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_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)
# Finally execute corresponding functions
## Analyze Flowcell
if "analyze_fc_dirs" in args:
LOG.info(
"Starting flowcell analysis of flowcell {} "
"{}".format(inflector.plural("directory", len(args.analyze_fc_dirs)), ", ".join(args.analyze_fc_dirs))
)
flowcell.process_demultiplexed_flowcells(
args.analyze_fc_dirs,
args.restrict_to_projects,
args.restrict_to_samples,
args.restart_failed_jobs,
args.restart_finished_jobs,
args.restart_running_jobs,
keep_existing_data=args.keep_existing_data,
no_qc=args.no_qc,
quiet=args.quiet,
manual=True,
generate_bqsr_bam=args.generate_bqsr_bam,
)
## Analyze Project
elif "analyze_project_dirs" in args:
for analyze_project_dir in args.analyze_project_dirs:
try:
project_dir = locate_project(analyze_project_dir)
except ValueError as e:
LOG.error(e)
continue
validate_dangerous_user_thing("delete existing data in Charon")
# Finally execute corresponding functions
## Analyze Flowcell
if 'analyze_fc_dirs' in args:
LOG.info('Starting flowcell analysis of flowcell {} '
'{}'.format(inflector.plural("directory", len(args.analyze_fc_dirs)),
", ".join(args.analyze_fc_dirs)))
flowcell.process_demultiplexed_flowcells(args.analyze_fc_dirs,
args.restrict_to_projects,
args.restrict_to_samples,
args.restart_failed_jobs,
args.restart_finished_jobs,
args.restart_running_jobs,
keep_existing_data=args.keep_existing_data,
no_qc=args.no_qc,
quiet=args.quiet,
manual=True,
generate_bqsr_bam=args.generate_bqsr_bam)
## Analyze Project
elif 'analyze_project_dirs' in args:
for analyze_project_dir in args.analyze_project_dirs:
try:
project_dir = locate_project(analyze_project_dir)
except ValueError as e:
LOG.error(e)
continue
project_obj = \
