Add more fields when creating a population

Add more of the missing fields when creating a population, to ensure
that the created population works as expected.

4 files changed, 137 insertions, 8 deletions

diff --git a/uploader/population/models.py b/uploader/population/models.py
index 4485e52..782bc9f 100644
--- a/uploader/population/models.py
+++ b/uploader/population/models.py
@@ -26,21 +26,43 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
 
     return tuple()
 
+
+def population_families(conn) -> tuple:
+    """Fetch the families under which populations are grouped."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL")
+        return tuple(row["Family"] for row in cursor.fetchall())
+
+
+def population_genetic_types(conn) -> tuple:
+    """Fetch the families under which populations are grouped."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT DISTINCT(GeneticType) FROM InbredSet WHERE GeneticType IS "
+            "NOT NULL")
+        return tuple(row["GeneticType"] for row in cursor.fetchall())
+
+
 def save_population(conn: mdb.Connection, population_details: dict) -> dict:
     """Save the population details to the db."""
     with conn.cursor(cursorclass=DictCursor) as cursor:
+        #TODO: Handle FamilyOrder here
         cursor.execute(
             "INSERT INTO InbredSet("
             "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
-            "MenuOrderId, Description"
+            "public, MappingMethodId, GeneticType, Family, MenuOrderId, "
+            "InbredSetCode, Description"
             ") "
             "VALUES ("
             "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
-            "%(FullName)s, %(MenuOrderId)s, %(Description)s"
+            "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, "
+            "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s"
             ")",
             {
                 "MenuOrderId": 0,
                 "InbredSetId": 0,
+                "public": 2,
                 **population_details
             })
         new_id = cursor.lastrowid
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 84dffdb..5be19ae 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -18,7 +18,9 @@ from uploader.species.models import (all_species,
                                      order_species_by_family)
 
 from .models import (save_population,
+                     population_families,
                      populations_by_species,
+                     population_genetic_types,
                      population_by_species_and_id)
 
 __active_link__ = "populations"
@@ -100,6 +102,14 @@ def create_population(species_id: int):
             return render_template(
                 "populations/create-population.html",
                 species=species,
+                families = population_families(conn),
+                genetic_types = population_genetic_types(conn),
+                mapping_methods=(
+                    {"id": "0", "value": "No mapping support"},
+                    {"id": "1", "value": "GEMMA, QTLReaper, R/qtl"},
+                    {"id": "2", "value": "GEMMA"},
+                    {"id": "3", "value": "R/qtl"},
+                    {"id": "4", "value": "GEMMA, PLINK"}),
                 activelink="create-population",
                 **error_values)
 
@@ -142,8 +152,11 @@ def create_population(species_id: int):
             "Name": population_name,
             "InbredSetName": population_fullname,
             "FullName": population_fullname,
-            "Family": request.form.get("inbredset_family") or None,
-            "Description": request.form.get("population_description") or None
+            "InbredSetCode": request.form.get("population_code") or None,
+            "Description": request.form.get("population_description") or None,
+            "Family": request.form.get("population_family") or None,
+            "MappingMethodId": request.form.get("population_mapping_method_id"),
+            "GeneticType": request.form.get("population_genetic_type") or None
         })
 
         return redirect(url_for("species.populations.view_population",
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html
index 6a96148..12811fd 100644
--- a/uploader/templates/populations/create-population.html
+++ b/uploader/templates/populations/create-population.html
@@ -88,8 +88,7 @@
         <p>
           This is a short representative, but constrained name for your
           population.
-        </p>
-        <p>
+          <br />
           The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens
           and underscores. Any other character will cause the name to be
           rejected.
@@ -97,6 +96,20 @@
       </small>
     </div>
 
+    <div class="form-group">
+      <label for="txt-population-code" class="form-label">Population Code</label>
+      <input type="text"
+             id="txt-population-code"
+             name="population_code"
+             maxLength="5"
+             minLength="3"
+             value="{{error_values.population_code or ''}}"
+             class="form-control" />
+      <small class="form-text text-muted">
+        … document what this field is for …
+      </small>
+    </div>
+
     <div {%if errors.population_description%}
          class="form-group has-error"
          {%else%}
@@ -119,14 +132,82 @@
           This is a more detailed description for your population. This is
           useful to communicate with other researchers some details regarding
           your population, and what its about.
-        </p>
-        <p>
+          <br />
           Put, here, anything that describes your population but does not go
           cleanly under metadata.
         </p>
       </small>
     </div>
 
+    <div {%if errors.population_family%}
+         class="form-group has-error"
+         {%else%}
+         class="form-group"
+         {%endif%}>
+      <label for="select-population-family" class="form-label">Family</label>
+      <select id="select-population-family"
+              name="population_family"
+              class="form-control"
+              required="required">
+        <option value="">Please select a family</option>
+        {%for family in families%}
+        <option value="{{family}}"
+                {%if error_values.population_family == family%}
+                selected="selected"
+                {%endif%}>{{family}}</option>
+        {%endfor%}
+      </select>
+      <small class="form-text text-muted">
+        <p>… provide some documentation on what this field does …</p>
+      </small>
+    </div>
+
+    <div {%if errors.population_mapping_method_id%}
+         class="form-group has-error"
+         {%else%}
+         class="form-group"
+         {%endif%}>
+      <label for="select-population-mapping-methods"
+             class="form-label">Mapping Methods</label>
+
+      <select id="select-population-mapping-methods"
+              name="population_mapping_method_id"
+              class="form-control"
+              required="required">
+        <option value="">Select appropriate mapping methods</option>
+        {%for mmethod in mapping_methods%}
+        <option value="{{mmethod.id}}"
+                {%if error_values.population_mapping_method_id == mmethod.id%}
+                selected="selected"
+                {%endif%}>{{mmethod.value}}</option>
+        {%endfor%}
+      </select>
+
+      <small class="form-text text-muted">
+        <p>Select the mapping methods that your population will support.</p>
+      </small>
+    </div>
+
+    <div {%if errors.population_genetic_type%}
+         class="form-group has-error"
+         {%else%}
+         class="form-group"
+         {%endif%}>
+      <label for="select-population-genetic-type"
+             class="form-label">Genetic Type</label>
+      <select id="select-population-genetic-type"
+              name="population_genetic_type"
+              class="form-control">
+        <option value="">Select proper genetic type</option>
+        {%for gtype in genetic_types%}
+        <option value="{{gtype}}"
+                {%if error_values.population_genetic_type == gtype%}
+                selected="selected"
+                {%endif%}>{{gtype}}</option>
+        {%endfor%}
+      </select>
+    </div>
+
     <div class="form-group">
       <input type="submit"
              value="create population"
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 7eb1362..3ae76ab 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -29,12 +29,25 @@
     <dt>FullName</dt>
     <dd>{{population.FullName}}</dd>
 
+    <dt>Code</dt>
+    <dd>{{population.InbredSetCode}}</dd>
+
+    <dt>Genetic Type</dt>
+    <dd>{{population.GeneticType}}</dd>
+
+    <dt>Family</dt>
+    <dd>{{population.Family}}</dd>
+
     <dt>Description</dt>
     <dd><pre>{{population.Description or "-"}}</pre></dd>
   </dl>
 </div>
 
 <div class="row">
+  … maybe provide a way to organise populations in the same family here …
+</div>
+
+<div class="row">
   <h3>Actions</h3>
 
   <p>