src/pybel/io/neo4j.py
def to_neo4j(graph, neo_connection, use_tqdm: bool = False):
    """Upload a BEL graph to a Neo4j graph database using :mod:`py2neo`.

    :param pybel.BELGraph graph: A BEL Graph
    :param neo_connection: A :mod:`py2neo` connection object. Refer to the
     `py2neo documentation <http://py2neo.org/v3/database.html#the-graph>`_ for how to build this object.
    :type neo_connection: str or py2neo.Graph

    Example Usage:

    >>> import py2neo
    >>> import pybel
    >>> from pybel.examples import sialic_acid_graph
    >>> neo_graph = py2neo.Graph("http://localhost:7474/db/data/")  # use your own connection settings
    >>> pybel.to_neo4j(sialic_acid_graph, neo_graph)
    """
    import py2neo

    if isinstance(neo_connection, str):
        neo_connection = py2neo.Graph(neo_connection)

    tx = neo_connection.begin()

    node_map = {}

    nodes = list(graph)
    if use_tqdm:
        nodes = tqdm(nodes, desc='nodes')

    for node in nodes:
        if NAMESPACE not in node or VARIANTS in node or MEMBERS in node or FUSION in node:
            attrs = {'name': node.as_bel()}
        else:
            attrs = {'namespace': node.namespace}

            if node.name and node.identifier:
                attrs['name'] = node.name
                attrs['identifier'] = node.identifier
            elif node.identifier and not node.name:
                attrs['name'] = node.identifier
            elif node.name and not node.identifier:
                attrs['name'] = node.name

        node_map[node] = py2neo.Node(node.function, **attrs)

        tx.create(node_map[node])

    edges = graph.edges(keys=True, data=True)
    if use_tqdm:
        edges = tqdm(edges, desc='edges')

    for u, v, key, node in edges:
        rel_type = node[RELATION]

        d = node.copy()
        del d[RELATION]

        attrs = {}

        annotations = d.pop(ANNOTATIONS, None)
        if annotations:
            for annotation, values in annotations.items():
                attrs[annotation] = list(values)

        citation = d.pop(CITATION, None)
        if citation:
            attrs[CITATION] = citation.curie

        if EVIDENCE in d:
            attrs[EVIDENCE] = d[EVIDENCE]

        for side in (SOURCE_MODIFIER, TARGET_MODIFIER):
            side_data = d.get(side)
            if side_data:
                attrs.update(flatten_dict(side_data, parent_key=side))

        rel = py2neo.Relationship(node_map[u], rel_type, node_map[v], key=key, **attrs)
        tx.create(rel)

    tx.commit()
Upload a BEL graph to a Neo4j graph database using :mod:`py2neo`.

    :param pybel.BELGraph graph: A BEL Graph
    :param neo_connection: A :mod:`py2neo` connection object. Refer to the
     `py2neo documentation <http://py2neo.org/v3/database.html#the-graph>`_ for how to build this object.
    :type neo_connection: str or py2neo.Graph

    Example Usage:

    >>> import py2neo
    >>> import pybel
    >>> from pybel.examples import sialic_acid_graph
    >>> neo_graph = py2neo.Graph("http://localhost:7474/db/data/")  # use your own connection settings
    >>> pybel.to_neo4j(sialic_acid_graph, neo_graph)
    
