diff options
| -rw-r--r-- | qc_app/dbinsert.py | 14 | ||||
| -rw-r--r-- | qc_app/entry.py | 12 | ||||
| -rw-r--r-- | qc_app/samples.py | 13 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 2 | ||||
| -rw-r--r-- | scripts/insert_samples.py | 3 |
5 files changed, 29 insertions, 15 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py index 881c913..a878ff5 100644 --- a/qc_app/dbinsert.py +++ b/qc_app/dbinsert.py @@ -11,8 +11,10 @@ from flask import ( flash, request, url_for, Blueprint, redirect, render_template, current_app as app) +from qc_app.db_utils import with_db_connection, database_connection +from qc_app.db import species, species_by_id, populations_by_species + from . import jobs -from .db_utils import with_db_connection, database_connection dbinsertbp = Blueprint("dbinsert", __name__) @@ -91,7 +93,8 @@ def tissues() -> tuple: 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: + with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, + database_connection(app.config["SQL_URI"]) as conn): job = jobs.job(rconn, job_id) if job: filename = job["filename"] @@ -102,7 +105,7 @@ def select_platform(): return render_template( "select_platform.html", filename=filename, filetype=job["filetype"], totallines=int(job["currentline"]), - default_species=default_species, species=species(), + default_species=default_species, species=species(conn), genechips=gchips[default_species], genechips_data=json.dumps(gchips)) return render_error(f"File '{filename}' no longer exists.") @@ -124,7 +127,10 @@ def select_study(): the_studies = studies_by_species_and_platform(speciesid, genechipid) the_groups = reduce( - organise_groups_by_family, groups_by_species(speciesid), {}) + organise_groups_by_family, + with_db_connection( + lambda conn: populations_by_species(conn, speciesid)), + {}) return render_template( "select_study.html", filename=form["filename"], filetype=form["filetype"], totallines=form["totallines"], diff --git a/qc_app/entry.py b/qc_app/entry.py index bf78037..0cd34c5 100644 --- a/qc_app/entry.py +++ b/qc_app/entry.py @@ -14,7 +14,8 @@ from flask import ( render_template, current_app as app) -from .dbinsert import species +from qc_app.db import species +from qc_app.db_utils import with_db_connection entrybp = Blueprint("entry", __name__) @@ -78,14 +79,16 @@ def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]: def upload_file(): """Enables uploading the files""" if request.method == "GET": - return render_template("index.html", species = species()) + return render_template( + "index.html", species=with_db_connection(species)) upload_dir = app.config["UPLOAD_FOLDER"] request_errors = errors(request) if request_errors: for error in request_errors: flash(error, "alert-error") - return render_template("index.html", species = species()), 400 + return render_template( + "index.html", species=with_db_connection(species)), 400 filename = secure_filename(request.files["qc_text_file"].filename) if not os.path.exists(upload_dir): @@ -98,7 +101,8 @@ def upload_file(): if zip_errors: for error in zip_errors: flash(error, "alert-error") - return render_template("index.html", species = species()), 400 + return render_template( + "index.html", species=with_db_connection(species)), 400 return redirect(url_for( "parse.parse", filename=filename, diff --git a/qc_app/samples.py b/qc_app/samples.py index 107e889..8f56ee1 100644 --- a/qc_app/samples.py +++ b/qc_app/samples.py @@ -22,11 +22,15 @@ from quality_control.parsing import take from qc_app import jobs from qc_app.files import save_file -from qc_app.dbinsert import species_by_id, groups_by_species from qc_app.db_utils import ( with_db_connection, database_connection, with_redis_connection) +from qc_app.db import ( + species_by_id, + save_population, + population_by_id, + populations_by_species) samples = Blueprint("samples", __name__) @@ -43,7 +47,8 @@ def select_species(): return render_template( "samples/select-population.html", species=species, - populations=groups_by_species(species_id)) + populations=with_db_connection( + lambda conn: populations_by_species(conn, species_id))) flash("Invalid species selected!", "alert-error") flash("You need to select a species", "alert-error") return index_page @@ -65,7 +70,7 @@ def create_population(): "alert-error error-create-population") return species_page - pop_id = save_population(conn, { + pop = save_population(conn, { "SpeciesId": species["SpeciesId"], "Name": pop_name, "InbredSetName": pop_fullname, @@ -79,7 +84,7 @@ def create_population(): "samples/upload-samples.html", species=species, population=with_db_connection( - lambda conn: population_by_id(conn, pop_id))) + lambda conn: population_by_id(conn, pop["population_id"]))) @samples.route("/upload/select-population", methods=["POST"]) def select_population(): diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 06edfee..aabcea9 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -19,7 +19,7 @@ rqtl2 = Blueprint("rqtl2", __name__) def select_species(): """Select the species.""" if request.method == "GET": - return render_template("rqtl2/index.html", species=all_species()) + return render_template("rqtl2/index.html", species=with_db_connection(all_species)) species_id = request.form.get("species_id") species = with_db_connection( diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py index 6b6faf1..8431462 100644 --- a/scripts/insert_samples.py +++ b/scripts/insert_samples.py @@ -9,9 +9,8 @@ from redis import Redis from qc_app.db_utils import database_connection from qc_app.check_connections import check_db, check_redis +from qc_app.db import species_by_id, population_by_id from qc_app.samples import ( - species_by_id, - population_by_id, save_samples_data, read_samples_file, cross_reference_samples) |