diff options
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/upload/rqtl2.py | 716 |
1 files changed, 387 insertions, 329 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 41663ff..d42780f 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -1,12 +1,13 @@ """Module to handle uploading of R/qtl2 bundles.""" import sys import json -from typing import Union from pathlib import Path from datetime import date from uuid import UUID, uuid4 from zipfile import ZipFile, is_zipfile +from typing import Union, Callable, Optional, Iterable +import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor from flask import ( @@ -14,6 +15,7 @@ from flask import ( request, url_for, redirect, + Response, Blueprint, render_template, current_app as app) @@ -47,7 +49,7 @@ from qc_app.db.datasets import ( rqtl2 = Blueprint("rqtl2", __name__) @rqtl2.route("/", methods=["GET", "POST"]) -@rqtl2.route("/select-species", methods=["POST"]) +@rqtl2.route("/select-species", methods=["GET", "POST"]) def select_species(): """Select the species.""" if request.method == "GET": @@ -249,94 +251,156 @@ def rqtl2_bundle_qc_status(jobid: UUID): except jobs.JobNotFound: return render_template("rqtl2/no-such-job.html", jobid=jobid) -def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements] - """Check for select errors in the forms and return a page to redirect to.""" - species_id = kwargs.get("species_id") or request.form.get("species_id") - population_id = (kwargs.get("population_id") - or request.form.get("population_id")) - species = species_by_id(conn, species_id) - population = population_by_species_and_id(conn, species_id, population_id) - - if "species" in args and not bool(species): - flash("Invalid species!", "alert-error error-rqtl2") - return redirect(url_for("upload.rqtl2.select_species")) - - if "population" in args and not bool(population): - flash("Invalid Population!", "alert-error error-rqtl2") - return redirect( - url_for("upload.rqtl2.select_population", pgsrc="error"), - code=307) - - if "rqtl2_bundle_file" in args: - fileuploadpage = redirect(url_for("upload.rqtl2.upload_rqtl2_bundle", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - if not bool(request.form.get("rqtl2_bundle_file")): - flash("There is no file to process.", "alert-error error-rqtl2") - return fileuploadpage +def form_errors(formargs, *errorcheckers) -> Iterable[tuple[str, Response]]: + """Retrieve all errors from the form inputs""" + return (checker(formargs) for checker in errorcheckers) - if not Path(fullpath(request.form["rqtl2_bundle_file"])).exists(): - flash("No R/qtl2 bundle with the given name exists.", - "alert-error error-rqtl2") - return fileuploadpage - - if ("geno-dataset" in args and - not bool(request.form.get("geno-dataset-id"))): - flash("No genotype dataset was provided!", "alert-error error-rqtl2") - return redirect(url_for("upload.rqtl2.select_geno_dataset", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - - summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) +def redirect_on_error(flaskroute, **kwargs): + """Utility to redirect on error""" + return redirect(url_for(flaskroute, **kwargs, pgsrc="error"), + code=(307 if request.method == "POST" else 302)) + +def check_species(conn: mdb.Connection, formargs: dict) -> Optional[ + tuple[str, Response]]: + """ + Check whether the 'species_id' value is provided, and whether a + corresponding species exists in the database. - if ("probe-study-id" in args and - not bool(request.form.get("probe-study-id"))): - flash("No probeset study was selected!", "alert-error error-rqtl2") - return summary_page + Maybe give the function a better name...""" + speciespage = redirect_on_error("upload.rqtl2.select_species") + if "species_id" not in formargs: + return "You MUST provide the Species identifier.", speciespage - if ("probe-dataset-id" in args and - not bool(request.form.get("probe-dataset-id"))): - flash("No probeset dataset was selected!", "alert-error error-rqtl2") - return summary_page + if not bool(species_by_id(conn, formargs["species_id"])): + return "No species with the provided identifier exists.", speciespage return None +def check_population(conn: mdb.Connection, + formargs: dict, + species_id) -> Optional[tuple[str, Response]]: + """ + Check whether the 'population_id' value is provided, and whether a + corresponding population exists in the database. + + Maybe