def setup_job(self, jiha, archive_source, archive_type):
if archive_type != "url":
external_chown(
archive_source,
jiha.job.user.system_user_pwent(
self.app.config.real_system_username),
self.app.config.external_chown_script,
"history import archive")
external_chown(
jiha.archive_dir,
jiha.job.user.system_user_pwent(
self.app.config.real_system_username),
self.app.config.external_chown_script,
"history import archive directory")
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 create_paramfile(trans, uploaded_datasets):
"""
Create the upload tool's JSON "param" file.
"""
tool_params = []
json_file_path = None
for uploaded_dataset in uploaded_datasets:
data = uploaded_dataset.data
if uploaded_dataset.type == 'composite':
# we need to init metadata before the job is dispatched
data.init_meta()
for meta_name, meta_value in uploaded_dataset.metadata.items():
setattr(data.metadata, meta_name, meta_value)
trans.sa_session.add(data)
trans.sa_session.flush()
params = dict(
file_type=uploaded_dataset.file_type,
dataset_id=data.dataset.id,
dbkey=uploaded_dataset.dbkey,
type=uploaded_dataset.type,
metadata=uploaded_dataset.metadata,
primary_file=uploaded_dataset.primary_file,
composite_file_paths=uploaded_dataset.composite_files,
composite_files={
k: v.__dict__
for k, v in data.datatype.get_composite_files(
data).items()
})
else:
try:
is_binary = uploaded_dataset.datatype.is_binary
except Exception:
is_binary = None
try:
link_data_only = uploaded_dataset.link_data_only
except Exception:
link_data_only = 'copy_files'
try:
uuid_str = uploaded_dataset.uuid
except Exception:
uuid_str = None
try:
purge_source = uploaded_dataset.purge_source
except Exception:
purge_source = True
try:
user_ftp_dir = os.path.abspath(trans.user_ftp_dir)
except Exception:
user_ftp_dir = None
if user_ftp_dir and uploaded_dataset.path.startswith(user_ftp_dir):
uploaded_dataset.type = 'ftp_import'
params = dict(
file_type=uploaded_dataset.file_type,
ext=uploaded_dataset.ext,
name=uploaded_dataset.name,
dataset_id=data.dataset.id,
dbkey=uploaded_dataset.dbkey,
type=uploaded_dataset.type,
is_binary=is_binary,
link_data_only=link_data_only,
uuid=uuid_str,
to_posix_lines=getattr(uploaded_dataset, "to_posix_lines",
True),
auto_decompress=getattr(uploaded_dataset, "auto_decompress",
True),
purge_source=purge_source,
space_to_tab=uploaded_dataset.space_to_tab,
run_as_real_user=trans.app.config.external_chown_script
is not None,
check_content=trans.app.config.check_upload_content,
path=uploaded_dataset.path)
# TODO: This will have to change when we start bundling inputs.
# Also, in_place above causes the file to be left behind since the
# user cannot remove it unless the parent directory is writable.
if link_data_only == 'copy_files' and trans.user:
external_chown(uploaded_dataset.path,
trans.user.system_user_pwent(
trans.app.config.real_system_username),
trans.app.config.external_chown_script,
description="uploaded file")
tool_params.append(params)
with tempfile.NamedTemporaryFile(mode="w",
prefix='upload_params_',
delete=False) as fh:
json_file_path = fh.name
dump(tool_params, fh)
return json_file_path
