def registry_runner(registry_, rtasks, output_dir): # this will emit the PTs to an output dir d = os.path.abspath(os.path.expanduser(output_dir)) r = registry_ log.info("Writing Pipeline Templates to ") print "Emitting pipelines to output dir {d}".format(d=d) write_pipeline_templates_to_avro(r.pipelines.values(), rtasks, d) log.info("Successful wrote {n} pipelines to {d}".format(n=len(r.pipelines), d=d)) return 0
def run_show_templates(output_dir=None): import pbsmrtpipe.loader as L from pbsmrtpipe.pb_io import write_pipeline_templates_to_avro rtasks_d, _, _, pts = L.load_all() print pretty_registered_pipelines(pts) if output_dir is not None: write_pipeline_templates_to_avro(pts.values(), rtasks_d, output_dir) return 0
def registry_runner(registry_, rtasks, output_dir): # this will emit the PTs to an output dir d = os.path.abspath(os.path.expanduser(output_dir)) r = registry_ log.info("Writing Pipeline Templates to {o}".format(o=output_dir)) print "Emitting pipelines to output dir {d}".format(d=d) write_pipeline_templates_to_avro(r.pipelines.values(), rtasks, d) for p in r.pipelines.values(): file_name = p.idx + "_pipeline.xml" path = os.path.join(output_dir, file_name) xml = pipeline_to_xml(p) with open(path, 'w') as f: f.write(str(xml)) log.info("writing pipeline {x}".format(x=path)) log.info("Successfully wrote {n} pipelines to {d}".format(n=len(r.pipelines), d=d)) return 0
def run_show_templates(avro_output_dir=None, json_output_dir=None, show_all=False): import pbsmrtpipe.loader as L from pbsmrtpipe.pb_io import (write_pipeline_templates_to_avro, write_pipeline_templates_to_json) rtasks_d, _, _, pts = L.load_all() print pretty_registered_pipelines(pts, show_all=show_all) if not show_all: print "Run with --show-all to display (unsupported) developer/internal pipelines" if avro_output_dir is not None: write_pipeline_templates_to_avro(pts.values(), rtasks_d, avro_output_dir) if json_output_dir is not None: write_pipeline_templates_to_json(pts.values(), rtasks_d, json_output_dir) return 0