give the function a better name...""" + poppage = redirect_on_error( + "upload.rqtl2.select_species", species_id=species_id) + if "population_id" not in formargs: + return "You MUST provide the Population identifier.", poppage + + if not bool(population_by_species_and_id( + conn, species_id, formargs["population_id"])): + return "No population with the provided identifier exists.", poppage + + return None + +def check_r_qtl2_bundle(formargs: dict, + species_id, + population_id) -> Optional[tuple[str, Response]]: + """Check for the existence of the R/qtl2 bundle.""" + fileuploadpage = redirect_on_error("upload.rqtl2.upload_rqtl2_bundle", + species_id=species_id, + population_id=population_id) + if not "rqtl2_bundle_file" in formargs: + return ( + "You MUST provide a R/qtl2 zip bundle for upload.", fileuploadpage) + + if not Path(fullpath(formargs["rqtl2_bundle_file"])).exists(): + return "No R/qtl2 bundle with the given name exists.", fileuploadpage + + return None + +def check_geno_dataset(formargs: dict, + species_id, + population_id) -> Optional[tuple[str, Response]]: + """Check for the Genotype dataset.""" + genodsetpg = redirect_on_error("upload.rqtl2.select_geno_dataset", + species_id=species_id, + population_id=population_id) + if not bool(formargs.get("geno-dataset-id")): + return ( + "You MUST provide a valid Genotype dataset identifier", genodsetpg) + + return None + +def check_probe_study(formargs: dict, + species_id, + population_id) -> Optional[tuple[str, Response]]: + """Check for the ProbeSet study.""" + dsetinfopg = redirect_on_error("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id) + if not bool(formargs.get("probe-study-id")): + return "No probeset study was selected!", dsetinfopg + + return None + +def check_probe_dataset(formargs: dict, + species_id, + population_id) -> Optional[tuple[str, Response]]: + """Check for the ProbeSet dataset.""" + dsetinfopg = redirect_on_error("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id) + if not bool(formargs.get("probe-dataset-id")): + return "No probeset dataset was selected!", dsetinfopg + + return None + +def with_errors(conn: mdb.Connection, endpointthunk: Callable, *checkerstrings): + """Run 'endpointthunk' with error checking.""" + formargs = {**dict(request.args), **dict(request.form)} + species_id = formargs.get("species_id") or 0 + population_id = formargs.get("population_id") or 0 + fns = { + "species": lambda fargs: check_species(conn, fargs), + "population": lambda fargs: check_population( + conn, fargs, species_id), + "rqtl2_bundle_file": lambda fargs: check_r_qtl2_bundle( + fargs, species_id, population_id), + "geno_dataset": lambda fargs: check_geno_dataset( + fargs, species_id, population_id), + "probeset_study": lambda fargs: check_probe_study( + fargs, species_id, population_id), + "probeset_dataset": lambda fargs: check_probe_dataset( + fargs, species_id, population_id) + } + errors = tuple(item for item in form_errors( + formargs, *(fns[chkstr] for chkstr in checkerstrings)) if item is not None) + if len(errors) > 0: + flash(errors[0][0], "alert-error error-rqtl2") + return errors[0][1] + + return endpointthunk() + @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-geno-dataset"), methods=["POST"]) def select_geno_dataset(species_id: int, population_id: int): """Select from existing geno datasets.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset") - if bool(error): - return error - - geno_dset = geno_datasets_by_species_and_population( - conn, species_id, population_id) - if not bool(geno_dset): - flash("No genotype dataset was provided!", - "alert-error error-rqtl2") - return redirect(url_for("upload.rqtl2.select_geno_dataset", + def __thunk__(): + geno_dset = geno_datasets_by_species_and_population( + conn, species_id, population_id) + if not bool(geno_dset): + flash("No genotype dataset was provided!", + "alert-error error-rqtl2") + return redirect(url_for("upload.rqtl2.select_geno_dataset", + species_id=species_id, + population_id=population_id, + pgsrc="error"), + code=307) + + flash("Genotype accepted", "alert-success error-rqtl2") + return redirect(url_for("upload.rqtl2.select_dataset_info", species_id=species_id, population_id=population_id, - pgsrc="error"), + pgsrc="upload.rqtl2.select_geno_dataset"), code=307) - flash("Genotype accepted", "alert-success error-rqtl2") - return redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="upload.rqtl2.select_geno_dataset"), - code=307) + return with_errors( + conn, __thunk__, "species", "population", "rqtl2_bundle_file", "geno_dataset") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-geno-dataset"), @@ -344,50 +408,50 @@ def select_geno_dataset(species_id: int, population_id: int): def create_geno_dataset(species_id: int, population_id: int): """Create a new geno dataset.