Initialise "Platforms" section.

1 files changed, 86 insertions, 0 deletions

diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
new file mode 100644
index 0000000..56390ab
--- /dev/null
+++ b/uploader/platforms/views.py
@@ -0,0 +1,86 @@
+"""The endpoints for the platforms"""
+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 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 = safe_int(request.args.get("start_from") or 0)
+        if start_from < 0:
+            start_from = 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:
+        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")
+
+        raise NotImplementedError("This still needs to be implemented.")