def create_item_slug(self, sa_session, item) -> bool:
"""Create/set item slug.
Slug is unique among user's importable items for item's class.
:param sa_session: Database session context.
:param item: The item to create/update its slug.
:type item: [type]
:return: Returns true if item's slug was set/changed; false otherwise.
:rtype: bool
"""
cur_slug = item.slug
# Setup slug base.
if cur_slug is None or cur_slug == '':
# Item can have either a name or a title.
item_name = ''
if hasattr(item, 'name'):
item_name = item.name
elif hasattr(item, 'title'):
item_name = item.title
slug_base = ready_name_for_url(item_name.lower())
else:
slug_base = cur_slug
# Using slug base, find a slug that is not taken. If slug is taken,
# add integer to end.
new_slug = slug_base
count = 1
# Ensure unique across model class and user and don't include this item
# in the check in case it has previously been assigned a valid slug.
while sa_session.query(item.__class__).filter(
item.__class__.user == item.user, item.__class__.slug
== new_slug, item.__class__.id != item.id).count() != 0:
# Slug taken; choose a new slug based on count. This approach can
# handle numerous items with the same name gracefully.
new_slug = f'{slug_base}-{count}'
count += 1
# Set slug and return.
item.slug = new_slug
return item.slug == cur_slug
def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
trans.check_user_activation()
#
# Get history to export.
#
incoming = incoming or {}
history = None
for name, value in incoming.items():
if isinstance(value, trans.app.model.History):
history_param_name = name
history = value
del incoming[history_param_name]
break
if not history:
raise Exception('There is no history to export.')
#
# Create the job and output dataset objects
#
job = trans.app.model.Job()
job.galaxy_version = trans.app.config.version_major
session = trans.get_galaxy_session()
job.session_id = session and session.id
history_id = history.id
job.history_id = history_id
job.tool_id = tool.id
if trans.user:
# If this is an actual user, run the job as that individual. Otherwise we're running as guest.
job.user_id = trans.user.id
job.state = job.states.WAITING # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
trans.sa_session.add(job)
compressed = incoming['compress']
exporting_to_uri = "directory_uri" in incoming
if not exporting_to_uri:
# see comment below about how this should be transitioned to occuring in a
# job handler or detached MQ-driven thread
jeha = trans.app.model.JobExportHistoryArchive.create_for_history(
history, job, trans.sa_session, trans.app.object_store, compressed
)
store_directory = jeha.temp_directory
else:
# creating a job directory in the web thread is bad (it is slow, bypasses
# dynamic objectstore assignment, etc..) but it is arguably less bad than
# creating a dataset (like above for dataset export case).
# ensure job.id is available
trans.sa_session.flush()
job_directory = create_working_directory_for_job(trans.app.object_store, job)
store_directory = os.path.join(job_directory, "working", "_object_export")
os.makedirs(store_directory)
#
# Setup job and job wrapper.
#
cmd_line = f"--galaxy-version '{job.galaxy_version}'"
if compressed:
cmd_line += " -G"
cmd_line = f"{cmd_line} {store_directory}"
#
# Add parameters to job_parameter table.
#
# Set additional parameters.
incoming['__HISTORY_TO_EXPORT__'] = history.id
incoming['__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__'] = cmd_line
if exporting_to_uri:
directory_uri = incoming["directory_uri"]
file_name = incoming.get("file_name")
if file_name is None:
hname = ready_name_for_url(history.name)
human_timestamp = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
if compressed:
extension = ".tar.gz"
else:
extension = ".tar"
file_name = f"Galaxy-History-{hname}-{human_timestamp}.{extension}"
file_name = os.path.basename(os.path.abspath(file_name))
sep = "" if directory_uri.endswith("/") else "/"
incoming['__EXPORT_TO_URI__'] = f"{directory_uri}{sep}{file_name}"
for name, value in tool.params_to_strings(incoming, trans.app).items():
job.add_parameter(name, value)
trans.sa_session.flush()
job_wrapper = JobExportHistoryArchiveWrapper(trans.app, job.id)
job_wrapper.setup_job(
history,
store_directory,
include_hidden=incoming['include_hidden'],
include_deleted=incoming['include_deleted'],
compressed=compressed)
return job, {}