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors(conn, "species", "population", "rqtl2_bundle_file") - if bool(error): - return error - - sgeno_page = redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset" - if not bool(request.form.get("dataset-name")): - flash("You must provide the dataset name", errorclasses) - return sgeno_page - if not bool(request.form.get("dataset-fullname")): - flash("You must provide the dataset full name", errorclasses) - return sgeno_page - public = 2 if request.form.get("dataset-public") == "on" else 0 - - with conn.cursor(cursorclass=DictCursor) as cursor: - datasetname = request.form["dataset-name"] - new_dataset = { - "name": datasetname, - "fname": request.form.get("dataset-fullname"), - "sname": request.form.get("dataset-shortname") or datasetname, - "today": date.today().isoformat(), - "pub": public, - "isetid": population_id - } - cursor.execute( - "INSERT INTO GenoFreeze(" - "Name, FullName, ShortName, CreateTime, public, InbredSetId" - ") " - "VALUES(" - "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s" - ")", - new_dataset) - flash("Created dataset successfully.", "alert-success") - return render_template( - "rqtl2/create-geno-dataset-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset={**new_dataset, "id": cursor.lastrowid}) + def __thunk__(): + sgeno_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id, + pgsrc="error"), + code=307) + errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset" + if not bool(request.form.get("dataset-name")): + flash("You must provide the dataset name", errorclasses) + return sgeno_page + if not bool(request.form.get("dataset-fullname")): + flash("You must provide the dataset full name", errorclasses) + return sgeno_page + public = 2 if request.form.get("dataset-public") == "on" else 0 + + with conn.cursor(cursorclass=DictCursor) as cursor: + datasetname = request.form["dataset-name"] + new_dataset = { + "name": datasetname, + "fname": request.form.get("dataset-fullname"), + "sname": request.form.get("dataset-shortname") or datasetname, + "today": date.today().isoformat(), + "pub": public, + "isetid": population_id + } + cursor.execute( + "INSERT INTO GenoFreeze(" + "Name, FullName, ShortName, CreateTime, public, InbredSetId" + ") " + "VALUES(" + "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s" + ")", + new_dataset) + flash("Created dataset successfully.", "alert-success") + return render_template( + "rqtl2/create-geno-dataset-success.html", + species=species_by_id(conn, species_id), + population=population_by_species_and_id( + conn, species_id, population_id), + rqtl2_bundle_file=request.form["rqtl2_bundle_file"], + geno_dataset={**new_dataset, "id": cursor.lastrowid}) + + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-probeset-study"), @@ -395,21 +459,19 @@ def create_geno_dataset(species_id: int, population_id: int): def select_probeset_study(species_id: int, population_id: int): """Select or create a probeset study.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset", - "probe-study-id") - if bool(error): - return error + def __thunk__(): + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id), + code=307) + if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): + flash("Invalid study selected!", "alert-error error-rqtl2") + return summary_page - summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): - flash("Invalid study selected!", "alert-error error-rqtl2") return summary_page - - return summary_page + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file", "geno_dataset", + "probeset_study") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-probeset-dataset"), @@ -417,21 +479,20 @@ def select_probeset_study(species_id: int, population_id: int): def select_probeset_dataset(species_id: int, population_id: int): """Select or create a probeset dataset.