Fix issues caught by linter. HEAD main

1 files changed, 0 insertions, 105 deletions

diff --git a/scripts/compute-phenotype-means.py b/scripts/compute-phenotype-means.py
deleted file mode 100644
index 3b876b7..0000000
--- a/scripts/compute-phenotype-means.py
+++ /dev/null
@@ -1,105 +0,0 @@
-"""Compute phenotype means."""
-import sys
-import logging
-from pathlib import Path
-from typing import TypeVar
-from argparse import Namespace, ArgumentParser
-
-import MySQLdb
-
-from gn_libs import mysqldb
-from uploader import setup_modules_logging
-from .load_phenotypes_to_db import update_means
-
-logger = logging.getLogger(__name__)
-logging.basicConfig(
-        encoding="utf-8",
-        format="%(asctime)s - %(name)s - %(levelname)s — %(message)s",
-        level=logging.INFO)
-
-
-def fetch_xref_id(conn: mysqldb.Connection, population_id: int) -> tuple[int, ...]:
-    """Fetch a population's cross-reference IDs."""
-    logger.debug("Fetching the xref IDs.")
-    with conn.cursor(cursorclass=MySQLdb.cursors.DictCursor) as cursor:
-        query = "SELECT Id FROM PublishXRef WHERE InbredSetId=%(population_id)s"
-        cursor.execute(query, {"population_id": population_id})
-        return tuple(int(row["Id"]) for row in cursor.fetchall())
-
-
-def run(args) -> int:
-    """Run the script."""
-    logger.debug("Running the script!")
-    with mysqldb.database_connection(args.db_uri) as mariadb_conn:
-        xref_ids = args.cross_ref_ids or fetch_xref_id(mariadb_conn, args.population_id)
-        if len(xref_ids):
-            update_means(mariadb_conn,
-                         args.population_id,
-                         xref_ids)
-            logger.debug("Successfully computed means for %02d phenotypes.",
-                         len(xref_ids))
-            return 0
-        _reasons = (
-            "no population exists with the ID '%s'",
-            "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)
-        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(","))
-
-
-def comma_separated_list_of_integers(val: str) -> tuple[int, ...]:
-    """Convert 'val' into list of items of type 'int'."""
-    return comma_separated_list(val, int)
-
-
-if __name__ == "__main__":
-    def parse_args() -> Namespace:
-        """Define and parse the CLI parsers accepted by this script."""
-        parser = ArgumentParser(
-            "compute-phenotype-means",
-            description="Compute/Recompute the phenotype means.")
-        parser.add_argument("db_uri",
-                            metavar="db-uri",
-                            type=str,
-                            help="MariaDB/MySQL connection URL")
-        parser.add_argument("jobs_db_path",
-                            metavar="jobs-db-path",
-                            type=Path,
-                            help="Path to jobs' SQLite database.")
-        parser.add_argument("population_id",
-                            metavar="population-id",
-                            type=int,
-                            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_argument(
-            "--cross-ref-ids",
-            type=comma_separated_list_of_integers,
-            help=("Provide cross-reference IDs to narrow the number of "
-                  "phenotypes that the means are computed against."),
-            default=[])
-
-        return parser.parse_args()
-
-    def main() -> int:
-        """compute-phenotype-means: Entry-point function."""
-        args = parse_args()
-        logger.setLevel(getattr(logging, args.log_level.upper()))
-        setup_modules_logging(logger, ("scripts.load_phenotypes_to_db",))
-        return run(args)
-
-    sys.exit(main())