Python Sqlalchemy mysql “Cannot add or update a child row: a foreign key constraint fails”

Question

I'm trying to create a simple realtional database using sqlalchemy and mysql. I'm not sure what I'm doing wrong, although I think it could be something to do with the way I'm adding the rows to the table. My models are below and the code that creates all the entries below that.

This is the error I'm getting:

2014-03-12 14:53:52,109 INFO sqlalchemy.engine.base.Engine BEGIN (implicit)
INFO:sqlalchemy.engine.base.Engine:BEGIN (implicit)
2014-03-12 14:53:52,139 INFO sqlalchemy.engine.base.Engine INSERT INTO accession_numbers (accession_number, gene) VALUES (%s, %s)
INFO:sqlalchemy.engine.base.Engine:INSERT INTO accession_numbers (accession_number, gene) VALUES (%s, %s)
2014-03-12 14:53:52,140 INFO sqlalchemy.engine.base.Engine (('AB009589', <__main__.Gene object at 0xe8ba090>), ('AB014887', <__main__.Gene object at 0xe220890>), ('AB019534', <__main__.Gene object at 0xe8baf10>), ('AB038490', <__main__.Gene object at 0xe8b8150>), ('AB046409', <__main__.Gene object at 0xe8b86d0>), ('AB051625', <__main__.Gene object at 0xe8b8c50>), ('AB051627', <__main__.Gene object at 0xe8b8ed0>), ('AB060808', <__main__.Gene object at 0xe8dd110>)  ... displaying 10 of 1317 total bound parameter sets ...  ('EU266531', <__main__.Gene object at 0x15093b50>), ('EU286279', <__main__.Gene object at 0x15093cd0>))
INFO:sqlalchemy.engine.base.Engine:(('AB009589', <__main__.Gene object at 0xe8ba090>), ('AB014887', <__main__.Gene object at 0xe220890>), ('AB019534', <__main__.Gene object at 0xe8baf10>), ('AB038490', <__main__.Gene object at 0xe8b8150>), ('AB046409', <__main__.Gene object at 0xe8b86d0>), ('AB051625', <__main__.Gene object at 0xe8b8c50>), ('AB051627', <__main__.Gene object at 0xe8b8ed0>), ('AB060808', <__main__.Gene object at 0xe8dd110>)  ... displaying 10 of 1317 total bound parameter sets ...  ('EU266531', <__main__.Gene object at 0x15093b50>), ('EU286279', <__main__.Gene object at 0x15093cd0>))
2014-03-12 14:53:52,143 INFO sqlalchemy.engine.base.Engine ROLLBACK
INFO:sqlalchemy.engine.base.Engine:ROLLBACK
---------------------------------------------------------------------------
IntegrityError                            Traceback (most recent call last)
<ipython-input-17-96f4786cad50> in <module>()
     29         session.add(acc)
     30 
---> 31 session.commit()

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
    719                 raise sa_exc.InvalidRequestError("No transaction is begun.")
    720 
--> 721         self.transaction.commit()
    722 
    723     def prepare(self):

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
    352         self._assert_active(prepared_ok=True)
    353         if self._state is not PREPARED:
--> 354             self._prepare_impl()
    355 
    356         if self._parent is None or self.nested:

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in _prepare_impl(self)
    332                 if self.session._is_clean():
    333                     break
--> 334                 self.session.flush()
    335             else:
    336                 raise exc.FlushError(

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in flush(self, objects)
   1822         try:
   1823             self._flushing = True
-> 1824             self._flush(objects)
   1825         finally:
   1826             self._flushing = False

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
   1940         except:
   1941             with util.safe_reraise():
-> 1942                 transaction.rollback(_capture_exception=True)
   1943 
   1944     def is_modified(self, instance, include_collections=True,

/usr/lib64/python2.7/site-packages/sqlalchemy/util/langhelpers.pyc in __exit__(self, type_, value, traceback)
     56             exc_type, exc_value, exc_tb = self._exc_info
     57             self._exc_info = None   # remove potential circular references
---> 58             compat.reraise(exc_type, exc_value, exc_tb)
     59         else:
     60             self._exc_info = None   # remove potential circular references

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
   1904             self._warn_on_events = True
   1905             try:
-> 1906                 flush_context.execute()
   1907             finally:
   1908                 self._warn_on_events = False

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self)
    370                                     self.dependencies,
    371                                     postsort_actions):
--> 372                 rec.execute(self)
    373 
    374     def finalize_flush_changes(self):

