def _job_dataset( self, name, path ):
metadata = dict( )
hda = HistoryDatasetAssociation( name=name, metadata=metadata )
hda.dataset = Dataset( id=123, external_filename=path )
hda.dataset.metadata = dict()
hda.children = []
jida = JobToInputDatasetAssociation( name=name, dataset=hda )
return jida
def _job_dataset(self, name, path):
metadata = dict()
hda = HistoryDatasetAssociation(name=name, metadata=metadata)
hda.dataset = Dataset(id=123, external_filename=path)
hda.dataset.metadata = dict()
hda.children = []
jida = JobToInputDatasetAssociation(name=name, dataset=hda)
return jida
def prototype_elements(self):
left_association = DatasetCollectionElement(
element=HistoryDatasetAssociation(),
element_identifier=FORWARD_IDENTIFIER,
)
right_association = DatasetCollectionElement(
element=HistoryDatasetAssociation(),
element_identifier=REVERSE_IDENTIFIER,
)
yield left_association
yield right_association
def test_check_required_metadata_inherited():
app = GalaxyDataTestApp()
app.datatypes_registry.datatypes_by_extension[
'inherited'] = CheckRequiredInherited
hda = HistoryDatasetAssociation(sa_session=app.model.session,
extension='inherited')
assert hda.metadata.spec['columns'].check_required_metadata
assert not hda.metadata.spec['something'].check_required_metadata
def create_bed_data(sa_session, string_size):
hda = HistoryDatasetAssociation(extension="bed")
big_string = "0" * string_size
sa_session.add(hda)
hda.metadata.column_names = [big_string]
assert hda.metadata.column_names
sa_session.flush()
return hda
def _create_hda(model,
object_store,
history,
path,
visible=True,
include_metadata_file=False):
hda = HistoryDatasetAssociation(extension="bam",
create_dataset=True,
sa_session=model.context)
hda.visible = visible
model.context.add(hda)
model.context.flush([hda])
object_store.update_from_file(hda, file_name=path, create=True)
if include_metadata_file:
hda.metadata.from_JSON_dict(
json_dict={
"bam_index":
MetadataTempFile.from_JSON({
"kwds": {},
"filename": path
})
})
_check_metadata_file(hda)
hda.set_size()
history.add_dataset(hda)
hda.add_item_annotation(model.context, history.user, hda,
"annotation #%d" % hda.hid)
return hda
def write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata):
for i, file_dict in enumerate(tool_provided_metadata.get_new_datasets_for_metadata_collection(), start=1):
filename = file_dict["filename"]
new_dataset_filename = os.path.join(tool_job_working_directory, "working", filename)
new_dataset = Dataset(id=-i, external_filename=new_dataset_filename)
extra_files = file_dict.get('extra_files', None)
if extra_files is not None:
new_dataset._extra_files_path = os.path.join(tool_job_working_directory, "working", extra_files)
new_dataset.state = new_dataset.states.OK
new_dataset_instance = HistoryDatasetAssociation(id=-i, dataset=new_dataset, extension=file_dict.get('ext', 'data'))
set_meta(new_dataset_instance, file_dict)
file_dict['metadata'] = json.loads(new_dataset_instance.metadata.to_JSON_dict()) # storing metadata in external form, need to turn back into dict, then later jsonify
tool_provided_metadata.rewrite()
def hda(id, name, path):
hda = HistoryDatasetAssociation(name=name, metadata=dict())
hda.dataset = Dataset(id=id, external_filename=path)
hda.dataset.metadata = dict()
hda.children = []
return hda
def test_check_required_metadata_true():
app = GalaxyDataTestApp()
app.datatypes_registry.datatypes_by_extension['true'] = CheckRequiredTrue
hda = HistoryDatasetAssociation(sa_session=app.model.session,
extension='true')
assert hda.metadata.spec['columns'].check_required_metadata