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Permission and ownership tweaks in LSS catalog writing functions #190

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Permission and ownership tweaks in LSS catalog writing functions #190

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792df1a
Added mode parameter
misharash Mar 18, 2026
01b8c18
Added chgrp desi
misharash Mar 18, 2026
6d2827d
Unset execution bits for FITS/HDF5 files
misharash Mar 18, 2026
a0a3e53
Added clarification
misharash Mar 18, 2026
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10 changes: 6 additions & 4 deletions py/LSS/common_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1855,7 +1855,7 @@ def convert_fits2h5(filename):
write_LSShdf5_scratchcp(ff, filename.replace('.fits', '.h5'))


def write_LSShdf5_scratchcp(ff, outf, logger=None):
def write_LSShdf5_scratchcp(ff, outf, logger=None, mode=0o664):
import h5py
import hdf5plugin # need to be in the cosmodesi test environment, as of Sep 4th 25

Expand Down Expand Up @@ -1897,7 +1897,8 @@ def write_LSShdf5_scratchcp(ff, outf, logger=None):
shutil.copy2(tmpfn, outftmp)
os.rename(outftmp, outf)
# os.system('chmod 775 ' + outf) #this should fix permissions for the group
os.chmod(outf, 0o775)
shutil.chown(outf, group='desi') # essentially chgrp desi. good to ensure at NERSC, but may fail elsewhere, do we need to account for that?
os.chmod(outf, mode) # now that the file's group is desi, could set permissions to 660 for more security
printlog('moved output to ' + outf, logger)
df = 0
# printlog('checking read of column ' + testcol, logger)
Expand Down Expand Up @@ -1941,7 +1942,7 @@ def read_hdf5_blosc(filename, columns=None, extname='LSS'):
return data


def write_LSS_scratchcp(ff, outf, comments=None, extname='LSS', logger=None):
def write_LSS_scratchcp(ff, outf, comments=None, extname='LSS', logger=None, mode=0o664):
'''
ff is the structured array/Table to be written out as an LSS catalog
outf is the full path to write out
Expand Down Expand Up @@ -1979,7 +1980,8 @@ def write_LSS_scratchcp(ff, outf, comments=None, extname='LSS', logger=None):
shutil.copy2(tmpfn, outftmp)
os.rename(outftmp, outf)
# os.system('chmod 775 ' + outf) #this should fix permissions for the group
os.chmod(outf, 0o775)
shutil.chown(outf, group='desi') # essentially chgrp desi. good to ensure at NERSC, but may fail elsewhere, do we need to account for that?
os.chmod(outf, mode) # now that the file's group is desi, could set permissions to 660 for more security

# os.system('cp ' + tmpfn + ' ' + outf)
# os.system('chmod 775 ' + outf) #this should fix permissions for the group
Expand Down