diff --git a/src/ingest_validation_tests/fastq_validator.py b/src/ingest_validation_tests/fastq_validator.py index e8cb8b8..b30ca75 100644 --- a/src/ingest_validation_tests/fastq_validator.py +++ b/src/ingest_validation_tests/fastq_validator.py @@ -12,7 +12,7 @@ class FASTQValidator(Validator): def collect_errors(self, **kwargs) -> List[Optional[str]]: threads = kwargs.get("coreuse", None) or cpu_count() // 4 or 1 - _log(f"Threading at {threads}") + _log(f"Threading at FastQValidator with {threads}") validator = FASTQValidatorLogic(verbose=True) validator.validate_fastq_files_in_path(self.paths, threads) if validator.errors: diff --git a/src/ingest_validation_tests/gz_validator.py b/src/ingest_validation_tests/gz_validator.py index ff3b2a5..bac33ec 100644 --- a/src/ingest_validation_tests/gz_validator.py +++ b/src/ingest_validation_tests/gz_validator.py @@ -36,7 +36,7 @@ class GZValidator(Validator): def collect_errors(self, **kwargs) -> List[Optional[str]]: data_output2 = [] threads = kwargs.get("coreuse", None) or cpu_count() // 4 or 1 - _log(f"Threading at {threads}") + _log(f"Threading at GZValidator with {threads}") file_list = [] for path in self.paths: for glob_expr in ["**/*.gz"]: diff --git a/src/ingest_validation_tests/ome_tiff_validator.py b/src/ingest_validation_tests/ome_tiff_validator.py index d967d60..ffcfaa4 100644 --- a/src/ingest_validation_tests/ome_tiff_validator.py +++ b/src/ingest_validation_tests/ome_tiff_validator.py @@ -7,6 +7,10 @@ from ingest_validation_tools.plugin_validator import Validator +def _log(message: str): + print(message) + + def _check_ome_tiff_file(file: str) -> Optional[str]: try: with tifffile.TiffFile(file) as tf: @@ -25,6 +29,7 @@ class OmeTiffValidator(Validator): def collect_errors(self, **kwargs) -> List[Optional[str]]: threads = kwargs.get("coreuse", None) or cpu_count() // 4 or 1 pool = Pool(threads) + _log(f"Threading at OmeTiffValidator with {threads}") filenames_to_test = [] for glob_expr in [ "**/*.ome.tif", diff --git a/src/ingest_validation_tests/tiff_validator.py b/src/ingest_validation_tests/tiff_validator.py index 0dbf16f..87bc07d 100644 --- a/src/ingest_validation_tests/tiff_validator.py +++ b/src/ingest_validation_tests/tiff_validator.py @@ -39,6 +39,7 @@ class TiffValidator(Validator): def collect_errors(self, **kwargs) -> List[Optional[str]]: threads = kwargs.get("coreuse", None) or cpu_count() // 4 or 1 + _log(f"Threading at TiffValidator with {threads}") pool = Pool(threads) filenames_to_test = [] for glob_expr in ["**/*.tif", "**/*.tiff", "**/*.TIFF", "**/*.TIF"]: