if files are in a workflow result, the files are copied to the workflow directory

Author: djarecka

pydra/engine/helpers.py

@@ -10,7 +10,7 @@
 import subprocess as sp
 
 from .specs import Runtime, File, attr_fields
-from .helpers_file import is_existing_file, hash_file
+from .helpers_file import is_existing_file, hash_file, copyfile, is_existing_file
 
 
 def ensure_list(obj, tuple2list=False):
@@ -112,13 +112,27 @@ def save(task_path: Path, result=None, task=None):
         raise ValueError("Nothing to be saved")
     task_path.mkdir(parents=True, exist_ok=True)
     if result:
+        if Path(task_path).name.startswith("Workflow"):
+            # copy files to the workflow directory
+            result = copyfile_workflow(wf_path=task_path, result=result)
         with (task_path / "_result.pklz").open("wb") as fp:
             cp.dump(result, fp)
     if task:
         with (task_path / "_task.pklz").open("wb") as fp:
             cp.dump(task, fp)
 
 
+def copyfile_workflow(wf_path, result):
+    """ if file in the wf results, the file will be copied to the workflow directory"""
+    for field in attr_fields(result.output):
+        value = getattr(result.output, field.name)
+        if is_existing_file(value):
+            new_path = wf_path / value.name
+            copyfile(originalfile=value, newfile=new_path, copy=True, use_hardlink=True)
+            setattr(result.output, field.name, new_path)
+    return result
+
+
 def task_hash(task):
     """
     Calculate the checksum of a task.

pydra/engine/helpers_file.py

@@ -516,6 +516,8 @@ def is_local_file(f):
 
 def is_existing_file(f):
     """ checking if an object is an existing file"""
+    if not f:
+        return False
     try:
         return Path(f).exists()
     except TypeError:

pydra/engine/tests/test_shelltask.py

@@ -2018,6 +2018,8 @@ def test_shell_cmd_outputspec_wf_1(plugin):
     res = wf.result()
     assert res.output.stdout == ""
     assert res.output.newfile.exists()
+    # checking if the file was copied to the wf dir
+    assert res.output.newfile.parent == wf.output_dir
 
 
 def no_fsl():