$ bio2bel_excape populate --reset
Deleting the previous instance of the database
Creating new models
2019-03-02 11:22:31,882 - bio2bel.downloading - INFO - downloading https://zenodo.org/record/173258/files/pubchem.chembl.dataset4publication_inchi_smiles.tsv.xz?download=1 to /Users/cthoyt/.bio2bel/excape/pubchem.chembl.dataset4publication_inchi_smiles.tsv.xz
35it [55:24, 98.78s/it] Traceback (most recent call last):
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1236, in _execute_context
cursor, statement, parameters, context
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 536, in do_execute
cursor.execute(statement, parameters)
psycopg2.IntegrityError: duplicate key value violates unique constraint "excape_interaction_chemical_id_target_id_db_assay_id_key"
DETAIL: Key (chemical_id, target_id, db, assay_id)=(50238, 16, chembl20, 845169) already exists.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/manager/abstract_manager.py", line 38, in populate_wrapped
cls._populate_original(self, *populate_args, **populate_kwargs)
File "/Users/cthoyt/dev/excape/src/bio2bel_excape/manager.py", line 71, in populate
self.session.commit()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/scoping.py", line 162, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1023, in commit
self.transaction.commit()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 487, in commit
self._prepare_impl()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 466, in _prepare_impl
self.session.flush()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2446, in flush
self._flush(objects)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2584, in _flush
transaction.rollback(_capture_exception=True)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 67, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 277, in reraise
raise value
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2544, in _flush
flush_context.execute()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 416, in execute
rec.execute(self)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 583, in execute
uow,
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj
insert,
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1116, in _emit_insert_statements
statement, params
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 980, in execute
return meth(self, multiparams, params)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 273, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1099, in _execute_clauseelement
distilled_params,
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1240, in _execute_context
e, statement, parameters, cursor, context
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1458, in _handle_dbapi_exception
util.raise_from_cause(sqlalchemy_exception, exc_info)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 296, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 276, in reraise
raise value.with_traceback(tb)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1236, in _execute_context
cursor, statement, parameters, context
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 536, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "excape_interaction_chemical_id_target_id_db_assay_id_key"
DETAIL: Key (chemical_id, target_id, db, assay_id)=(50238, 16, chembl20, 845169) already exists.
[SQL: 'INSERT INTO excape_interaction (chemical_id, target_id, db, assay_id, pxc50, activity_flag) VALUES (%(chemical_id)s, %(target_id)s, %(db)s, %(assay_id)s, %(pxc50)s, %(activity_flag)s) RETURNING excape_interaction.id'] [parameters: {'chemical_id': 50238, 'target_id': 16, 'db': 'chembl20', 'assay_id': 845169, 'pxc50': 5.99, 'activity_flag': 'A'}] (Background on this error at: http://sqlalche.me/e/gkpj)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/cthoyt/.virtualenvs/hbp/bin/bio2bel_excape", line 11, in <module>
load_entry_point('bio2bel-excape', 'console_scripts', 'bio2bel_excape')()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/decorators.py", line 27, in new_func
return f(get_current_context().obj, *args, **kwargs)
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/manager/abstract_manager.py", line 320, in populate
manager.populate()
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/manager/abstract_manager.py", line 40, in populate_wrapped
self._store_populate_failed()
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/manager/connection_manager.py", line 93, in _store_populate_failed
Action.store_populate_failed(self.module_name, session=self.session)
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/models.py", line 95, in store_populate_failed
_store_helper(action, session=session)
File "/Users/cthoyt/dev/bio2bel/src/bio2bel/models.py", line 140, in _store_helper
session.commit()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/scoping.py", line 162, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1023, in commit
self.transaction.commit()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 485, in commit
self._assert_active(prepared_ok=True)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 288, in _assert_active
% self._rollback_exception
sqlalchemy.exc.InvalidRequestError: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: (psycopg2.IntegrityError) duplicate key value violates unique constraint "excape_interaction_chemical_id_target_id_db_assay_id_key"
DETAIL: Key (chemical_id, target_id, db, assay_id)=(50238, 16, chembl20, 845169) already exists.
[SQL: 'INSERT INTO excape_interaction (chemical_id, target_id, db, assay_id, pxc50, activity_flag) VALUES (%(chemical_id)s, %(target_id)s, %(db)s, %(assay_id)s, %(pxc50)s, %(activity_flag)s) RETURNING excape_interaction.id'] [parameters: {'chemical_id': 50238, 'target_id': 16, 'db': 'chembl20', 'assay_id': 845169, 'pxc50': 5.99, 'activity_flag': 'A'}] (Background on this error at: http://sqlalche.me/e/gkpj)
