def review(ctx, type, customer, skip_update, email, output):
"""Generates information about novel ST"""
# Trace exists by some samples having pubMLST_ST filled in. Make trace function later
ctx.obj["config"]["regex"]["mail_recipient"] = email
ext_refs = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
if not skip_update:
ext_refs.update_refs()
ext_refs.resync()
click.echo("INFO - Version check done. Generating output")
if type == "report":
codemonkey = Reporter(config=ctx.obj["config"],
log=ctx.obj["log"],
output=output)
codemonkey.report(type="st_update", customer=customer)
elif type == "list":
ext_refs.resync(type=type)
done()
def overwrite(ctx, sample_name, force):
"""Flags sample as resolved"""
ext_refs = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
ext_refs.resync(type="overwrite", sample=sample_name, ignore=force)
done()