<commit_before>from sqlalchemy import Column, Integer, String, Table, ForeignKey
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship

SQLAlchemyModel = declarative_base()

study_sample_join_table = Table("current_study_sample", SQLAlchemyModel.metadata,
    Column("sample_internal_id", Integer, ForeignKey("current_samples.internal_id")),
    Column("study_internal_id", Integer, ForeignKey("current_studies.internal_id"))
)

class SQLAlchemyNamedModel(SQLAlchemyModel):
    __abstract__ = True
    name = Column(String)


class SQLAlchemyInternalIdModel(SQLAlchemyModel):
    __abstract__ = True
    internal_id = Column(Integer, primary_key=True)


class SQLAlchemyAccessionNumberModel(SQLAlchemyModel):
    __abstract__ = True
    accession_number = Column(String)


class SQLAlchemyIsCurrentModel(SQLAlchemyModel):
    __abstract__ = True
    is_current = Column(Integer)


class SQLAlchemySample(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyAccessionNumberModel,
                       SQLAlchemyIsCurrentModel):
    __tablename__ = "current_samples"
    organism = Column(String)
    common_name = Column(String)
    taxon_id = Column(String)
    gender = Column(String)
    ethnicity = Column(String)
    cohort = Column(String)
    country_of_origin = Column(String)
    geographical_region = Column(String)
    studies = relationship("SQLAlchemyStudy", secondary=study_sample_join_table)


class SQLAlchemyStudy(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyAccessionNumberModel,
                      SQLAlchemyIsCurrentModel):
    __tablename__ = "current_studies"
    study_type = Column(String)
    description = Column(String)
    study_title = Column(String)
    study_visibility = Column(String)
    faculty_sponsor = Column(String)
    samples = relationship("SQLAlchemySample", secondary=study_sample_join_table)


class SQLAlchemyLibrary(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyIsCurrentModel):
    __tablename__ = "current_library_tubes"
    library_type = Column(String)


class SQLAlchemyMultiplexedLibrary(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel,
                                   SQLAlchemyIsCurrentModel):
    __tablename__ = "current_multiplexed_library_tubes"


# TODO: doesn"t look like this model name fits the domain very well (Wells?)
class SQLAlchemyWell(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyIsCurrentModel):
    __tablename__ = "current_wells"
<commit_msg>Corrected study-sample join table name (again!).<commit_after>from sqlalchemy import Column, Integer, String, Table, ForeignKey
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship

SQLAlchemyModel = declarative_base()

study_sample_join_table = Table("current_study_samples", SQLAlchemyModel.metadata,
    Column("sample_internal_id", Integer, ForeignKey("current_samples.internal_id")),
    Column("study_internal_id", Integer, ForeignKey("current_studies.internal_id"))
)

class SQLAlchemyNamedModel(SQLAlchemyModel):
    __abstract__ = True
    name = Column(String)


class SQLAlchemyInternalIdModel(SQLAlchemyModel):
    __abstract__ = True
    internal_id = Column(Integer, primary_key=True)


class SQLAlchemyAccessionNumberModel(SQLAlchemyModel):
    __abstract__ = True
    accession_number = Column(String)


class SQLAlchemyIsCurrentModel(SQLAlchemyModel):
    __abstract__ = True
    is_current = Column(Integer)


class SQLAlchemySample(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyAccessionNumberModel,
                       SQLAlchemyIsCurrentModel):
    __tablename__ = "current_samples"
    organism = Column(String)
    common_name = Column(String)
    taxon_id = Column(String)
    gender = Column(String)
    ethnicity = Column(String)
    cohort = Column(String)
    country_of_origin = Column(String)
    geographical_region = Column(String)
    studies = relationship("SQLAlchemyStudy", secondary=study_sample_join_table)


class SQLAlchemyStudy(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyAccessionNumberModel,
                      SQLAlchemyIsCurrentModel):
    __tablename__ = "current_studies"
    study_type = Column(String)
    description = Column(String)
    study_title = Column(String)
    study_visibility = Column(String)
    faculty_sponsor = Column(String)
    samples = relationship("SQLAlchemySample", secondary=study_sample_join_table)


class SQLAlchemyLibrary(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyIsCurrentModel):
    __tablename__ = "current_library_tubes"
    library_type = Column(String)


class SQLAlchemyMultiplexedLibrary(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel,
                                   SQLAlchemyIsCurrentModel):
    __tablename__ = "current_multiplexed_library_tubes"


class SQLAlchemyWell(SQLAlchemyNamedModel, SQLAlchemyInternalIdModel, SQLAlchemyIsCurrentModel):
    __tablename__ = "current_wells"
{'fraction_non_alphanumeric': 0.071285140562249, 'fraction_numerical': 0.0, 'mean_word_length': 5.394094993581515, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6880189', 'n_tokens_mistral': 1539, 'n_tokens_neox': 1420, 'n_words': 254}