Initialise the populations package and update references.

5 files changed, 118 insertions, 1 deletions

diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 7431767..fd6010b 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -45,6 +45,7 @@
       <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('populations.index')}}">Populations</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}" >Expression Data</a></li>
       </ul>
     </aside>
diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html
new file mode 100644
index 0000000..1033927
--- /dev/null
+++ b/uploader/templates/populations/base.html
@@ -0,0 +1,12 @@
+{%extends "base.html"%}
+
+{%block breadcrumbs%}
+<li {%if activelink=="populations"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('populations.index')}}">Populations</a>
+</li>
+{%block lvl3_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html
new file mode 100644
index 0000000..14cf547
--- /dev/null
+++ b/uploader/templates/populations/index.html
@@ -0,0 +1,16 @@
+{%extends "populations/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Populations{%endblock%}
+
+{%block pagetitle%}Populations{%endblock%}
+
+
+{%block contents%}
+<div class="row">
+  To continue, you need to select the species:
+
+  {{select_species_form(url_for("populations.index"), species)}}
+</div>
+{%endblock%}
diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html
new file mode 100644
index 0000000..bf6cf98
--- /dev/null
+++ b/uploader/templates/populations/list-populations.html
@@ -0,0 +1,87 @@
+{%extends "populations/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Populations{%endblock%}
+
+{%block pagetitle%}Populations{%endblock%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="list-populations"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('populations.list_species_populations',
+           species_id=species.SpeciesId)}}">List</a>
+</li>
+{%endblock%}
+
+
+{%block contents%}
+<div class="row">
+  <p>
+    The following populations/groups exist for the '{{species.FullName}}'
+    species.
+  </p>
+  <p>
+    Click on the population's name to select and continue using the population.
+  </p>
+</div>
+
+<div class="row">
+  <p>
+    If the population you need for the species '{{species.FullName}}' does not
+    exist, click on the "Create Population" button below to create a new one.
+  </p>
+  <p>
+    <a href="{{url_for('populations.create_population',
+             species_id=species.SpeciesId)}}"
+       title="Create a new population for species '{{species.FullName}}'."
+       class="btn btn-danger">
+      Create Population
+    </a>
+  </p>
+</div>
+
+<div class="row">
+  <table class="table">
+    <caption>Populations for {{species.FullName}}</caption>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Full Name</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for population in populations%}
+      <tr>
+        <td>
+          <a href="#{{population.InbredSetId}}"
+             title="Population '{{population.FullName}}' for species '{{species.FullName}}'.">
+            {{population.Name}}
+          </a>
+        </td>
+        <td>{{population.FullName}}</td>
+        <td>{{population.Description}}</td>
+      </tr>
+      {%else%}
+      <tr>
+        <td colspan="3">
+          <p class="text-danger">
+            <span class="glyphicon glyphicon-exclamation-mark"></span>
+            There were no populations found for {{species.FullName}}!
+          </p>
+        </td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+&hellip; maybe provide species details here, perhaps? &hellip;
+{%endblock%}
diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html
index a0eb54b..0a3b0dd 100644
--- a/uploader/templates/species/view-species.html
+++ b/uploader/templates/species/view-species.html
@@ -60,7 +60,8 @@
          title="Upload genotypes for {{species.FullName}}">Upload Genotypes</a>
     </li>
     <li>
-      <a href="#"
+      <a href="{{url_for('species.populations.list_species_populations',
+               species_id=species.SpeciesId)}}"
          title="Create/Edit populations for {{species.FullName}}">
         Manage populations</a>
     </li>