CenterForOpenScience / SHARE / 4872982462

import pytest

from share.util.graph import MutableGraph, MutableGraphError

work_id = '_:6203fec461bb4b3fa956772acbd9c50d'

org_id = '_:d486fd737bea4fbe9566b7a2842651ef'

uni_id = '_:d486fd737beeffbe9566b7a2842651ef'

person_id = '_:f4cec0271c7d4085bac26dbb2b32a002'

creator_id = '_:a17f28109536459ca02d99bf777400ae'

identifier_id = '_:a27f2810e536459ca02d99bf707400be'

@pytest.fixture

def example_graph_nodes():

    return [

        {'@id': uni_id, '@type': 'Institution', 'name': 'University of Whales'},

        {'@id': org_id, '@type': 'Organization', 'name': 'Department of Physics'},

        {'@id': '_:org-uni', '@type': 'IsMemberOf', 'subject': {'@id': org_id, '@type': 'Organization'}, 'related': {'@id': uni_id, '@type': 'Institution'}},

        {'@id': '_:tag1', '@type': 'Tag', 'name': 'you\'re'},

        {'@id': '_:tag2', '@type': 'Tag', 'name': 'it'},

        {'@id': '_:ttag1', '@type': 'ThroughTags', 'tag': {'@id': '_:tag1', '@type': 'Tag'}, 'creative_work': {'@id': work_id, '@type': 'Article'}},

        {'@id': '_:ttag2', '@type': 'ThroughTags', 'tag': {'@id': '_:tag2', '@type': 'Tag'}, 'creative_work': {'@id': work_id, '@type': 'Article'}},

        {'@id': '_:c4f10e02785a4b4d878f48d08ffc7fce', 'related': {'@type': 'Organization', '@id': org_id}, '@type': 'IsAffiliatedWith', 'subject': {'@type': 'Person', '@id': '_:7e742fa3377e4f119e36f8629144a0bc'}},

        {'@id': '_:7e742fa3377e4f119e36f8629144a0bc', 'agent_relations': [{'@type': 'IsAffiliatedWith', '@id': '_:c4f10e02785a4b4d878f48d08ffc7fce'}], '@type': 'Person', 'family_name': 'Prendergast', 'given_name': 'David'},

        {'@id': '_:687a4ba2cbd54ab7a2f2c3cd1777ea8a', '@type': 'Creator', 'creative_work': {'@type': 'Article', '@id': work_id}, 'agent': {'@type': 'Person', '@id': '_:7e742fa3377e4f119e36f8629144a0bc'}},

        {'@id': '_:69e859cefed140bd9b717c5b610d300c', '@type': 'Organization', 'name': 'NMRC, University College, Cork, Ireland'},

        {'@id': '_:2fd829eeda214adca2d4d34d02b10328', 'related': {'@type': 'Organization', '@id': '_:69e859cefed140bd9b717c5b610d300c'}, '@type': 'IsAffiliatedWith', 'subject': {'@type': 'Person', '@id': '_:ed3cc2a50f6d499db933a28d16bca5d6'}},

        {'@id': '_:ed3cc2a50f6d499db933a28d16bca5d6', 'agent_relations': [{'@type': 'IsAffiliatedWith', '@id': '_:2fd829eeda214adca2d4d34d02b10328'}], '@type': 'Person', 'family_name': 'Nolan', 'given_name': 'M.'},

        {'@id': '_:27961f3c7c644101a500772477aff304', '@type': 'Creator', 'creative_work': {'@type': 'Article', '@id': work_id}, 'agent': {'@type': 'Person', '@id': '_:ed3cc2a50f6d499db933a28d16bca5d6'}},

        {'@id': '_:d4f10e02785a4b4d878f48d08ffc7fce', 'related': {'@type': 'Organization', '@id': org_id}, '@type': 'IsAffiliatedWith', 'subject': {'@type': 'Person', '@id': '_:9a1386475d314b9bb524931e24361aaa'}},

