diff options
| -rw-r--r-- | scripts/compute_phenotype_means.py (renamed from scripts/compute-phenotype-means.py) | 20 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 10 | ||||
| -rw-r--r-- | uploader/route_utils.py | 12 |
3 files changed, 17 insertions, 25 deletions
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: |