Merge pull request #61 from hubmapconsortium/sunset666/logging_thread…

…count

Adding logging to plugins for thread counting

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:

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"]:

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",

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"]: