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"Handle inserting data into the database"
import os
import json
import datetime
from functools import reduce
import requests
from redis import Redis
from MySQLdb.cursors import DictCursor
from flask import (
flash, request, url_for, Blueprint, redirect, render_template,
current_app as app)
from . import jobs
from .db_utils import database_connection
dbinsertbp = Blueprint("dbinsert", __name__)
def render_error(error_msg):
"Render the generic error page"
return render_template("dbupdate_error.html", error_message=error_msg), 400
def make_menu_items_grouper(grouping_fn=lambda item: item):
"Build function to be used to group menu items."
def __grouper__(acc, row):
grouping = grouping_fn(row[2])
row_values = (row[0].strip(), row[1].strip())
if acc.get(grouping) is None:
return {**acc, grouping: (row_values,)}
return {**acc, grouping: (acc[grouping] + (row_values,))}
return __grouper__
def species() -> tuple:
"Retrieve the species from the database."
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
"FROM Species")
return tuple(cursor.fetchall())
return tuple()
def genechips():
"Retrieve the genechip information from the database"
def __organise_by_species__(acc, chip):
speciesid = chip["SpeciesId"]
if acc.get(speciesid) is None:
return {**acc, speciesid: (chip,)}
return {**acc, species: acc[speciesid] + (chip,)}
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC")
return reduce(__organise_by_species__, cursor.fetchall(), {})
return {}
def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
"Retrieve the studies by the related species and gene platform"
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
query = (
"SELECT Species.SpeciesId, ProbeFreeze.* "
"FROM Species INNER JOIN InbredSet "
"ON Species.SpeciesId=InbredSet.SpeciesId "
"INNER JOIN ProbeFreeze "
"ON InbredSet.InbredSetId=ProbeFreeze.InbredSetId "
"WHERE Species.SpeciesId = %s "
"AND ProbeFreeze.ChipId = %s")
cursor.execute(query, (speciesid, genechipid))
return tuple(cursor.fetchall())
return tuple()
def groups_by_species(speciesid:int) -> tuple:
"Retrieve group (InbredSet) information from the database."
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
query = "SELECT * FROM InbredSet WHERE SpeciesId=%s"
cursor.execute(query, (speciesid,))
return tuple(cursor.fetchall())
return tuple()
def organise_groups_by_family(acc:dict, group:dict) -> dict:
"Organise the group (InbredSet) information by the group field"
family = group["Family"]
if acc.get(family):
return {**acc, family: acc[family] + (group,)}
return {**acc, family: (group,)}
def tissues() -> tuple:
"Retrieve type (Tissue) information from the database."
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM Tissue ORDER BY Name")
return tuple(cursor.fetchall())
return tuple()
@dbinsertbp.route("/platform", methods=["POST"])
def select_platform():
"Select the platform (GeneChipId) used for the data."
job_id = request.form["job_id"]
with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
job = jobs.job(rconn, job_id)
if job:
filename = job["filename"]
filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
if os.path.exists(filepath):
default_species = 1
gchips = genechips()
return render_template(
"select_platform.html", filename=filename,
filetype=job["filetype"], default_species=default_species,
species=species(), genechips=gchips[default_species],
genechips_data=json.dumps(gchips))
return render_error(f"File '{filename}' no longer exists.")
return render_error(f"Job '{job_id}' no longer exists.")
return render_error("Unknown error")
@dbinsertbp.route("/study", methods=["POST"])
def select_study():
"View to select/create the study (ProbeFreeze) associated with the data."
form = request.form
try:
assert form.get("filename"), "filename"
assert form.get("filetype"), "filetype"
assert form.get("species"), "species"
assert form.get("genechipid"), "platform"
speciesid = form["species"]
genechipid = form["genechipid"]
the_studies = studies_by_species_and_platform(speciesid, genechipid)
the_groups = reduce(
organise_groups_by_family, groups_by_species(speciesid), {})
return render_template(
"select_study.html", filename=form["filename"],
filetype=form["filetype"], species=speciesid, genechipid=genechipid,
studies=the_studies, groups=the_groups, tissues = tissues(),
selected_group=int(form.get("inbredsetid", -13)),
selected_tissue=int(form.get("tissueid", -13)))
except AssertionError as aserr:
return render_error(f"Missing data: {aserr.args[0]}")
@dbinsertbp.route("/create-study", methods=["POST"])
def create_study():
"Create a new study (ProbeFreeze)."
form = request.form
try:
assert form.get("filename"), "filename"
assert form.get("filetype"), "filetype"
assert form.get("species"), "species"
assert form.get("genechipid"), "platform"
assert form.get("studyname"), "study name"
assert form.get("inbredsetid"), "group"
assert form.get("tissueid"), "type/tissue"
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT MAX(Id) AS last_id FROM ProbeFreeze")
new_studyid = cursor.fetchone()["last_id"] + 1
values = (
new_studyid, new_studyid, form["genechipid"],
form["tissueid"], form["studyname"],
form.get("studyfullname", ""),
form.get("studyshortname", ""),
datetime.datetime.now().date().strftime("%Y-%m-%d"),
form["inbredsetid"])
query = (
"INSERT INTO ProbeFreeze() "
"VALUES(%s, %s, %s, %s, %s, %s, %s, %s, %s)")
cursor.execute(query, values)
flash("Study created successfully", "alert-success")
return render_template(
"continue_from_create_study.html",
filename=form["filename"], filetype=form["filetype"],
species=form["species"], genechipid=form["genechipid"],
studyid=new_studyid)
except AssertionError as aserr:
flash(f"Missing data: {aserr.args[0]}", "alert-error")
return redirect(url_for("dbinsert.select_study"), code=307)
def datasets_by_study(studyid:int) -> tuple:
"Retrieve datasets associated with a study with the ID `studyid`."
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s"
print(f"QUERY: {query}\n\tPARAMS: ({studyid},)")
cursor.execute(query, (studyid,))
return tuple(cursor.fetchall())
return tuple()
@dbinsertbp.route("/dataset", methods=["POST"])
def select_dataset():
"Select the dataset to add the file contents against"
form = request.form
try:
assert form.get("filename"), "filename"
assert form.get("filetype"), "filetype"
assert form.get("species"), "species"
assert form.get("genechipid"), "platform"
assert form.get("studyid"), "study"
studyid = form["studyid"]
datasets = datasets_by_study(studyid)
return render_template(
"select_dataset.html", filename=form["filename"],
filetype=form["filetype"], species=form["species"],
genechipid=form["genechipid"], studyid=studyid, datasets=datasets)
except AssertionError as aserr:
return render_error(f"Missing data: {aserr.args[0]}")
@dbinsertbp.route("/insert_data", methods=["POST"])
def insert_data():
"Preview the data before triggering entry into the database"
form = request.form
filename = form["filename"]
filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
if os.path.exists(filepath):
try:
species = form["species"]
filetype = form["filetype"]
datasetid = int(form["dataset"])
genechipid = int(form["genechipid"])
return (f"Would insert '{species}' data in '{filetype}' file "
f"'{filepath}' into the database with the dataset "
f"'{datasetid}' and genechip '{genechipid}'.")
except ValueError as verr:
msg = "::".join(verr.args)
return render_error(f"Invalid value: {msg}")
return render_error(f"File '{filename}' no longer exists.")
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