def _add_versions(samples): """Add tool and data versions to the summary. """ samples[0]["versions"] = { "tools": programs.write_versions(samples[0]["dirs"], samples[0]["config"]), "data": provenancedata.write_versions(samples[0]["dirs"], samples) } return samples
def _add_provenance(items, dirs, config): p = programs.write_versions(dirs, config) versioncheck.testall(items) p_db = diagnostics.initialize(dirs) out = [] for item in items: entity_id = diagnostics.store_entity(item) item["config"]["resources"]["program_versions"] = p item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db} out.append([item]) return out
def _add_provenance(items, dirs, parallel, config): p = programs.write_versions(dirs, config, is_wrapper=parallel.get("wrapper") is not None) p_db = diagnostics.initialize(dirs) system.write_info(dirs, parallel, config) out = [] for item in items: entity_id = diagnostics.store_entity(item) item["config"]["resources"]["program_versions"] = p item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db} out.append([item]) return out
def _add_provenance(items, dirs, config): p = programs.write_versions(dirs, config=config) versioncheck.testall(items) p_db = diagnostics.initialize(dirs) out = [] for item in items: entity_id = diagnostics.store_entity(item) item["config"]["resources"]["program_versions"] = p item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db} out.append([item]) return out
def _add_provenance(items, dirs, run_parallel, parallel, config): p = programs.write_versions(dirs, config) system.write_info(dirs, run_parallel, parallel, config) out = [] for item in items: if item.get("upload") and item["upload"].get("fc_name"): entity_id = "%s.%s.%s" % (item["upload"]["fc_date"], item["upload"]["fc_name"], item["description"]) else: entity_id = item["description"] item["config"]["resources"]["program_versions"] = p item["provenance"] = {"programs": p, "entity": entity_id} out.append([item]) return out
def _add_provenance(items, dirs, parallel, config): p = programs.write_versions(dirs, config, is_wrapper=parallel.get("wrapper") is not None) system.write_info(dirs, parallel, config) out = [] for item in items: if item.get("upload") and item["upload"].get("fc_name"): entity_id = "%s.%s.%s" % (item["upload"]["fc_date"], item["upload"]["fc_name"], item["description"]) else: entity_id = item["description"] item["config"]["resources"]["program_versions"] = p item["provenance"] = {"programs": p, "entity": entity_id} out.append([item]) return out
def _add_provenance(items, dirs, config): p = programs.write_versions(dirs, config) out = [] for item_info in items: item = item_info[2] if item.get("upload"): entity_id = "%s.%s.%s" % (item["upload"]["fc_date"], item["upload"]["fc_name"], item["description"]) else: entity_id = item["description"] item["provenance"] = {"programs": p, "entity": entity_id} cur = list(item_info) cur[2] = item out.append(cur) return out
if kwargs.get("workflow"): kwargs["inputs"] = inputs kwargs["config_file"] = global_config kwargs["fc_dir"] = fc_dir kwargs["run_info_yaml"] = run_info_yaml return kwargs if __name__ == "__main__": kwargs = parse_cl_args(sys.argv[1:]) if "upgrade" in kwargs and kwargs["upgrade"]: install.upgrade_bcbio(kwargs["args"]) elif "server" in kwargs and kwargs["server"]: server_main.start(kwargs["args"]) elif "runfn" in kwargs and kwargs["runfn"]: runfn.process(kwargs["args"]) elif "graph" in kwargs and kwargs["graph"]: graph.bootstrap(kwargs["args"]) elif "version" in kwargs and kwargs["version"]: programs.write_versions({"work": kwargs["args"].workdir}) elif "sequencer" in kwargs and kwargs["sequencer"]: machine.check_and_postprocess(kwargs["args"]) else: if kwargs.get("workflow"): setup_info = workflow.setup(kwargs["workflow"], kwargs.pop("inputs")) if setup_info is None: # no automated run after setup sys.exit(0) workdir, new_kwargs = setup_info os.chdir(workdir) kwargs.update(new_kwargs) main(**kwargs)
def _add_versions(samples): """Add tool and data versions to the summary. """ samples[0]["versions"] = {"tools": programs.write_versions(samples[0]["dirs"], samples[0]["config"]), "data": provenancedata.write_versions(samples[0]["dirs"], samples)} return samples
kwargs["config_file"] = global_config kwargs["fc_dir"] = fc_dir kwargs["run_info_yaml"] = run_info_yaml return kwargs if __name__ == "__main__": kwargs = parse_cl_args(sys.argv[1:]) if "upgrade" in kwargs and kwargs["upgrade"]: install.upgrade_bcbio(kwargs["args"]) elif "server" in kwargs and kwargs["server"]: server_main.start(kwargs["args"]) elif "runfn" in kwargs and kwargs["runfn"]: runfn.process(kwargs["args"]) elif "graph" in kwargs and kwargs["graph"]: graph.bootstrap(kwargs["args"]) elif "version" in kwargs and kwargs["version"]: programs.write_versions({"work": kwargs["args"].workdir}) elif "sequencer" in kwargs and kwargs["sequencer"]: machine.check_and_postprocess(kwargs["args"]) else: if kwargs.get("workflow"): setup_info = workflow.setup(kwargs["workflow"], kwargs.pop("inputs")) if setup_info is None: # no automated run after setup sys.exit(0) workdir, new_kwargs = setup_info os.chdir(workdir) kwargs.update(new_kwargs) main(**kwargs)