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-rw-r--r--qc_app/upload/rqtl2.py716
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):