        {'@id': '_:9a1386475d314b9bb524931e24361aaa', 'agent_relations': [{'@type': 'IsAffiliatedWith', '@id': '_:d4f10e02785a4b4d878f48d08ffc7fce'}], '@type': 'Person', 'family_name': 'Filippi', 'given_name': 'Claudia'},

        {'@id': '_:bf7726af4542405888463c796e5b7686', '@type': 'Creator', 'creative_work': {'@type': 'Article', '@id': work_id}, 'agent': {'@type': 'Person', '@id': '_:9a1386475d314b9bb524931e24361aaa'}},

        {'@id': '_:e4f10e02785a4b4d878f48d08ffc7fce', 'related': {'@type': 'Organization', '@id': org_id}, '@type': 'IsAffiliatedWith', 'subject': {'@type': 'Person', '@id': '_:78639db07e2e4ee88b422a8920d8a095'}},

        {'@id': '_:78639db07e2e4ee88b422a8920d8a095', 'agent_relations': [{'@type': 'IsAffiliatedWith', '@id': '_:e4f10e02785a4b4d878f48d08ffc7fce'}], '@type': 'Person', 'family_name': 'Fahy', 'given_name': 'Stephen'},

        {'@id': '_:18d151204d7c431388a7e516defab1bc', '@type': 'Creator', 'creative_work': {'@type': 'Article', '@id': work_id}, 'agent': {'@type': 'Person', '@id': '_:78639db07e2e4ee88b422a8920d8a095'}},

        {'@id': '_:5fd829eeda214adca2d4d34d02b10328', 'related': {'@type': 'Organization', '@id': '_:69e859cefed140bd9b717c5b610d300c'}, '@type': 'IsAffiliatedWith', 'subject': {'@type': 'Person', '@id': person_id}},

        {'@id': person_id, 'agent_relations': [{'@type': 'IsAffiliatedWith', '@id': '_:5fd829eeda214adca2d4d34d02b10328'}], '@type': 'Person', 'family_name': 'Greer', 'given_name': 'J.'},

        {'@id': creator_id, '@type': 'Creator', 'creative_work': {'@type': 'Article', '@id': work_id}, 'agent': {'@type': 'Person', '@id': person_id}},

        {'@id': identifier_id, '@type': 'WorkIdentifier', 'creative_work': {'@type': 'Article', '@id': work_id}, 'uri': 'http://example.com/things'},

        {'@id': work_id, 'date_updated': '2016-10-20T00:00:00+00:00', 'identifiers': [{'@type': 'WorkIdentifier', '@id': identifier_id}], 'agent_relations': [{'@type': 'Creator', '@id': '_:687a4ba2cbd54ab7a2f2c3cd1777ea8a'}, {'@type': 'Creator', '@id': '_:27961f3c7c644101a500772477aff304'}, {'@type': 'Creator', '@id': '_:bf7726af4542405888463c796e5b7686'}, {'@type': 'Creator', '@id': '_:18d151204d7c431388a7e516defab1bc'}, {'@type': 'Creator', '@id': creator_id}], 'title': 'Impact of Electron-Electron Cusp on Configuration Interaction Energies', '@type': 'Article', 'description': '  The effect of the electron-electron cusp on the convergence of configuration\ninteraction (CI) wave functions is examined. By analogy with the\npseudopotential approach for electron-ion interactions, an effective\nelectron-electron interaction is developed which closely reproduces the\nscattering of the Coulomb interaction but is smooth and finite at zero\nelectron-electron separation. The exact many-electron wave function for this\nsmooth effective interaction has no cusp at zero electron-electron separation.\nWe perform CI and quantum Monte Carlo calculations for He and Be atoms, both\nwith the Coulomb electron-electron interaction and with the smooth effective\nelectron-electron interaction. We find that convergence of the CI expansion of\nthe wave function for the smooth electron-electron interaction is not\nsignificantly improved compared with that for the divergent Coulomb interaction\nfor energy differences on the order of 1 mHartree. This shows that, contrary to\npopular belief, description of the electron-electron cusp is not a limiting\nfactor, to within chemical accuracy, for CI calculations.\n'}  # noqa

