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fix DB download/update permissions
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@oschwengers
oschwengers committed Jan 22, 2024
1 parent c09d8d4 commit 1a0413c
Showing 1 changed file with 19 additions and 10 deletions.
29 changes: 19 additions & 10 deletions bakta/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,10 @@ def main():
try:
db_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH) # set write permissions on old (existing) directory with updated content
for db_file_path in db_path.iterdir():
db_file_path.chmod(stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH)
if(db_file_path.is_dir()):
db_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
else:
db_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IROTH)
except:
sys.exit(f'ERROR: cannot set read|execute permissions on new database! path={db_path}, owner={db_path.owner()}, group={db_path.group()}, permissions={oct(db_path.stat().st_mode )[-3:]}')

Expand Down Expand Up @@ -266,15 +269,15 @@ def main():
sys.exit()
required_version = compatible_sorted[0]

tarball_path = output_path.joinpath(f"{'db-light' if args.type == 'light' else 'db'}.tar.gz")
db_url = f"https://zenodo.org/record/{required_version['record']}/files/{'db-light' if args.type == 'light' else 'db'}.tar.gz"
tarball_path = tmp_path.joinpath(f"{'db-light' if db_old_info['type'] == 'light' else 'db'}.tar.gz")
db_url = f"https://zenodo.org/record/{required_version['record']}/files/{'db-light' if db_old_info['type'] == 'light' else 'db'}.tar.gz"
print(f"Download database: v{required_version['major']}.{required_version['minor']}, type={db_old_info['type']}, {required_version['date']}, DOI: {required_version['doi']}, URL: {db_url}...")
download(db_url, tarball_path)
print('\t... done')

print('Check MD5 sum...')
md5_sum = calc_md5_sum(tarball_path)
required_md5 = required_version['md5-light' if args.type == 'light' else 'md5']
required_md5 = required_version['md5-light' if db_old_info['type'] == 'light' else 'md5']
if(md5_sum == required_md5):
print(f'\t...database file OK: {md5_sum}')
else:
Expand All @@ -284,17 +287,17 @@ def main():
untar(tarball_path, tmp_path)
tarball_path.unlink()

db_new_path = tmp_path.joinpath('db-light' if args.type == 'light' else 'db')
db_new_path = tmp_path.joinpath('db-light' if db_old_info['type'] == 'light' else 'db')
db_new_info = check(db_new_path)
if(db_new_info['major'] != required_version['major']):
sys.exit(f"ERROR: wrong major db detected! required={required_version['major']}, detected={db_new_info['major']}")
elif(db_new_info['minor'] != required_version['minor']):
sys.exit(f"ERROR: wrong minor db detected! required={required_version['minor']}, detected={db_new_info['minor']}")
elif(db_new_info['type'] != args.type == 'light'):
sys.exit(f"ERROR: wrong db type detected! required={args.type}, detected={db_new_info['type']}")
elif(db_new_info['type'] != db_old_info['type'] == 'light'):
sys.exit(f"ERROR: wrong db type detected! required={db_old_info['type']}, detected={db_new_info['type']}")
print('Successfully downloaded Bakta DB:')
print(f"\tversion: {required_version['major']}.{required_version['minor']}")
print(f"\tType: {args.type}")
print(f"\tType: {db_new_info['type']}")
print(f"\tDOI: {required_version['doi']}")
print(f'\tpath: {db_new_path}')
print('Remove old database...')
Expand All @@ -316,7 +319,10 @@ def main():
try:
db_new_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR) # set write permissions on db_new_path directory
for db_new_file_path in db_new_path.iterdir():
db_new_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR)
if(db_new_file_path.is_dir()):
db_new_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
else:
db_new_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IROTH)
except:
sys.exit(f'ERROR: cannot set read|write|execute permissions on new database! path={db_new_path}, owner={db_new_path.owner()}, group={db_new_path.group()}, permissions={oct(db_new_path.stat().st_mode )[-3:]}')
try:
Expand All @@ -330,7 +336,10 @@ def main():
try:
db_old_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH) # set write permissions on old (existing) directory with updated content
for db_old_file_path in db_old_path.iterdir():
db_old_file_path.chmod(stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH)
if(db_old_file_path.is_dir()):
db_old_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
else:
db_old_file_path.chmod(stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IROTH)
except:
sys.exit(f'ERROR: cannot set read(|execute) permissions on new database! path={db_old_path}, owner={db_old_path.owner()}, group={db_old_path.group()}, permissions={oct(db_old_path.stat().st_mode )[-3:]}')

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