1 files changed, 112 insertions, 0 deletions
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
new file mode 100644
index 0000000..2d61b6a
--- /dev/null
+++ b/uploader/platforms/views.py
@@ -0,0 +1,112 @@
+"""The endpoints for the platforms"""
+from MySQLdb.cursors import DictCursor
+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
+from uploader.datautils import safe_int, order_by_family, enumerate_sequence
+
+from .models import (save_new_platform,
+                     platforms_by_species,
+                     species_platforms_count)
+
+platformsbp = Blueprint("platforms", __name__)
+render_template = make_template_renderer("platforms")
+
+@platformsbp.route("platforms", methods=["GET"])
+@require_login
+def index():
+    """Entry-point to the platforms feature."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        if not bool(request.args.get("species_id")):
+            return render_template(
+                "platforms/index.html",
+                species=order_by_family(all_species(conn)),
+                activelink="platforms")
+
+        species = species_by_id(conn, request.args["species_id"])
+        if not bool(species):
+            flash("No species selected.", "alert-danger")
+            return redirect(url_for("species.platforms.index"))
+
+        return redirect(url_for("species.platforms.list_platforms",
+                                species_id=species["SpeciesId"]))
+
+
+@platformsbp.route("<int:species_id>/platforms", methods=["GET"])
+@require_login
+def list_platforms(species_id: int):
+    """List all the available genetic sequencing platforms."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("No species provided.", "alert-danger")
+            return redirect(url_for("species.platforms.index"))
+
+        start_from = max(safe_int(request.args.get("start_from") or 0), 0)
+        count = safe_int(request.args.get("count") or 20)
+        return render_template(
+            "platforms/list-platforms.html",
+            species=species,
+            platforms=enumerate_sequence(
+                platforms_by_species(conn,
+                                     species_id,
+                                     offset=start_from,
+                                     limit=count),
+                start=start_from+1),
+            start_from=start_from,
+            count=count,
+            total_platforms=species_platforms_count(conn, species_id),
+            activelink="list-platforms")
+
+
+@platformsbp.route("<int:species_id>/platforms/create", methods=["GET", "POST"])
+@require_login
+def create_platform(species_id: int):
+    """Create a new genetic sequencing platform."""
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          conn.cursor(cursorclass=DictCursor) as cursor):
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("No species provided.", "alert-danger")
+            return redirect(url_for("species.platforms.index"))
+
+        if request.method == "GET":
+            return render_template(
+                "platforms/create-platform.html",
+                species=species,
+                activelink="create-platform")
+
+        try:
+            form = request.form
+            _new_platform = save_new_platform(
+                cursor,
+                species_id,
+                form["geo-platform"],
+                form["platform-name"],
+                form["platform-shortname"],
+                form["platform-title"],
+                form.get("go-tree-value") or None)
+        except KeyError as _kerr:
+            flash(f"Required value for field {_kerr.args[0]} was not provided.",
+                  "alert-danger")
+            return redirect(url_for("species.platforms.create_platform",
+                                    species_id=species_id))
+        except AssertionError as _aerr:
+            flash(f"Platform with GeoPlatform value of '{form['geo-platform']}'"
+                  f" already exists for species '{species['FullName']}'.",
+                  "alert-danger")
+            return redirect(url_for("species.platforms.create_platform",
+                                    species_id=species_id))
+
+    flash("Platform created successfully", "alert-success")
+    return redirect(url_for("species.platforms.list_platforms",
+                            species_id=species_id))