def test_migrate_v3_to_v4(self):
"""Test function migrate_v3_to_v4"""
from aiida import get_version
# Get metadata.json and data.json as dicts from v0.4 file archive
metadata_v4, data_v4 = get_json_files('export_v0.4_simple.aiida', **self.core_archive)
verify_metadata_version(metadata_v4, version='0.4')
# Get metadata.json and data.json as dicts from v0.3 file archive
# Cannot use 'get_json_files' for 'export_v0.3_simple.aiida',
# because we need to pass the SandboxFolder to 'migrate_v3_to_v4'
dirpath_archive = get_archive_file('export_v0.3_simple.aiida', **self.core_archive)
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(dirpath_archive):
extract_zip(dirpath_archive, folder, silent=True)
elif tarfile.is_tarfile(dirpath_archive):
extract_tar(dirpath_archive, folder, silent=True)
else:
raise ValueError('invalid file format, expected either a zip archive or gzipped tarball')
try:
with io.open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle:
data_v3 = jsonload(fhandle)
with io.open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle:
metadata_v3 = jsonload(fhandle)
except IOError:
raise NotExistent('export archive does not contain the required file {}'.format(fhandle.filename))
verify_metadata_version(metadata_v3, version='0.3')
# Migrate to v0.4
migrate_v3_to_v4(metadata_v3, data_v3, folder)
verify_metadata_version(metadata_v3, version='0.4')
# Remove AiiDA version, since this may change irregardless of the migration function
metadata_v3.pop('aiida_version')
metadata_v4.pop('aiida_version')
# Assert conversion message in `metadata.json` is correct and then remove it for later assertions
self.maxDiff = None # pylint: disable=invalid-name
conversion_message = 'Converted from version 0.3 to 0.4 with AiiDA v{}'.format(get_version())
self.assertEqual(
metadata_v3.pop('conversion_info')[-1],
conversion_message,
msg='The conversion message after migration is wrong'
)
metadata_v4.pop('conversion_info')
# Assert changes were performed correctly
self.assertDictEqual(
metadata_v3,
metadata_v4,
msg='After migration, metadata.json should equal intended metadata.json from archives'
)
self.assertDictEqual(
data_v3, data_v4, msg='After migration, data.json should equal intended data.json from archives'
)
def test_migrate_recursively(self):
"""Test function 'migrate_recursively'"""
import io
import tarfile
import zipfile
from aiida.common.exceptions import NotExistent
from aiida.common.folders import SandboxFolder
from aiida.common.json import load as jsonload
from aiida.tools.importexport.common.archive import extract_tar, extract_zip
# Get metadata.json and data.json as dicts from v0.1 file archive
# Cannot use 'get_json_files' for 'export_v0.1_simple.aiida',
# because we need to pass the SandboxFolder to 'migrate_recursively'
dirpath_archive = get_archive_file('export_v0.1_simple.aiida',
**self.core_archive)
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(dirpath_archive):
extract_zip(dirpath_archive, folder, silent=True)
elif tarfile.is_tarfile(dirpath_archive):
extract_tar(dirpath_archive, folder, silent=True)
else:
raise ValueError(
'invalid file format, expected either a zip archive or gzipped tarball'
)
try:
with io.open(folder.get_abs_path('data.json'),
'r',
encoding='utf8') as fhandle:
data = jsonload(fhandle)
with io.open(folder.get_abs_path('metadata.json'),
'r',
encoding='utf8') as fhandle:
metadata = jsonload(fhandle)
except IOError:
raise NotExistent(
'export archive does not contain the required file {}'.
format(fhandle.filename))
verify_metadata_version(metadata, version='0.1')
# Migrate to newest version
new_version = migrate_recursively(metadata, data, folder)
verify_metadata_version(metadata, version=newest_version)
self.assertEqual(new_version, newest_version)
def test_migrate_v3_to_v4_complete(self):
"""Test migration for file containing complete v0.3 era possibilities"""
# Get metadata.json and data.json as dicts from v0.3 file archive
dirpath_archive = get_archive_file('export_v0.3.aiida', **self.external_archive)
# Migrate
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(dirpath_archive):
extract_zip(dirpath_archive, folder, silent=True)
elif tarfile.is_tarfile(dirpath_archive):
extract_tar(dirpath_archive, folder, silent=True)
else:
raise ValueError('invalid file format, expected either a zip archive or gzipped tarball')
try:
with io.open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle:
data = jsonload(fhandle)
with io.open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle:
metadata = jsonload(fhandle)
except IOError:
raise NotExistent('export archive does not contain the required file {}'.format(fhandle.filename))
verify_metadata_version(metadata, version='0.3')
# Save pre-migration info
links_count_org = len(data['links_uuid'])
work_uuids = {
value['uuid']
for value in data['export_data']['Node'].values()
if value['type'].startswith('calculation.function') or value['type'].startswith('calculation.work')
}
illegal_links = []
for link in data['links_uuid']:
if link['input'] in work_uuids and link['type'] == 'createlink':
illegal_links.append(link)
# Migrate to v0.4
migrate_v3_to_v4(metadata, data, folder)
verify_metadata_version(metadata, version='0.4')