@pytest.fixture

def example_graph(example_graph_nodes):

    return MutableGraph.from_jsonld(example_graph_nodes)

class TestMutableGraph:

    def test_graph(self, example_graph):

        assert example_graph.number_of_nodes() == 25

    @pytest.mark.parametrize('node_id', [work_id, org_id, person_id, creator_id])

    def test_get_node(self, example_graph, node_id):

        assert example_graph.get_node(node_id).id == node_id

    def test_get_nonexistent_node(self, example_graph):

        assert example_graph.get_node('not_an_id') is None

    def test_edge(self, example_graph):

        creator_node = example_graph.get_node(creator_id)

        assert creator_node['creative_work'] == example_graph.get_node(work_id)

        assert creator_node['agent'] == example_graph.get_node(person_id)

    @pytest.mark.parametrize('node_id, key, value', [

        (work_id, 'title', 'title title'),

        (work_id, 'description', 'woo'),

        (identifier_id, 'creative_work', None),

        (identifier_id, 'foo', 'bar'),

    def test_set_attrs(self, example_graph, node_id, key, value):

        n = example_graph.get_node(node_id)

        n[key] = value

        assert n[key] == value

    @pytest.mark.parametrize('set_none', [True, False])

    def test_del_attrs(self, example_graph, set_none):

        work = example_graph.get_node(work_id)

        assert work['title']

        if set_none:

            work['title'] = None

            del work['title']

        assert work['title'] is None

        assert 'title' not in work.attrs()

        identifier = example_graph.get_node(identifier_id)

        assert identifier['creative_work'] == work

        if set_none:

            identifier['creative_work'] = None

            del identifier['creative_work']

    @pytest.mark.parametrize('node_id, reverse_edge_name, count', [

        (work_id, 'agent_relations', 5),

        (work_id, 'incoming_creative_work_relations', 0),

        (work_id, 'identifiers', 1),

        (org_id, 'incoming_agent_relations', 3),

        (org_id, 'outgoing_agent_relations', 1),

    def test_reverse_edge(self, example_graph, node_id, reverse_edge_name, count):

        node = example_graph.get_node(node_id)

        assert len(node[reverse_edge_name]) == count

    @pytest.mark.parametrize('node_id, m2m_name, count', [

        (work_id, 'related_agents', 5),

        (work_id, 'related_works', 0),

        (work_id, 'subjects', 0),

        (work_id, 'tags', 2),

        (org_id, 'related_works', 0),

        (org_id, 'related_agents', 4),

    def test_many_to_many(self, example_graph, node_id, m2m_name, count):

        node = example_graph.get_node(node_id)

        assert len(node[m2m_name]) == count

    @pytest.mark.parametrize('node_id, count', [

        (work_id, 16),

        (org_id, 20),

        (person_id, 22),

        (creator_id, 24),

    def test_remove_node_cascades(self, example_graph, node_id, count):

        example_graph.remove_node(node_id)

        assert example_graph.number_of_nodes() == count

    def test_add_node(self, example_graph):

        identifier_id = '_:foo'

        uri = 'mailto:person@example.com'

        person = example_graph.get_node(person_id)

        node_count = example_graph.number_of_nodes()

        assert len(person['identifiers']) == 0

        example_graph.add_node(identifier_id, 'AgentIdentifier', {'uri': uri, 'agent': person})

        assert example_graph.number_of_nodes() == node_count + 1

        identifier_node = example_graph.get_node(identifier_id)

        assert identifier_node['uri'] == uri

        assert identifier_node['agent'] == person

        identifiers = person['identifiers']

        assert len(identifiers) == 1

        assert identifier_node == next(iter(identifiers))

