def test_convert_to_d_and_load(self):
import pbsmrtpipe.loader as L
import pprint
rtasks, rfile_types, chunk_operators, pipelines = L.load_all()
for pipeline in pipelines.values():
pipeline_d = IO.pipeline_template_to_dict(pipeline, rtasks)
#print "Raw Pipeline converted to dict"
#print pprint.pformat(pipeline_d)
pipeline_loaded = IO.load_pipeline_template_from(pipeline_d)
#print "Pipeline task options loaded from dict"
#print pprint.pformat(pipeline_loaded.task_options)
self.assertEqual(pipeline.idx, pipeline_loaded.idx)
self.assertEqual(pipeline.display_name,
pipeline_loaded.display_name)
self.assertEqual(len(pipeline.all_bindings),
len(pipeline_loaded.all_bindings))
self.assertEqual(len(pipeline.entry_bindings),
len(pipeline_loaded.entry_bindings))
# note that the internally registered pipeline does not necessarily
# have any task_options at this point, so we can't simply test for
# equality. however after another cycle they should be identical
if len(pipeline.task_options) > 0:
self.assertGreater(len(pipeline_loaded.task_options), 0)
pipeline_d2 = IO.pipeline_template_to_dict(
pipeline_loaded, rtasks)
#print pprint.pformat(pipeline_d)
pipeline_loaded2 = IO.load_pipeline_template_from(pipeline_d2)
self.assertEqual(len(pipeline_loaded.task_options),
len(pipeline_loaded2.task_options))
n = 1
for k, v in pipeline.task_options.iteritems():
if k in pipeline_loaded2.task_options:
v2 = pipeline_loaded2.task_options[k]
msg = "task option #{n} {k} expected '{v}' got '{x}'".format(
k=k, v=v, x=v2, n=n)
self.assertEqual(v, v2, msg)
print "Valid " + msg
n += 1
def test_convert_to_d_and_load(self):
import pbsmrtpipe.loader as L
rtasks, rfile_types, chunk_operators, pipelines = L.load_all()
for pipeline in pipelines.values():
pipeline_d = IO.pipeline_template_to_dict(pipeline, rtasks)
pipeline_loaded = IO.load_pipeline_template_from(pipeline_d)
self.assertEqual(pipeline.idx, pipeline_loaded.idx)
self.assertEqual(pipeline.display_name, pipeline_loaded.display_name)
self.assertEqual(len(pipeline.all_bindings), len(pipeline_loaded.all_bindings))
self.assertEqual(len(pipeline.entry_bindings), len(pipeline_loaded.entry_bindings))
def test_convert_to_d_and_load(self):
import pbsmrtpipe.loader as L
rtasks, rfile_types, chunk_operators, pipelines = L.load_all()
for pipeline in pipelines.values():
pipeline_d = IO.pipeline_template_to_dict(pipeline, rtasks)
pipeline_loaded = IO.load_pipeline_template_from(pipeline_d)
self.assertEqual(pipeline.idx, pipeline_loaded.idx)
self.assertEqual(pipeline.display_name, pipeline_loaded.display_name)
self.assertEqual(len(pipeline.all_bindings), len(pipeline_loaded.all_bindings))
self.assertEqual(len(pipeline.entry_bindings), len(pipeline_loaded.entry_bindings))
# note that the internally registered pipeline does not necessarily
# have any task_options at this point, so we can't simply test for
# equality. however after another cycle they should be identical
if len(pipeline.task_options) > 0:
self.assertGreater(len(pipeline_loaded.task_options), 0)
pipeline_d2 = IO.pipeline_template_to_dict(pipeline_loaded, rtasks)
pipeline_loaded2 = IO.load_pipeline_template_from(pipeline_d2)
self.assertEqual(len(pipeline_loaded.task_options),
len(pipeline_loaded2.task_options))
for k,v in pipeline.task_options.iteritems():
if k in pipeline_loaded2.task_options:
self.assertEqual(v, pipeline_loaded2.task_options[k])
def _load_resolved_pipeline_template_json_from_dir(dir_name):
"""
:rtype: list[Pipeline]
"""
import pbsmrtpipe.pb_io as IO
pipelines = []
if os.path.exists(dir_name):
for file_name in os.listdir(dir_name):
if file_name.endswith(".json"):
try:
p = IO.load_pipeline_template_from(os.path.join(dir_name, file_name))
pipelines.append(p)
except Exception as e:
log.warn("Unable to load Resolved Pipeline Template from {}. {}".format(dir_name, str(e)))
else:
log.warn("Unable to load Resolved Pipeline Template from {}. Path does not exist.".format(dir_name))
return pipelines
def load_resolved_pipeline_template_jsons_from_dir(dir_name):
"""
:rtype: list[Pipeline]
"""
import pbsmrtpipe.pb_io as IO
pipelines = []
if os.path.exists(dir_name):
for file_name in os.listdir(dir_name):
if file_name.endswith(".json"):
try:
p = IO.load_pipeline_template_from(os.path.join(dir_name, file_name))
pipelines.append(p)
except Exception as e:
log.warn("Unable to load Resolved Pipeline Template from {}. {}".format(dir_name, str(e)))
else:
log.warn("Unable to load Resolved Pipeline Template from {}. Path does not exist.".format(dir_name))
return pipelines
def test_load_pipeline_template_json(self):
path = os.path.join(TEST_DATA_DIR, "example_pipeline_template_01.json")
pipeline_loaded = IO.load_pipeline_template_from(path)
self.assertEqual(len(pipeline_loaded.task_options), 1)
def test_load_pipeline_template_json(self):
path = os.path.join(TEST_DATA_DIR, "example_pipeline_template_01.json")
pipeline_loaded = IO.load_pipeline_template_from(path)
self.assertEqual(len(pipeline_loaded.task_options), 1)
