fix logging

Author: mr-c

cwl_utils/cwl_expression_refactor.py

@@ -5,22 +5,19 @@
 import shutil
 import sys
 from pathlib import Path
-from typing import (
-    Any,
-    Callable,
-    Dict,
-    List,
-    MutableSequence,
-    Optional,
-    Tuple,
-    Union,
-)
-from typing_extensions import Protocol
+from typing import Any, Callable, Dict, List, MutableSequence, Optional, Tuple, Union
 
 from cwltool.loghandler import _logger as _cwltoollogger
 from ruamel import yaml
+from typing_extensions import Protocol
 
-from . import (
+_logger = logging.getLogger("cwl-expression-refactor")  # pylint: disable=invalid-name
+defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name
+_logger.addHandler(defaultStreamHandler)
+_logger.setLevel(logging.INFO)
+_cwltoollogger.setLevel(100)
+
+from cwl_utils import (
     cwl_v1_0_expression_refactor,
     cwl_v1_1_expression_refactor,
     cwl_v1_2_expression_refactor,
@@ -29,12 +26,6 @@
     parser_v1_2,
 )
 
-_logger = logging.getLogger("cwl-expression-refactor")  # pylint: disable=invalid-name
-defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name
-_logger.addHandler(defaultStreamHandler)
-_logger.setLevel(logging.INFO)
-_cwltoollogger.setLevel(100)
-
 save_type = Union[Dict[str, str], List[Union[Dict[str, str], List[Any], None]], None]
 
 
@@ -97,18 +88,19 @@ def run(args: argparse.Namespace) -> int:
         with open(document, "r") as doc_handle:
             result = yaml.main.round_trip_load(doc_handle, preserve_quotes=True)
         version = result["cwlVersion"]
+        uri = Path(document).as_uri()
         if version == "v1.0":
-            top = parser_v1_0.load_document_by_yaml(result, document)
+            top = parser_v1_0.load_document_by_yaml(result, uri)
             traverse: Callable[
                 [Any, bool, bool, bool, bool], Tuple[Any, bool]
             ] = cwl_v1_0_expression_refactor.traverse
             save: saveCWL = parser_v1_0.save
         elif version == "v1.1":
-            top = parser_v1_1.load_document_by_yaml(result, document)
+            top = parser_v1_1.load_document_by_yaml(result, uri)
             traverse = cwl_v1_1_expression_refactor.traverse
             save = parser_v1_1.save
         elif version == "v1.2":
-            top = parser_v1_2.load_document_by_yaml(result, document)
+            top = parser_v1_2.load_document_by_yaml(result, uri)
             traverse = cwl_v1_2_expression_refactor.traverse
             save = parser_v1_2.save
         else:

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -20,7 +20,6 @@
 
 from cwltool.errors import WorkflowException
 from cwltool.expression import do_eval, interpolate
-from cwltool.loghandler import _logger as _cwltoollogger
 from cwltool.sandboxjs import JavascriptException
 from cwltool.utils import CWLObjectType, CWLOutputType
 from ruamel import yaml
@@ -29,12 +28,6 @@
 
 import cwl_utils.parser_v1_0 as cwl
 
-_logger = logging.getLogger("cwl-expression-refactor")  # pylint: disable=invalid-name
-defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name
-_logger.addHandler(defaultStreamHandler)
-_logger.setLevel(logging.INFO)
-_cwltoollogger.setLevel(100)
-
 
 def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool:
     """Rewrite the "type: stdout" shortcut to use an explicit random filename."""
@@ -129,7 +122,7 @@ def get_expression(
                     fullJS=True,
                     escaping_behavior=2,
                     convert_to_expression=True,
-                )
+                ),
             )
     return None
 

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -20,7 +20,6 @@
 
 from cwltool.errors import WorkflowException
 from cwltool.expression import do_eval, interpolate
-from cwltool.loghandler import _logger as _cwltoollogger
 from cwltool.sandboxjs import JavascriptException
 from cwltool.utils import CWLObjectType, CWLOutputType
 from ruamel import yaml
@@ -29,12 +28,6 @@
 
 import cwl_utils.parser_v1_1 as cwl
 
-_logger = logging.getLogger("cwl-expression-refactor")  # pylint: disable=invalid-name
-defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name
-_logger.addHandler(defaultStreamHandler)
-_logger.setLevel(logging.INFO)
-_cwltoollogger.setLevel(100)
-
 
 def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool:
     """Rewrite the "type: stdout" shortcut to use an explicit random filename."""
@@ -129,7 +122,7 @@ def get_expression(
                     fullJS=True,
                     escaping_behavior=2,
                     convert_to_expression=True,
-                )
+                ),
             )
     return None
 

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -20,7 +20,6 @@
 
 from cwltool.errors import WorkflowException
 from cwltool.expression import do_eval, interpolate
-from cwltool.loghandler import _logger as _cwltoollogger
 from cwltool.sandboxjs import JavascriptException
 from cwltool.utils import CWLObjectType, CWLOutputType
 from ruamel import yaml
@@ -29,12 +28,6 @@
 
 import cwl_utils.parser_v1_2 as cwl
 
-_logger = logging.getLogger("cwl-expression-refactor")  # pylint: disable=invalid-name
-defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name
-_logger.addHandler(defaultStreamHandler)
-_logger.setLevel(logging.INFO)
-_cwltoollogger.setLevel(100)
-
 
 def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool:
     """Rewrite the "type: stdout" shortcut to use an explicit random filename."""
@@ -129,7 +122,7 @@ def get_expression(
                     fullJS=True,
                     escaping_behavior=2,
                     convert_to_expression=True,
-                )
+                ),
             )
     return None