Separate dir creation from compilation

src/sophios/api/pythonapi.py

@@ -758,7 +758,7 @@ def run(self) -> None:
 
         post_compile.cwl_docker_extract(args, self.process_name)
         rose_tree = post_compile.remove_entrypoints(args, rose_tree)
-
+        post_compile.find_and_create_output_dirs(rose_tree)
         # Do NOT capture stdout and/or stderr and pipe warnings and errors into a black hole.
         retval = run_local_module.run_local(args, rose_tree, args.cachedir, args.cwl_runner, True)
 

src/sophios/compiler.py

@@ -880,11 +880,6 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 newval['format'] = in_format
             new_keyval = {key: newval}
         elif 'Directory' == in_dict['type']:
-            if not args.ignore_dir_path:
-                ldir = Path(in_dict['value'])
-                if not ldir.is_absolute():
-                    ldir = Path('autogenerated') / ldir
-                ldir.mkdir(parents=True, exist_ok=True)
             newval = {'class': 'Directory', 'location': in_dict['value']}
             new_keyval = {key: newval}
         # TODO: Check for all valid types?

src/sophios/main.py

@@ -196,7 +196,7 @@ def main() -> None:
         pc.cwl_docker_extract(args, yaml_stem)
         rose_tree = pc.remove_entrypoints(args, rose_tree)
         io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
-
+        pc.find_and_create_output_dirs(rose_tree)
         run_local.run_local(args, rose_tree, args.cachedir, args.cwl_runner, False)
 
         # Finally, since there is an output file copying bug in cwltool,

src/sophios/post_compile.py

@@ -1,11 +1,55 @@
 import argparse
 from pathlib import Path
 import subprocess as sub
-
+from typing import Dict, Union
 from . import plugins
 from .wic_types import RoseTree
 
 
+def find_output_dirs(data: Union[RoseTree, Dict, list]) -> list:
+    """
+    Recursively searches through a nested structure and finds all dictionaries 
+    that contain the key 'location', and a key 'class' with a value of 'Directory'.
+
+    Args:
+        data (any): The data to search through, which can be a dictionary, list, 
+        or any other structure.
+
+    Returns:
+        list: A list of location values.
+    """
+    results = []
+    if isinstance(data, Dict):
+        if "class" in data and data["class"] == "Directory" and "location" in data:
+            results.append(data["location"])
+        for value in data.values():
+            results.extend(find_output_dirs(value))
+    elif isinstance(data, list):
+        for item in data:
+            results.extend(find_output_dirs(item))
+
+    return results
+
+
+def create_output_dirs(output_dirs: list, basepath: str = 'autogenerated') -> None:
+    """
+    Creates all the directories that are needed for the outputs of a workflow.
+    """
+    for output_dir in output_dirs:
+        dir_path = Path(output_dir)
+        if not dir_path.is_absolute():
+            dir_path = Path(basepath) / dir_path
+        dir_path.mkdir(parents=True, exist_ok=True)
+
+
+def find_and_create_output_dirs(rose_tree: RoseTree, basepath: str = 'autogenerated') -> None:
+    """
+    Finds all output directories in the workflow and creates them.
+    """
+    output_dirs = find_output_dirs(rose_tree.data.workflow_inputs_file)
+    create_output_dirs(output_dirs, basepath)
+
+
 def cwl_docker_extract(args: argparse.Namespace, file_name: str) -> None:
     """Helper function to do the cwl_docker_extract"""
     # cwl-docker-extract recursively `docker pull`s all images in all subworkflows.

tests/test_examples.py

@@ -22,7 +22,7 @@
 from sophios import auto_gen_header
 from sophios.cli import get_args
 from sophios.utils_yaml import wic_loader
-from sophios.post_compile import cwl_docker_extract, remove_entrypoints
+from sophios.post_compile import cwl_docker_extract, remove_entrypoints, find_and_create_output_dirs
 from sophios.wic_types import NodeData, StepId, Yaml, YamlTree, Json
 from sophios.utils_graphs import get_graph_reps
 
@@ -223,6 +223,7 @@ def run_workflows(yml_path_str: str, yml_path: Path, cwl_runner: str, args: argp
         rose_tree = sophios.plugins.cwl_update_outputs_optional_rosetree(rose_tree)
         sophios.input_output.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
     # NOTE: Do not use --cachedir; we want to actually test everything.
+    find_and_create_output_dirs(rose_tree)
     retval = sophios.run_local.run_local(args, rose_tree, None, cwl_runner, True)
     assert retval == 0