selenocysteine conversion about metadome HOT 6 CLOSED

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ERROR: test_three_letter_amino_acid_residue_pyrrolysine (tests.unit.domain.models.entities.test_codon.Test_codon)
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Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/ext/declarative/clsregistry.py", line 281, in __call__
    x = eval(self.arg, globals(), self._dict)
  File "<string>", line 1, in <module>
NameError: name 'Protein' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/tests/unit/domain/models/entities/test_codon.py", line 26, in test_three_letter_amino_acid_residue_pyrrolysine
    _mappings.append(Mapping(base_pair='T', codon='TAG', codon_base_pair_position=0, amino_acid_residue='U', cDNA_position=1, chromosome_position=1))
  File "<string>", line 2, in __init__
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/instrumentation.py", line 347, in _new_state_if_none
    state = self._state_constructor(instance, self)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/langhelpers.py", line 767, in __get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/instrumentation.py", line 177, in _state_constructor
    self.dispatch.first_init(self, self.class_)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/event/attr.py", line 256, in __call__
    fn(*args, **kw)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/mapper.py", line 2983, in _event_on_first_init
    configure_mappers()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/mapper.py", line 2873, in configure_mappers
    mapper._post_configure_properties()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/mapper.py", line 1766, in _post_configure_properties
    prop.init()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/interfaces.py", line 184, in init
    self.do_init()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/relationships.py", line 1653, in do_init
    self._process_dependent_arguments()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/relationships.py", line 1710, in _process_dependent_arguments
    self.target = self.mapper.mapped_table
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/langhelpers.py", line 767, in __get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/relationships.py", line 1626, in mapper
    argument = self.argument()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/ext/declarative/clsregistry.py", line 293, in __call__
    (self.prop.parent, self.arg, n.args[0], self.cls)
sqlalchemy.exc.InvalidRequestError: When initializing mapper Mapper|Mapping|mappings, expression 'Protein' failed to locate a name ("name 'Protein' is not defined"). If this is a class name, consider adding this relationship() to the <class 'metadome.domain.models.mapping.Mapping'> class after both dependent classes have been defined.

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ERROR: test_three_letter_amino_acid_residue_selenocysteine (tests.unit.domain.models.entities.test_codon.Test_codon)
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Traceback (most recent call last):
  File "/usr/src/app/tests/unit/domain/models/entities/test_codon.py", line 15, in test_three_letter_amino_acid_residue_selenocysteine
    _mappings.append(Mapping(base_pair='T', codon='TGA', codon_base_pair_position=0, amino_acid_residue='U', cDNA_position=1, chromosome_position=1))
  File "<string>", line 2, in __init__
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/instrumentation.py", line 347, in _new_state_if_none
    state = self._state_constructor(instance, self)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/langhelpers.py", line 767, in __get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/instrumentation.py", line 177, in _state_constructor
    self.dispatch.first_init(self, self.class_)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/event/attr.py", line 256, in __call__
    fn(*args, **kw)
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/mapper.py", line 2983, in _event_on_first_init
    configure_mappers()
  File "/usr/local/lib/python3.5/site-packages/sqlalchemy/orm/mapper.py", line 2870, in configure_mappers
    raise e
sqlalchemy.exc.InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Triggering mapper: 'Mapper|Mapping|mappings'. Original exception was: When initializing mapper Mapper|Mapping|mappings, expression 'Protein' failed to locate a name ("name 'Protein' is not defined"). If this is a class name, consider adding this relationship() to the <class 'metadome.domain.models.mapping.Mapping'> class after both dependent classes have been defined.

./run_tests.sh -t tests/unit/domain/models/entities/test_codon.py

docker-compose -f docker-compose.yml -f docker-compose-dev.yml run --no-deps --rm celery nosetests -v -a !disabled --with-coverage --cover-inclusive --cover-package metadome tests/unit/domain/models/entities/test_codon.py