Python process_nodes Examples

Example #1

File: ncbi_taxa_bulk_loader_multiple_edges.py Project: kbaseIncubator/relation_engine_incubator

def main():
    a = parse_args()
    nodes = os.path.join(a.dir, NODES_IN_FILE)
    names = os.path.join(a.dir, NAMES_IN_FILE)

    nodes_out = os.path.join(a.dir, NODES_OUT_FILE)
    edges_out = os.path.join(a.dir, EDGES_OUT_FILE)

    with open(nodes) as infile, open(names) as namesfile, open(
            nodes_out, 'w') as node_out:
        nodeprov = NCBINodeProvider(namesfile, infile)
        process_nodes(nodeprov, a.load_version, a.load_timestamp, node_out)

    with ExitStack() as stack:
        infile = stack.enter_context(open(nodes))
        files = {
            1: stack.enter_context(open(edges_out + '_1', 'w')),
            2: stack.enter_context(open(edges_out + '_2', 'w')),
            3: stack.enter_context(open(edges_out + '_3', 'w'))
        }
        edgeprov = NCBIEdgeProvider(infile)
        for e in edgeprov:
            e = process_edge(e, a.load_version, a.load_timestamp)
            fileno = int(e['id']) % 3 + 1
            files[fileno].write(json.dumps(e) + '\n')

Example #2

File: ncbi_taxa_bulk_loader.py Project: MrCreosote/relation_engine_importers

def main():
    a = parse_args()
    nodes = os.path.join(a.dir, NODES_IN_FILE)
    names = os.path.join(a.dir, NAMES_IN_FILE)

    nodes_out = os.path.join(a.dir, NODES_OUT_FILE)
    edges_out = os.path.join(a.dir, EDGES_OUT_FILE)

    with open(nodes) as infile, open(names) as namesfile, open(nodes_out, 'w') as node_out:
        nodeprov = NCBINodeProvider(namesfile, infile)
        process_nodes(nodeprov, a.load_version, a.load_timestamp, node_out)

    with open(nodes) as infile, open(edges_out, 'w') as edgef:
        edgeprov = NCBIEdgeProvider(infile)
        process_edges(edgeprov, a.load_version, a.load_timestamp, edgef)