Merge pull request #42 from common-workflow-language/expr_refactor_cwl_v12

Expr refactor for CWL v1.1+1.2

Author: mr-c

cwl_utils/cwl_expression_refactor.py cwl_utils/cwl_v1_0_expression_refactor.pycwl_utils/cwl_expression_refactor.py renamed to cwl_utils/cwl_v1_0_expression_refactor.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+"""CWL Expression refactoring tool for CWL v1.0 ."""
 import argparse
 import copy
 import hashlib
@@ -42,8 +43,9 @@
 def parse_args(args: List[str]) -> argparse.Namespace:
     """Argument parser."""
     parser = argparse.ArgumentParser(
-        description="Tool to upgrade refactor CWL documents so that any CWL expression "
-        "are separate steps as either ExpressionTools or CommandLineTools."
+        description="Tool to refactor CWL v1.0 documents so that any CWL expression "
+        "are separate steps as either ExpressionTools or CommandLineTools. Exit code 7 "
+        "means a single CWL document was provided but it did not need modification."
     )
     parser.add_argument(
         "--etools",
@@ -83,11 +85,14 @@ def run(args: argparse.Namespace) -> int:
         top = cwl.load_document(document)
         output = Path(args.dir) / Path(document).name
         result, modified = traverse(
-            top, not args.etools, args.skip_some1, args.skip_some2
+            top, not args.etools, False, args.skip_some1, args.skip_some2
         )
         if not modified:
-            shutil.copyfile(document, output)
-            continue
+            if len(args.inputs) > 1:
+                shutil.copyfile(document, output)
+                continue
+            else:
+                return 7
         if not isinstance(result, MutableSequence):
             result_json = cwl.save(
                 result,
@@ -242,15 +247,18 @@ def etool_to_cltool(
 process.stdout.write(JSON.stringify(ret));"""
     )
     contents = escape_expression_field(contents)
-    listing = [cwl.Dirent("expression.js", contents, writable=None)]
+    listing = [cwl.Dirent(entryname="expression.js", entry=contents, writable=None)]
     iwdr = cwl.InitialWorkDirRequirement(listing)
     containerReq = cwl.DockerRequirement(dockerPull="node:slim")
+    softwareHint = cwl.SoftwareRequirement(
+        packages=[cwl.SoftwarePackage(package="nodejs")]
+    )
     return cwl.CommandLineTool(
         inputs=inputs,
         outputs=outputs,
         id=etool.id,
         requirements=[iwdr],
-        hints=[containerReq],
+        hints=[containerReq, softwareHint],
         label=etool.label,
         doc=etool.doc,
         cwlVersion=etool.cwlVersion,
@@ -263,10 +271,10 @@ def etool_to_cltool(
 
 def traverse(
     process: Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow],
-    replace_etool: bool = False,
-    inside: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    inside: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> Tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
     """Convert the given process and any subprocesess."""
     if not inside and isinstance(process, cwl.CommandLineTool):
@@ -348,9 +356,9 @@ def traverse(
 
 def load_step(
     step: cwl.WorkflowStep,
-    replace_etool: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> bool:
     """If the step's Process is not inline, load and process it."""
     modified = False
@@ -700,7 +708,7 @@ def process_workflow_inputs_and_outputs(
 
 
 def process_workflow_reqs_and_hints(
-    workflow: cwl.Workflow, replace_etool: bool = False
+    workflow: cwl.Workflow, replace_etool: bool
 ) -> bool:
     """
     Convert any expressions in a workflow's reqs and hints.
@@ -1029,9 +1037,9 @@ def process_level_reqs(
     process: cwl.CommandLineTool,
     step: cwl.WorkflowStep,
     parent: cwl.Workflow,
-    replace_etool: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> bool:
     """Convert expressions inside a process into new adjacent steps."""
     # This is for reqs inside a Process (CommandLineTool, ExpressionTool)
@@ -1301,9 +1309,9 @@ def traverse_CommandLineTool(
     clt: cwl.CommandLineTool,
     parent: cwl.Workflow,
     step: cwl.WorkflowStep,
-    replace_etool: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> bool:
     """Extract any CWL Expressions within the given CommandLineTool into sibling steps."""
     modified = False
@@ -1592,7 +1600,7 @@ def simplify_step_id(uri: str) -> str:
 
 def remove_JSReq(
     process: Union[cwl.CommandLineTool, cwl.WorkflowStep, cwl.Workflow],
-    skip_command_line1: bool = False,
+    skip_command_line1: bool,
 ) -> None:
     """Since the InlineJavascriptRequiment is longer needed, remove it."""
     if skip_command_line1 and isinstance(process, cwl.CommandLineTool):
@@ -1621,7 +1629,7 @@ def replace_step_clt_expr_with_etool(
     workflow: cwl.Workflow,
     target: cwl.InputParameter,
     step: cwl.WorkflowStep,
-    replace_etool: bool = False,
+    replace_etool: bool,
     self_name: Optional[str] = None,
 ) -> None:
     """Convert a step level CWL Expression to a sibling expression step."""
@@ -1656,7 +1664,7 @@ def replace_clt_hintreq_expr_with_etool(
     workflow: cwl.Workflow,
     target: cwl.InputParameter,
     step: cwl.WorkflowStep,
-    replace_etool: bool = False,
+    replace_etool: bool,
     self_name: Optional[str] = None,
 ) -> Union[cwl.CommandLineTool, cwl.ExpressionTool]:
     """Factor out an expression inside a CommandLineTool req or hint into a sibling step."""
@@ -1815,9 +1823,9 @@ def generate_etool_from_expr2(
 def traverse_step(
     step: cwl.WorkflowStep,
     parent: cwl.Workflow,
-    replace_etool: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> bool:
     """Process the given WorkflowStep."""
     modified = False
@@ -1915,7 +1923,12 @@ def traverse_step(
                 inp.source = "{}/result".format(etool_id)
     # TODO: skip or special process for sub workflows?
     process_modified = process_level_reqs(
-        original_process, step, parent, replace_etool, skip_command_line1
+        original_process,
+        step,
+        parent,
+        replace_etool,
+        skip_command_line1,
+        skip_command_line2,
     )
     if process_modified:
         modified = True
@@ -1958,7 +1971,7 @@ def replace_step_valueFrom_expr_with_etool(
     original_process: Union[cwl.CommandLineTool, cwl.ExpressionTool],
     original_step_ins: List[cwl.WorkflowStepInput],
     source: Union[str, List[Any]],
-    replace_etool: bool = False,
+    replace_etool: bool,
     source_type: Optional[Union[cwl.InputParameter, cwl.CommandInputParameter]] = None,
 ) -> None:
     """Replace a WorkflowStep level 'valueFrom' expression with a sibling ExpressionTool step."""
@@ -2030,9 +2043,9 @@ def replace_step_valueFrom_expr_with_etool(
 
 def traverse_workflow(
     workflow: cwl.Workflow,
-    replace_etool: bool = False,
-    skip_command_line1: bool = False,
-    skip_command_line2: bool = False,
+    replace_etool: bool,
+    skip_command_line1: bool,
+    skip_command_line2: bool,
 ) -> Tuple[cwl.Workflow, bool]:
     """Traverse a workflow, processing each step."""
     modified = False
@@ -2049,7 +2062,7 @@ def traverse_workflow(
     for step in workflow.steps:
         if not step.id.startswith("_expression"):
             step_modified = traverse_step(
-                step, workflow, skip_command_line1, skip_command_line2
+                step, workflow, replace_etool, skip_command_line1, skip_command_line2
             )
             if step_modified:
                 modified = True