def _run_jihaw_cleanup(archive_dir, app=None):
app = app or _mock_app()
job = model.Job()
job.tool_stderr = ''
jiha = model.JobImportHistoryArchive(job=job, archive_dir=archive_dir)
app.model.context.current.add_all([job, jiha])
app.model.context.flush()
jihaw = JobImportHistoryArchiveWrapper(app, job.id) # yeehaw!
return app, jihaw.cleanup_after_job()
def _run_jihaw_cleanup(history_archive, msg):
app = MockApp()
job = model.Job()
job.stderr = ''
jiha = model.JobImportHistoryArchive(job=job, archive_dir=history_archive.arc_directory)
app.model.context.current.add_all([job, jiha])
app.model.context.flush()
jihaw = JobImportHistoryArchiveWrapper(app, 1) # yeehaw!
try:
jihaw.cleanup_after_job()
data = app.object_store.get_data(model.Dataset(1))
assert data != 'insecure', msg
except MalformedContents:
pass
def _run_jihaw_cleanup(history_archive, msg):
app = MockApp()
job = model.Job()
job.stderr = ''
jiha = model.JobImportHistoryArchive(job=job, archive_dir=history_archive.arc_directory)
app.model.context.current.add_all([job, jiha])
app.model.context.flush()
jihaw = JobImportHistoryArchiveWrapper(app, 1) # yeehaw!
try:
jihaw.cleanup_after_job()
data = app.object_store.get_data(model.Dataset(1))
assert data != 'insecure', msg
except MalformedContents:
pass
def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
#
# Create job.
#
incoming = incoming or {}
trans.check_user_activation()
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
if history:
history_id = history.id
elif trans.history:
history_id = trans.history.id
else:
history_id = None
job.history_id = history_id
job.tool_id = tool.id
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)
trans.sa_session.flush() # ensure job.id are available
#
# Setup job and job wrapper.
#
# Add association for keeping track of job, history relationship.
# Use abspath because mkdtemp() does not, contrary to the documentation,
# always return an absolute path.
archive_dir = os.path.abspath(tempfile.mkdtemp())
jiha = trans.app.model.JobImportHistoryArchive(job=job, archive_dir=archive_dir)
trans.sa_session.add(jiha)
job_wrapper = JobImportHistoryArchiveWrapper(trans.app, job)
job_wrapper.setup_job(jiha, incoming['__ARCHIVE_SOURCE__'], incoming["__ARCHIVE_TYPE__"])
#
# Add parameters to job_parameter table.
#
# Set additional parameters.
incoming['__DEST_DIR__'] = jiha.archive_dir
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
return job, {}