annotate planemo/lib/python3.7/site-packages/prov/graph.py @ 1:56ad4e20f292 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

from __future__ import (absolute_import, division, print_function,
                        unicode_literals)

import networkx as nx
from prov.model import (
    ProvDocument, ProvRecord, ProvElement, ProvEntity, ProvActivity, ProvAgent,
    ProvRelation, PROV_ATTR_ENTITY, PROV_ATTR_ACTIVITY, PROV_ATTR_AGENT,
    PROV_ATTR_TRIGGER, PROV_ATTR_GENERATED_ENTITY, PROV_ATTR_USED_ENTITY,
    PROV_ATTR_DELEGATE, PROV_ATTR_RESPONSIBLE, PROV_ATTR_SPECIFIC_ENTITY,
    PROV_ATTR_GENERAL_ENTITY, PROV_ATTR_ALTERNATE1, PROV_ATTR_ALTERNATE2,
    PROV_ATTR_COLLECTION, PROV_ATTR_INFORMED, PROV_ATTR_INFORMANT
)

__author__ = 'Trung Dong Huynh'
__email__ = '[e-mail]'


INFERRED_ELEMENT_CLASS = {
    PROV_ATTR_ENTITY: ProvEntity,
    PROV_ATTR_ACTIVITY: ProvActivity,
    PROV_ATTR_AGENT: ProvAgent,
    PROV_ATTR_TRIGGER: ProvEntity,
    PROV_ATTR_GENERATED_ENTITY: ProvEntity,
    PROV_ATTR_USED_ENTITY: ProvEntity,
    PROV_ATTR_DELEGATE: ProvAgent,
    PROV_ATTR_RESPONSIBLE: ProvAgent,
    PROV_ATTR_SPECIFIC_ENTITY: ProvEntity,
    PROV_ATTR_GENERAL_ENTITY: ProvEntity,
    PROV_ATTR_ALTERNATE1: ProvEntity,
    PROV_ATTR_ALTERNATE2: ProvEntity,
    PROV_ATTR_COLLECTION: ProvEntity,
    PROV_ATTR_INFORMED: ProvActivity,
    PROV_ATTR_INFORMANT: ProvActivity
}


def prov_to_graph(prov_document):
    """
    Convert a :class:`~prov.model.ProvDocument` to a `MultiDiGraph
    <https://networkx.readthedocs.io/en/stable/reference/classes.multigraph.html>`_
    instance of the `NetworkX <https://networkx.github.io/>`_ library.

    :param prov_document: The :class:`~prov.model.ProvDocument` instance to convert.
    """
    g = nx.MultiDiGraph()
    unified = prov_document.unified()
    node_map = dict()
    for element in unified.get_records(ProvElement):
        g.add_node(element)
        node_map[element.identifier] = element

    for relation in unified.get_records(ProvRelation):
        # taking the first two elements of a relation
        attr_pair_1, attr_pair_2 = relation.formal_attributes[:2]
        # only need the QualifiedName (i.e. the value of the attribute)
        qn1, qn2 = attr_pair_1[1], attr_pair_2[1]
        if qn1 and qn2:  # only proceed if both ends of the relation exist
            try:
                if qn1 not in node_map:
                    node_map[qn1] = \
                        INFERRED_ELEMENT_CLASS[attr_pair_1[0]](None, qn1)
                if qn2 not in node_map:
                    node_map[qn2] = \
                        INFERRED_ELEMENT_CLASS[attr_pair_2[0]](None, qn2)
            except KeyError:
                # Unsupported attribute; cannot infer the type of the element
                continue  # skipping this relation
            g.add_edge(node_map[qn1], node_map[qn2], relation=relation)
    return g


def graph_to_prov(g):
    """
    Convert a `MultiDiGraph
    <https://networkx.readthedocs.io/en/stable/reference/classes.multigraph.html>`_
    that was previously produced by :func:`prov_to_graph` back to a
    :class:`~prov.model.ProvDocument`.

    :param g: The graph instance to convert.
    """
    prov_doc = ProvDocument()
    for n in g.nodes_iter():
        if isinstance(n, ProvRecord) and n.bundle is not None:
            prov_doc.add_record(n)
    for _, _, edge_data in g.edges_iter(data=True):
        try:
            relation = edge_data['relation']
            if isinstance(relation, ProvRecord):
                prov_doc.add_record(relation)
        except KeyError:
            pass

    return prov_doc