def _import_export(app, h, dest_export=None):
if dest_export is None:
dest_parent = mkdtemp()
dest_export = os.path.join(dest_parent, "moo.tgz")
jeha = model.JobExportHistoryArchive(job=None, history=h,
dataset=None,
compressed=True)
wrapper = JobExportHistoryArchiveWrapper(app, 1)
wrapper.setup_job(jeha)
from galaxy.tools.imp_exp import export_history
ret = export_history.main(["--gzip", jeha.temp_directory, dest_export])
assert ret == 0, ret
_, imported_history = import_archive(dest_export, app=app)
assert imported_history
return imported_history
def _import_export(app, h, dest_export=None):
if dest_export is None:
dest_parent = tempfile.mkdtemp()
dest_export = os.path.join(dest_parent, "moo.tgz")
job = model.Job()
jeha = model.JobExportHistoryArchive.create_for_history(
h, job, app.model.context, app.object_store, compressed=True
)
wrapper = JobExportHistoryArchiveWrapper(app, job.id)
wrapper.setup_job(h, jeha.temp_directory)
from galaxy.tools.imp_exp import export_history
ret = export_history.main(["--gzip", jeha.temp_directory, dest_export])
assert ret == 0, ret
_, imported_history = import_archive(dest_export, app=app)
assert imported_history
return imported_history
def execute(self,
tool,
trans,
incoming={},
set_output_hid=False,
overwrite=True,
history=None,
**kwargs):
#
# Get history to export.
#
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()
session = trans.get_galaxy_session()
job.session_id = session and session.id
if history:
history_id = history.id
else:
history_id = trans.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
start_job_state = job.state # should be job.states.NEW
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)
# Create dataset that will serve as archive.
archive_dataset = trans.app.model.Dataset()
trans.sa_session.add(archive_dataset)
trans.sa_session.flush(
) # ensure job.id and archive_dataset.id are available
trans.app.object_store.create(
archive_dataset
) # set the object store id, create dataset (if applicable)
#
# Setup job and job wrapper.
#
# Add association for keeping track of job, history, archive relationship.
jeha = trans.app.model.JobExportHistoryArchive(
job=job,
history=history,
dataset=archive_dataset,
compressed=incoming['compress'])
trans.sa_session.add(jeha)
job_wrapper = JobExportHistoryArchiveWrapper(job)
cmd_line = job_wrapper.setup_job(
trans,
jeha,
include_hidden=incoming['include_hidden'],
include_deleted=incoming['include_deleted'])
#
# Add parameters to job_parameter table.
#
# Set additional parameters.
incoming['__HISTORY_TO_EXPORT__'] = history.id
incoming['__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__'] = cmd_line
for name, value in tool.params_to_strings(incoming, trans.app).items():
job.add_parameter(name, value)
job.state = start_job_state # job inputs have been configured, restore initial job state
job.set_handler(tool.get_job_handler(None))
trans.sa_session.flush()
# Queue the job for execution
trans.app.job_manager.job_queue.put(job.id, tool.id)
trans.log_event("Added export history job to the job queue, id: %s" %
str(job.id),
tool_id=job.tool_id)
return job, odict()
def execute(self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, **kwargs):
#
# Get history to export.
#
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()
session = trans.get_galaxy_session()
job.session_id = session and session.id
if history:
history_id = history.id
else:
history_id = trans.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
start_job_state = job.state # should be job.states.NEW
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)
# Create dataset that will serve as archive.
archive_dataset = trans.app.model.Dataset()
trans.sa_session.add(archive_dataset)
trans.sa_session.flush() # ensure job.id and archive_dataset.id are available
trans.app.object_store.create(archive_dataset) # set the object store id, create dataset (if applicable)
#
# Setup job and job wrapper.
#
# Add association for keeping track of job, history, archive relationship.
jeha = trans.app.model.JobExportHistoryArchive(job=job, history=history,
dataset=archive_dataset,
compressed=incoming['compress'])
trans.sa_session.add(jeha)
job_wrapper = JobExportHistoryArchiveWrapper(job)
cmd_line = job_wrapper.setup_job(trans, jeha, include_hidden=incoming['include_hidden'],
include_deleted=incoming['include_deleted'])
#
# Add parameters to job_parameter table.
#
# Set additional parameters.
incoming['__HISTORY_TO_EXPORT__'] = history.id
incoming['__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__'] = cmd_line
for name, value in tool.params_to_strings(incoming, trans.app).items():
job.add_parameter(name, value)
job.state = start_job_state # job inputs have been configured, restore initial job state
job.set_handler(tool.get_job_handler(None))
trans.sa_session.flush()
# Queue the job for execution
trans.app.job_manager.job_queue.put(job.id, tool.id)
trans.log_event("Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id)
return job, odict()
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, {}