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset", - "probe-study-id", "probe-dataset-id") - if bool(error): - return error + def __thunk__(): + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id), + code=307) + if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): + flash("Invalid study selected!", "alert-error error-rqtl2") + return summary_page - summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): - flash("Invalid study selected!", "alert-error error-rqtl2") return summary_page - return summary_page + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file", "geno_dataset", + "probeset_study", "probeset_dataset") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-probeset-study"), @@ -439,42 +500,41 @@ def select_probeset_dataset(species_id: int, population_id: int): def create_probeset_study(species_id: int, population_id: int): """Create a new probeset study.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset") - if bool(error): - return error - - form = request.form - select_study_page = redirect( - url_for("upload.rqtl2.select_probeset_study", - species_id=species_id, - population_id=population_id), - code=307) - - if not (bool(form.get("platformid")) and - bool(platform_by_id(conn, int(form["platformid"])))): - flash("Invalid platform selected.", "alert-error error-rqtl2") - return select_study_page - - if not (bool(form.get("tissueid")) and - bool(tissue_by_id(conn, int(form["tissueid"])))): - flash("Invalid tissue selected.", "alert-error error-rqtl2") - return select_study_page - - study = probeset_create_study( - conn, population_id, int(form["platformid"]), int(form["tissueid"]), - form["studyname"], form.get("studyfullname") or "", - form.get("studyshortname") or "") - return render_template( - "rqtl2/create-probe-study-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset=geno_dataset_by_id( - conn, - int(request.form["geno-dataset-id"])), - study=study) + def __thunk__(): + form = request.form + select_study_page = redirect( + url_for("upload.rqtl2.select_probeset_study", + species_id=species_id, + population_id=population_id), + code=307) + + if not (bool(form.get("platformid")) and + bool(platform_by_id(conn, int(form["platformid"])))): + flash("Invalid platform selected.", "alert-error error-rqtl2") + return select_study_page + + if not (bool(form.get("tissueid")) and + bool(tissue_by_id(conn, int(form["tissueid"])))): + flash("Invalid tissue selected.", "alert-error error-rqtl2") + return select_study_page + + study = probeset_create_study( + conn, population_id, int(form["platformid"]), int(form["tissueid"]), + form["studyname"], form.get("studyfullname") or "", + form.get("studyshortname") or "") + return render_template( + "rqtl2/create-probe-study-success.html", + species=species_by_id(conn, species_id), + population=population_by_species_and_id( + conn, species_id, population_id), + rqtl2_bundle_file=request.form["rqtl2_bundle_file"], + geno_dataset=geno_dataset_by_id( + conn, + int(request.form["geno-dataset-id"])), + study=study) + + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file", "geno_dataset") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-probeset-dataset"), @@ -482,57 +542,56 @@ def create_probeset_study(species_id: int, population_id: int): def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements] """Create a new probeset dataset.""" with database_connection(app.config["SQL_URI"]) as conn: - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset", - "probe-study-id") - if bool(error): - return error - - form = request.form - summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(form.get("averageid")): - flash("Averaging method not selected!", "alert-error error-rqtl2") - return summary_page - if not bool(form.get("datasetname")): - flash("Dataset name not provided!", "alert-error error-rqtl2") - return summary_page - if not bool(form.get("datasetfullname")): - flash("Dataset full name not provided!", "alert-error error-rqtl2") - return summary_page - - study = probeset_study_by_id(conn, int(form["probe-study-id"])) - if not bool(study): - flash("Invalid ProbeSet study provided!", "alert-error error-rqtl2") - return summary_page - - avgmethod = averaging_method_by_id(conn, int(form["averageid"])) - if not bool(avgmethod): - flash("Invalid averaging method provided!", "alert-error error-rqtl2") - return summary_page + def __thunk__(): + form = request.form + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id), + code=307) + if