def clean(context, force, date, case_name):
"""Clean up files for an analysis."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(context, case_name, date)
if force or click.confirm('Are you sure?'):
api.clean_up(context.obj['root'], run_obj, force=force)
manager.commit()
def scout(context, madeline_exe, date, replace, case_name):
"""Prepare a config and files for Scout."""
madeline_exe = madeline_exe or context.obj['madeline_exe']
manager = api.manager(context.obj['database'])
root_path = context.obj['root']
run_obj = run_orabort(context, case_name, date)
if not run_obj.pipeline_version.startswith('v4'):
log.error("unsupported pipeline version: %s", run_obj.pipeline_version)
context.abort()
existing_conf = (api.assets(category='scout-config', run_id=run_obj.id)
.first())
if existing_conf:
if replace:
log.info("deleting existing scout config: %s", existing_conf.path)
api.delete_asset(existing_conf)
existing_mad = (api.assets(category='madeline', run_id=run_obj.id)
.first())
if existing_mad:
log.info("deleting existing madeline: %s", existing_mad.path)
api.delete_asset(existing_mad)
manager.commit()
else:
log.error("scout config already generated")
context.abort()
prepare_scout(run_obj, root_path, madeline_exe)
manager.commit()
def extend(context, no_link, date, category, sample, archive_type, case_name,
asset_path):
"""Add an additional asset to a run."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(context, case_name, date)
if sample:
sample_map = {smpl.name: smpl for smpl in run_obj.samples}
sample_obj = sample_map[sample]
else:
sample_obj = None
new_asset = api.add_asset(run_obj, asset_path, category, archive_type,
sample=sample_obj)
root_path = context.obj['root']
run_root = get_rundir(root_path, run_obj.case.name, run_obj)
filename = new_asset.basename()
if no_link:
new_path = asset_path
else:
new_path = run_root.joinpath(filename)
log.debug("link asset: %s -> %s", new_asset.original_path, new_path)
path(new_asset.original_path).link(new_path)
new_asset.path = new_path
run_obj.assets.append(new_asset)
log.info("add asset: %s", new_asset.path)
manager.commit()
def postpone(context, days, case_name):
"""Ask Housekeeper for a file."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(case_name)
api.postpone(run_obj, time=datetime.timedelta(days=days))
manager.commit()
click.echo("analysis will be archived on: {}"
.format(run_obj.will_cleanup_at))
def status(context, date, now, run_date, sample_status, run_status,
extra_status, identifier):
"""Mark dates for resources."""
manager = api.manager(context.obj['database'])
# determine which date to set: custom or now!
if date:
status_date = parse_date(date)
elif now:
status_date = datetime.datetime.now()
else:
status_date = None
if sample_status:
# update a date for a sample
model_obj = api.sample(identifier)
if model_obj is None:
click.echo("can't find sample")
context.abort()
# types are predefined; no need to check!
status_type = sample_status
else:
# update a date for an analysis run
model_obj = run_orabort(context, identifier, run_date)
# types are predefined as well
status_type = run_status
if extra_status:
if model_obj.extra is None:
log.info("adding extra data record")
model_obj.extra = ExtraRunData()
manager.commit()
extra_date_key = "{}_date".format(extra_status)
if status_date is None:
# show a custom date for an analysis run
current_date = getattr(model_obj.extra, extra_date_key)
else:
# update a custom date for a run
setattr(model_obj.extra, extra_date_key, status_date)
status_field = extra_status
else:
status_field = "{}_at".format(status_type)
if status_date is None:
# show a predfined date for a model
current_date = getattr(model_obj, status_field)
else:
# update a predefined date on a model
setattr(model_obj, status_field, status_date)
if status_date is None:
if current_date is None:
context.abort()
else:
click.echo(current_date)
else:
log.info("updating %s -> %s", status_field, status_date)
manager.commit()
def delete_analysis(context, date, yes, case_name):
"""Delete an analysis run and files."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(context, case_name, date)
root_path = context.obj['root']
run_root = get_rundir(root_path, case_name, run_obj)
click.echo("you are about to delete: {}".format(run_root))
if yes or click.confirm('Are you sure?'):
api.delete(root_path, run_obj)
manager.commit()
def archive(context, date, force, case_name):
"""Archive compiled assets to PDC."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(context, case_name, date)
if not run_obj.compiled_at:
log.warn("run not compiled yet: %s", case_name)
if force or click.confirm("do you want to compile the run?"):
date_str = run_obj.analyzed_at.date().isoformat()
context.invoke(compile_cmd, date=date_str, force=True,
case_name=case_name)
# refresh the run object
run_obj = AnalysisRun.query.get(run_obj.id)
else:
context.abort()
if force or click.confirm("are you sure you want to archive the run?"):
archive_run(run_obj, force=force)
manager.commit()
