def migrate(file_input, file_output, force, silent, archive_format):
"""
An entry point to migrate existing AiiDA export archives between version numbers
"""
import os, json, sys
import tarfile, zipfile
from aiida.common.folders import SandboxFolder
from aiida.common.archive import extract_zip, extract_tar
if os.path.exists(file_output) and not force:
print >> sys.stderr, 'Error: the output file already exists'
sys.exit(2)
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(file_input):
extract_zip(file_input, folder, silent=silent)
elif tarfile.is_tarfile(file_input):
extract_tar(file_input, folder, silent=silent)
else:
print >> sys.stderr, 'Error: invalid file format, expected either a zip archive or gzipped tarball'
sys.exit(2)
try:
with open(folder.get_abs_path('data.json')) as f:
data = json.load(f)
with open(folder.get_abs_path('metadata.json')) as f:
metadata = json.load(f)
except IOError as e:
raise ValueError(
'export archive does not contain the required file {}'.format(
e.filename))
old_version = verify_metadata_version(metadata)
try:
if old_version == '0.1':
migrate_v1_to_v2(metadata, data)
elif old_version == '0.2':
try:
migrate_v2_to_v3(metadata, data)
except DanglingLinkError as e:
print "An exception occured!"
print e
raise RuntimeError(
"You're export file is broken because it contains dangling links"
)
else:
raise ValueError(
'cannot migrate from version {}'.format(old_version))
except ValueError as exception:
print >> sys.stderr, 'Error:', exception
sys.exit(2)
new_version = verify_metadata_version(metadata)
with open(folder.get_abs_path('data.json'), 'w') as f:
json.dump(data, f)
with open(folder.get_abs_path('metadata.json'), 'w') as f:
json.dump(metadata, f)
if archive_format == 'zip' or archive_format == 'zip-uncompressed':
compression = zipfile.ZIP_DEFLATED if archive_format == 'zip' else zipfile.ZIP_STORED
with zipfile.ZipFile(file_output,
mode='w',
compression=compression,
allowZip64=True) as archive:
src = folder.abspath
for dirpath, dirnames, filenames in os.walk(src):
relpath = os.path.relpath(dirpath, src)
for fn in dirnames + filenames:
real_src = os.path.join(dirpath, fn)
real_dest = os.path.join(relpath, fn)
archive.write(real_src, real_dest)
elif archive_format == 'tar.gz':
with tarfile.open(file_output,
'w:gz',
format=tarfile.PAX_FORMAT,
dereference=True) as archive:
archive.add(folder.abspath, arcname='')
if not silent:
print 'Successfully migrated the archive from version {} to {}'.format(
old_version, new_version)
def migrate(input_file, output_file, force, silent, archive_format):
# pylint: disable=too-many-locals,too-many-statements,too-many-branches
"""
Migrate an existing export archive file to the most recent version of the export format
"""
import os
import json
import tarfile
import zipfile
from aiida.common.folders import SandboxFolder
from aiida.common.archive import extract_zip, extract_tar
if os.path.exists(output_file) and not force:
echo.echo_critical('the output file already exists')
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(input_file):
extract_zip(input_file, folder, silent=silent)
elif tarfile.is_tarfile(input_file):
extract_tar(input_file, folder, silent=silent)
else:
echo.echo_critical('invalid file format, expected either a zip archive or gzipped tarball')
try:
with open(folder.get_abs_path('data.json')) as handle:
data = json.load(handle)
with open(folder.get_abs_path('metadata.json')) as handle:
metadata = json.load(handle)
except IOError:
echo.echo_critical('export archive does not contain the required file {}'.format(handle.filename))
old_version = verify_metadata_version(metadata)
try:
if old_version == '0.1':
migrate_v1_to_v2(metadata, data)
elif old_version == '0.2':
try:
migrate_v2_to_v3(metadata, data)
except DanglingLinkError:
echo.echo_critical('export file is invalid because it contains dangling links')
else:
echo.echo_critical('cannot migrate from version {}'.format(old_version))
except ValueError as exception:
echo.echo_critical(exception)
new_version = verify_metadata_version(metadata)
with open(folder.get_abs_path('data.json'), 'w') as handle:
json.dump(data, handle)
with open(folder.get_abs_path('metadata.json'), 'w') as handle:
json.dump(metadata, handle)
if archive_format == 'zip' or archive_format == 'zip-uncompressed':
compression = zipfile.ZIP_DEFLATED if archive_format == 'zip' else zipfile.ZIP_STORED
with zipfile.ZipFile(output_file, mode='w', compression=compression, allowZip64=True) as archive:
src = folder.abspath
for dirpath, dirnames, filenames in os.walk(src):
relpath = os.path.relpath(dirpath, src)
for filename in dirnames + filenames:
real_src = os.path.join(dirpath, filename)
real_dest = os.path.join(relpath, filename)
archive.write(real_src, real_dest)
elif archive_format == 'tar.gz':
with tarfile.open(output_file, 'w:gz', format=tarfile.PAX_FORMAT, dereference=True) as archive:
archive.add(folder.abspath, arcname='')
if not silent:
echo.echo_success('migrated the archive from version {} to {}'.format(old_version, new_version))