Bamboost
bamboostindexschema

bamboost.index.schema

Source: https://gitlab.com/cmbm-ethz/bamboost/-/blob/main/bamboost/index_/schema.py

SQLAlchemy Core schema definitions for the BAMBOOST index database.

Attributes

  • metadata=MetaData()
  • collections_table=Table(TABLENAME_COLLECTIONS, metadata, Column('uid', String, primary_key=True), Column('path', String, nullable=False), Column('created_at', DateTime, nullable=True), Column('description', String, nullable=False, default='', server_default=''), Column('tags', JSON, nullable=False, default=list, server_default='[]'), Column('aliases', JSON, nullable=False, default=list, server_default='[]'), Column('author', JSON, nullable=True, default=None, server_default='null'))
  • simulations_table=Table(TABLENAME_SIMULATIONS, metadata, Column('id', Integer, primary_key=True, autoincrement=True), Column('collection_uid', String, ForeignKey(f'{TABLENAME_COLLECTIONS}.uid', ondelete='CASCADE')), Column('name', String, nullable=False), Column('created_at', DateTime, nullable=False, default=(datetime.now)), Column('modified_at', DateTime, nullable=False, default=(datetime.now)), Column('description', String, nullable=True), Column('status', String, nullable=False, default='initialized', server_default='initialized'), Column('submitted', Boolean, nullable=False, default=False, server_default='0'), UniqueConstraint('collection_uid', 'name', name='uix_collection_name'))
  • parameters_table=Table(TABLENAME_PARAMETERS, metadata, Column('id', Integer, primary_key=True, autoincrement=True), Column('simulation_id', Integer, ForeignKey(f'{TABLENAME_SIMULATIONS}.id', ondelete='CASCADE'), nullable=False), Column('key', String, nullable=False), Column('value', JSON, nullable=False), UniqueConstraint('simulation_id', 'key', name='uix_simulation_key'))

Functions

create_all(engine) -> None

Create all tables defined in this module.

Arguments:
  • engine

Classes

ParameterRecord

ParameterRecord(self, id, simulation_id, key, value) -> None
Arguments:
  • id:int
  • simulation_id:int
  • key:str
  • value:typing.Any
Attributes:
  • id:int
  • simulation_id:int
  • key:str
  • value:typing.Any

SimulationRecord

SimulationRecord(self, id, collection_uid, name, created_at, modified_at, description, status, submitted, parameters=list()) -> None
Arguments:
  • id:int
  • collection_uid:str
  • name:str
  • created_at:datetime.datetime
  • modified_at:datetime.datetime
  • description:str | None
  • status:str
  • submitted:bool
  • parameters:list[ParameterRecord]=list()
Attributes:
  • id:int
  • collection_uid:str
  • name:str
  • created_at:datetime.datetime
  • modified_at:datetime.datetime
  • description:str | None
  • status:str
  • submitted:bool
  • parameters:list[ParameterRecord]=field(default_factory=list)
  • parameter_dict:dict[str, typing.Any]
SimulationRecord.as_dict_metadata(self) -> dict[str, Any]
SimulationRecord.as_dict(self, standalone=True) -> dict[str, Any]
Arguments:
  • standalone:bool=True

CollectionMetadata

CollectionMetadata(self, uid, created_at=None, tags=list(), aliases=list(), author=None, description=None) -> None

Collection metadata container. Can load/save from/to dicts, storing unknown fields in an extras dictionary.

Arguments:
  • uid:str
  • created_at:datetime.datetime | None=None
  • tags:list[str]=list()
  • aliases:list[str]=list()
  • author:str | dict | None=None
  • description:str | None=None
Attributes:
  • uid:str

    Unique identifier of the collection.

  • created_at:datetime.datetime | None=field(default=None)

    Creation timestamp.

  • tags:list[str]=field(default_factory=list)

    List of tags associated with the collection.

  • aliases:list[str]=field(default_factory=list)

    List of aliases for the collection.

  • author:str | dict | None=field(default=None)

    Author information, can be a string or a dictionary.

  • description:str | None=field(default=None)

    Completely optional description of the collection.

  • _extras:dict[str, typing.Any]=field(default_factory=dict, init=False, repr=False)
CollectionMetadata.__post_init__(self)
CollectionMetadata.to_dict(self) -> dict[str, Any]
CollectionMetadata.from_dict(cls, data, *_) -> Self

Create an instance from a dictionary, storing unknown fields in the extras dictionary.

Arguments:
  • cls
  • data:dict[str, typing.Any]

    The input dictionary.

  • _=()

CollectionRecord

CollectionRecord(self, uid, created_at=None, tags=list(), aliases=list(), author=None, description=None, path='', simulations=list()) -> None

Collection record, including metadata and associated simulations. Used for exposing (read only) a record in the collection table in the sql database.

Arguments:
  • uid:str
  • created_at:datetime.datetime | None=None
  • tags:list[str]=list()
  • aliases:list[str]=list()
  • author:str | dict | None=None
  • description:str | None=None
  • path:str=''
  • simulations:list[SimulationRecord] | property=list()
Attributes:
  • path:str=field(default='')

    Path to the collection on disk. Guaranteed to be not null.

  • simulations:list[SimulationRecord] | property=field(default_factory=list, repr=False)

    List of simulations associated with the collection.

  • parameters:list[ParameterRecord]
CollectionRecord.get_parameter_keys(self) -> tuple[list[str], list[int]]
CollectionRecord.to_pandas(self, flatten=True) -> 'DataFrame'
Arguments:
  • flatten:bool=True
CollectionRecord.filtered(self, filter, sorter) -> Self
Arguments:

base

Indexing of bamboost collections and their simulations/parameters. SQLAlchemy is used to interact with the SQLite database.

store

SQLAlchemy Core helper utilities for the BAMBOOST index database.

On this page

Attributes
Functions
create_all
Classes
ParameterRecord
SimulationRecord
as_dict_metadata
as_dict
CollectionMetadata
__post_init__
to_dict
from_dict
CollectionRecord
get_parameter_keys
to_pandas
filtered