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"""Code regarding samples"""
import csv
from pathlib import Path
from typing import Iterator
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from quality_control.parsing import take
from .files import save_file
from .db_utils import with_db_connection
from .dbinsert import species_by_id, groups_by_species
samples = Blueprint("samples", __name__)
@samples.route("/upload/species", methods=["POST"])
def select_species():
"""Select the species."""
index_page = redirect(url_for("entry.upload_file"))
species_id = request.form.get("species_id")
if bool(species_id):
species_id = int(species_id)
species = species_by_id(species_id)
if bool(species):
return render_template(
"samples/select-population.html",
species=species,
populations=groups_by_species(species_id))
flash("Invalid species selected!", "alert-error")
flash("You need to select a species", "alert-error")
return index_page
def save_population(conn: mdb.Connection, population_details: dict) -> int:
"""Save the population details to the db."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT MAX(Id) AS last_id FROM InbredSet")
new_id = cursor.fetchone()["last_id"] + 1
cursor.execute(
"INSERT INTO InbredSet("
"Id, InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
"MenuOrderId, Description"
") "
"VALUES ("
"%(Id)s, %(InbredSetId)s, %(InbredSetName)s, %(Name)s, "
"%(SpeciesId)s, %(FullName)s, %(MenuOrderId)s, %(Description)s"
")",
{
"Id": new_id,
"InbredSetId": new_id,
"MenuOrderId": 0,
**population_details
})
return new_id
def population_by_id(conn: mdb.Connection, population_id: int) -> dict:
"""Get the grouping/population by id."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
(population_id,))
return cursor.fetchone()
@samples.route("/upload/create-population", methods=["POST"])
def create_population():
"""Create new grouping/population."""
species_page = redirect(url_for("samples.select_species"), code=307)
species = species_by_id(request.form.get("species_id"))
pop_name = request.form.get("inbredset_name").strip()
pop_fullname = request.form.get("inbredset_fullname").strip()
if not bool(species):
flash("Invalid species!", "alert-error error-create-population")
return species_page
if (not bool(pop_name)) or (not bool(pop_fullname)):
flash("You *MUST* provide a grouping/population name",
"alert-error error-create-population")
return species_page
pop_id = with_db_connection(lambda conn: save_population(conn, {
"SpeciesId": species["SpeciesId"],
"Name": pop_name,
"InbredSetName": pop_fullname,
"FullName": pop_fullname,
"Family": request.form.get("inbredset_family") or None,
"Description": request.form.get("description") or None
}))
flash("Grouping/Population created successfully.", "alert-success")
return render_template(
"samples/upload-samples.html",
species=species,
population=with_db_connection(
lambda conn: population_by_id(conn, pop_id)))
@samples.route("/upload/select-population", methods=["POST"])
def select_population():
"""Select from existing groupings/populations."""
species_page = redirect(url_for("samples.select_species"), code=307)
species = species_by_id(request.form.get("species_id"))
pop_id = int(request.form.get("inbredset_id"))
population = with_db_connection(lambda conn: population_by_id(conn, pop_id))
if not bool(species):
flash("Invalid species!", "alert-error error-select-population")
return species_page
if not bool(population):
flash("Invalid grouping/population!",
"alert-error error-select-population")
return species_page
return render_template("samples/upload-samples.html",
species=species,
population=population)
def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs) -> Iterator[dict]:
"""Read the samples file."""
with open(filepath, "r", encoding="utf-8") as inputfile:
reader = csv.DictReader(
inputfile,
fieldnames=(
None if firstlineheading
else ("Name", "Name2", "Symbol", "Alias")),
delimiter=separator,
quotechar=kwargs.get("quotechar", '"'))
for row in reader:
yield row
def save_samples_data(conn: mdb.Connection,
speciesid: int,
file_data: Iterator[dict]):
"""Save the samples to DB."""
data = ({**row, "SpeciesId": speciesid} for row in file_data)
with conn.cursor() as cursor:
while True:
batch = take(data, 5000)
if len(batch) == 0:
break
cursor.executemany(
"INSERT INTO Strain(Name, Name2, SpeciesId, Symbol, Alias) "
"VALUES("
" %(Name)s, %(Name2)s, %(SpeciesId)s, %(Symbol)s, %(Alias)s"
") ON DUPLICATE KEY UPDATE Name=Name",
batch)
def cross_reference_samples(conn: mdb.Connection,
species_id: int,
population_id: int,
strain_names: Iterator[str]):
"""Link samples to their population."""
with conn.cursor(cursorclass=DictCursor) as cursor:
while True:
batch = take(strain_names, 5000)
if len(batch) == 0:
break
params_str = ", ".join(["%s"] * len(batch))
## This query is slow -- investigate.
cursor.execute(
"SELECT s.Id FROM Strain AS s LEFT JOIN StrainXRef AS sx "
"ON s.Id = sx.StrainId WHERE s.SpeciesId=%s AND s.Name IN "
f"({params_str}) AND sx.StrainId IS NULL",
(species_id,) + tuple(batch))
strain_ids = (sid["Id"] for sid in cursor.fetchall())
cursor.execute(
"SELECT MAX(OrderId) AS loid FROM StrainXRef WHERE InbredSetId=%s",
(population_id,))
last_order_id = cursor.fetchone()["loid"]
cursor.executemany(
"INSERT INTO StrainXRef( "
" InbredSetId, StrainId, OrderId, Used_for_mapping, PedigreeStatus"
")"
"VALUES ("
" %(pop_id)s, %(strain_id)s, %(order_id)s, %(mapping)s, "
" %(pedigree)s"
")",
tuple({
"pop_id": population_id,
"strain_id": strain_id,
"order_id": order_id,
"mapping": "N",
"pedigree": None
} for order_id, strain_id in
enumerate(strain_ids, start=(last_order_id+10))))
@samples.route("/upload/samples", methods=["POST"])
def upload_samples():
"""Upload the samples."""
samples_uploads_page = redirect(url_for("samples.select_population"),
code=307)
species = species_by_id(request.form.get("species_id"))
if not bool(species):
flash("Invalid species!", "alert-error")
return samples_uploads_page
population = with_db_connection(
lambda conn: population_by_id(
conn, int(request.form.get("inbredset_id"))))
if not bool(population):
flash("Invalid grouping/population!", "alert-error")
return samples_uploads_page
samples_file = save_file(request.files["samples_file"], Path(app.config["UPLOAD_FOLDER"]))
if not bool(samples_file):
flash("You need to provide a file with the samples data.")
return samples_uploads_page
firstlineheading = (request.form.get("first_line_heading") == "on")
separator = request.form.get("separator")
if separator == "other":
separator = request.form.get("other_separator")
if not bool(separator):
flash("You need to provide a separator character.", "alert-error")
return samples_uploads_page
def __insert_samples__(conn: mdb.Connection):
save_samples_data(
conn,
species["SpeciesId"],
read_samples_file(samples_file, separator, firstlineheading))
cross_reference_samples(
conn,
species["SpeciesId"],
population["InbredSetId"],
(row["Name"] for row in read_samples_file(samples_file, separator, firstlineheading)))
with_db_connection(__insert_samples__)
return "SUCCESS: Respond with a better UI than this."
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