def metadata_command(self, output_datasets, output_collections=None):
output_collections = output_collections or {}
metadata_compute_strategy = get_metadata_compute_strategy(
self.app.config, self.job.id)
self.metadata_compute_strategy = metadata_compute_strategy
exec_dir = None
dataset_files_path = self.app.model.Dataset.file_path
config_root = self.app.config.root
config_file = None
datatypes_config = os.path.join(self.job_working_directory, 'metadata',
'registry.xml')
safe_makedirs(os.path.join(self.job_working_directory, 'metadata'))
self.app.datatypes_registry.to_xml_file(path=datatypes_config)
job_metadata = os.path.join(self.tool_working_directory,
self.tool.provided_metadata_file)
output_fnames = [
DatasetPath(o.dataset.id, o.dataset.file_name, None)
for o in output_datasets.values()
]
command = metadata_compute_strategy.setup_external_metadata(
output_datasets,
output_collections,
self.app.model.session,
exec_dir=exec_dir,
tmp_dir=self.
job_working_directory, # set in jobs/runners.py - better if was default.
dataset_files_path=dataset_files_path,
config_root=config_root,
config_file=config_file,
datatypes_config=datatypes_config,
job_metadata=job_metadata,
output_fnames=output_fnames,
tool=self.tool,
job=self.job,
object_store_conf=self.app.object_store.to_dict(),
max_metadata_value_size=10000)
return command
def execute_via_app(self,
tool,
app,
session_id,
history_id,
user=None,
incoming=None,
set_output_hid=False,
overwrite=True,
history=None,
job_params=None):
"""
Execute using application.
"""
incoming = incoming or {}
for name, value in incoming.items():
# Why are we looping here and not just using a fixed input name? Needed?
if not name.startswith("input"):
continue
if isinstance(value, app.model.HistoryDatasetAssociation):
dataset = value
dataset_name = name
type = 'hda'
break
elif isinstance(value, app.model.LibraryDatasetDatasetAssociation):
dataset = value
dataset_name = name
type = 'ldda'
break
else:
raise Exception(
'The dataset to set metadata on could not be determined.')
sa_session = app.model.context
# Create the job object
job = app.model.Job()
job.galaxy_version = app.config.version_major
job.session_id = session_id
job.history_id = history_id
job.tool_id = tool.id
if user:
job.user_id = user.id
if job_params:
job.params = dumps(job_params)
start_job_state = job.state # should be job.states.NEW
try:
# For backward compatibility, some tools may not have versions yet.
job.tool_version = tool.version
except AttributeError:
job.tool_version = "1.0.1"
job.dynamic_tool = tool.dynamic_tool
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
sa_session.add(job)
sa_session.flush() # ensure job.id is available
# add parameters to job_parameter table
# Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)?
incoming['__ORIGINAL_DATASET_STATE__'] = dataset.state
input_paths = [
DatasetPath(dataset.id, real_path=dataset.file_name, mutable=False)
]
app.object_store.create(job,
base_dir='job_work',
dir_only=True,
extra_dir=str(job.id))
job_working_dir = app.object_store.get_filename(job,
base_dir='job_work',
dir_only=True,
extra_dir=str(job.id))
datatypes_config = os.path.join(job_working_dir, 'registry.xml')
app.datatypes_registry.to_xml_file(path=datatypes_config)
external_metadata_wrapper = get_metadata_compute_strategy(
app.config, job.id, tool_id=tool.id)
output_datatasets_dict = {
dataset_name: dataset,
}
validate_outputs = asbool(incoming.get("validate", False))
cmd_line = external_metadata_wrapper.setup_external_metadata(
output_datatasets_dict, {},
sa_session,
exec_dir=None,
tmp_dir=job_working_dir,
dataset_files_path=app.model.Dataset.file_path,
output_fnames=input_paths,
config_root=app.config.root,
config_file=app.config.config_file,
datatypes_config=datatypes_config,
job_metadata=os.path.join(job_working_dir, 'working',
tool.provided_metadata_file),
include_command=False,
max_metadata_value_size=app.config.max_metadata_value_size,
validate_outputs=validate_outputs,
job=job,
kwds={'overwrite': overwrite})
incoming['__SET_EXTERNAL_METADATA_COMMAND_LINE__'] = cmd_line
for name, value in tool.params_to_strings(incoming, app).items():
job.add_parameter(name, value)
# add the dataset to job_to_input_dataset table
if type == 'hda':
job.add_input_dataset(dataset_name, dataset)
elif type == 'ldda':
job.add_input_library_dataset(dataset_name, dataset)
# Need a special state here to show that metadata is being set and also allow the job to run
# i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state
dataset._state = dataset.states.SETTING_METADATA
job.state = start_job_state # job inputs have been configured, restore initial job state
sa_session.flush()
# clear e.g. converted files
dataset.datatype.before_setting_metadata(dataset)
return job, {}