def __init__(self,
graph=None,
host=None,
ports=None,
username=None,
password=None,
**args):
super(NeoTransformer, self).__init__(graph)
self.http_driver = None
if ports is None:
# read from config
with open('config.yml', 'r') as ymlfile:
cfg = yaml.load(ymlfile)
if 'http_port' in cfg['neo4j']:
http_uri = "http://{}:{}".format(cfg['neo4j']['host'],
cfg['neo4j']['http_port'])
logging.debug(
"Initializing http driver with URI: {}".format(
http_uri))
self.http_driver = http_gdb(http_uri,
username=username,
password=password)
else:
if 'http' in ports:
http_uri = "http://{}:{}".format(host, ports['http'])
self.http_driver = http_gdb(http_uri,
username=username,
password=password)
def __init__(self,
graph: nx.MultiDiGraph = None,
uri: str = None,
username: str = None,
password: str = None):
"""
Initialize an instance of NeoTransformer.
"""
super(NeoTransformer, self).__init__(graph)
self.http_driver = None
self.http_driver = http_gdb(uri, username=username, password=password)
def __init__(self,
graph=None,
host=None,
port=None,
username=None,
password=None):
super(NeoTransformer, self).__init__(graph)
self.http_driver = None
http_uri = f'http://{host}:{port}'
self.http_driver = http_gdb(http_uri,
username=username,
password=password)
def test_neo_to_graph_download():
""" downloads a neo4j graph
"""
return
subject_label = 'gene'
object_label = None
edge_type = None
stop_after = 100
output_transformer = JsonTransformer()
G = output_transformer.graph
driver = http_gdb('http://localhost:7474', username='', password='')
subject_label = ':`{}`'.format(subject_label) if isinstance(
subject_label, str) else ''
object_label = ':`{}`'.format(object_label) if isinstance(
object_label, str) else ''
edge_type = ':`{}`'.format(edge_type) if isinstance(edge_type, str) else ''
match = 'match (n{})-[e{}]->(m{})'.format(subject_label, edge_type,
object_label)
results = driver.query('{} return count(*)'.format(match))
print('Using cyper query: {} return n, e, m'.format(match))
for a, in results:
size = a
break
if size == 0:
print('No data available')
quit()
page_size = 1_000
skip_flag = False
for i in range(0, size, page_size):
q = '{} return n, e, m skip {} limit {}'.format(match, i, page_size)
results = driver.query(q)
for n, e, m in results:
subject_attr = n['data']
object_attr = m['data']
edge_attr = e['data']
if 'id' not in subject_attr or 'id' not in object_attr:
if not skip_flag:
print('Skipping records that have no id attribute')
skip_flag = True
continue
s = subject_attr['id']
o = object_attr['id']
if 'edge_label' not in edge_attr:
edge_attr['edge_label'] = e['metadata']['type']
if 'category' not in subject_attr:
subject_attr['category'] = n['metadata']['labels']
if 'category' not in object_attr:
object_attr['category'] = m['metadata']['labels']
if s not in G:
G.add_node(s, **subject_attr)
if o not in G:
G.add_node(o, **object_attr)
G.add_edge(s, o, key=edge_attr['edge_label'], **edge_attr)
if stop_after is not None and G.number_of_edges() > stop_after:
break
def neo4j_download(config: dict, address: str, username: str, password: str,
output: str, output_type: str, subject_label: str,
object_label: str, edge_label: str, directed: bool,
page_size: int, stop_after: int):
"""
Download nodes and edges from Neo4j database.
