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-rw-r--r--uploader/genotypes/models.py41
-rw-r--r--uploader/genotypes/views.py39
2 files changed, 78 insertions, 2 deletions
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")