Print out progress to STDOUT.

1 files changed, 8 insertions, 8 deletions

diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index a9097d5..699c291 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -181,7 +181,7 @@ def qc_phenocovar_file(
             filepath.name,
             f"{fqkey}:logs") as logger,
           Redis.from_url(redisuri, decode_responses=True) as rconn):
-        logger.info("Running QC on file: %s", filepath.name)
+        print("Running QC on file: ", filepath.name)
         _csvfile = rqtl2.read_csv_file(filepath, separator, comment_char)
         _headings = tuple(heading.lower() for heading in next(_csvfile))
         _errors: tuple[InvalidValue, ...] = tuple()
@@ -289,7 +289,7 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments]
             filepath.name,
             f"{fqkey}:logs") as logger,
           Redis.from_url(redisuri, decode_responses=True) as rconn):
-        logger.info("Running QC on file: %s", filepath.name)
+        print("Running QC on file: ", filepath.name)
         save_error = partial(
             push_error, rconn, file_fqkey(fqkey, "errors", filepath))
         _csvfile = rqtl2.read_csv_file(filepath, separator, comment_char)
@@ -376,7 +376,7 @@ def run_qc(# pylint: disable=[too-many-locals]
         args: Namespace
 ) -> int:
     """Run quality control checks on the bundle."""
-    logger.debug("Beginning the quality assurance checks.")
+    print("Beginning the quality assurance checks.")
     results = check_for_averages_files(
         **check_for_mandatory_pheno_keys(
             **validate(args.rqtl2bundle, logger)))
@@ -401,7 +401,7 @@ def run_qc(# pylint: disable=[too-many-locals]
              for ftype in ("pheno", "phenocovar", "phenose", "phenonum")))
 
     #       - Fetch samples/individuals from database.
-    logger.debug("Fetching samples/individuals from the database.")
+    print("Fetching samples/individuals from the database.")
     samples = tuple(#type: ignore[var-annotated]
         item for item in set(reduce(
             lambda acc, item: acc + (
@@ -418,7 +418,7 @@ def run_qc(# pylint: disable=[too-many-locals]
                json.dumps(tuple(f"{fullyqualifiedjobid}:phenocovar:{_file}"
                                 for _file in cdata.get("phenocovar", []))))
     with mproc.Pool(mproc.cpu_count() - 1) as pool:
-        logger.debug("Check for errors in 'phenocovar' file(s).")
+        print("Check for errors in 'phenocovar' file(s).")
         _phenocovar_qc_res = merge_dicts(*pool.starmap(qc_phenocovar_file, tuple(
             (extractiondir.joinpath(_file),
              args.redisuri,
@@ -440,7 +440,7 @@ def run_qc(# pylint: disable=[too-many-locals]
             "Expected a non-negative number with at least one decimal "
             "place."))
 
-        logger.debug("Check for errors in 'pheno' file(s).")
+        print("Check for errors in 'pheno' file(s).")
         _pheno_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple((
             extractiondir.joinpath(_file),
             args.redisuri,
@@ -459,7 +459,7 @@ def run_qc(# pylint: disable=[too-many-locals]
         #       - Check the 3 checks above for phenose and phenonum values too
         # qc_phenose_files(…)
         # qc_phenonum_files(…)
-        logger.debug("Check for errors in 'phenose' file(s).")
+        print("Check for errors in 'phenose' file(s).")
         _phenose_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple((
             extractiondir.joinpath(_file),
             args.redisuri,
@@ -475,7 +475,7 @@ def run_qc(# pylint: disable=[too-many-locals]
             dec_err_fn
         ) for _file in cdata.get("phenose", []))))
 
-        logger.debug("Check for errors in 'phenonum' file(s).")
+        print("Check for errors in 'phenonum' file(s).")
         _phenonum_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple((
             extractiondir.joinpath(_file),
             args.redisuri,