    @pytest.mark.parametrize('count, filter', [

        (5, lambda n, g: n.type == 'person'),

        (0, lambda n, g: not g.degree(n.id)),

        (1, lambda n, g: len(g.out_edges(n.id)) == 1),

    def test_filter_nodes(self, example_graph, filter, count):

        filtered = list(example_graph.filter_nodes(lambda n: filter(n, example_graph)))

        assert len(filtered) == count

    def test_jsonld(self, example_graph_nodes, example_graph):

        def clean_jsonld(value):

            if isinstance(value, list):

                return [clean_jsonld(n) for n in sorted(value, key=lambda n: n['@id'])]

            if isinstance(value, dict):

                return {

                    k: v.lower() if k == '@type' else clean_jsonld(v)

                    for k, v in value.items() if not isinstance(v, list)

            return value

        expected_nodes = clean_jsonld(example_graph_nodes)

        actual = example_graph.to_jsonld(in_edges=False)

        actual_nodes = clean_jsonld(actual['@graph'])

        assert expected_nodes == actual_nodes

        assert actual['central_node_id'] is None

class TestCentralWork:

    def test_obvious_example(self, example_graph):

        assert example_graph.central_node_id is None

        assert example_graph.get_central_node() is None

        guessed = example_graph.get_central_node(guess=True)

        assert guessed.id == work_id

        assert example_graph.central_node_id == work_id

        assert example_graph.get_central_node() == guessed

    def test_no_central_node(self):

        graph = MutableGraph()

        agent = graph.add_node(None, 'agent')

        graph.add_node(None, 'agentidentifier', {'agent': agent})

        assert graph.get_central_node() is None

        assert graph.get_central_node(guess=True) is None

        assert graph.central_node_id is None

    def test_explicit_central_node(self):

        central_id = '_:center'

        graph = MutableGraph.from_jsonld({

            'central_node_id': central_id,

            '@graph': [

                {'@id': central_id, '@type': 'creativework'},

                {'@id': '_:other', '@type': 'creativework', 'title': 'looks like the center'},

        assert graph.central_node_id == central_id

        assert graph.get_central_node().id == central_id

        assert graph.get_central_node(guess=True).id == central_id

    def test_ambiguous_central_node(self):

        graph = MutableGraph.from_jsonld({

            '@graph': [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'looks like the center'},

                {'@id': '_:thing2', '@type': 'creativework', 'title': 'also looks like the center'},

        with pytest.raises(MutableGraphError):

            graph.get_central_node(guess=True)

    @pytest.mark.parametrize('graph_nodes, expected_guess', [

        (

            [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'only thing'},

            '_:thing1',

        (

            [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'one thing'},

                {'@id': '_:thing2', '@type': 'creativework', 'title': 'another thing', 'description': 'tiebreaker'},

            '_:thing2',

        (

            [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'looks like the center'},

                {'@id': '_:thing2', '@type': 'creativework', 'title': 'also looks like the center'},

                {

                    '@id': '_:tiebreaker',

                    '@type': 'workidentifier',

                    'uri': 'http://example.com/woo',

                    'creative_work': {'@id': '_:thing2', '@type': 'creativework'},

            '_:thing2',

        (

            [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'looks like the center', 'description': 'confounder'},

                {'@id': '_:thing2', '@type': 'creativework', 'title': 'also looks like the center'},

                {

                    '@id': '_:tiebreaker',

                    '@type': 'workidentifier',

                    'uri': 'http://example.com/woo',

                    'creative_work': {'@id': '_:thing2', '@type': 'creativework'},

            '_:thing2',

        (

            [

                {'@id': '_:thing1', '@type': 'creativework', 'title': 'parent'},

                {'@id': '_:thing2', '@type': 'creativework', 'title': 'child'},

                {

                    '@id': '_:choose-the-child',

                    '@type': 'ispartof',

                    'subject': {'@id': '_:thing2', '@type': 'creativework'},

                    'related': {'@id': '_:thing1', '@type': 'creativework'},

            '_:thing2',

    def test_guessing(self, graph_nodes, expected_guess):

        graph = MutableGraph.from_jsonld({'@graph': graph_nodes})

        guessed = graph.get_central_node(guess=True)

        assert guessed.id == expected_guess