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fix: pass converter commands as argv lists instead of via a shell #114

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fix: pass converter commands as argv lists instead of via a shell #114

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24 changes: 13 additions & 11 deletions PyReconstruct/modules/gui/main/main_window.py
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Original file line number Diff line number Diff line change
Expand Up @@ -411,7 +411,7 @@ def srcToZarr(self, create_new=True):
str(zarr_converter.absolute()),
"convert_zarr",
str(cores),
f"\"{self.series.src_dir}\"",
self.series.src_dir,
zarr_fp
]

Expand All @@ -421,19 +421,20 @@ def srcToZarr(self, create_new=True):
str(zarr_converter.absolute()),
"convert_zarr",
str(cores),
f"\"{self.series.src_dir}\""
self.series.src_dir
]

# Pass argv as a list on every platform, never through a shell, so paths
# read from the series file stay single literal arguments.
if os.name == 'nt':

subprocess.Popen(
convert_cmd, creationflags=subprocess.CREATE_NO_WINDOW
)

else:

convert_cmd = " ".join(convert_cmd)
subprocess.Popen(convert_cmd, shell=True, stdout=None, stderr=None)
subprocess.Popen(convert_cmd, stdout=None, stderr=None)

def changeUsername(self, new_name : str = None):
"""Edit the login name used to track history.
Expand Down Expand Up @@ -1997,7 +1998,7 @@ def exportToZarr(self):
convert_cmd = launch_prefix + [
str(zarr_converter.absolute()),
"create_ng_zarr",
f"\"{self.series.jser_fp}\""
self.series.jser_fp
]

for argname, arg in args.items():
Expand All @@ -2010,24 +2011,25 @@ def exportToZarr(self):

convert_cmd += [
"--output",
f"\"{arg}\""
str(arg)
]

else:

convert_cmd += [argname] + str(arg).split()

# Pass argv as a list on every platform, never through a shell, so paths
# read from the series file stay single literal arguments.
if os.name == 'nt':

subprocess.Popen(
convert_cmd,
creationflags=subprocess.CREATE_NO_WINDOW
)

else:

convert_cmd = " ".join(convert_cmd)
subprocess.Popen(convert_cmd, shell=True, stdout=None, stderr=None)
subprocess.Popen(convert_cmd, stdout=None, stderr=None)

# AUTOSEG FUNCTIONS TEMPORARILY REMOVED

Expand Down