             class="form-control"
+             required="required" />
+      <small class="form-text text-muted">Provide the scientific name for the
+        species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small>
+    </div>
+
+    <div class="form-group">
+      <input type="submit"
+             value="create new species"
+             class="btn btn-primary" />
+    </div>
+
+  </form>
+</div>
+{%endblock%}
+
+{%block javascript%}
+<script>
+  var lastTaxonId = null;
+
+  var fetch_taxonomy = (taxonId) => {
+      var uri = (
+          "https://rest.uniprot.org/taxonomy/" + encodeURIComponent(taxonId));
+      $.get(
+          uri,
+          {},
+          (data, textStatus, jqXHR) => {
+              if(textStatus == "success") {
+                  lastTaxonId = taxonId;
+                  $("#txt-species-scientific").val(data.scientificName);
+                  $("#txt-species-name").val(data.commonName);
+                  return false;
+              }
+              msg = (
+                  "Request to '${uri}' failed with message '${textStatus}'. "
+                  + "Please try again later, or fill the details manually.");
+              alert(msg);
+              console.error(msg, data, textStatus);
+              return false;
+          },
+          "json");
+  };
+
+  $("#btn-search-taxonid").on("click", (event) => {
+      event.preventDefault();
+      taxonId = $("#txt-taxonomy-id").val();
+      if((taxonId !== "") && (taxonId !== lastTaxonId)) {
+          fetch_taxonomy(taxonId);
+      }
+  });
+</script>
+{%endblock%}
diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html
new file mode 100644
index 0000000..42094c1
--- /dev/null
+++ b/uploader/templates/species/list-species.html
@@ -0,0 +1,68 @@
+{%extends "species/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}List Species{%endblock%}
+
+{%block pagetitle%}List Species{%endblock%}
+
+{%block contents%}
+<div class="row">
+  <p>
+    All data in GeneNetwork revolves around species. This is the core of the
+    system.</p>
+  <p>Here you can see a list of all the species available in GeneNetwork.
+    Click on the link besides each species to view greater detail on the species,
+    and access further operations that are possible for said species.</p>
+</div>
+
+<div class="row">
+  <p>If you cannot find the species you are looking for below, click the button
+    below to create it</p>
+  <p><a href="{{url_for('species.create_species')}}"
+        title="Add a new species to GeneNetwork"
+        class="btn btn-danger">Create Species</a></p>
+</div>
+
+<div class="row">
+  <table class="table">
+    <caption>Available Species</caption>
+    <thead>
+      <tr>
+        <th>Common Name</th>
+        <th>Scientific Name</th>
+        <th>TaxonId</th>
+        <th>Use</th>
+      </tr>
+    </thead>
+    <tbody>
+      {%for species in allspecies%}
+      <tr>
+        <td>{{species["SpeciesName"]}}</td>
+        <td>{{species["FullName"]}}</td>
+        <td>
+          <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species['TaxonomyId']}}"
+             title="View species details on NCBI"
+             target="_blank">{{species["TaxonomyId"]}}</a>
+        </td>
+        <td>
+          <a href="{{url_for('species.view_species',
+                   species_id=species['SpeciesId'])}}"
+             title="">
+            {{species["SpeciesName"]}} ({{species["FullName"]}})
+          </a>
+        </td>
+      </tr>
+      {%else%}
+      <tr>
+        <td colspan="3">
+          <p class="text-danger">
+            <span class="glyphicon glyphicon-exclamation-mark"></span>
+            There were no species found!
+          </p>
+        </td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+</div>
+{%endblock%}
-- 
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