Fix issues caught by type-checker.

1 files changed, 14 insertions, 13 deletions

diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py
index 89cc3ec..7d58402 100644
--- a/scripts/run_qtlreaper.py
+++ b/scripts/run_qtlreaper.py
@@ -6,8 +6,8 @@ import secrets
 import logging
 import subprocess
 from pathlib import Path
-from typing import Union
 from functools import reduce
+from typing import Union, Iterator
 from argparse import Namespace, ArgumentParser
 
 from gn_libs import mysqldb
@@ -56,7 +56,7 @@ def reconcile_samples(
 def generate_qtlreaper_traits_file(
         outdir: Path,
         samples: tuple[str, ...],
-        traits_data: dict[str, Union[int, float]],
+        traits_data: tuple[dict[str, Union[int, float]], ...],
         filename_prefix: str = ""
 ) -> Path:
     """Generate a file for use with qtlreaper that contains the traits' data."""
@@ -65,7 +65,7 @@ def generate_qtlreaper_traits_file(
     _dialect.quoting=0
 
     _traitsfile = outdir.joinpath(
-        f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv")
+        f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined]
     with _traitsfile.open(mode="w", encoding="utf-8") as outptr:
         writer = csv.DictWriter(
             outptr, fieldnames=("Trait",) + samples, dialect=_dialect)
@@ -79,7 +79,7 @@ def generate_qtlreaper_traits_file(
     return _traitsfile
 
 
-def parse_tsv_file(results_file: Path) -> list[dict]:
+def parse_tsv_file(results_file: Path) -> Iterator[dict]:
     """Parse the rust-qtlreaper output into usable python objects."""
     with results_file.open("r", encoding="utf-8") as readptr:
         _dialect = csv.unix_dialect()
@@ -96,7 +96,7 @@ def __qtls_by_trait__(qtls, current):
     }
 
 
-def save_qtl_values_to_db(conn, qtls: dict):
+def save_qtl_values_to_db(conn, qtls: tuple[dict, ...]):
     """Save computed QTLs to the database."""
     with conn.cursor() as cursor:
         cursor.executemany(
@@ -131,11 +131,11 @@ def dispatch(args: Namespace) -> int:
                              ", ".join(_samples_not_in_genofile))
 
             # Fetch traits data: provided list, or all traits in db
-            _traitsdata = phenotypes_vector_data(
+            _traitsdata = tuple(phenotypes_vector_data(
                 conn,
                 args.species_id,
                 args.population_id,
-                xref_ids=tuple(args.xref_ids)).values()
+                xref_ids=tuple(args.xref_ids)).values())
             logger.debug("Successfully got traits data. Generating the QTLReaper's traits file…")
             _traitsfile = generate_qtlreaper_traits_file(
                 args.working_dir,
@@ -145,7 +145,7 @@ def dispatch(args: Namespace) -> int:
             logger.debug("QTLReaper's Traits file: %s", _traitsfile)
 
             _qtlreaper_main_output = args.working_dir.joinpath(
-                f"main-output-{secrets.token_urlsafe(15)}.tsv")
+                f"main-output-{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined]
             logger.debug("Main output filename: %s", _qtlreaper_main_output)
             with subprocess.Popen(
                     ("qtlreaper",
@@ -156,11 +156,12 @@ def dispatch(args: Namespace) -> int:
                 while _qtlreaper.poll() is None:
                     logger.debug("QTLReaper process running…")
                     time.sleep(1)
-                    results = tuple(max(qtls, key=lambda qtl: qtl["LRS"])
-                                    for qtls in
-                                    reduce(__qtls_by_trait__,
-                                           parse_tsv_file(_qtlreaper_main_output),
-                                           {}).values())
+                    results = tuple(#type: ignore[var-annotated]
+                        max(qtls, key=lambda qtl: qtl["LRS"])
+                        for qtls in
+                        reduce(__qtls_by_trait__,
+                               parse_tsv_file(_qtlreaper_main_output),
+                               {}).values())
             save_qtl_values_to_db(conn, results)
             logger.debug("Cleaning up temporary files.")
             _traitsfile.unlink()