def test_edge_update_nested_lists():
graph = GraphDocument(force_undirected=True)
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
graph.add_single_edge(doc0, doc1)
edge_key = graph._get_edge_key(doc0.id, doc1.id)
graph.edge_features[edge_key] = {
'hey': {
'nested': True,
'list': ['elem1', 'elem2', {
'inlist': 'here'
}]
},
'hoy': [0, 1],
}
graph.edge_features[edge_key]['hey']['nested'] = False
graph.edge_features[edge_key]['hey']['list'][1] = True
graph.edge_features[edge_key]['hey']['list'][2]['inlist'] = 'not here'
graph.edge_features[edge_key]['hoy'][0] = 1
assert graph.edge_features[edge_key]['hey']['nested'] is False
assert graph.edge_features[edge_key]['hey']['list'][1] is True
assert graph.edge_features[edge_key]['hey']['list'][2][
'inlist'] == 'not here'
assert graph.edge_features[edge_key]['hoy'][0] == 1
def test_graph_add_multiple_nodes():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_nodes([doc0, doc1, doc2, doc3])
assert graph.num_nodes == 4
assert graph.num_edges == 0
def test_add_single_edge_from_id_strings_non_existing_nodes():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
with pytest.raises(AssertionError):
graph.add_single_edge(doc0.id,
doc1.id,
features={'text': 'I connect Doc0 and Doc1'})
def test_undirected_graph():
graph = GraphDocument()
assert graph.undirected is False
undirected_graph = GraphDocument(force_undirected=True)
assert undirected_graph.undirected is True
graph_from_undirected_no_force = GraphDocument(undirected_graph)
assert graph_from_undirected_no_force.undirected is True
graph_from_undirected_proto_no_force = GraphDocument(
undirected_graph.proto)
assert graph_from_undirected_proto_no_force.undirected is True
def test_from_dgl_graph_without_edges():
from dgl import DGLGraph
dummy_graph = DGLGraph()
dummy_graph.add_nodes(2)
jina_graph = GraphDocument.load_from_dgl_graph(dummy_graph)
assert jina_graph.num_nodes == 2
def test_from_dgl_graph(graph):
dgl_graph = graph.to_dgl_graph()
jina_graph = GraphDocument.load_from_dgl_graph(dgl_graph)
assert graph.num_nodes == jina_graph.num_nodes
assert graph.num_edges == jina_graph.num_edges
assert (graph.adjacency.col == jina_graph.adjacency.col).all()
assert (graph.adjacency.col == jina_graph.adjacency.col).all()
def node_and_graph_encode(self, docs: DocumentArray, **kwargs):
"""
This executor is going to add for each node an embedding computed as the sum of outgoing and incoming edges.
Then is going to assign a graph embedding as the sum of the embeddings of all its nodes multiplied by the `feature` weight of each edge.
.. # noqa: DAR201
:param docs: Array of GraphDocuments
"""
for doc in docs:
graph = GraphDocument(doc)
for node in graph.nodes:
node.embedding = np.array(
[graph.get_out_degree(node) + graph.get_in_degree(node)])
sum = 0
for node in graph.nodes:
node_embedding = node.embedding[0]
for out_node in graph.get_outgoing_nodes(node):
node_embedding = (
node_embedding *
graph.edge_features[f'{node.id}-{out_node.id}']
['weight'])
for in_node in graph.get_incoming_nodes(node):
node_embedding = (
node_embedding *
graph.edge_features[f'{in_node.id}-{node.id}']
['weight'])
sum += node_embedding
graph.embedding = np.array([sum])
def graph():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_single_edge(doc0, doc1, features={'weight': 1})
graph.add_single_edge(doc0, doc2, features={'weight': 1})
graph.add_single_edge(doc2, doc1, features={'weight': 10})
graph.add_single_edge(doc1, doc3, features={'weight': 1})
graph.add_single_edge(doc2, doc3, features={'weight': 1})
return graph
def test_add_multiple_edges_from_string():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_nodes([doc0, doc1, doc2, doc3])
