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-rw-r--r--uploader/population/views.py55
-rw-r--r--uploader/templates/populations/create-population.html118
-rw-r--r--uploader/templates/populations/view-population.html2
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>