Create populations (InbredSet groups) under Species.

3 files changed, 164 insertions, 11 deletions

diff --git a/uploader/population/views.py b/uploader/population/views.py
index e21465c..fe318e1 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -1,4 +1,8 @@
 """Views dealing with populations/inbredsets"""
+import re
+import json
+import base64
+
 from flask import (flash,
                    request,
                    url_for,
@@ -54,12 +58,30 @@ def list_species_populations(species_id: int):
             activelink="list-populations")
 
 
-def valid_population_name(population_name) -> bool:
-    """Check whether the given name is a valid population name."""
-    raise NotImplementedError("Please implement this…")
+def valid_population_name(population_name: str) -> bool:
+    """
+    Check whether the given name is a valid population name.
+
+    Parameters
+    ----------
+    population_name: a string of characters.
+
+    Checks For
+    ----------
+    * The name MUST start with an alphabet [a-zA-Z]
+    * The name MUST end with an alphabet [a-zA-Z] or number [0-9]
+    * The name MUST be composed of alphabets [a-zA-Z], numbers [0-9],
+      underscores (_) and/or hyphens (-).
+
+    Returns
+    -------
+    Boolean indicating whether or not the name is valid.
+    """
+    pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$")
+    return bool(pattern.match(population_name))
 
 
-@popbp.route("/<int:species_id>/create-population/", methods=["GET", "POST"])
+@popbp.route("/<int:species_id>/populations/create", methods=["GET", "POST"])
 @require_login
 def create_population(species_id: int):
     """Create a new population."""
@@ -67,10 +89,18 @@ def create_population(species_id: int):
         species = species_by_id(conn, species_id)
 
         if request.method == "GET":
+            error_values = request.args.get("error_values")
+            if bool(error_values):
+                base64.b64encode(
+                json.dumps(dict(request.form)).encode("utf8"))
+                error_values = json.loads(
+                    base64.b64decode(
+                        error_values.encode("utf8")).decode("utf8"))
             return render_template(
                 "populations/create-population.html",
                 species=species,
-                continue_to=request.args.get("continue_uri"))
+                activelink="create-population",
+                **error_values)
 
         error = False
 
@@ -78,7 +108,8 @@ def create_population(species_id: int):
             flash("You must select a species.", "alert-danger")
             error = True
 
-        population_name = request.form.get("population_name", "").strip()
+        population_name = (request.form.get(
+            "population_name") or "").strip()
         if not bool(population_name):
             flash("You must provide a name for the population!", "alert-danger")
             error = True
@@ -89,15 +120,19 @@ def create_population(species_id: int):
                   "alert-danger")
             error = True
 
-        population_fullname = request.form.get("inbredset_fullname", "").strip()
+        population_fullname = (request.form.get(
+            "population_fullname") or "").strip()
         if not bool(population_fullname):
-            flash("You MUST provide a Full Name for the population."
+            flash("You MUST provide a Full Name for the population.",
                   "alert-danger")
             error = True
 
         if error:
+            values = base64.b64encode(
+                json.dumps(dict(request.form)).encode("utf8"))
             return redirect(url_for("species.populations.create_population",
-                                    **dict(request.args)))
+                                    species_id=species["SpeciesId"],
+                                    error_values=values))
 
         new_population = save_population(conn, {
             "SpeciesId": species["SpeciesId"],
@@ -105,7 +140,7 @@ def create_population(species_id: int):
             "InbredSetName": population_fullname,
             "FullName": population_fullname,
             "Family": request.form.get("inbredset_family") or None,
-            "Description": request.form.get("description") or None
+            "Description": request.form.get("population_description") 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
new file mode 100644
index 0000000..a27a134
--- /dev/null
+++ b/uploader/templates/populations/create-population.html
@@ -0,0 +1,118 @@
+{%extends "populations/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Create Population{%endblock%}
+
+{%block pagetitle%}Create Population{%endblock%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="create-population"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.create_population',
+           species_id=species.SpeciesId)}}">create population</a>
+</li>
+{%endblock%}
+
+
+{%block contents%}
+<div class="row">
+  <p>The population is the next hierarchical node under Species. Data is grouped under a specific population, under a particular species.</p>
+  <p>
+    This page enables you to create a new population, in the case that you
+    cannot find the population you want in the
+    <a
+      href="{{url_for('species.populations.list_species_populations',
+            species_id=species.SpeciesId)}}"
+      title="Population for species '{{species.FullName}}'.">
+      list of species populations
+    </a>
+  </p>
+</div>
+
+<div class="row">
+  <form method="POST"
+        action="{{url_for('species.populations.create_population',
+                species_id=species.SpeciesId)}}">
+
+    <legend>Create Population</legend>
+
+    <div class="form-group">
+      <label for="txt-population-fullname" class="form-label">Full Name</label>
+      <input type="text"
+             id="txt-population-fullname"
+             name="population_fullname"
+             required="required"
+             minLength="3"
+             maxLength="100"
+             value="{{population_fullname or ''}}"
+             class="form-control" />
+      <small class="form-text text-muted">
+        <p>
+          This is a descriptive name for your population &mdash; useful for
+          humans.
+        </p>
+      </small>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-population-name" class="form-label">Name</label>
+      <input type="text"
+             id="txt-population-name"
+             name="population_name"
+             required="required"
+             minLength="3"
+             maxLength="30"
+             value="{{population_name or ''}}"
+             class="form-control" />
+      <small class="form-text text-muted">
+        <p>
+          This is a short representative, but constrained name for your
+          population.
+        </p>
+        <p>
+          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.
+        </p>
+      </small>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-population-description" class="form-label">
+        Description
+      </label>
+      <textarea id="txt-population-description"
+                name="population_description"
+                required="required"
+                class="form-control"
+                rows="5">{{population_description or ''}}</textarea>
+      <small class="form-text text-muted">
+        <p>
+          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>
+          Put, here, anything that describes your population but does not go
+          cleanly under metadata.
+        </p>
+      </small>
+    </div>
+
+    <div class="form-group">
+      <input type="submit"
+             value="create population"
+             class="btn btn-primary"  />
+    </div>
+
+  </form>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+<p>&hellip; maybe provide species details here, perhaps? &hellip;</p>
+{%endblock%}
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 2ab7ca3..7eb1362 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -30,7 +30,7 @@
     <dd>{{population.FullName}}</dd>
 
     <dt>Description</dt>
-    <dd>{{population.Description or "-"}}</dd>
+    <dd><pre>{{population.Description or "-"}}</pre></dd>
   </dl>
 </div>