graph.add_edges(
[doc0.id, doc0.id, doc2.id, doc1.id, doc2.id],
[doc1.id, doc2.id, doc1.id, doc3.id, doc3.id],
edge_features=[
{
'text': 'I connect Doc0 and Doc1'
},
{
'text': 'I connect Doc0 and Doc2'
},
{
'text': 'I connect Doc2 and Doc1'
},
{
'text': 'I connect Doc1 and Doc3'
},
{
'text': 'I connect Doc2 and Doc3'
},
],
)
validate_graph(graph)
def graph():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_edge(doc0, doc1, features={'text': 'I connect Doc0 and Doc1'})
graph.add_edge(doc0, doc2, features={'text': 'I connect Doc0 and Doc2'})
graph.add_edge(doc2, doc1, features={'text': 'I connect Doc2 and Doc1'})
graph.add_edge(doc1, doc3, features={'text': 'I connect Doc1 and Doc3'})
graph.add_edge(doc2, doc3, features={'text': 'I connect Doc2 and Doc3'})
return graph
def test_undirected_graph_to_dgl(graph):
dgl_graph = graph.to_dgl_graph()
dgl_adj_coo = dgl_graph.adjacency_matrix(scipy_fmt='coo')
assert dgl_graph.num_nodes() == graph.num_nodes
assert dgl_graph.num_edges() == graph.num_edges
assert (graph.adjacency.row == dgl_adj_coo.row).all()
assert (graph.adjacency.col == dgl_adj_coo.col).all()
undirected_graph = GraphDocument(graph, force_undirected=True)
dgl_undirected_graph = undirected_graph.to_dgl_graph()
dgl_undirected_adj_coo = dgl_undirected_graph.adjacency_matrix(
scipy_fmt='coo')
assert dgl_undirected_graph.num_nodes() == graph.num_nodes
assert dgl_undirected_graph.num_edges() == graph.num_edges * 2
assert (np.concatenate(
(undirected_graph.adjacency.row,
undirected_graph.adjacency.col)) == dgl_undirected_adj_coo.row).all()
assert (np.concatenate(
(undirected_graph.adjacency.col,
undirected_graph.adjacency.row)) == dgl_undirected_adj_coo.col).all()
def test_remove_single_node_from_string_non_existing():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
graph.add_node(doc0)
assert graph.num_nodes == 1
graph.remove_single_node(doc1.id)
assert graph.num_nodes == 1
def test_remove_single_node_from_string():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_single_node(doc0)
graph.add_single_node(doc1)
graph.add_single_node(doc2)
graph.add_single_node(doc3)
assert len(graph.nodes) == 4
assert doc0.id in graph.nodes
graph.remove_single_node(doc0.id)
assert len(graph.nodes) == 3
assert doc0.id not in graph.nodes
def validate_resp(resp):
assert len(resp.data.docs) == 1
for doc in resp.data.docs:
graph = GraphDocument(doc)
assert graph.embedding[0] == 64
assert len(graph.nodes) == 4
for i, node in enumerate(graph.nodes):
if i == 0:
assert node.embedding[0] == 2
if i == 1:
assert node.embedding[0] == 3
if i == 2:
assert node.embedding[0] == 3
if i == 3:
assert node.embedding[0] == 2
def test_add_remove_node_deprecated():
graph = GraphDocument()
d1 = Document(id='1')
d2 = Document(id='2')
graph.add_node(d1)
graph.add_node(d2)
assert len(graph.nodes) == 2
graph.remove_node(d1)
graph.remove_node(d2)
assert len(graph.nodes) == 0
def test_add_remove_edge_deprecated():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
graph.add_edge(doc0, doc1, features={'text': 'I connect Doc0 and Doc1'})
assert graph.num_nodes == 2
assert graph.num_edges == 1
graph.remove_edge(doc0, doc1)
assert graph.num_nodes == 2
assert graph.num_edges == 0
def test_remove_single_edge_from_string():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_nodes([doc0, doc1, doc2, doc3])
graph.add_single_edge(doc0.id,
doc1.id,
features={'text': 'I connect Doc0 and Doc1'})
graph.add_single_edge(doc0.id,
doc2.id,
features={'text': 'I connect Doc0 and Doc2'})
graph.add_single_edge(doc2.id,
doc1.id,
features={'text': 'I connect Doc2 and Doc1'})
graph.add_single_edge(doc1.id,
doc3.id,
features={'text': 'I connect Doc1 and Doc3'})
