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glasgowcompbio / PALS

Ranking metabolite (and other omics sets) by their activity levels via SVD
https://pals.glasgowcompbio.org
MIT License
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Error loading PALS when neo4j user/password is not defined and/or is incorrect #6

Closed RonanDaly closed 4 years ago

RonanDaly commented 4 years ago 
/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/bin/python /Users/ronan/work/PALS/notebooks/PALS_beer_analysis.py
2019-11-22 12:23:44.161 | WARNING  | pals.reactome:get_neo4j_driver:14 - Using a default neo4j server: bolt://localhost:7687
2019-11-22 12:23:44.161 | WARNING  | pals.reactome:get_neo4j_driver:19 - Using a default neo4j username or password: neo4j
2019-11-22 12:23:44.304 | WARNING  | pals.reactome:get_neo4j_driver:27 - Failed to connect to graph database: The client is unauthorized due to authentication failure.
Traceback (most recent call last):
  File "/Users/ronan/work/PALS/notebooks/PALS_beer_analysis.py", line 8, in <module>
    from pals.feature_extraction import DataSource
  File "/Users/ronan/work/PALS/pals/feature_extraction.py", line 8, in <module>
    from .reactome import get_pathway_dict, get_compound_mapping_dict, load_entity_dict, get_protein_entity_dict, \
  File "/Users/ronan/work/PALS/pals/reactome.py", line 31, in <module>
    driver = get_neo4j_driver()
  File "/Users/ronan/work/PALS/pals/reactome.py", line 28, in get_neo4j_driver
    raise e
  File "/Users/ronan/work/PALS/pals/reactome.py", line 23, in get_neo4j_driver
    auth=basic_auth(NEO4J_USER, NEO4J_PASSWORD))
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neo4j/__init__.py", line 120, in driver
    return Driver(uri, **config)
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neo4j/__init__.py", line 161, in __new__
    return subclass(uri, **config)
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neo4j/__init__.py", line 235, in __new__
    pool.release(pool.acquire())
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 719, in acquire
    return self.acquire_direct(self.address)
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 612, in acquire_direct
    connection = self.connector(address, error_handler=self.connection_error_handler)
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neo4j/__init__.py", line 232, in connector
    return connect(address, **dict(config, **kwargs))
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 976, in connect
    raise last_error
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 968, in connect
    connection = _handshake(s, address, der_encoded_server_certificate, **config)
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 930, in _handshake
    connection.init()
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 237, in init
    self.sync()
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 531, in sync
    detail_delta, summary_delta = self.fetch()
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 422, in fetch
    return self._fetch()
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 464, in _fetch
    response.on_failure(summary_metadata or {})
  File "/Users/ronan/.local/share/virtualenvs/PALS-OBSDRA2Y/lib/python3.7/site-packages/neobolt/direct.py", line 778, in on_failure
    raise AuthError(message)
neobolt.exceptions.AuthError: The client is unauthorized due to authentication failure.

Process finished with exit code 1