def migrate(self) -> bool:
""" Migrate the given LabBook to the most recent schema AND branch version.
Returns:
Boolean indicating whether a migration was performed (False if already up-to-date)
"""
if self.repository.schema == CURRENT_LABBOOK_SCHEMA:
logger.info(f"{str(self.labbook)} already migrated.")
return False
if 'gm.workspace' not in BranchManager(self.labbook).active_branch:
raise GitWorkflowException(
'Must be on a gm.workspace branch to migrate')
im = InventoryManager(self.labbook.client_config.config_file)
gitworkflows_utils.migrate_labbook_branches(self.labbook)
self.repository = im.load_labbook_from_directory(self.labbook.root_dir)
gitworkflows_utils.migrate_labbook_schema(self.labbook)
self.repository = im.load_labbook_from_directory(self.labbook.root_dir)
gitworkflows_utils.migrate_labbook_untracked_space(self.labbook)
self.repository = im.load_labbook_from_directory(self.labbook.root_dir)
# Pushes up the new master branch
if self.repository.has_remote:
self.sync(username='')
return True
def check_projects(config: Configuration, username: str) -> Dict[str, Any]:
""" Crawl through all projects to check for errors on loading or accessing imporant fields.
Warning: This method may take a while.
Args:
config: Configuration to include root gigantum directory
username: Active username - if none provided crawl for all users.
Returns:
Dictionary mapping a project path to errors
Schema:
{
'errors': {
'username/owner/labbooks/project-name': 'This is the error msg'
},
'_collectionTimeSec': 2.0
}
"""
gigantum_root = config.app_workdir
project_paths = glob.glob(f'{gigantum_root}/{username}/*/labbooks/*')
inventory = InventoryManager(config.config_file)
t0 = time.time()
errors: Dict[str, Any] = {'errors': {}}
for project_path in project_paths:
try:
# Try to load the labbook, and it's important fields.
labbook = inventory.load_labbook_from_directory(project_path)
_ = labbook.creation_date, labbook.modified_on, labbook.data
except Exception as e:
logger.error(e)
errors['errors'][project_path.replace(gigantum_root, '')] = str(e)
tfin = time.time()
errors['_collectionTimeSec'] = float(f'{tfin - t0:.2f}')
return errors
def test_query_owner_fail(self, mock_config_file):
inv_manager = InventoryManager(mock_config_file[0])
lb = inv_manager.create_labbook("test",
"test",
"labbook1",
description="my first labbook")
new_location = shutil.move(lb.root_dir, '/tmp')
try:
lb = inv_manager.load_labbook_from_directory(new_location)
with pytest.raises(InventoryException):
inv_manager.query_owner(lb)
finally:
shutil.rmtree(new_location)
def test_should_migrate_on_old_project(self, mock_config_file):
p = resource_filename('gtmcore', 'workflows')
p2 = os.path.join(p, 'tests', 'lb-to-migrate-197b6a.zip')
with tempfile.TemporaryDirectory() as tempdir:
lbp = shutil.copyfile(p2, os.path.join(tempdir,
'lb-to-migrate.zip'))
subprocess.run(f'unzip lb-to-migrate.zip'.split(),
check=True,
cwd=tempdir)
im = InventoryManager(mock_config_file[0])
lb = im.load_labbook_from_directory(
os.path.join(tempdir, 'lb-to-migrate'))
wf = LabbookWorkflow(lb)
assert wf.should_migrate() is True
wf.migrate()
assert wf.labbook.active_branch == 'master'
assert wf.should_migrate() is False
wf.labbook.git.checkout('gm.workspace')
assert wf.should_migrate() is False
