def upload_cbn_dir(dir_path, manager): """Uploads CBN data to edge store :param str dir_path: Directory full of CBN JGIF files :param pybel.Manager manager: """ t = time.time() for jfg_path in os.listdir(dir_path): if not jfg_path.endswith('.jgf'): continue path = os.path.join(dir_path, jfg_path) log.info('opening %s', path) with open(path) as f: cbn_jgif_dict = json.load(f) graph = pybel.from_cbn_jgif(cbn_jgif_dict) out_path = os.path.join(dir_path, jfg_path.replace('.jgf', '.bel')) with open(out_path, 'w') as o: pybel.to_bel(graph, o) strip_annotations(graph) enrich_pubmed_citations(manager=manager, graph=graph) pybel.to_database(graph, manager=manager) log.info('') log.info('done in %.2f', time.time() - t)
def save_model(self, path, output_format=None): """Save the :class:`pybel.BELGraph` using one of the outputs from :py:mod:`pybel` Parameters ---------- path : str The path to output to output_format : Optional[str] Output format as ``cx``, ``pickle``, ``json`` or defaults to ``bel`` """ if output_format == 'pickle': pybel.to_pickle(self.model, path) else: with open(path, 'w') as fh: if output_format == 'json': pybel.to_json_file(self.model, fh) elif output_format == 'cx': pybel.to_cx_file(self.model, fh) else: # output_format == 'bel': pybel.to_bel(self.model, fh)
def main(file): """Provide BEL Statements from BEL graph.""" df = get_equivalences_df() graph = build_equivalences_graph(df) pybel.to_bel(graph, file)
def main(): """Provide BEL Statements from BEL graph.""" df = get_relations_df() graph = build_relations_graph(df) with open("famplex.bel", "w") as file: to_bel(graph, file)
def to_bel_file(self, file): graph = self.to_bel_graph() pybel.to_bel(graph, file=file)