## Following checks are based on the archive-file
## Which means there are more legal entities, they are simply not relevant here.
self.maxDiff = None # pylint: disable=invalid-name
# Check schema-changes
new_node_attrs = {'node_type', 'process_type'}
for change in new_node_attrs:
# data.json
for node in data['export_data']['Node'].values():
self.assertIn(change, node, msg="'{}' not found for {}".format(change, node))
# metadata.json
self.assertIn(
change,
metadata['all_fields_info']['Node'],
msg="'{}' not found in metadata.json for Node".format(change)
)
# Check Node types
legal_node_types = {
'data.float.Float.', 'data.int.Int.', 'data.dict.Dict.', 'data.code.Code.', 'data.structure.StructureData.',
'data.folder.FolderData.', 'data.remote.RemoteData.', 'data.upf.UpfData.', 'data.array.ArrayData.',
'data.array.bands.BandsData.', 'data.array.kpoints.KpointsData.', 'data.array.trajectory.TrajectoryData.',
'process.workflow.workchain.WorkChainNode.', 'process.calculation.calcjob.CalcJobNode.'
}
legal_process_types = {'', 'aiida.calculations:quantumespresso.pw'}
for node in data['export_data']['Node'].values():
self.assertIn(
node['node_type'],
legal_node_types,
msg='{} is not a legal node_type. Legal node types: {}'.format(node['node_type'], legal_node_types)
)
self.assertIn(
node['process_type'],
legal_process_types,
msg='{} is not a legal process_type. Legal process types: {}'.format(
node['process_type'], legal_node_types
)
)
# Check links
# Make sure the two illegal create links were removed during the migration
self.assertEqual(
len(data['links_uuid']),
links_count_org - 2,
msg='Two of the org. {} links should have been removed during the migration, '
'instead there are now {} links'.format(links_count_org, len(data['links_uuid']))
)
legal_link_types = {'unspecified', 'create', 'return', 'input_calc', 'input_work', 'call_calc', 'call_work'}
for link in data['links_uuid']:
self.assertIn(link['type'], legal_link_types)
for link in illegal_links:
self.assertNotIn(link, data['links_uuid'], msg='{} should not be in the migrated export file'.format(link))
# Check Groups
# There is one Group in the export file, it is a user group
updated_attrs = {'label', 'type_string'}
legal_group_type = {'user'}
for attr in updated_attrs:
# data.json
for group in data['export_data']['Group'].values():
self.assertIn(attr, group, msg='{} not found in Group {}'.format(attr, group))
self.assertIn(
group['type_string'],
legal_group_type,
msg='{} is not a legal Group type_string'.format(group['type_string'])
)
# metadata.json
self.assertIn(attr, metadata['all_fields_info']['Group'], msg='{} not found in metadata.json'.format(attr))
# Check node_attributes*
calcjob_nodes = []
process_nodes = []
for node_id, content in data['export_data']['Node'].items():
if content['node_type'] == 'process.calculation.calcjob.CalcJobNode.':
calcjob_nodes.append(node_id)
elif content['node_type'].startswith('process.'):
process_nodes.append(node_id)
mandatory_updated_calcjob_attrs = {'resources', 'parser_name'}
optional_updated_calcjob_attrs = {'custom_environment_variables': 'environment_variables'}
updated_process_attrs = {'process_label'}
fields = {'node_attributes', 'node_attributes_conversion'}
for field in fields:
for node_id in calcjob_nodes:
for attr in mandatory_updated_calcjob_attrs:
self.assertIn(
attr,
data[field][node_id],
msg="Updated attribute name '{}' not found in {} for node_id: {}".format(attr, field, node_id)
)
for old, new in optional_updated_calcjob_attrs.items():
self.assertNotIn(
old,
data[field][node_id],
msg="Old attribute '{}' found in {} for node_id: {}. "
"It should now be updated to '{}' or not exist".format(old, field, node_id, new)
)
for node_id in process_nodes:
for attr in updated_process_attrs:
self.assertIn(
attr,
data[field][node_id],
msg="Updated attribute name '{}' not found in {} for node_id: {}".format(attr, field, node_id)
)
# Check TrajectoryData
# There should be minimum one TrajectoryData in the export file
trajectorydata_nodes = []
for node_id, content in data['export_data']['Node'].items():
if content['node_type'] == 'data.array.trajectory.TrajectoryData.':
