Provide generic way to select species.

2 files changed, 57 insertions, 1 deletions

diff --git a/uploader/species/models.py b/uploader/species/models.py
index 481f8be..53e7de0 100644
--- a/uploader/species/models.py
+++ b/uploader/species/models.py
@@ -1,5 +1,7 @@
 """Database functions for species."""
+import math
 from typing import Optional
+from functools import reduce
 
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
@@ -9,11 +11,27 @@ def all_species(conn: mdb.Connection) -> tuple:
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             "SELECT Id AS SpeciesId, SpeciesName, LOWER(Name) AS Name, "
-            "MenuName, FullName, TaxonomyId FROM Species")
+            "MenuName, FullName, TaxonomyId, Family, FamilyOrderId, OrderId "
+            "FROM Species ORDER BY FamilyOrderId ASC, OrderID ASC")
         return tuple(cursor.fetchall())
 
     return tuple()
 
+def order_species_by_family(species: tuple[dict, ...]) -> list:
+    """Order the species by their family"""
+    def __family_order_id__(item):
+        orderid = item["FamilyOrderId"]
+        return math.inf if orderid is None else orderid
+    def __order__(ordered, current):
+        _key = (__family_order_id__(current), current["Family"])
+        return {
+            **ordered,
+            _key: ordered.get(_key, tuple()) + (current,)
+        }
+    ordered = reduce(__order__, species, {})
+    return sorted(tuple(ordered.items()), key=lambda item: item[0][0])
+
+
 def species_by_id(conn: mdb.Connection, speciesid) -> dict:
     "Retrieve the species from the database by id."
     with conn.cursor(cursorclass=DictCursor) as cursor:
diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html
new file mode 100644
index 0000000..3dbfc95
--- /dev/null
+++ b/uploader/templates/species/macro-select-species.html
@@ -0,0 +1,38 @@
+{%macro select_species_form(form_action, species)%}
+{%if species | length > 0%}
+<form method="GET" action="{{form_action}}">
+  <legend>Select Species</legend>
+
+  <div class="form-group">
+    <label for="select-species" class="form-label">Select Species</label>
+    <select id="select-species"
+            name="species_id"
+            class="form-control"
+            required="required">
+      <option value="">Select Species</option>
+      {%for group in species%}
+      {{group}}
+      <optgroup {%if group[0][1] is not none%}
+                label="{{group[0][1].capitalize()}}"
+                {%else%}
+                label="Undefined"
+                {%endif%}>
+        {%for aspecies in group[1]%}
+        <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
+        {%endfor%}
+      </optgroup>
+      {%endfor%}
+    </select>
+  </div>
+
+  <div class="form-group">
+    <input type="submit" value="Select" class="btn btn-primary" />
+  </div>
+</form>
+{%else%}
+<p class="text-danger">
+  <span class="glyphicon glyphicon-exclamation-mark"></span>
+  We could not find species to select from!
+</p>
+{%endif%}
+{%endmacro%}