graph.add_single_edge(doc2.id,
doc3.id,
features={'text': 'I connect Doc2 and Doc3'})
assert graph.num_nodes == 4
assert graph.num_edges == 5
graph.remove_single_edge(doc0.id, doc1.id)
assert graph.num_nodes == 4
assert graph.num_edges == 4
def test_add_single_edge_from_id_strings():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_nodes([doc0, doc1, doc2, doc3])
graph.add_single_edge(doc0.id,
doc1.id,
features={'text': 'I connect Doc0 and Doc1'})
graph.add_single_edge(doc0.id,
doc2.id,
features={'text': 'I connect Doc0 and Doc2'})
graph.add_single_edge(doc2.id,
doc1.id,
features={'text': 'I connect Doc2 and Doc1'})
graph.add_single_edge(doc1.id,
doc3.id,
features={'text': 'I connect Doc1 and Doc3'})
graph.add_single_edge(doc2.id,
doc3.id,
features={'text': 'I connect Doc2 and Doc3'})
validate_graph(graph)
dgl_undirected_adj_coo = dgl_undirected_graph.adjacency_matrix(
scipy_fmt='coo')
assert dgl_undirected_graph.num_nodes() == graph.num_nodes
assert dgl_undirected_graph.num_edges() == graph.num_edges * 2
assert (np.concatenate(
(undirected_graph.adjacency.row,
undirected_graph.adjacency.col)) == dgl_undirected_adj_coo.row).all()
assert (np.concatenate(
(undirected_graph.adjacency.col,
undirected_graph.adjacency.row)) == dgl_undirected_adj_coo.col).all()
@pytest.mark.parametrize(
'graph, expected_output',
[(GraphDocument(force_undirected=True), 1), (GraphDocument(), 2)],
)
def test_graph_edge_behaviour_creation(graph, expected_output):
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
graph.add_single_edge(doc0, doc1)
graph.add_single_edge(doc1, doc0)
assert graph.num_edges == expected_output
@pytest.mark.parametrize(
'graph, expected_output',
[(GraphDocument(force_undirected=True), 1), (GraphDocument(), 2)],
)
def test_graph_add_multiple_edges():
graph = GraphDocument()
doc0 = Document(text='Document0')
doc1 = Document(text='Document1')
doc2 = Document(text='Document2')
doc3 = Document(text='Document3')
graph.add_edges(
[doc0, doc0, doc2, doc1, doc2],
[doc1, doc2, doc1, doc3, doc3],
edge_features=[
{
'text': 'I connect Doc0 and Doc1'
},
{
'text': 'I connect Doc0 and Doc2'
},
{
'text': 'I connect Doc2 and Doc1'
},
{
'text': 'I connect Doc1 and Doc3'
},
{
'text': 'I connect Doc2 and Doc3'
},
],
)
assert graph.num_nodes == 4
assert graph.num_edges == 5
doc0 = graph.chunks[0]
assert doc0.text == 'Document0'
doc1 = graph.chunks[1]
assert doc1.text == 'Document1'
doc2 = graph.chunks[2]
assert doc2.text == 'Document2'
doc3 = graph.chunks[3]
assert doc3.text == 'Document3'
edge_features = graph.edge_features
for i, (d1, d2) in enumerate(graph):
if i == 0:
assert (edge_features[f'{d1.id}-{d2.id}']['text'] ==
'I connect Doc0 and Doc1')
assert d1.text == 'Document0'
assert d2.text == 'Document1'
if i == 1:
assert (edge_features[f'{d1.id}-{d2.id}']['text'] ==
'I connect Doc0 and Doc2')
assert d1.text == 'Document0'
assert d2.text == 'Document2'
if i == 2:
assert (edge_features[f'{d1.id}-{d2.id}']['text'] ==
'I connect Doc2 and Doc1')
assert d1.text == 'Document2'
assert d2.text == 'Document1'
if i == 3:
assert (edge_features[f'{d1.id}-{d2.id}']['text'] ==
'I connect Doc1 and Doc3')
assert d1.text == 'Document1'
assert d2.text == 'Document3'
if i == 4:
assert (edge_features[f'{d1.id}-{d2.id}']['text'] ==
'I connect Doc2 and Doc3')
assert d1.text == 'Document2'
assert d2.text == 'Document3'
def test_graph_document_from_graph(graph):
graph2 = GraphDocument(graph)
validate_graph(graph2)
def test_graph_document_from_proto(graph):
graph2 = GraphDocument(graph._pb_body)
validate_graph(graph2)
def test_validate_iteration_graph_without_edges():
graph = GraphDocument()
assert len([x for x in graph]) == 0