Upload a BEL graph to a Neo4j graph database using :mod:`py2neo`.
Upload a BEL graph to a Neo4j graph database using : mod : ` py2neo ` .
def to_neo4j(graph, neo_connection, use_tqdm: bool = False):
    import py2neo
    if isinstance(neo_connection, str):
        neo_connection = py2neo.Graph(neo_connection)
    tx = neo_connection.begin()
    node_map = {}
    nodes = list(graph)
    if use_tqdm:
        nodes = tqdm(nodes, desc='nodes')
    for node in nodes:
        if NAMESPACE not in node or VARIANTS in node or MEMBERS in node or FUSION in node:
            attrs = {'name': node.as_bel()}
        else:
            attrs = {'namespace': node.namespace}
            if node.name and node.identifier:
                attrs['name'] = node.name
                attrs['identifier'] = node.identifier
            elif node.identifier and not node.name:
                attrs['name'] = node.identifier
            elif node.name and not node.identifier:
                attrs['name'] = node.name
        node_map[node] = py2neo.Node(node.function, **attrs)
        tx.create(node_map[node])
    edges = graph.edges(keys=True, data=True)
    if use_tqdm:
        edges = tqdm(edges, desc='edges')
    for u, v, key, node in edges:
        rel_type = node[RELATION]
        d = node.copy()
        del d[RELATION]
        attrs = {}
        annotations = d.pop(ANNOTATIONS, None)
        if annotations:
            for annotation, values in annotations.items():
                attrs[annotation] = list(values)
        citation = d.pop(CITATION, None)
        if citation:
            attrs[CITATION] = citation.curie
        if EVIDENCE in d:
            attrs[EVIDENCE] = d[EVIDENCE]
        for side in (SOURCE_MODIFIER, TARGET_MODIFIER):
            side_data = d.get(side)
            if side_data:
                attrs.update(flatten_dict(side_data, parent_key=side))
        rel = py2neo.Relationship(node_map[u], rel_type, node_map[v], key=key, **attrs)
        tx.create(rel)
    tx.commit()
def to_neo4j ( graph , neo_connection , use_tqdm : bool = False ) : import py2neo if isinstance ( neo_connection , str ) : neo_connection = py2neo . Graph ( neo_connection ) tx = neo_connection . begin ( ) node_map = { } nodes = list ( graph ) if use_tqdm : nodes = tqdm ( nodes , desc = 'nodes' ) for node in nodes : if NAMESPACE not in node or VARIANTS in node or MEMBERS in node or FUSION in node : attrs = { 'name' : node . as_bel ( ) } else : attrs = { 'namespace' : node . namespace } if node . name and node . identifier : attrs [ 'name' ] = node . name attrs [ 'identifier' ] = node . identifier elif node . identifier and not node . name : attrs [ 'name' ] = node . identifier elif node . name and not node . identifier : attrs [ 'name' ] = node . name node_map [ node ] = py2neo . Node ( node . function , ** attrs ) tx . create ( node_map [ node ] ) edges = graph . edges ( keys = True , data = True ) if use_tqdm : edges = tqdm ( edges , desc = 'edges' ) for u , v , key , node in edges : rel_type = node [ RELATION ] d = node . copy ( ) del d [ RELATION ] attrs = { } annotations = d . pop ( ANNOTATIONS , None ) if annotations : for annotation , values in annotations . items ( ) : attrs [ annotation ] = list ( values ) citation = d . pop ( CITATION , None ) if citation : attrs [ CITATION ] = citation . curie if EVIDENCE in d : attrs [ EVIDENCE ] = d [ EVIDENCE ] for side in ( SOURCE_MODIFIER , TARGET_MODIFIER ) : side_data = d . get ( side ) if side_data : attrs . update ( flatten_dict ( side_data , parent_key = side ) ) rel = py2neo . Relationship ( node_map [ u ] , rel_type , node_map [ v ] , key = key , ** attrs ) tx . create ( rel ) tx . commit ( )
Upload a BEL graph to a Neo4j graph database using :mod:`py2neo`.
Upload a BEL graph to a Neo4j graph database using : mod : ` py2neo ` .
"""Upload a BEL graph to a Neo4j graph database using :mod:`py2neo`.

    :param pybel.BELGraph graph: A BEL Graph
    :param neo_connection: A :mod:`py2neo` connection object. Refer to the
     `py2neo documentation <http://py2neo.org/v3/database.html#the-graph>`_ for how to build this object.
    :type neo_connection: str or py2neo.Graph

    Example Usage:

    >>> import py2neo
    >>> import pybel
    >>> from pybel.examples import sialic_acid_graph
    >>> neo_graph = py2neo.Graph("http://localhost:7474/db/data/")  # use your own connection settings
    >>> pybel.to_neo4j(sialic_acid_graph, neo_graph)
    """
graph
A BEL Graph
A BEL Graph
neo_connection
A :mod:`py2neo` connection object. Refer to the
`py2neo documentation `_ for how to build this object.
A : mod : ` py2neo ` connection object . Refer to the ` py2neo documentation ` _ for how to build this object .
use_tqdm
bool