def test_workflows(self):
config_file_path = locate_ngi_config()
config = load_yaml_config(config_file_path)
for workflow_name, workflow_dict in config.get("test_data", {}).get(
"workflows", {}).iteritems():
# Load and rewrite config file as needed
customize_config_dict = workflow_dict.get("customize_config")
if customize_config_dict:
config = update_dict(config, customize_config_dict)
#self._install_test_files(workflow_dict)
LOG.info(
'Starting test analysis pipeline for workflow "{}"'.format(
workflow_name))
try:
local_files = workflow_dict["local_files"]
except KeyError:
raise ValueError(
"Required paths to input files for testing do not"
"exist in config file (test_data.workflows."
"{}.local_files); cannot proceed.".format(workflow_name))
try:
flowcell_path = local_files["flowcell"]
except KeyError:
raise ValueError(
"Path to flowcell is required and not specified "
"in configuration file (test_data.workflows."
"{}.local_files.flowcell); cannot proceed.".format(
workflow_name))
try:
test_project = workflow_dict["test_project"]
test_proj_id = test_project["project_id"]
test_proj_name = test_project["project_name"]
test_proj_bpa = test_project["bpa"]
except KeyError as e:
raise ValueError(
"Test project information is missing from config "
"file (under test_data.workflows.{}.test_project "
"({}); cannot proceed.".format(workflow_name, e.msg))
charon_session = CharonSession(config=config)
try:
charon_session.project_delete(projectid=test_proj_id)
except CharonError:
pass
charon_session.project_create(projectid=test_proj_id,
name=test_proj_name,
status="OPEN",
best_practice_analysis=test_proj_bpa)
process_demultiplexed_flowcells([flowcell_path],
fallback_libprep="A",
config=config)
def test_create_charon_entries_from_project(self):
# Create the NGIObjects
project_obj = NGIProject(name=self.p_name,
dirname=self.p_name,
project_id=self.p_id,
base_path=self.p_bp)
sample_obj = project_obj.add_sample(name=self.s_id, dirname=self.s_id)
libprep_obj = sample_obj.add_libprep(name=self.l_id, dirname=self.l_id)
seqrun_obj = libprep_obj.add_seqrun(name=self.sr_id,
dirname=self.sr_id)
try:
# Create them in the db
create_charon_entries_from_project(project_obj)
finally:
charon_session = CharonSession()
charon_session.project_delete(project_obj.project_id)
def test_workflows(self):
config_file_path = locate_ngi_config()
config = load_yaml_config(config_file_path)
for workflow_name, workflow_dict in config.get("test_data", {}).get("workflows", {}).iteritems():
# Load and rewrite config file as needed
customize_config_dict = workflow_dict.get("customize_config")
if customize_config_dict:
config = update_dict(config, customize_config_dict)
#self._install_test_files(workflow_dict)
LOG.info('Starting test analysis pipeline for workflow "{}"'.format(workflow_name))
try:
local_files = workflow_dict["local_files"]
except KeyError:
raise ValueError("Required paths to input files for testing do not"
"exist in config file (test_data.workflows."
"{}.local_files); cannot proceed.".format(workflow_name))
try:
flowcell_path = local_files["flowcell"]
except KeyError:
raise ValueError("Path to flowcell is required and not specified "
"in configuration file (test_data.workflows."
"{}.local_files.flowcell); cannot proceed.".format(workflow_name))
try:
test_project = workflow_dict["test_project"]
test_proj_id = test_project["project_id"]
test_proj_name = test_project["project_name"]
test_proj_bpa = test_project["bpa"]
except KeyError as e:
raise ValueError("Test project information is missing from config "
"file (under test_data.workflows.{}.test_project "
"({}); cannot proceed.".format(workflow_name, e.msg))
charon_session = CharonSession(config=config)
try:
charon_session.project_delete(projectid=test_proj_id)
except CharonError:
pass
charon_session.project_create(projectid=test_proj_id, name=test_proj_name,
status="OPEN", best_practice_analysis=test_proj_bpa)
process_demultiplexed_flowcells([flowcell_path], fallback_libprep="A",
config=config)
def test_create_charon_entries_from_project(self):
# Create the NGIObjects
project_obj = NGIProject(name=self.p_name,
dirname=self.p_name,
project_id=self.p_id,
base_path=self.p_bp)
sample_obj = project_obj.add_sample(name=self.s_id,
dirname=self.s_id)
libprep_obj = sample_obj.add_libprep(name=self.l_id,
dirname=self.l_id)
seqrun_obj = libprep_obj.add_seqrun(name=self.sr_id,
dirname=self.sr_id)
try:
# Create them in the db
create_charon_entries_from_project(project_obj)
finally:
charon_session = CharonSession()
charon_session.project_delete(project_obj.project_id)