not bool(form.get("averageid")): + flash("Averaging method not selected!", "alert-error error-rqtl2") + return summary_page + if not bool(form.get("datasetname")): + flash("Dataset name not provided!", "alert-error error-rqtl2") + return summary_page + if not bool(form.get("datasetfullname")): + flash("Dataset full name not provided!", "alert-error error-rqtl2") + return summary_page + + study = probeset_study_by_id(conn, int(form["probe-study-id"])) + if not bool(study): + flash("Invalid ProbeSet study provided!", "alert-error error-rqtl2") + return summary_page + + avgmethod = averaging_method_by_id(conn, int(form["averageid"])) + if not bool(avgmethod): + flash("Invalid averaging method provided!", "alert-error error-rqtl2") + return summary_page + + dset = probeset_create_dataset(conn, + int(form["probe-study-id"]), + int(form["averageid"]), + form["datasetname"], + form["datasetfullname"], + form["datasetshortname"], + form["datasetpublic"] == "on", + form.get("datasetdatascale", "log2")) + return render_template( + "rqtl2/create-probe-dataset-success.html", + species=species_by_id(conn, species_id), + population=population_by_species_and_id( + conn, species_id, population_id), + rqtl2_bundle_file=request.form["rqtl2_bundle_file"], + geno_dataset=geno_dataset_by_id( + conn, + int(request.form["geno-dataset-id"])), + study=study, + avgmethod=avgmethod, + dataset=dset) - dset = probeset_create_dataset(conn, - int(form["probe-study-id"]), - int(form["averageid"]), - form["datasetname"], - form["datasetfullname"], - form["datasetshortname"], - form["datasetpublic"] == "on", - form.get("datasetdatascale", "log2")) - return render_template( - "rqtl2/create-probe-dataset-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset=geno_dataset_by_id( - conn, - int(request.form["geno-dataset-id"])), - study=study, - avgmethod=avgmethod, - dataset=dset) + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file", "geno_dataset", + "probeset_study") @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/dataset-info"), @@ -544,63 +603,63 @@ def select_dataset_info(species_id: int, population_id: int): """ form = request.form with database_connection(app.config["SQL_URI"]) as conn: - error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file") - if bool(error_page): - return error_page - - species = species_by_id(conn, species_id) - population = population_by_species_and_id( - conn, species_id, population_id) - thefile = fullpath(form["rqtl2_bundle_file"]) - with ZipFile(str(thefile), "r") as zfile: - cdata = r_qtl2.control_data(zfile) - if "geno" in cdata and not bool(form.get("geno-dataset-id")): - return render_template( - "rqtl2/select-geno-dataset.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - datasets=geno_datasets_by_species_and_population( - conn, species_id, population_id)) - geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"])) + def __thunk__(): + species = species_by_id(conn, species_id) + population = population_by_species_and_id( + conn, species_id, population_id) + thefile = fullpath(form["rqtl2_bundle_file"]) + with ZipFile(str(thefile), "r") as zfile: + cdata = r_qtl2.control_data(zfile) + if "geno" in cdata and not bool(form.get("geno-dataset-id")): + return render_template( + "rqtl2/select-geno-dataset.html", + species=species, + population=population, + rqtl2_bundle_file=thefile.name, + datasets=geno_datasets_by_species_and_population( + conn, species_id, population_id)) + geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"])) + + if "pheno" in cdata and not bool(form.get("probe-study-id")): + return render_template( + "rqtl2/select-probeset-study-id.html", + species=species, + population=population, + rqtl2_bundle_file=thefile.name, + geno_dataset=geno_dataset, + studies=probeset_studies_by_species_and_population( + conn, species_id, population_id), + platforms=platforms_by_species(conn, species_id), + tissues=all_tissues(conn)) + probeset_study = probeset_study_by_id( + conn, int(form["probe-study-id"])) + + if "pheno" in cdata and not bool(form.get("probe-dataset-id")): + return render_template( + "rqtl2/select-probeset-dataset.html", + species=species, + population=population, + rqtl2_bundle_file=thefile.name, + geno_dataset=geno_dataset, + probe_study=probeset_study, + datasets=probeset_datasets_by_study( + conn, int(form["probe-study-id"])), + avgmethods=averaging_methods(conn)) + probeset_study = probeset_study_by_id( + conn, int(form["probe-study-id"])) + probeset_dataset = probeset_dataset_by_id( + conn, int(form["probe-dataset-id"])) + + return render_template("rqtl2/summary-info.html", + species=species, + population=population, + rqtl2_bundle_file=thefile.name, + geno_dataset=geno_dataset, + probe_study=probeset_study, + probe_dataset=probeset_dataset) - if "pheno" in cdata and not bool(form.get("probe-study-id")): - return render_template( - "rqtl2/select-probeset-study-id.