def __init__(self, implicit_output_name=None, job=None, hid=1):
self.id = 124
self.copied_from_history_dataset_collection_association = None
self.history_content_type = "dataset_collection"
self.implicit_output_name = implicit_output_name
self.hid = 1
self.collection = model.DatasetCollection()
self.creating_job_associations = []
element = model.DatasetCollectionElement(
collection=self.collection,
element=model.HistoryDatasetAssociation(),
element_index=0,
element_identifier="moocow",
)
element.dataset_instance.dataset = model.Dataset()
element.dataset_instance.dataset.state = "ok"
creating = model.JobToOutputDatasetAssociation(
implicit_output_name,
element.dataset_instance,
)
creating.job = job
element.dataset_instance.creating_job_associations = [
creating,
]
self.collection.elements = [element]
def _new_hda( self ):
hda = model.HistoryDatasetAssociation()
hda.visible = True
hda.dataset = model.Dataset()
self.app.model.context.add( hda )
self.app.model.context.flush( )
return hda
def __add_dataset(self, state='ok'):
hda = model.HistoryDatasetAssociation()
hda.dataset = model.Dataset()
hda.dataset.state = 'ok'
hda.dataset.external_filename = "/tmp/datasets/dataset_001.dat"
self.history.add_dataset(hda)
self.app.model.context.flush()
return hda
def test_dataset_job_relationship(self):
model = self.model
dataset = model.Dataset()
job = model.Job()
dataset.job = job
self.persist(job, dataset)
loaded_dataset = model.session.query(model.Dataset).filter(model.Dataset.id == dataset.id).one()
assert loaded_dataset.job_id == job.id
def _setup_test_output(self):
dataset = model.Dataset()
dataset.external_filename = "example_output" # This way object store isn't asked about size...
self.hda = model.HistoryDatasetAssociation(name="test", dataset=dataset)
job = model.Job()
job.add_output_dataset(DEFAULT_TOOL_OUTPUT, self.hda)
self.app.model.context.add(job)
self.job = job
self.history = self._new_history(hdas=[self.hda])
self.outputs = {DEFAULT_TOOL_OUTPUT: self.hda}
def create(self, trans, flush=True, **kwargs):
"""
Create and return a new Dataset object.
"""
# default to NEW state on new datasets
kwargs.update(
dict(state=(kwargs.get('state', model.Dataset.states.NEW))))
dataset = model.Dataset(**kwargs)
self.app.model.context.add(dataset)
if flush:
self.app.model.context.flush()
return dataset
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 create(self, manage_roles=None, access_roles=None, flush=True, **kwargs):
"""
Create and return a new Dataset object.
"""
# default to NEW state on new datasets
kwargs.update(dict(state=(kwargs.get('state', model.Dataset.states.NEW))))
dataset = model.Dataset(**kwargs)
self.session().add(dataset)
self.permissions.set(dataset, manage_roles, access_roles, flush=False)
if flush:
self.session().flush()
return dataset
def main():
options, args = doc_optparse.parse( __doc__ )
try:
extension = options.ext
except:
doc_optparse.exception()
# create datatype
data = model.Dataset( extension=extension, id=int( args[0] ) )
data.file_path = "/home/ian/trunk/database/files/"
if options.metadata:
data.metadata = util.string_to_object( options.metadata )
errors = data.datatype.validate( data )
print util.object_to_string(errors)
def __init__(self, test_dataset=None, name="Test Dataset", id=1):
if not test_dataset:
test_dataset = model.Dataset()
test_dataset.state = model.Dataset.states.OK
self.states = model.HistoryDatasetAssociation.states
self.deleted = False
self.dataset = test_dataset
self.visible = True
self.conversion_destination = (None, None)
self.extension = "txt"
self.dbkey = "hg19"
self.implicitly_converted_parent_datasets = False
self.name = name
self.hid = id
self.id = id
self.children = []
self.tags = []
def __init__(self, test_dataset=None, name="Test Dataset", id=1):
if not test_dataset:
test_dataset = model.Dataset()
self.states = model.HistoryDatasetAssociation.states
self.deleted = False
self.dataset = test_dataset
self.visible = True
self.datatype_matches = True
self.conversion_destination = (None, None)
self.datatype = bunch.Bunch(
matches_any=lambda formats: self.datatype_matches, )
self.dbkey = "hg19"
self.implicitly_converted_parent_datasets = False
self.name = name
self.hid = id
self.id = id
self.children = []
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")
dataset = model.Dataset(id=100)
jeha = model.JobExportHistoryArchive(job=model.Job(),
history=h,
dataset=dataset,
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
