def __test_evaluation_with_path_rewrites(self):
# Various things can cause dataset paths to be rewritten (Task
# splitting, config.outputs_to_working_directory). This tests that
# functionality.
self._setup_test_bwa_job()
job_path_1 = "%s/dataset_1.dat" % self.test_directory
job_path_2 = "%s/dataset_2.dat" % self.test_directory
self._set_compute_environment(
input_paths=[DatasetPath(1, '/galaxy/files/dataset_1.dat', false_path=job_path_1)],
output_paths=[DatasetPath(2, '/galaxy/files/dataset_2.dat', false_path=job_path_2)],
)
command_line, extra_filenames, _ = self.evaluator.build()
self.assertEquals(command_line, "bwa --thresh=4 --in=%s --out=%s" % (job_path_1, job_path_2))
def test_dataset_path():
dataset_path_1 = DatasetPath(1, "/galaxy/database/files/dataset_1.dat")
assert dataset_path_1.dataset_id == 1
assert dataset_path_1.real_path == "/galaxy/database/files/dataset_1.dat"
assert dataset_path_1.false_path is None
assert dataset_path_1.mutable
assert str(dataset_path_1) == "/galaxy/database/files/dataset_1.dat"
dataset_path_2 = DatasetPath(2, "/galaxy/database/files/dataset_2.dat", false_path="/mnt/galaxyData/files/dataset_2.dat", mutable=False)
assert dataset_path_2.dataset_id == 2
assert dataset_path_2.real_path == "/galaxy/database/files/dataset_2.dat"
assert dataset_path_2.false_path == "/mnt/galaxyData/files/dataset_2.dat"
assert not dataset_path_2.mutable
assert str(dataset_path_2) == "/mnt/galaxyData/files/dataset_2.dat"
def test_dataset_false_extra_files_path():
dataset = MockDataset()
wrapper = DatasetFilenameWrapper(dataset)
assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
new_path = "/new/path/dataset_123.dat"
dataset_path = DatasetPath(123, MOCK_DATASET_PATH, false_path=new_path)
wrapper = DatasetFilenameWrapper(dataset, dataset_path=dataset_path)
# Setting false_path is not enough to override
assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
new_files_path = "/new/path/dataset_123_files"
dataset_path = DatasetPath(123, MOCK_DATASET_PATH, false_path=new_path, false_extra_files_path=new_files_path)
wrapper = DatasetFilenameWrapper(dataset, dataset_path=dataset_path)
assert wrapper.extra_files_path == new_files_path
def execute_via_app( self, tool, app, session_id, history_id, user=None,
incoming = {}, set_output_hid = False, overwrite = True,
history=None, job_params=None ):
"""
Execute using application.
"""
for name, value in incoming.iteritems():
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.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:
job.tool_version = "1.0.1"
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
job.set_handler(tool.get_job_handler( job_params ))
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))
external_metadata_wrapper = JobExternalOutputMetadataWrapper( job )
cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,
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 = app.datatypes_registry.integrated_datatypes_configs,
job_metadata = None,
include_command = False,
kwds = { 'overwrite' : overwrite } )
incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line
for name, value in tool.params_to_strings( incoming, app ).iteritems():
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()
# Queue the job for execution
app.job_queue.put( job.id, tool.id )
# FIXME: need to add event logging to app and log events there rather than trans.
#trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
#clear e.g. converted files
dataset.datatype.before_setting_metadata( dataset )
return job, odict()
