From 17defa03f395aa9895b524ef3125e138b3987507 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 17 Sep 2024 16:57:39 -0500
Subject: Display some genotype information.

---
 uploader/genotypes/models.py | 41 +++++++++++++++++++++++++++++++++++++++++
 uploader/genotypes/views.py  | 39 +++++++++++++++++++++++++++++++++++++--
 2 files changed, 78 insertions(+), 2 deletions(-)
 create mode 100644 uploader/genotypes/models.py

(limited to 'uploader/genotypes')

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
new file mode 100644
index 0000000..53c5fb8
--- /dev/null
+++ b/uploader/genotypes/models.py
@@ -0,0 +1,41 @@
+"""Functions for handling genotypes."""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+from uploader.db_utils import debug_query
+
+def genocode_by_population(
+        conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
+    """Get the allele/genotype codes."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GenoCode WHERE InbredSetId=%s",
+                       (population_id,))
+        return tuple(dict(item) for item in cursor.fetchall())
+
+
+def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
+    """Find the total count of the genotype markers for a species."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT COUNT(Name) AS markers_count FROM Geno WHERE SpeciesId=%s",
+            (species_id,))
+        return int(cursor.fetchone()["markers_count"])
+
+
+def genotype_markers(
+        conn: mdb.Connection,
+        species_id: int,
+        offset: int = 0,
+        limit: Optional[int] = None
+) -> tuple[dict, ...]:
+    """Retrieve markers from the database."""
+    _query = "SELECT * FROM Geno WHERE SpeciesId=%s"
+    if bool(limit) and limit > 0:
+        _query = _query + f" LIMIT {limit} OFFSET {offset}"
+
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, (species_id,))
+        debug_query(cursor)
+        return tuple(dict(row) for row in cursor.fetchall())
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 885e008..0618949 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -7,13 +7,17 @@ from flask import (flash,
                    render_template,
                    current_app as app)
 
-from uploader.datautils import order_by_family
 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"])
@@ -72,4 +76,35 @@ def select_population(species_id: int):
 @require_login
 def list_genotypes(species_id: int, population_id: int):
     """List genotype details for species and population."""
-    return f"Would list geno info for population {population_id} from species {species_id}"
+    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))
+
+        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-genotypes.html",
+                               species=species,
+                               population=population,
+                               genocode=genocode_by_population(
+                                   conn, population_id),
+                               total_markers=genotype_markers_count(
+                                   conn, species_id),
+                               start_from=start_from,
+                               count=count,
+                               markers=markers,
+                               activelink="list-genotypes")
-- 
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