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Expose the output_type option when streaming, and allow both stdout/stderr to be captured #209

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merged 4 commits into from
Oct 25, 2023
Merged

Expose the output_type option when streaming, and allow both stdout/stderr to be captured #209

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3bafb4c
allow both output stdout stderr to be emitted. Expose option to allow…
Oct 25, 2023
55c477a
updted changlog, version bump, error message
Oct 25, 2023
56747e1
added a basic stream test
Oct 25, 2023
c00ecb3
linting and pin black to 23.3.0
vsoch Oct 25, 2023
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4 changes: 3 additions & 1 deletion spython/main/execute.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ def execute(
sudo_options=None,
quiet=True,
environ=None,
stream_type="stdout"
):
"""execute: send a command to a container

Expand All @@ -51,6 +52,7 @@ def execute(
and message result not (default)
quiet: Do not print verbose output.
environ: extra environment to add.
stream_type: Sets which output stream from the singularity command should be return. Values are 'stdout', 'stderr', 'both'.
"""
from spython.utils import check_install

Expand Down Expand Up @@ -115,7 +117,7 @@ def execute(
quiet=quiet,
environ=environ,
)
return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
return stream_command(cmd, sudo=sudo, sudo_options=sudo_options, output_type=stream_type)

bot.exit("Please include a command (list) to execute.")

Expand Down
6 changes: 4 additions & 2 deletions spython/utils/terminal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,12 +122,14 @@ def stream_command(
sudo_options: string or list of strings that will be passed as options to sudo

"""
if output_type not in ["stdout", "stderr"]:
if output_type not in ["stdout", "stderr", "both"]:
bot.exit("Invalid output type %s. Must be stderr or stdout." % output_type)
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Suggested change
bot.exit("Invalid output type %s. Must be stderr or stdout." % output_type)
bot.exit("Invalid output type %s. Must be stderr, stdout, or both" % output_type)

cmd = _process_sudo_cmd(cmd, sudo, sudo_options)

stderr_pipe = subprocess.STDOUT if output_type == "both" else subprocess.PIPE

process = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True
cmd, stdout=subprocess.PIPE, stderr=stderr_pipe, universal_newlines=True
)

# Allow the runner to choose streaming output or error
Expand Down