1 files changed, 127 insertions, 0 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
new file mode 100644
index 0000000..2ff9965
--- /dev/null
+++ b/uploader/genotypes/views.py
@@ -0,0 +1,127 @@
+"""Views for the genotypes."""
+from flask import (flash,
+                   request,
+                   url_for,
+                   redirect,
+                   Blueprint,
+                   render_template,
+                   current_app as app)
+
+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 uploader.population.models import (populations_by_species,
+                                        population_by_species_and_id)
+
+from .models import (genotype_markers,
+                     genotype_markers_count,
+                     genocode_by_population)
+
+genotypesbp = Blueprint("genotypes", __name__)
+
+@genotypesbp.route("populations/genotypes", methods=["GET"])
+@require_login
+def index():
+    """Direct entry-point for genotypes."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        if not bool(request.args.get("species_id")):
+            return render_template("genotypes/index.html",
+                                   species=order_by_family(all_species(conn)),
+                                   activelink="genotypes")
+        species = species_by_id(conn, request.args.get("species_id"))
+        if not bool(species):
+            flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
+                  "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+        return redirect(url_for("species.populations.genotypes.select_population",
+                                species_id=species["SpeciesId"]))
+
+
+@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population",
+                   methods=["GET"])
+@require_login
+def select_population(species_id: int):
+    """Select the population under which the genotypes go."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("Invalid species provided!", "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+
+        if not bool(request.args.get("population_id")):
+            return render_template("genotypes/select-population.html",
+                                   species=species,
+                                   populations=order_by_family(
+                                       populations_by_species(conn, species_id),
+                                       order_key="FamilyOrder"),
+                                   activelink="genotypes")
+
+        population = population_by_species_and_id(
+            conn, species_id, request.args.get("population_id"))
+        if not bool(population):
+            flash("Invalid population selected!", "alert-danger")
+            return redirect(url_for(
+                "species.populations.genotypes.select_population",
+                species_id=species_id))
+
+        return redirect(url_for("species.populations.genotypes.list_genotypes",
+                                species_id=species_id,
+                                population_id=population["Id"]))
+
+
+@genotypesbp.route(
+    "/<int:species_id>/populations/<int:population_id>/genotypes",
+    methods=["GET"])
+@require_login
+def list_genotypes(species_id: int, population_id: int):
+    """List genotype details for species and population."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("Invalid species provided!", "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+
+        population = population_by_species_and_id(
+            conn, species_id, population_id)
+        if not bool(population):
+            flash("Invalid population selected!", "alert-danger")
+            return redirect(url_for(
+                "species.populations.genotypes.select_population",
+                species_id=species_id))
+
+        return render_template("genotypes/list-genotypes.html",
+                               species=species,
+                               population=population,
+                               genocode=genocode_by_population(
+                                   conn, population_id),
+                               total_markers=genotype_markers_count(
+                                   conn, species_id),
+                               activelink="list-genotypes")
+
+
+@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
+@require_login
+def list_markers(species_id: int):
+    """List a species' genetic markers."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("Invalid species provided!", "alert-danger")
+            return redirect(url_for("species.populations.genotypes.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)
+        markers = enumerate_sequence(
+            genotype_markers(conn, species_id, offset=start_from, limit=count),
+            start=start_from+1)
+        return render_template("genotypes/list-markers.html",
+                               species=species,
+                               total_markers=genotype_markers_count(
+                                   conn, species_id),
+                               start_from=start_from,
+                               count=count,
+                               markers=markers,
+                               activelink="list-markers")