\f
Parameters
----------
config: dict
A dictionary containing the configuration for kgx.cli
address: str
The full HTTP address for Neo4j database
username: str
Username for authentication
password: str
Password for authentication
output: str
Where to write the output (stdout, by default)
output_type: str
The output type (``csv``, by default)
subject_label: str
The label for subject node in an association
object_label: str
The label for object node in an association
edge_label: str
The label for the edge in an association
directed: bool
Whether or not the edge is supposed to be directed (``true``, by default)
stop_after: int
The max number of edges to fetch
page_size: int
The page size to use while fetching associations from Neo4j (``10000``, by default)
"""
if not is_writable(output):
try:
with open(output, 'w+') as f:
pass
except:
error(f'Cannot write to {output}')
output_transformer = get_transformer(output_type)()
G = output_transformer.graph
driver = http_gdb(address, username=username, password=password)
subject_label = ':`{}`'.format(subject_label) if isinstance(
subject_label, str) else ''
object_label = ':`{}`'.format(object_label) if isinstance(
object_label, str) else ''
edge_label = ':`{}`'.format(edge_label) if isinstance(edge_label,
str) else ''
if directed:
query = 'match (n{})-[e{}]->(m{})'.format(subject_label, edge_label,
object_label)
else:
query = 'match (n{})-[e{}]-(m{})'.format(subject_label, edge_label,
object_label)
results = driver.query('{} return count(*)'.format(query))
size = [x[0] for x in results][0]
print("SIZE: {}".format(size))
if size == 0:
click.echo('No records found.')
return
click.echo('Using cypher query: {} return n, e, m'.format(query))
page_size = 1_000
skip_flag = False
with click.progressbar(
list(range(0, size, page_size)),
label='Downloading {} many edges'.format(size)) as bar:
for i in bar:
q = '{} return n, e, m skip {} limit {}'.format(
query, i, page_size)
results = driver.query(q)
for n, e, m in results:
subject_attr = n['data']
object_attr = m['data']
edge_attr = e['data']
if 'id' not in subject_attr or 'id' not in object_attr:
if not skip_flag:
click.echo(
'Skipping records that have no id attribute')
skip_flag = True
continue
s = subject_attr['id']
o = object_attr['id']
if 'edge_label' not in edge_attr:
edge_attr['edge_label'] = e['metadata']['type']
if 'category' not in subject_attr:
subject_attr['category'] = n['metadata']['labels']
if 'category' not in object_attr:
object_attr['category'] = m['metadata']['labels']
if s not in G:
G.add_node(s, **subject_attr)
if o not in G:
G.add_node(o, **object_attr)
G.add_edge(s, o, key=edge_attr['edge_label'], **edge_attr)
if stop_after is not None and G.number_of_edges() > stop_after:
break
output_transformer.save(output, extension=output_type)
def neo4j_edge_summary(config: dict,
address: str,
username: str,
password: str,
output: str = None):
"""
Get a summary of all the edges in a Neo4j database.
\f
Parameters
----------
config: dict
A dictionary containing the configuration for kgx.cli
address: str
The full HTTP address for Neo4j database
username: str
Username for authentication
password: str
Password for authentication
output: str
Where to write the output (stdout, by default)
"""
if output is not None and not is_writable(output):
error(f'Cannot write to {output}')
http_driver = http_gdb(address, username=username, password=password)
query = """
MATCH (x) RETURN DISTINCT x.category AS category
"""
records = http_driver.query(query)
categories = set()
for record in records:
category = record[0]
if isinstance(category, str):
categories.add(category)
elif isinstance(category, (list, set, tuple)):
categories.update(category)
elif category is None:
continue
else:
error('Unrecognized value for node.category: {}'.format(category))
categories = list(categories)
query = """
MATCH (n)-[r]-(m)
WHERE
(n.category = {category1} OR {category1} IN n.category) AND
(m.category = {category2} OR {category2} IN m.category)
RETURN DISTINCT
{category1} AS subject_category,
{category2} AS object_category,
type(r) AS edge_type,
split(n.id, ':')[0] AS subject_prefix,
split(m.id, ':')[0] AS object_prefix,
COUNT(*) AS frequency
ORDER BY subject_category, object_category, frequency DESC;
"""
combinations = [(c1, c2) for c1 in categories for c2 in categories]
rows = []
with click.progressbar(combinations, length=len(combinations)) as bar:
for category1, category2 in bar:
records = http_driver.query(query,
params={
'category1': category2,
'category2': category2
})
for r in records:
rows.append({
'subject_category': r[0],
'object_category': r[1],
'subject_prefix': r[3],
'object_prefix': r[4],
'frequency': r[5]
})
df = pd.DataFrame(rows)
df = df[[
'subject_category', 'subject_prefix', 'object_category',
'object_prefix', 'frequency'
]]
if output is None:
with pd.option_context('display.max_rows', None, 'display.max_columns',
None):
click.echo(df)
else:
df.to_csv(output, sep='|', header=True)
click.echo('Saved report to {}'.format(output))
def neo4j_node_summary(config: dict,
address: str,
username: str,
password: str,
output: str = None):
"""
Get a summary of all the nodes in a Neo4j database.
