Skip to content

fix(ProcessExecution): pass io parameter through input_data to get_fi… #13

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mhusbynflow merged 1 commit into from
Mar 20, 2026
Merged

fix(ProcessExecution): pass io parameter through input_data to get_fi… #13

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions nextflow/models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,15 +105,15 @@ def full_path(self):
return Path(self.execution.path, "work", self.path)


def input_data(self, include_path=True):
def input_data(self, include_path=True, io=None):
"""A list of files passed to the process execution as inputs.

:param bool include_path: if ``False``, only filenames returned.
:param io: an optional custom io object to handle file operations.
:type: ``list``"""

inputs = []
if not self.path: return []
run = get_file_text(self.full_path / ".command.run")
run = get_file_text(self.full_path / ".command.run", io=io)
stage = re.search(r"nxf_stage\(\)((.|\n|\r)+?)}", run)
if not stage: return []
contents = stage[1]
Expand All @@ -135,7 +135,7 @@ def all_output_data(self, include_path=True, io=None):

outputs = []
if not self.path: return []
inputs = self.input_data(include_path=False)
inputs = self.input_data(include_path=False, io=io)
listdir = io.listdir if io else os.listdir
for f in listdir(self.full_path):
full_path = Path(f"{self.full_path}/{f}")
Expand Down
2 changes: 1 addition & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

setup(
name="nextflowpy",
version="0.12.1",
version="0.13.0",
description="A Python wrapper around Nextflow.",
long_description=long_description,
long_description_content_type="text/x-rst",
Expand Down
36 changes: 24 additions & 12 deletions tests/unit/test_process_executions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,8 @@ def test_can_get_input_data(self, mock_text, mock_path):
self.process_execution.input_data(),
["/work/25/7eaa7786ca/file1.dat", "/work/fe/3b80569ba5/file2.dat"]
)
mock_text.assert_called_with(Path("/loc/.command.run"))
mock_text.assert_called_with(Path("/loc/.command.run"), io=None)


@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
@patch("nextflow.models.get_file_text")
Expand All @@ -119,8 +119,8 @@ def test_can_get_input_data_filenames(self, mock_text, mock_path):
self.process_execution.input_data(include_path=False),
["file1.dat", "file2.dat"]
)
mock_text.assert_called_with(Path("/loc/.command.run"))
mock_text.assert_called_with(Path("/loc/.command.run"), io=None)


@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
@patch("nextflow.models.get_file_text")
Expand All @@ -130,8 +130,8 @@ def test_can_handle_no_command_run_file(self, mock_text, mock_path):
self.assertEqual(
self.process_execution.input_data(include_path=False), []
)
mock_text.assert_called_with(Path("/loc/.command.run"))
mock_text.assert_called_with(Path("/loc/.command.run"), io=None)


@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
@patch("nextflow.models.get_file_text")
Expand All @@ -141,7 +141,7 @@ def test_can_handle_no_staging(self, mock_text, mock_path):
self.assertEqual(
self.process_execution.input_data(include_path=False), []
)
mock_text.assert_called_with(Path("/loc/.command.run"))
mock_text.assert_called_with(Path("/loc/.command.run"), io=None)


@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
Expand Down Expand Up @@ -178,7 +178,19 @@ def test_can_handle_staging_by_copying(self, mock_text, mock_path):
self.process_execution.input_data(),
["/work/25/7eaa7786ca/file1.dat", "/work/fe/3b80569ba5/file2.dat"]
)
mock_text.assert_called_with(Path("/loc/.command.run"))
mock_text.assert_called_with(Path("/loc/.command.run"), io=None)


@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
def test_can_get_input_data_with_custom_io(self, mock_path):
mock_path.return_value = Path("/loc")
io = Mock()
io.read.return_value = self.text
self.assertEqual(
self.process_execution.input_data(io=io),
["/work/25/7eaa7786ca/file1.dat", "/work/fe/3b80569ba5/file2.dat"]
)
io.read.assert_called_with(Path("/loc/.command.run"))



Expand All @@ -195,9 +207,9 @@ def test_can_get_all_output_data(self, mock_dir, mock_path, mock_input):
self.make_process_execution().all_output_data(),
[str(Path("/loc/file1")), str(Path("/loc/file3"))]
)
mock_input.assert_called_with(include_path=False)
mock_input.assert_called_with(include_path=False, io=None)
mock_dir.assert_called_with(mock_path.return_value)


@patch("nextflow.models.ProcessExecution.input_data")
@patch("nextflow.models.ProcessExecution.full_path", new_callable=PropertyMock)
Expand All @@ -210,7 +222,7 @@ def test_can_get_all_output_filenames(self, mock_dir, mock_path, mock_input):
self.make_process_execution().all_output_data(include_path=False),
["file1", "file3"]
)
mock_input.assert_called_with(include_path=False)
mock_input.assert_called_with(include_path=False, io=None)
mock_dir.assert_called_with(mock_path.return_value)


Expand Down Expand Up @@ -239,4 +251,4 @@ def test_can_use_custom_io(self, mock_path, mock_input):
self.make_process_execution().all_output_data(io=io),
[str(Path("/loc/file1")), str(Path("/loc/file3"))]
)
mock_input.assert_called_with(include_path=False)
mock_input.assert_called_with(include_path=False, io=io)
Loading