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self, uow)
    523         persistence.save_obj(self.mapper,
    524             uow.states_for_mapper_hierarchy(self.mapper, False, False),
--> 525             uow
    526         )
    527 

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/persistence.pyc in save_obj(base_mapper, states, uowtransaction, single)
     62             _emit_insert_statements(base_mapper, uowtransaction,
     63                                     cached_connections,
---> 64                                     table, insert)
     65 
     66     _finalize_insert_update_commands(base_mapper, uowtransaction,

/usr/lib64/python2.7/site-packages/sqlalchemy/orm/persistence.pyc in _emit_insert_statements(base_mapper, uowtransaction, cached_connections, table, insert)
    539             multiparams = [rec[2] for rec in records]
    540             c = cached_connections[connection].\
--> 541                                 execute(statement, multiparams)
    542 
    543             for (state, state_dict, params, mapper,

/usr/lib64/python2.7/site-packages/sqlalchemy/engine/base.pyc in execute(self, object, *multiparams, **params)
    660                                                 object,
    661                                                 multiparams,
--> 662                                                 params)
    663         else:
    664             raise exc.InvalidRequestError(

/usr/lib64/python2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_clauseelement(self, elem, multiparams, params)
    759             compiled_sql,
    760             distilled_params,
--> 761             compiled_sql, distilled_params
    762         )
    763         if self._has_events:

/usr/lib64/python2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
    872                                 parameters,
    873                                 cursor,
--> 874                                 context)
    875 
    876         if self._has_events:

/usr/lib64/python2.7/site-packages/sqlalchemy/engine/base.pyc in _handle_dbapi_exception(self, e, statement, parameters, cursor, context)
   1022                                         self.dialect.dbapi.Error,
   1023                                         connection_invalidated=self._is_disconnect),
-> 1024                                     exc_info
   1025                                 )
   1026 

/usr/lib64/python2.7/site-packages/sqlalchemy/util/compat.pyc in raise_from_cause(exception, exc_info)
    194         # the code line where the issue occurred
    195         exc_type, exc_value, exc_tb = exc_info
--> 196         reraise(type(exception), exception, tb=exc_tb)
    197 
    198 

/usr/lib64/python2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
    854                                     statement,
    855                                     parameters,
--> 856                                     context)
    857             elif not parameters and context.no_parameters:
    858                 self.dialect.do_execute_no_params(

/usr/lib64/python2.7/site-packages/sqlalchemy/connectors/mysqldb.pyc in do_executemany(self, cursor, statement, parameters, context)
     58 
     59     def do_executemany(self, cursor, statement, parameters, context=None):
---> 60         rowcount = cursor.executemany(statement, parameters)
     61         if context is not None:
     62             context._rowcount = rowcount

/usr/lib64/python2.7/site-packages/MySQLdb/cursors.pyc in executemany(self, query, args)
    204             r = 0
    205             for a in args:
--> 206                 r = r + self.execute(query, a)
    207             return r
    208         p = m.start(1)

/usr/lib64/python2.7/site-packages/MySQLdb/cursors.pyc in execute(self, query, args)
    172             del tb
    173             self.messages.append((exc, value))
--> 174             self.errorhandler(self, exc, value)
    175         self._executed = query
    176         if not self._defer_warnings: self._warning_check()

/usr/lib64/python2.7/site-packages/MySQLdb/connections.pyc in defaulterrorhandler(***failed resolving arguments***)
     34     del cursor
     35     del connection
---> 36     raise errorclass, errorvalue
     37 
     38 re_numeric_part = re.compile(r"^(\d+)")

IntegrityError: (IntegrityError) (1452, 'Cannot add or update a child row: a foreign key constraint fails (`chromo9`.`accession_numbers`, CONSTRAINT `accession_numbers_ibfk_1` FOREIGN KEY (`gene`) REFERENCES `genes` (`gene_identifier`))') 'INSERT INTO accession_numbers (accession_number, gene) VALUES (%s, %s)' (('AB009589', <__main__.Gene object at 0xe8ba090>), ('AB014887', <__main__.Gene object at 0xe220890>), ('AB019534', <__main__.Gene object at 0xe8baf10>), ('AB038490', <__main__.Gene object at 0xe8b8150>), ('AB046409', <__main__.Gene object at 0xe8b86d0>), ('AB051625', <__main__.Gene object at 0xe8b8c50>), ('AB051627', <__main__.Gene object at 0xe8b8ed0>), ('AB060808', <__main__.Gene object at 0xe8dd110>)  ... displaying 10 of 1317 total bound parameter sets ...  ('EU266531', <__main__.Gene object at 0x15093b50>), ('EU286279', <__main__.Gene object at 0x15093cd0>))

my models:

from sqlalchemy import create_engine
from sqlalchemy import Column, Integer, String, Text
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy import ForeignKey
from sqlalchemy.orm import sessionmaker

