diff --git a/scripts/compute-phenotype-means.py b/scripts/compute_phenotype_means.py
index 3b876b7..ef2fabc 100644
--- a/scripts/compute-phenotype-means.py
+++ b/scripts/compute_phenotype_means.py
@@ -9,6 +9,8 @@ import MySQLdb
from gn_libs import mysqldb
from uploader import setup_modules_logging
+
+from .cli_parser import add_logging_option
from .load_phenotypes_to_db import update_means
logger = logging.getLogger(__name__)
@@ -40,19 +42,18 @@ def run(args) -> int:
len(xref_ids))
return 0
_reasons = (
- "no population exists with the ID '%s'",
+ f"no population exists with the ID {args.population_id}",
"the population exists but it has no phenotypes linked to it yet")
logger.error(
- ("No cross-reference IDs to run against. Likely causes are: "
- + " OR ".join(_reasons) + "."),
- args.population_id)
+ "No cross-reference IDs to run against. Likely causes are: %s",
+ " OR ".join(_reasons) + ".")
return 1
T = TypeVar("T")
def comma_separated_list(val: str, itemstype: T = str) -> tuple[T, ...]:
- """Convert val into a list of items of type 'itemstype'."""
- return tuple(itemstype(item.strip()) for item in val.split(","))
+ """Convert val into a list of items of type 'itemstype'."""
+ return tuple(itemstype(item.strip()) for item in val.split(","))
def comma_separated_list_of_integers(val: str) -> tuple[int, ...]:
@@ -80,12 +81,7 @@ if __name__ == "__main__":
help=("Identifier for the InbredSet group/"
"population to run means against."))
## Optional arguments
- parser.add_argument(
- "--log-level",
- type=str,
- help="Determines what is logged out.",
- choices=("debug", "info", "warning", "error", "critical"),
- default="info")
+ parser = add_logging_option(parser)
parser.add_argument(
"--cross-ref-ids",
type=comma_separated_list_of_integers,
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index cefa6f2..7002ccd 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -234,11 +234,6 @@ def view_phenotype(# pylint: disable=[unused-argument]
population["Id"],
dataset["Id"],
xref_id)
- def __non_empty__(value) -> bool:
- if isinstance(value, str):
- return value.strip() != ""
- return bool(value)
-
return render_template(
"phenotypes/view-phenotype.html",
species=species,
@@ -1020,14 +1015,13 @@ def load_data_success(
species_redirect_uri="species.populations.phenotypes.index",
population_redirect_uri="species.populations.phenotypes.select_population",
redirect_uri="species.populations.phenotypes.list_datasets")
-def recompute_means(
+def recompute_means(# pylint: disable=[unused-argument]
species: dict,
population: dict,
dataset: dict,
**kwargs
):
"""Compute/Recompute the means for phenotypes in a particular population."""
- form = request.form
_jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]
_job_id = uuid.uuid4()
_xref_ids = tuple(int(item.split("_")[-1])
@@ -1038,7 +1032,7 @@ def recompute_means(
sys.executable,
"-u",
"-m",
- "scripts.compute-phenotype-means",
+ "scripts.compute_phenotype_means",
app.config["SQL_URI"],
_jobs_db,
str(population["Id"]),
diff --git a/uploader/route_utils.py b/uploader/route_utils.py
index 63b2852..53247e6 100644
--- a/uploader/route_utils.py
+++ b/uploader/route_utils.py
@@ -1,5 +1,5 @@
"""Generic routing utilities."""
-import json
+import logging
from json.decoder import JSONDecodeError
from flask import (flash,
@@ -15,6 +15,8 @@ from uploader.datautils import base64_encode_dict, base64_decode_to_dict
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
+logger = logging.getLogger(__name__)
+
def generic_select_population(
# pylint: disable=[too-many-arguments, too-many-positional-arguments]
species: dict,
@@ -56,9 +58,9 @@ def redirect_to_next(default: dict):
assert "uri" in default, "You must provide at least the 'uri' value."
try:
next_page = base64_decode_to_dict(request.args.get("next"))
- return redirect(url_for(
- next_page["uri"],
- **{key:value for key,value in next_page.items()}))
+ _uri = next_page["uri"]
+ next_page.pop("uri")
+ return redirect(url_for(_uri, **next_page))
except (TypeError, JSONDecodeError) as _err:
logger.debug("We could not decode the next value '%s'",
next_page,
@@ -66,7 +68,7 @@ def redirect_to_next(default: dict):
return redirect(url_for(
default["uri"],
- **{key:value for key,value in default.items()}))
+ **{key:value for key,value in default.items() if key != "uri"}))
def build_next_argument(uri: str, **kwargs) -> str:
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