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - studies=probeset_studies_by_species_and_population( - conn, species_id, population_id), - platforms=platforms_by_species(conn, species_id), - tissues=all_tissues(conn)) - probeset_study = probeset_study_by_id( - conn, int(form["probe-study-id"])) - - if "pheno" in cdata and not bool(form.get("probe-dataset-id")): - return render_template( - "rqtl2/select-probeset-dataset.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - probe_study=probeset_study, - datasets=probeset_datasets_by_study( - conn, int(form["probe-study-id"])), - avgmethods=averaging_methods(conn)) - probeset_study = probeset_study_by_id( - conn, int(form["probe-study-id"])) - probeset_dataset = probeset_dataset_by_id( - conn, int(form["probe-dataset-id"])) - - return render_template("rqtl2/summary-info.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - probe_study=probeset_study, - probe_dataset=probeset_dataset) + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file") @@ -612,50 +671,49 @@ def confirm_bundle_details(species_id: int, population_id: int): redisuri = app.config["REDIS_URL"] with (database_connection(app.config["SQL_URI"]) as conn, Redis.from_url(redisuri, decode_responses=True) as rconn): - error = check_errors( - conn, "species", "population", "rqtl2_bundle_file", "geno-dataset", - "probe-study-id", "probe-dataset-id") - if bool(error): - return error - - redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"] - jobid = str(uuid4()) - _job = jobs.launch_job( - jobs.initialise_job( - rconn, - jobs.jobsnamespace(), - jobid, - [ - sys.executable, "-m", "scripts.process_rqtl2_bundle", - app.config["SQL_URI"], app.config["REDIS_URL"], - jobs.jobsnamespace(), jobid, "--redisexpiry", - str(redis_ttl_seconds)], - "R/qtl2 Bundle Upload", - redis_ttl_seconds, - { - "bundle-metadata": json.dumps({ - "speciesid": species_id, - "populationid": population_id, - "rqtl2-bundle-file": str(fullpath( - request.form["rqtl2_bundle_file"])), - "geno-dataset-id": request.form.get( - "geno-dataset-id", ""), - "probe-study-id": request.form.get( - "probe-study-id", ""), - "probe-dataset-id": request.form.get( - "probe-dataset-id", ""), - **({ - "platformid": probeset_study_by_id( - conn, - int(request.form["probe-study-id"]))["ChipId"] - } if bool(request.form.get("probe-study-id")) else {}) - }) - }), - redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") - - return redirect(url_for("upload.rqtl2.rqtl2_processing_status", - jobid=jobid)) + def __thunk__(): + redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"] + jobid = str(uuid4()) + _job = jobs.launch_job( + jobs.initialise_job( + rconn, + jobs.jobsnamespace(), + jobid, + [ + sys.executable, "-m", "scripts.process_rqtl2_bundle", + app.config["SQL_URI"], app.config["REDIS_URL"], + jobs.jobsnamespace(), jobid, "--redisexpiry", + str(redis_ttl_seconds)], + "R/qtl2 Bundle Upload", + redis_ttl_seconds, + { + "bundle-metadata": json.dumps({ + "speciesid": species_id, + "populationid": population_id, + "rqtl2-bundle-file": str(fullpath( + request.form["rqtl2_bundle_file"])), + "geno-dataset-id": request.form.get( + "geno-dataset-id", ""), + "probe-study-id": request.form.get( + "probe-study-id", ""), + "probe-dataset-id": request.form.get( + "probe-dataset-id", ""), + **({ + "platformid": probeset_study_by_id( + conn, + int(request.form["probe-study-id"]))["ChipId"] + } if bool(request.form.get("probe-study-id")) else {}) + }) + }), + redisuri, + f"{app.config['UPLOAD_FOLDER']}/job_errors") + + return redirect(url_for("upload.rqtl2.rqtl2_processing_status", + jobid=jobid)) + + return with_errors(conn, __thunk__, "species", "population", + "rqtl2_bundle_file", "geno_dataset", + "probeset_study", "probeset_dataset") @rqtl2.route("/status/<uuid:jobid>") def rqtl2_processing_status(jobid: UUID): |