SETTINGS = {
            'DB':{
                  'USER':'root',
                  'LOCATION':'localhost',
                  'PORT':'3306',
                  'DATABASE_NAME':'chromo9',
                  },
            }

class Settings:
    def __init__(self, **attrs):
        for key, value in attrs.iteritems():
            if type(value) is dict:
                attrs[key] = Settings(**value)
        self.__dict__.update(attrs)

SETTINGS = Settings(**SETTINGS)

if not hasattr(SETTINGS.DB, 'PASSWD'):
    SETTINGS.DB.PASSWD = raw_input('Enter passwd for mysql user {}'.format(SETTINGS.DB.USER))

conn_string = 'mysql+mysqldb://{user}:{passwd}@{location}:{port}'.format(
                                            user = SETTINGS.DB.USER,
                                            passwd = SETTINGS.DB.PASSWD,
                                            location = SETTINGS.DB.LOCATION,
                                            port = SETTINGS.DB.PORT,
                                                                         )
#engine = create_engine('sqlite:///:memory:', )#echo=True)
engine = create_engine(conn_string, echo=True)
engine.execute('CREATE DATABASE IF NOT EXISTS {}'.format(SETTINGS.DB.DATABASE_NAME))
engine.execute('USE {}'.format(SETTINGS.DB.DATABASE_NAME))

Base = declarative_base()

class Gene(Base):
    __tablename__ = 'genes'

    gene_identifier= Column(Integer, primary_key=True)
    nucleotide_sequence = Column(Text)
    chromosome_location = Column(String(8))    


class Accession(Base):
    __tablename__ = 'accession_numbers'

    accession_number = Column(String(8), primary_key=True)
    gene = Column(Integer, ForeignKey('genes.gene_identifier'))


class Exon(Base):
    __tablename__ = 'exons'

    id = Column(Integer, primary_key=True)
    start = Column(Integer)
    end = Column(Integer)
    gene = Column(Integer, ForeignKey('genes.gene_identifier'))


class Protein(Base):
    __tablename__ = 'proteins'

    id = Column(Integer, primary_key=True)    
    name = Column(String(128))
    sequence = Column(Text)
    gene = Column(Integer, ForeignKey('genes.gene_identifier'))


Base.metadata.create_all(engine) # create the tables

Creating all the objects:

Session = sessionmaker(bind=engine)
session = Session()

for record in records:
    gene = Gene(gene_identifier=record.gi ,nucleotide_sequence=record.sequence ,chromosome_location=record.locus)
    session.add(gene)

    for feature in record.features:

        if feature.key == 'CDS':
            translation, name  = None, None
            for qualifier in feature.qualifiers:
                if qualifier.key == '/translation=':
                    translation = qualifier.value
                if qualifier.key == '/product=':
                    name = qualifier.value
            # create protein object
            protein = Protein(name=name, sequence=translation, gene=gene)
            session.add(protein)

        if feature.key == 'exon':
            start, end = feature.location.split('..')
            start, end = int(''.join([d for d in start if d.isdigit()])), int(''.join([d for d in end if d.isdigit()]))
            exon = Exon(start=start,end=end,gene=gene)
            session.add(exon)

    for accession in record.accession:
        acc = Accession(accession_number=accession, gene=gene)
        session.add(acc)

session.commit()

Answer 1

There was a lot to look through, so I'm sure I missed something, but since I'm not sure how much you know about the database you're working with, I'll start with this and hope it helps:

It looks like you're trying to insert an Accession that references a Gene that doesn't exist. That's the Foreign Key that it's complaining about. It looks like you try to create the Gene and the Accession in the same session. You might need to call session.commit() after creating the Gene (and any other objects that are relied upon by later updates). That will put the Gene in the DB, which can then be referenced by the Accession.

That's a bit of a shot in the dark, as I'm not familiar with SQLAlchemy (and have no idea what an Accession is). I'm just relying on my knowledge of SQL here. But the issue is definitely getting any rows into the gene table BEFORE rows in tables that rely on the gene table are inserted.