Initialise the populations package and update references.

3 files changed, 177 insertions, 0 deletions

diff --git a/uploader/population/__init__.py b/uploader/population/__init__.py
new file mode 100644
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+++ b/uploader/population/__init__.py
@@ -0,0 +1,3 @@
+"""Package to handle creation and management of Populations/InbredSets"""
+
+from .views import popbp
diff --git a/uploader/population/models.py b/uploader/population/models.py
new file mode 100644
index 0000000..4485e52
--- /dev/null
+++ b/uploader/population/models.py
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+"""Functions for accessing the database relating to species populations."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def population_by_id(conn: mdb.Connection, population_id) -> dict:
+    """Get the grouping/population by id."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
+                       (population_id,))
+        return cursor.fetchone()
+
+def population_by_species_and_id(
+        conn: mdb.Connection, species_id, population_id) -> dict:
+    """Retrieve a population by its identifier and species."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s",
+                       (species_id, population_id))
+        return cursor.fetchone()
+
+def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
+    "Retrieve group (InbredSet) information from the database."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        query = "SELECT * FROM InbredSet WHERE SpeciesId=%s"
+        cursor.execute(query, (speciesid,))
+        return tuple(cursor.fetchall())
+
+    return tuple()
+
+def save_population(conn: mdb.Connection, population_details: dict) -> dict:
+    """Save the population details to the db."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "INSERT INTO InbredSet("
+            "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+            "MenuOrderId, Description"
+            ") "
+            "VALUES ("
+            "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
+            "%(FullName)s, %(MenuOrderId)s, %(Description)s"
+            ")",
+            {
+                "MenuOrderId": 0,
+                "InbredSetId": 0,
+                **population_details
+            })
+        new_id = cursor.lastrowid
+        cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
+                       (new_id, new_id))
+        return {
+            **population_details,
+            "Id": new_id,
+            "InbredSetId": new_id,
+            "population_id": new_id
+        }
diff --git a/uploader/population/views.py b/uploader/population/views.py
new file mode 100644
index 0000000..cd5e20b
--- /dev/null
+++ b/uploader/population/views.py
@@ -0,0 +1,120 @@
+"""Views dealing with populations/inbredsets"""
+from flask import (flash,
+                   request,
+                   url_for,
+                   redirect,
+                   Blueprint,
+                   current_app as app)
+
+from uploader.ui import make_template_renderer
+from uploader.authorisation import require_login
+from uploader.db_utils import database_connection
+from uploader.species.models import (all_species,
+                                     species_by_id,
+                                     order_species_by_family)
+
+from .models import (save_population,
+                     populations_by_species)
+
+__active_link__ = "populations"
+popbp = Blueprint("populations", __name__)
+render_template = make_template_renderer("populations")
+
+
+@popbp.route("/", methods=["GET", "POST"])
+@require_login
+def index():
+    """Entry point for populations."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        if not bool(request.args.get("species_id")):
+            return render_template(
+                "populations/index.html",
+                species=order_species_by_family(all_species(conn)))
+        species = species_by_id(conn, request.args.get("species_id"))
+        if not bool(species):
+            flash("Invalid species identifier provided!", "alert-danger")
+            return redirect(url_for("populations.index"))
+        return redirect(url_for("populations.list_species_populations",
+                                species_id=species["SpeciesId"]))
+
+@popbp.route("/<int:species_id>", methods=["GET"])
+@require_login
+def list_species_populations(species_id: int):
+    """List a particular species' populations."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("No species was found for given ID.", "alert-danger")
+            return redirect(url_for("populations.index"))
+        return render_template(
+            "populations/list-populations.html",
+            species=species,
+            populations=populations_by_species(conn, species_id),
+            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…")
+
+
+@popbp.route("/<int:species_id>/create-population/", methods=["GET", "POST"])
+@require_login
+def create_population(species_id: int):
+    """Create a new population."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+
+        if request.method == "GET":
+            return render_template(
+                "populations/create-population.html",
+                species=species,
+                continue_to=request.args.get("continue_uri"))
+
+        error = False
+
+        if not bool(species):
+            flash("You must select a species.", "alert-danger")
+            error = True
+
+        population_name = request.form.get("population_name", "").strip()
+        if not bool(population_name):
+            flash("You must provide a name for the population!", "alert-danger")
+            error = True
+
+        if not valid_population_name(population_name):
+            flash("The population name can only contain letters, numbers, "
+                  "hyphens and underscores.",
+                  "alert-danger")
+            error = True
+
+        population_fullname = request.form.get("inbredset_fullname", "").strip()
+        if not bool(population_fullname):
+            flash("You MUST provide a Full Name for the population."
+                  "alert-danger")
+            error = True
+
+        if error:
+            return redirect(url_for("populations.create_population",
+                                    **dict(request.args)))
+
+        new_population = save_population(conn, {
+            "SpeciesId": species["SpeciesId"],
+            "Name": population_name,
+            "InbredSetName": population_fullname,
+            "FullName": population_fullname,
+            "Family": request.form.get("inbredset_family") or None,
+            "Description": request.form.get("description") or None
+        })
+
+        return redirect(url_for("populations.view_population",
+                                species_id=species["SpeciesId"],
+                                population_id=new_population["InbredSetId"]))
+
+
+@popbp.route("/<int:species_id>/populations/<int:population_id>",
+             methods=["GET"])
+@require_login
+def view_population(species_id: int, population_id: int):
+    """View the details of a population."""
+    raise NotImplementedError("Please implement this too …")