trajectorydata_nodes.append(node_id)
updated_attrs = {'symbols'}
fields = {'node_attributes', 'node_attributes_conversion'}
for field in fields:
for node_id in trajectorydata_nodes:
for attr in updated_attrs:
self.assertIn(
attr,
data[field][node_id],
msg="Updated attribute name '{}' not found in {} for TrajecteoryData node_id: {}".format(
attr, field, node_id
)
)
# Check Computer
removed_attrs = {'enabled'}
for attr in removed_attrs:
# data.json
for computer in data['export_data']['Computer'].values():
self.assertNotIn(
attr, computer, msg="'{}' should have been removed from Computer {}".format(attr, computer['name'])
)
# metadata.json
self.assertNotIn(
attr,
metadata['all_fields_info']['Computer'],
msg="'{}' should have been removed from Computer in metadata.json".format(attr)
)
# Check new entities
new_entities = {'Log', 'Comment'}
fields = {'all_fields_info', 'unique_identifiers'}
for entity in new_entities:
for field in fields:
self.assertIn(entity, metadata[field], msg='{} not found in {} in metadata.json'.format(entity, field))
# Check extras
# Dicts with key, vales equal to node_id, {} should be present
# This means they should be same length as data['export_data']['Node'] or 'node_attributes*'
attrs_count = len(data['node_attributes'])
new_fields = {'node_extras', 'node_extras_conversion'}
for field in new_fields:
self.assertIn(field, list(data.keys()), msg="New field '{}' not found in data.json".format(field))
self.assertEqual(
len(data[field]),
attrs_count,
msg="New field '{}' found to have only {} entries, but should have had {} entries".format(
field, len(data[field]), attrs_count
)
)
def test_illegal_create_links(self):
"""Test illegal create links from workchain are detected and removed from exports using v0.3"""
# Initialization
dirpath_archive = get_archive_file('export_v0.3.aiida', **self.external_archive)
known_illegal_links = 2
# Unpack archive, check data.json, and migrate to v0.4
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(dirpath_archive):
extract_zip(dirpath_archive, folder, silent=True)
elif tarfile.is_tarfile(dirpath_archive):
extract_tar(dirpath_archive, folder, silent=True)
else:
raise ValueError('invalid file format, expected either a zip archive or gzipped tarball')
try:
with io.open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle:
data = jsonload(fhandle)
with io.open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle:
metadata = jsonload(fhandle)
except IOError:
raise NotExistent('export archive does not contain the required file {}'.format(fhandle.filename))
# Check illegal create links are present in org. export file
links_count = len(data['links_uuid'])
links_count_migrated = links_count - known_illegal_links
workfunc_uuids = {
value['uuid']
for value in data['export_data']['Node'].values()
if value['type'].startswith('calculation.function') or value['type'].startswith('calculation.work')
}
violations = []
for link in data['links_uuid']:
if link['input'] in workfunc_uuids and link['type'] == 'createlink':
violations.append(link)
self.assertEqual(
len(violations),
known_illegal_links,
msg='{} illegal create links were expected, instead {} was/were found'.format(
known_illegal_links, len(violations)
)
)
# Migrate to v0.4
migrate_v3_to_v4(metadata, data, folder)
# Check illegal create links were removed
self.assertEqual(
len(data['links_uuid']),
links_count_migrated,
msg='{} links were expected, instead {} was/were found'.format(
links_count_migrated, len(data['links_uuid'])
)
)
workfunc_uuids = {
value['uuid']
for value in data['export_data']['Node'].values()
if value['node_type'].find('WorkFunctionNode') != -1 or value['node_type'].find('WorkChainNode') != -1
}
violations = []
for link in data['links_uuid']:
if link['input'] in workfunc_uuids and link['type'] == 'create':
violations.append(link)
self.assertEqual(
len(violations), 0, msg='0 illegal links were expected, instead {} was/were found'.format(len(violations))
)
def test_compare_migration_with_aiida_made(self):
"""
Compare the migration of a Workflow made and exported with version 0.3 to version 0.4,
and the same Workflow made and exported with version 0.4.