\f
Parameters
----------
config: dict
A dictionary containing the configuration for kgx.cli
address: str
The full HTTP address for Neo4j database
username: str
Username for authentication
password: str
Password for authentication
output: str
Where to write the output (stdout, by default)
"""
if output is not None and not is_writable(output):
error(f'Cannot write to {output}')
http_driver = http_gdb(address, username=username, password=password)
query = """
MATCH (x) RETURN DISTINCT x.category AS category
"""
records = http_driver.query(query)
categories = set()
for record in records:
category = record[0]
if isinstance(category, str):
categories.add(category)
elif isinstance(category, (list, set, tuple)):
categories.update(category)
elif category is None:
continue
else:
error('Unrecognized value for node.category: {}'.format(category))
rows = []
with click.progressbar(categories, length=len(categories)) as bar:
for category in bar:
query = f"""
MATCH (x) WHERE x.category = '{category}' OR '{category}' IN x.category
RETURN DISTINCT
'{category}' AS category,
split(x.id, ':')[0] AS prefix,
COUNT(*) AS frequency
ORDER BY category, frequency DESC;
"""
records = http_driver.query(query)
for record in records:
rows.append({
'category': record[0],
'prefix': record[1],
'frequency': record[2]
})
df = pd.DataFrame(rows)
df = df[['category', 'prefix', 'frequency']]
if output is None:
click.echo(df)
else:
df.to_csv(output, sep='|', header=True)
click.echo('Saved report to {}'.format(output))
def neo4j_download(config, page_size, stop_after, subject_label, object_label, edge_type, address, username, password, output, output_type):
if not is_writable(output):
try:
with open(output, 'w+') as f:
pass
except:
error(f'Cannot write to {output}')
output_transformer = get_transformer(get_type(output))()
G = output_transformer.graph
driver = http_gdb(address, username=username, password=password)
subject_label = ':`{}`'.format(subject_label) if isinstance(subject_label, str) else ''
object_label = ':`{}`'.format(object_label) if isinstance(object_label, str) else ''
edge_type = ':`{}`'.format(edge_type) if isinstance(edge_type, str) else ''
match = 'match (n{})-[e{}]->(m{})'.format(subject_label, edge_type, object_label)
results = driver.query('{} return count(*)'.format(match))
click.echo('Using cyper query: {} return n, e, m'.format(match))
for a, in results:
size = a
break
if size == 0:
click.echo('No data available')
quit()
page_size = 1_000
skip_flag = False
with click.progressbar(list(range(0, size, page_size)), label='Downloading {} many edges'.format(size)) as bar:
for i in bar:
q = '{} return n, e, m skip {} limit {}'.format(match, i, page_size)
results = driver.query(q)
for n, e, m in results:
subject_attr = n['data']
object_attr = m['data']
edge_attr = e['data']
if 'id' not in subject_attr or 'id' not in object_attr:
if not skip_flag:
click.echo('Skipping records that have no id attribute')
skip_flag = True
continue
s = subject_attr['id']
o = object_attr['id']
if 'edge_label' not in edge_attr:
edge_attr['edge_label'] = e['metadata']['type']
if 'category' not in subject_attr:
subject_attr['category'] = n['metadata']['labels']
if 'category' not in object_attr:
object_attr['category'] = m['metadata']['labels']
if s not in G:
G.add_node(s, **subject_attr)
if o not in G:
G.add_node(o, **object_attr)
G.add_edge(s, o, key=edge_attr['edge_label'], **edge_attr)
if stop_after is not None and G.number_of_edges() > stop_after:
break
output_transformer.save(output)