def test_model_create_context_persist_error_hda():
work_directory = mkdtemp()
with open(os.path.join(work_directory, "file1.txt"), "w") as f:
f.write("hello world\nhello world line 2")
target = {
"destination": {
"type": "hdas",
},
"elements": [{
"error_message": "Failed to download some URL I guess",
}],
}
app = _mock_app(store_by="uuid")
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(
temp_directory, serialize_dataset_objects=True) as export_store:
persist_target_to_export_store(target, export_store, app.object_store,
work_directory)
import_history = _import_directory_to_history(app, temp_directory,
work_directory)
assert len(import_history.datasets) == 1
imported_hda = import_history.datasets[0]
assert imported_hda.state == "error"
assert imported_hda.info == "Failed to download some URL I guess"
def test_persist_target_hdca():
work_directory = mkdtemp()
with open(os.path.join(work_directory, "file1.txt"), "w") as f:
f.write("hello world\nhello world line 2")
with open(os.path.join(work_directory, "file2.txt"), "w") as f:
f.write("file 2 contents")
target = {
"destination": {
"type": "hdca",
},
"name":
"My HDCA",
"collection_type":
"list",
"elements": [{
"filename": "file1.txt",
"ext": "txt",
"dbkey": "hg19",
"info": "dataset info",
"name": "my file",
}, {
"filename": "file2.txt",
"ext": "txt",
"dbkey": "hg18",
"info": "dataset info 2",
"name": "my file 2",
}]
}
app = _mock_app(store_by="uuid")
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(
temp_directory, serialize_dataset_objects=True) as export_store:
persist_target_to_export_store(target, export_store, app.object_store,
work_directory)
import_history = _import_directory_to_history(app, temp_directory,
work_directory)
assert len(import_history.dataset_collections) == 1
assert len(import_history.datasets) == 2
import_hdca = import_history.dataset_collections[0]
datasets = import_hdca.dataset_instances
assert len(datasets) == 2
dataset0 = datasets[0]
dataset1 = datasets[1]
with open(dataset0.file_name, "r") as f:
assert f.read().startswith("hello world\n")
with open(dataset1.file_name, "r") as f:
assert f.read().startswith("file 2 contents")
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
args = _arg_parser().parse_args(argv)
object_store_config = Bunch(
object_store_store_by="uuid",
object_store_config_file=args.object_store_config,
object_store_check_old_style=False,
jobs_directory=None,
new_file_path=None,
umask=os.umask(0o77),
gid=os.getgid(),
)
object_store = build_object_store_from_config(object_store_config)
galaxy.model.Dataset.object_store = object_store
galaxy.model.set_datatypes_registry(example_datatype_registry_for_sample())
from galaxy.model import mapping
mapping.init("/tmp",
"sqlite:///:memory:",
create_tables=True,
object_store=object_store)
with open(args.objects) as f:
targets = yaml.safe_load(f)
if not isinstance(targets, list):
targets = [targets]
export_path = args.export
export_type = args.export_type
if export_type is None:
export_type = "directory" if not export_path.endswith(
".tgz") else "bag_archive"
export_types = {
"directory": store.DirectoryModelExportStore,
"tar": store.TarModelExportStore,
"bag_directory": store.BagDirectoryModelExportStore,
"bag_archive": store.BagArchiveModelExportStore,
}
store_class = export_types[export_type]
export_kwds = {
"serialize_dataset_objects": True,
}
with store_class(export_path, **export_kwds) as export_store:
for target in targets:
persist_target_to_export_store(target, export_store, object_store,
".")
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 test_model_create_context_persist_hdas():
work_directory = mkdtemp()
with open(os.path.join(work_directory, "file1.txt"), "w") as f:
f.write("hello world\nhello world line 2")
target = {
"destination": {
"type": "hdas",
},
"elements": [{
"filename": "file1.txt",
"ext": "txt",
"dbkey": "hg19",
"name": "my file",
"md5": "e5d21b1ea57fc9a31f8ea0110531bf3d",
"tags": ["name:value"]
}],
}
app = _mock_app()
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(
temp_directory, serialize_dataset_objects=True) as export_store:
persist_target_to_export_store(target, export_store, app.object_store,
work_directory)
import_history = _import_directory_to_history(app, temp_directory,
work_directory)
assert len(import_history.datasets) == 1
imported_hda = import_history.datasets[0]
assert imported_hda.ext == "txt"
assert imported_hda.name == "my file"
assert imported_hda.metadata.data_lines == 2
assert len(imported_hda.dataset.hashes) == 1
assert imported_hda.dataset.hashes[
0].hash_value == "e5d21b1ea57fc9a31f8ea0110531bf3d"
tags = imported_hda.tags
assert len(tags) == 1
assert tags[0].value == "value"
with open(imported_hda.file_name) as f:
assert f.read().startswith("hello world\n")
