def confirm_downloaded_files(self):
try:
checksums_file = read_remote_file(self.database_url +
'/md5_checksums',
is_gzip=False).strip()
checksums = {}
except:
self.run.warning(
"Checksum file '%s' is not available in FTP, Anvi'o won't be able to verify downloaded files."
% (self.database_url + '/md5_checksums'))
return
for line in checksums_file.split('\n'):
checksum, file_name = [
item.strip() for item in line.strip().split()
]
checksums[file_name] = checksum
for file_name in self.files:
if not filesnpaths.is_file_exists(os.path.join(
self.pfam_data_dir, file_name),
dont_raise=True):
# TO DO: Fix messages :(
raise ConfigError("Have missing file %s, please run --reset" %
file_name)
hash_on_disk = utils.get_file_md5(
os.path.join(self.pfam_data_dir, file_name))
expected_hash = checksums[file_name]
if not expected_hash == hash_on_disk:
# TO DO: Fix messages :(
raise ConfigError(
"Please run with --reset, one file hash doesn't match. %s"
% file_name)
def confirm_downloaded_files(self):
try:
checksums_file = read_remote_file(self.database_url + '/md5_checksums', is_gzip=False).strip()
checksums = {}
except:
self.run.warning("Checksum file '%s' is not available in FTP, Anvi'o won't be able to verify downloaded files." % (self.database_url + '/md5_checksums'))
return
for line in checksums_file.split('\n'):
checksum, file_name = [item.strip() for item in line.strip().split()]
checksums[file_name] = checksum
for file_name in self.files:
if not filesnpaths.is_file_exists(os.path.join(self.pfam_data_dir, file_name), dont_raise=True):
# TO DO: Fix messages :(
raise ConfigError("Have missing file %s, please run --reset" % file_name)
hash_on_disk = utils.get_file_md5(os.path.join(self.pfam_data_dir, file_name))
expected_hash = checksums[file_name]
if not expected_hash == hash_on_disk:
# TO DO: Fix messages :(
raise ConfigError("Please run with --reset, one file hash doesn't match. %s" % file_name)
def confirm_downloaded_files(self):
try:
checksums_file = read_remote_file(self.database_url +
'/md5_checksums',
is_gzip=False).strip()
checksums = {}
except:
self.run.warning(
"Checksum file '%s' is not available in FTP, Anvi'o won't be able to verify downloaded files."
% (self.database_url + '/md5_checksums'))
return
for line in checksums_file.split('\n'):
checksum, file_name = [
item.strip() for item in line.strip().split()
]
checksums[file_name] = checksum
for file_name in self.files:
if not filesnpaths.is_file_exists(os.path.join(
self.pfam_data_dir, file_name),
dont_raise=True):
raise ConfigError(
f"Unfortunately, we failed to download the file {file_name}, please re-run setup "
"with the --reset flag.")
hash_on_disk = utils.get_file_md5(
os.path.join(self.pfam_data_dir, file_name))
expected_hash = checksums[file_name]
if not expected_hash == hash_on_disk:
raise ConfigError(
f"Please re-run setup with --reset, the file hash for {file_name} doesn't match to the hash "
"we expected. If you continue to get this error after doing that, try removing the entire "
f"Pfams data directory ({self.pfam_data_dir}) manually and running setup again (without the --reset flag)."
)