(AiiDA versions 0.12.3 versus 1.0.0b2)
NB: Since PKs and UUIDs will have changed, comparisons between 'data.json'-files will be made indirectly
"""
# Get metadata.json and data.json as dicts from v0.3 file archive and migrate
dirpath_archive = get_archive_file('export_v0.3.aiida', **self.external_archive)
# Migrate
with SandboxFolder(sandbox_in_repo=False) as folder:
if zipfile.is_zipfile(dirpath_archive):
extract_zip(dirpath_archive, folder, silent=True)
elif tarfile.is_tarfile(dirpath_archive):
extract_tar(dirpath_archive, folder, silent=True)
else:
raise ValueError('invalid file format, expected either a zip archive or gzipped tarball')
try:
with io.open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle:
data_v3 = jsonload(fhandle)
with io.open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle:
metadata_v3 = jsonload(fhandle)
except IOError:
raise NotExistent('export archive does not contain the required file {}'.format(fhandle.filename))
# Migrate to v0.4
migrate_v3_to_v4(metadata_v3, data_v3, folder)
# Get metadata.json and data.json as dicts from v0.4 file archive
metadata_v4, data_v4 = get_json_files('export_v0.4.aiida', **self.external_archive)
# Compare 'metadata.json'
self.maxDiff = None
metadata_v3.pop('conversion_info')
metadata_v3.pop('aiida_version')
metadata_v4.pop('aiida_version')
self.assertDictEqual(metadata_v3, metadata_v4)
self.maxDiff = None
# Compare 'data.json'
self.assertEqual(len(data_v3), len(data_v4))
entities = {
'Node': {
'migrated': [],
'made': []
},
'Computer': {
'migrated': [],
'made': []
},
'Group': {
'migrated': [],
'made': []
}
} # User is special, see below
for entity, details in entities.items():
for node in data_v3['export_data'][entity].values():
add = node.get('node_type', None) # Node
if not add:
add = node.get('hostname', None) # Computer
if not add:
add = node.get('type_string', None) # Group
self.assertIsNotNone(add, msg="Helper variable 'add' should never be None")
details['migrated'].append(add)
for node in data_v4['export_data'][entity].values():
add = node.get('node_type', None) # Node
if not add:
add = node.get('hostname', None) # Computer
if not add:
add = node.get('type_string', None) # Group
self.assertIsNotNone(add, msg="Helper variable 'add' should never be None")
details['made'].append(add)
#### Two extra Dicts are present for AiiDA made export 0.4 file ####
if entity == 'Node':
details['migrated'].extend(2 * ['data.dict.Dict.'])
self.assertListEqual(
sorted(details['migrated']),
sorted(details['made']),
msg='Number of {}-entities differ, see diff for details'.format(entity)
)
fields = {
'groups_uuid', 'node_attributes_conversion', 'node_attributes', 'node_extras', 'node_extras_conversion'
} # 'export_data' is special, see below
for field in fields:
if field != 'groups_uuid':
correction = 2 # Two extra Dicts in AiiDA made export v0.4 file
else:
correction = 0
self.assertEqual(
len(data_v3[field]),
len(data_v4[field]) - correction,
msg='Number of entities in {} differs for the export files'.format(field)
)
number_of_links_v3 = {
'unspecified': 0,
'create': 0,
'return': 0,
'input_calc': 0,
'input_work': 0,
'call_calc': 0,
'call_work': 0
}
for link in data_v3['links_uuid']:
number_of_links_v3[link['type']] += 1
number_of_links_v4 = {
'unspecified': 0,
'create': 0,
'return': 0,
'input_calc': -2, # Two extra Dict inputs to CalcJobNodes
'input_work': 0,
'call_calc': 0,
'call_work': 0
}
for link in data_v4['links_uuid']:
number_of_links_v4[link['type']] += 1
self.assertDictEqual(
number_of_links_v3,
number_of_links_v4,
msg='There are a different number of specific links in the migrated export file than the AiiDA made one.'
)
self.assertEqual(number_of_links_v3['unspecified'], 0)
self.assertEqual(number_of_links_v4['unspecified'], 0)
# Special for data['export_data']['User']
# There is an extra user in the migrated export v0.3 file
self.assertEqual(len(data_v3['export_data']['User']), len(data_v4['export_data']['User']) + 1)
# Special for data['export_data']
# There are Logs exported in the AiiDA made export v0.4 file
self.assertEqual(len(data_v3['export_data']) + 1, len(data_v4['export_data']))
