diff options
| -rw-r--r-- | qc_app/dbinsert.py | 25 | ||||
| -rw-r--r-- | qc_app/samples.py | 120 |
2 files changed, 74 insertions, 71 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py index ab1c350..2282c8d 100644 --- a/qc_app/dbinsert.py +++ b/qc_app/dbinsert.py @@ -5,6 +5,7 @@ from typing import Union from functools import reduce from datetime import datetime +import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor from flask import ( @@ -12,7 +13,7 @@ from flask import ( current_app as app) from . import jobs -from .db_utils import database_connection +from .db_utils import with_db_connection, database_connection dbinsertbp = Blueprint("dbinsert", __name__) @@ -41,17 +42,16 @@ def species() -> tuple: return tuple() -def species_by_id(speciesid) -> Union[dict, None]: +def species_by_id(conn: mdb.Connection, speciesid) -> Union[dict, None]: "Retrieve the species from the database by id." - with database_connection() as conn: - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute( - ( - "SELECT " - "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName " - "FROM Species WHERE SpeciesId=%s"), - (speciesid,)) - return cursor.fetchone() + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + ( + "SELECT " + "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName " + "FROM Species WHERE SpeciesId=%s"), + (speciesid,)) + return cursor.fetchone() def genechips(): "Retrieve the genechip information from the database" @@ -362,7 +362,8 @@ def final_confirmation(): filetype=form["filetype"], totallines=form["totallines"], species=speciesid, genechipid=genechipid, studyid=studyid, datasetid=datasetid, the_species=selected_keys( - species_by_id(speciesid), ("SpeciesName", "Name", "MenuName")), + with_db_connection(lambda conn: species_by_id(conn, speciesid)), + ("SpeciesName", "Name", "MenuName")), platform=selected_keys( platform_by_id(genechipid), ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")), diff --git a/qc_app/samples.py b/qc_app/samples.py index 1063fb8..dee08e5 100644 --- a/qc_app/samples.py +++ b/qc_app/samples.py @@ -17,8 +17,8 @@ from flask import ( 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 +from .db_utils import with_db_connection, database_connection samples = Blueprint("samples", __name__) @@ -29,7 +29,8 @@ def select_species(): species_id = request.form.get("species_id") if bool(species_id): species_id = int(species_id) - species = species_by_id(species_id) + species = with_db_connection( + lambda conn: species_by_id(conn, species_id)) if bool(species): return render_template( "samples/select-population.html", @@ -72,40 +73,42 @@ def population_by_id(conn: mdb.Connection, population_id: int) -> dict: 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))) + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, 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 = 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)) + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, 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") @@ -195,33 +198,33 @@ def upload_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 + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, 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"], @@ -232,5 +235,4 @@ def upload_samples(): 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." + return "SUCCESS: Respond with a better UI than this." |