def test_import_library_require_permissions():
"""Verify library creation (import) is off by default."""
app = _mock_app()
sa_session = app.model.context
u = model.User(email="*****@*****.**", password="******")
library = model.Library(name="my library 1",
description="my library description",
synopsis="my synopsis")
root_folder = model.LibraryFolder(name="my library 1",
description='folder description')
library.root_folder = root_folder
sa_session.add_all((library, root_folder))
sa_session.flush()
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory,
app=app) as export_store:
export_store.export_library(library)
error_caught = False
try:
import_model_store = store.get_import_model_store_for_directory(
temp_directory, app=app, user=u)
import_model_store.perform_import()
except AssertionError:
# TODO: throw and catch a better exception...
error_caught = True
assert error_caught
def _perform_import_from_directory(directory,
app,
user,
import_history,
import_options=None):
import_model_store = store.get_import_model_store_for_directory(
directory, app=app, user=user, import_options=import_options)
with import_model_store.target_history(default_history=import_history):
import_model_store.perform_import(import_history)
def import_archive(archive_path, app, user):
dest_parent = mkdtemp()
dest_dir = CompressedFile(archive_path).extract(dest_parent)
new_history = None
model_store = store.get_import_model_store_for_directory(dest_dir,
app=app,
user=user)
with model_store.target_history(default_history=None) as new_history:
model_store.perform_import(new_history)
shutil.rmtree(dest_parent)
return new_history
def cleanup_after_job(self):
""" Set history, datasets, collections and jobs' attributes
and clean up archive directory.
"""
#
# Import history.
#
jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(
job_id=self.job_id).first()
if not jiha:
return None
user = jiha.job.user
new_history = None
try:
archive_dir = jiha.archive_dir
if self.app.config.external_chown_script:
external_chown(
archive_dir,
jiha.job.user.system_user_pwent(getpass.getuser()),
self.app.config.external_chown_script,
"history import archive directory")
model_store = store.get_import_model_store_for_directory(
archive_dir,
app=self.app,
user=user,
tag_handler=self.app.tag_handler.create_tag_handler_session())
job = jiha.job
with model_store.target_history(
default_history=job.history) as new_history:
jiha.history = new_history
self.sa_session.flush()
model_store.perform_import(new_history,
job=job,
new_history=True)
# Cleanup.
if os.path.exists(archive_dir):
shutil.rmtree(archive_dir)
except Exception as e:
jiha.job.tool_stderr += f"Error cleaning up history import job: {e}"
self.sa_session.flush()
raise
return new_history
def test_sessionless_import_edit_datasets():
app, h, temp_directory, import_history = _setup_simple_export(
{"for_edit": True})
# Create a model store without a session and import it.
import_model_store = store.get_import_model_store_for_directory(
temp_directory,
import_options=store.ImportOptions(allow_dataset_object_edit=True,
allow_edit=True))
import_model_store.perform_import()
# Not using app.sa_session but a session mock that has a query/find pattern emulating usage
# of real sa_session.
d1 = import_model_store.sa_session.query(
model.HistoryDatasetAssociation).find(h.datasets[0].id)
d2 = import_model_store.sa_session.query(
model.HistoryDatasetAssociation).find(h.datasets[1].id)
assert d1 is not None
assert d2 is not None
def _import_directory_to_history(app, target, work_directory):
sa_session = app.model.context
u = model.User(email="*****@*****.**", password="******")
import_history = model.History(name="Test History for Import", user=u)
sa_session = app.model.context
sa_session.add_all([u, import_history])
sa_session.flush()
assert len(import_history.datasets) == 0
import_options = store.ImportOptions(allow_dataset_object_edit=True)
import_model_store = store.get_import_model_store_for_directory(
target, app=app, user=u, import_options=import_options)
with import_model_store.target_history(default_history=import_history):
import_model_store.perform_import(import_history)
return import_history
def _import_library_target(target, work_directory):
app = _mock_app(store_by="uuid")
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(
temp_directory, app=app,
serialize_dataset_objects=True) as export_store:
persist_target_to_export_store(target, export_store, app.object_store,
work_directory)
u = model.User(email="*****@*****.**", password="******")
import_options = store.ImportOptions(allow_dataset_object_edit=True,
allow_library_creation=True)
import_model_store = store.get_import_model_store_for_directory(
temp_directory, app=app, user=u, import_options=import_options)
import_model_store.perform_import()
sa_session = app.model.context
return sa_session
def import_archive(archive_path, app, user):
dest_parent = mkdtemp()
dest_dir = os.path.join(dest_parent, 'dest')
options = Dummy()
options.is_url = False
options.is_file = True
options.is_b64encoded = False
args = (archive_path, dest_dir)
unpack_tar_gz_archive.main(options, args)
new_history = None
model_store = store.get_import_model_store_for_directory(dest_dir,
app=app,
user=user)
with model_store.target_history(default_history=None) as new_history:
model_store.perform_import(new_history)
return new_history
def cleanup_after_job(self):
""" Set history, datasets, collections and jobs' attributes
and clean up archive directory.
"""
#
# Import history.
#
jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(
job_id=self.job_id).first()
if not jiha:
return None
user = jiha.job.user
new_history = None
try:
archive_dir = jiha.archive_dir
model_store = store.get_import_model_store_for_directory(
archive_dir, app=self.app, user=user)
job = jiha.job
with model_store.target_history(
default_history=job.history) as new_history:
jiha.history = new_history
self.sa_session.flush()
model_store.perform_import(new_history,
job=job,
new_history=True)
# Cleanup.
if os.path.exists(archive_dir):
shutil.rmtree(archive_dir)
except Exception as e:
jiha.job.tool_stderr += "Error cleaning up history import job: %s" % e
self.sa_session.flush()
raise
return new_history
def test_import_export_library():
"""Test basics of library, library folder, and library dataset import/export."""
app = _mock_app()
sa_session = app.model.context
u = model.User(email="*****@*****.**", password="******")
library = model.Library(name="my library 1",
description="my library description",
synopsis="my synopsis")
root_folder = model.LibraryFolder(name="my library 1",
description='folder description')
library.root_folder = root_folder
sa_session.add_all((library, root_folder))
sa_session.flush()
subfolder = model.LibraryFolder(name="sub folder 1",
description="sub folder")
root_folder.add_folder(subfolder)
sa_session.add(subfolder)
ld = model.LibraryDataset(folder=root_folder,
name="my name",
info="my library dataset")
ldda = model.LibraryDatasetDatasetAssociation(create_dataset=True,
flush=False)
ld.library_dataset_dataset_association = ldda
root_folder.add_library_dataset(ld)
sa_session.add(ld)
sa_session.add(ldda)
sa_session.flush()
assert len(root_folder.datasets) == 1
assert len(root_folder.folders) == 1
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory,
app=app) as export_store:
export_store.export_library(library)
import_model_store = store.get_import_model_store_for_directory(
temp_directory,
app=app,
user=u,
import_options=store.ImportOptions(allow_library_creation=True))
import_model_store.perform_import()
all_libraries = sa_session.query(model.Library).all()
assert len(all_libraries) == 2, len(all_libraries)
all_lddas = sa_session.query(model.LibraryDatasetDatasetAssociation).all()
assert len(all_lddas) == 2, len(all_lddas)
new_library = [l for l in all_libraries if l.id != library.id][0]
assert new_library.name == "my library 1"
assert new_library.description == "my library description"
assert new_library.synopsis == "my synopsis"
new_root = new_library.root_folder
assert new_root
assert new_root.name == "my library 1"
assert len(new_root.folders) == 1
assert len(new_root.datasets) == 1
