def test_app_paths():
# test with default root
paths = constants.app_paths()
root = os.path.expanduser('~/.mip2scout')
assert paths.app == root
assert paths.config == os.path.join(root, 'config.yaml')
# test with custom app root
paths = constants.app_paths('/tmp/mip2scout')
assert paths.out == '/tmp/mip2scout/static'
assert paths.log == '/tmp/mip2scout/logs/main.log'
def root(context, config, log, level, root_dir):
"""Process MIP output to prepare upload to Scout."""
if config and os.path.exists(config.name):
context.obj = yaml.load(config)
context.default_map = context.obj
else:
context.obj = {}
app_rootdir = root_dir or context.obj.get('root_dir') or APP_ROOT
paths = context.obj['paths'] = app_paths(app_rootdir)
build_folders(paths.app)
log_path = log or paths.log
# setup logging
init_log(log_path, email_auth=context.obj.get('email'), level=level)
def all_cmd(context, root_dir, vtype, force, no_upload):
"""Do all the preprocessing for an analysis."""
paths = app_paths(root_dir or context.obj["root_dir"] or APP_ROOT)
mip_case = context.obj["case"]
owner = mip_case.instance_tags[0]
case_root = build_case_root(paths.out, cust_id=owner, case_id=mip_case.family_id)
config_path = case_root.joinpath("{}.conf.ini".format(vtype))
madeline_path = case_root.joinpath("madeline.xml")
scout_db = scout_tools.ScoutDatabase(context.obj["mongodb"])
logger.debug("checking if case is loaded in Scout")
case_loaded = scout_db.case_is_loaded(owner, mip_case.family_id, mip_case.analyzed_at, vtype=vtype)
if not force and case_loaded:
logger.debug("case (%s) already uploaded", vtype)
elif (mip_case.is_old and not case_loaded) and not force:
logger.info("%s is from old analysis, use force", mip_case.family_id)
else:
if vtype == "clinical":
logger.info("generating madeline SVG file")
try:
context.invoke(svg, out=madeline_path.open("w"))
except SinglePedigreeError:
logger.debug("skipping pedigree generation, single sample")
except MadelineIncompatibleError:
logger.debug("skipping pedigree generation, no connections")
case_obj = scout_db.case(owner, mip_case.family_id)
if case_obj and not case_loaded:
logger.info("removing coverage from old analysis (%s)", case_obj.analysis_date)
context.invoke(coverage_cmd, remove=True)
logger.info("remove variants from frequency database")
context.invoke(frequency, remove=True)
logger.info("uploading coverage to chanjo database")
context.invoke(coverage_cmd)
logger.info("uploading variants to frequency database")
context.invoke(frequency)
logger.info("uploading genotypes to taboo database")
context.invoke(genotype, force=force)
logger.info("generating '%s' config file", vtype)
context.invoke(config, out=config_path.open("w"), vtype=vtype, madeline_path=madeline_path)
if not no_upload:
logger.info("uploading case and variants to scout")
context.invoke(upload, config=config_path, force=force)
# also upload research variants if the case is_research
if vtype == "clinical" and case_obj and case_obj.is_research:
logger.info("old case marked as research")
logger.info("generating research config file")
config_path = case_root.joinpath("research.conf.ini")
context.invoke(config, out=config_path, vtype="research")
logger.info("uploading research variants to scout")
context.invoke(upload, config=config_path, force=force)