cleanup

cwlkernel/CWLBuilder.py

@@ -32,7 +32,7 @@ def get_current_code(self) -> str:
         return self._code
 
     def build(self) -> WorkflowComponent:
-        code = yaml.load(StringIO(self._code), yaml.Loader)
+        code = yaml.safe_load(StringIO(self._code))
         if 'id' not in code:
             raise ValueError("the workflow must contain an id")
         if code['class'] == 'CommandLineTool':

cwlkernel/CWLExecuteConfigurator.py

@@ -16,11 +16,11 @@ class CWLExecuteConfigurator:
 
     def __init__(self):
         """Kernel configurations."""
-        for property, (default_value, validator) in self.properties.items():
-            value = os.environ.get(property, default_value)
+        for property_name, (default_value, validator) in self.properties.items():
+            value = os.environ.get(property_name, default_value)
             if not validator(value):
-                raise RuntimeError("Value {0} is not allowed for property {1}".format(value, property))
+                raise RuntimeError("Value {0} is not allowed for property {1}".format(value, property_name))
             self.__setattr__(
-                property,
+                property_name,
                 value
             )

cwlkernel/CWLKernel.py

@@ -167,7 +167,7 @@ def _execute_workflow(self, code_path: Path) -> Optional[Exception]:
         output_directory_for_that_run = str(run_id)
         for output in results:
             if isinstance(results[output], list):
-                for i, output_i in enumerate(results[output]):
+                for i, _ in enumerate(results[output]):
                     results[output][i]['id'] = f'{output}_{i + 1}'
                     results[output][i]['result_counter'] = self._results_manager.files_counter
                     self._results_manager.append_files(

cwlkernel/CoreExecutor.py

@@ -1,8 +1,8 @@
 import os
-import subprocess
 import sys
 import traceback
 from pathlib import Path
+from subprocess import DEVNULL
 from typing import (
     Dict,
     List,
@@ -46,9 +46,9 @@ def execute(self) -> Tuple[UUID, Dict, Optional[Exception]]:
         runtime_context = RuntimeContext()
         runtime_context.outdir = self.file_manager.ROOT_DIRECTORY
         runtime_context.basedir = self.file_manager.ROOT_DIRECTORY
-        runtime_context.default_stdin = subprocess.DEVNULL
-        runtime_context.default_stdout = subprocess.DEVNULL
-        runtime_context.default_stderr = subprocess.DEVNULL
+        runtime_context.default_stdin = DEVNULL
+        runtime_context.default_stdout = DEVNULL
+        runtime_context.default_stderr = DEVNULL
         os.chdir(self.file_manager.ROOT_DIRECTORY)
         factory = Factory(runtime_context=runtime_context)
         executable = factory.make(self._workflow_path)

cwlkernel/cwlrepository/CWLComponent.py

@@ -118,11 +118,6 @@ def steps(self):
                 steps[step]['run'] = f"{steps[step]['run']._id}.cwl"
         return deepcopy(steps)
 
-    """
-    A composite object can add or remove other components (both simple or
-    complex) to or from its child list.
-    """
-
     def add(self, component: WorkflowComponent, step_name: str) -> None:
         self._steps[step_name] = {
             'run': component,
@@ -188,7 +183,7 @@ def compose_requirements(self) -> Dict:
 
 class WorkflowComponentFactory:
     def get_workflow_component(self, yaml_string: str) -> WorkflowComponent:
-        component = yaml.load(StringIO(yaml_string), yaml.SafeLoader)
+        component = yaml.safe_load(StringIO(yaml_string))
         if 'id' not in component:
             component['id'] = str(uuid.uuid4())
         if component['class'] == 'CommandLineTool':

cwlkernel/cwlrepository/cwlrepository.py

@@ -28,9 +28,9 @@ def validate(self, tool: WorkflowComponent):
                 raise TypeError(f'WorkflowComponent expected but type of {type(tool)} given')
             if not isinstance(tool.id, str):
                 raise MissingIdError('Missing WorkflowComponent\'s id')
-            for input in tool.inputs:
-                if 'id' not in input:
-                    raise MissingIdError(f'Missing id for input: {input}')
+            for tool_input in tool.inputs:
+                if 'id' not in tool_input:
+                    raise MissingIdError(f'Missing id for input: {tool_input}')
             for output in tool.outputs:
                 if 'id' not in output:
                     raise MissingIdError(f'Missing id for outputs: {output}')