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-rw-r--r--qc_app/upload/rqtl2.py235
1 files changed, 184 insertions, 51 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 04bfa5b..8b5ac01 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."""
+"""Module to handle uploading of R/qtl2 bundles."""#pylint: disable=[too-many-lines]
import sys
import json
import traceback
from pathlib import Path
from datetime import date
from uuid import UUID, uuid4
+from functools import partial
from zipfile import ZipFile, is_zipfile
-from typing import Union, Callable, Optional, Iterable
+from typing import Union, Callable, Optional
import MySQLdb as mdb
from redis import Redis
@@ -262,11 +263,6 @@ def rqtl2_bundle_qc_status(jobid: UUID):
return render_template("rqtl2/no-such-job.html", jobid=jobid)
-def form_errors(formargs, *errorcheckers) -> Iterable[tuple[str, Response]]:
- """Retrieve all errors from the form inputs"""
- return (checker(formargs) for checker in errorcheckers)
-
-
def redirect_on_error(flaskroute, **kwargs):
"""Utility to redirect on error"""
return redirect(url_for(flaskroute, **kwargs, pgsrc="error"),
@@ -327,21 +323,61 @@ def check_r_qtl2_bundle(formargs: dict,
return None
-def check_geno_dataset(formargs: dict,
+def check_geno_dataset(conn: mdb.Connection,
+ formargs: dict,
species_id,
population_id) -> Optional[tuple[str, Response]]:
"""Check for the Genotype dataset."""
- genodsetpg = redirect_on_error("upload.rqtl2.select_geno_dataset",
+ genodsetpg = redirect_on_error("upload.rqtl2.select_dataset_info",
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)
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
+ (formargs["geno-dataset-id"],))
+ results = cursor.fetchall()
+ if not bool(results):
+ return ("No genotype dataset with the provided identifier exists.",
+ genodsetpg)
+ if len(results) > 1:
+ return (
+ "Data corruption: More than one genotype dataset with the same "
+ "identifier.",
+ genodsetpg)
+
+ return None
+
+def check_tissue(
+ conn: mdb.Connection,formargs: dict) -> Optional[tuple[str, Response]]:
+ """Check for tissue/organ/biological material."""
+ selectdsetpg = redirect_on_error("upload.rqtl2.select_dataset_info",
+ species_id=formargs["species_id"],
+ population_id=formargs["population_id"])
+ if not bool(formargs.get("tissueid", "").strip()):
+ return ("No tissue/organ/biological material provided.", selectdsetpg)
+
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM Tissue WHERE Id=%s",
+ (formargs["tissueid"],))
+ results = cursor.fetchall()
+ if not bool(results):
+ return ("No tissue/organ with the provided identifier exists.",
+ selectdsetpg)
+
+ if len(results) > 1:
+ return (
+ "Data corruption: More than one tissue/organ with the same "
+ "identifier.",
+ selectdsetpg)
+
return None
-def check_probe_study(formargs: dict,
+def check_probe_study(conn: mdb.Connection,
+ formargs: dict,
species_id,
population_id) -> Optional[tuple[str, Response]]:
"""Check for the ProbeSet study."""
@@ -351,10 +387,15 @@ def check_probe_study(formargs: dict,
if not bool(formargs.get("probe-study-id")):
return "No probeset study was selected!", dsetinfopg
+ if not bool(probeset_study_by_id(conn, formargs["probe-study-id"])):
+ return ("No probeset study with the provided identifier exists",
+ dsetinfopg)
+
return None
-def check_probe_dataset(formargs: dict,
+def check_probe_dataset(conn: mdb.Connection,
+ formargs: dict,
species_id,
population_id) -> Optional[tuple[str, Response]]:
"""Check for the ProbeSet dataset."""
@@ -364,29 +405,18 @@ def check_probe_dataset(formargs: dict,
if not bool(formargs.get("probe-dataset-id")):
return "No probeset dataset was selected!", dsetinfopg
+ if not bool(probeset_dataset_by_id(conn, formargs["probe-dataset-id"])):
+ return ("No probeset dataset with the provided identifier exists",
+ dsetinfopg)
+
return None
-def with_errors(conn: mdb.Connection, endpointthunk: Callable, *checkerstrings):
+def with_errors(endpointthunk: Callable, *checkfns):
"""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)
+ errors = tuple(item for item in (_fn(formargs=formargs) for _fn in checkfns)
+ if item is not None)
if len(errors) > 0:
flash(errors[0][0], "alert-error error-rqtl2")
return errors[0][1]
@@ -419,8 +449,17 @@ def select_geno_dataset(species_id: int, population_id: int):
pgsrc="upload.rqtl2.select_geno_dataset"),
code=307)
- return with_errors(
- conn, __thunk__, "species", "population", "rqtl2_bundle_file", "geno_dataset")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population, conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -484,8 +523,12 @@ def create_geno_dataset(species_id: int, population_id: int):
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")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population, conn=conn),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -505,8 +548,18 @@ def select_tissue(species_id: int, population_id: int):
pgsrc="upload.rqtl2.select_geno_dataset"),
code=307)
- return with_errors(
- conn, __thunk__, "species", "population", "rqtl2_bundle_file", "geno_dataset")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/create-tissue"),
@@ -568,9 +621,23 @@ def select_probeset_study(species_id: int, population_id: int):
return summary_page
return summary_page
- return with_errors(conn, __thunk__, "species", "population",
- "rqtl2_bundle_file", "geno_dataset",
- "probeset_study")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_tissue, conn=conn),
+ partial(check_probe_study,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -590,9 +657,27 @@ def select_probeset_dataset(species_id: int, population_id: int):
return summary_page
- return with_errors(conn, __thunk__, "species", "population",
- "rqtl2_bundle_file", "geno_dataset",
- "probeset_study", "probeset_dataset")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_tissue, conn=conn),
+ partial(check_probe_study,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_probe_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -642,8 +727,19 @@ def create_probeset_study(species_id: int, population_id: int):
int(request.form["geno-dataset-id"])),
study=study)
- return with_errors(conn, __thunk__, "species", "population",
- "rqtl2_bundle_file", "geno_dataset")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_tissue, conn=conn))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -713,9 +809,23 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl
avgmethod=avgmethod,
dataset=dset)
- return with_errors(conn, __thunk__, "species", "population",
- "rqtl2_bundle_file", "geno_dataset",
- "probeset_study")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_tissue, conn=conn),
+ partial(check_probe_study,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -796,8 +906,14 @@ def select_dataset_info(species_id: int, population_id: int):
probe_study=probeset_study,
probe_dataset=probeset_dataset)
- return with_errors(conn, __thunk__, "species", "population",
- "rqtl2_bundle_file")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
@@ -848,9 +964,26 @@ def confirm_bundle_details(species_id: int, population_id: int):
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")
+ return with_errors(__thunk__,
+ partial(check_species, conn=conn),
+ partial(check_population,
+ conn=conn,
+ species_id=species_id),
+ partial(check_r_qtl2_bundle,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_geno_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_probe_study,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id),
+ partial(check_probe_dataset,
+ conn=conn,
+ species_id=species_id,
+ population_id=population_id))
@rqtl2.route("/status/<uuid:jobid>")