Bamboost
bamboost/Index/base

bamboost.index.base

Source: https://gitlab.com/cmbm-ethz/bamboost/-/blob/next/bamboost/index/base.py

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

The index is generated on the fly or can be explicitly created by scanning the search_paths for collections. The index is stored as a SQLite database that stores the path of collections (characterized with a unique UID), as well as the metadata and parameters of all simulations.

The Index class provides the public API for interacting with the index. This works in paralell execution, but the class is designed to execute any operations on the database on the root process only. Methods that return something use bcast to cast the result to all processes. Any SQL operation is executed only on the root process!

Database schema:

  • collections: Contains information about the collections, namely uids and corresponding paths.
  • simulations: Contains information about the simulations, including names, statuses, and links to the corresponding parameters.
  • parameters: Contains the parameters associated with the simulations.

Attributes

  • log=BAMBOOST_LOGGER.getChild('Database')
  • IDENTIFIER_PREFIX='.bamboost-collection'
  • IDENTIFIER_SEPARATOR='-'

Functions

simulation_metadata_from_h5(file) -> Tuple[SimulationMetadataT, SimulationParameterT]

Extract metadata and parameters from a BAMBOOST simulation HDF5 file.

Reads the metadata and parameters from the HDF5 file and returns them as a tuple.

Arguments:
  • file:pathlib.Path

    Path to the HDF5 file.

create_identifier_file(path, uid) -> None

Create an identifier file in the collection directory.

Arguments:
  • path:StrPath

    Path to the collection directory

  • uid:str

    UID of the collection

get_identifier_filename(uid) -> str
Arguments:
  • uid:str
_sql_transaction(func) -> Callable[Concatenate[Index, _P], _T]

Decorator to add a session to the function signature.

Arguments:
  • func:typing.Callable[typing_extensions.Concatenate[Index, bamboost._typing._P], bamboost._typing._T]

    The function to decorate.

_validate_path(path, uid) -> bool
Arguments:
  • path:pathlib.Path
  • uid:str
_find_uid_from_path(path) -> Optional[str]
Arguments:
  • path:pathlib.Path
_find_collection(uid, root_dir) -> tuple[Path, ...]

Find the collection with UID under given root_dir.

Arguments:
  • uid:str

    UID to search for

  • root_dir:pathlib.Path

    root directory for search

_find_files(pattern, root_dir, exclude=None) -> Tuple[Path, ...]

Locate every file matching pattern under root_dir while pruning directory names listed in exclude (exact-match on the final path part).

Returns an immutable tuple of absolute paths (str) just like the POSIX helper.

Arguments:
  • pattern:str
  • root_dir:str | os.os.PathLike
  • exclude:typing.Iterable[str] | None=None
_scan_directory_for_collections(root_dir) -> tuple[tuple[str, Path], ...]

Scan the directory for collections.

Arguments:
  • root_dir:pathlib.Path

    Directory to scan for collections

Returns
tuple[tuple[str, pathlib.Path], ...]Tuple of tuples with the UID and path of the collection

Classes

CollectionUID

UID of a collection. If no UID is provided, a new one is generated.

CollectionUID.__new__(cls, uid=None, length=10)
Arguments:
  • cls
  • uid:typing.Optional[str]=None
  • length:int=10
CollectionUID.generate_uid(length) -> str
Arguments:
  • length:int

LazyDefaultIndex

LazyDefaultIndex(self) -> None
Attributes:
  • _instance=None
LazyDefaultIndex.__delete__(self, instance) -> None
Arguments:
  • instance:None
LazyDefaultIndex.__set__(self, instance, value) -> None
Arguments:
LazyDefaultIndex.__get__(self, instance, owner) -> Index
Arguments:
  • instance:None
  • owner:typing.Type[Index]

Index

Index(self, sql_file=None, comm=None, *, search_paths=None) -> None

API for indexing BAMBOOST collections and simulations.

Arguments:
  • sql_file:typing.Optional[StrPath]=None
  • comm:typing.Optional[Comm]=None
  • search_paths:typing.Optional[typing.Iterable[str | pathlib.Path]]=None
Attributes:
  • _comm=Communicator()
  • _engine:sqlalchemy.Engine
  • _sm:typing.Callable[..., sqlalchemy.orm.Session]
  • _s:sqlalchemy.orm.Session
  • search_paths:PathSet=PathSet(search_paths or config.index.searchPaths)

    Paths to scan for collections.

  • default:LazyDefaultIndex=LazyDefaultIndex()

    A default index instance. Uses the default SQLite database file and search paths from the configuration.

  • _file=bamboost.index.base.Index(sql_file) or bamboost.config.bamboost.config.index.bamboost.config.index.databaseFile

    The path to the SQLite database file.

  • _isolated=bamboost.config.bamboost.config.index.bamboost.config.index.isolated

    Whether project based indexing is used.

  • _url=f'sqlite:///{bamboost.index.base.Index(self).bamboost.index.base.Index(self)._file}'

    The URL to the SQLite database file.

  • all_collections:typing.Sequence[CollectionORM]

    Return all collections in the index. Eagerly loads the simulations and its parameters.

  • all_simulations:typing.Sequence[SimulationORM]

    Return all simulations in the index. Eagerly loads the parameters.

  • all_parameters:typing.Sequence[ParameterORM]

    Return all parameters in the index.

Usage

Create an instance of the Index class and use its methods to interact with the index. $ from bamboost.index import Index $ index = Index()

Scan for collections in known paths: $ index.scan_for_collections()

Resolve the path of a collection: $ index.resolve_path()

Get a simulation from its collection and simulation name: $ index.get_simulation(, )

Index.sql_transaction(self) -> Generator[Session, None, None]

Context manager for a SQL transaction.

If no transaction is active, a new transaction is started. If a transaction is active, the current session is used.

Usage

>>> with index.sql_transaction() as s:
...     s.execute(...)
Index.scan_for_collections(self, *, search_paths=None) -> list[tuple[str, Path]]

Scan known paths for collections and update the index.

Iterates through the search paths and searches files with the identifier file structure. If a collection is found, it is added to the cache.

Arguments:
  • search_paths:List[pathlib.Path]=None

    Paths to scan for collections. Defaults to config.index.searchPaths.

Index.check_integrity(self) -> None

Check the integrity of the cache.

This method checks if the paths stored in the cache are valid. If a path is not valid, it is removed from the cache.

Index.resolve_path(self, uid, *, search_paths=None) -> Path

Resolve and return the path of a collection from its UID. Raises a FileNotFoundError if the collection is not found in the search paths.

Arguments:
  • uid:str

    UID of the collection

  • search_paths:typing.Optional[typing.Set[StrPath]]=None

    Paths to search for the collection

Index.resolve_uid(self, path) -> CollectionUID

Resolve the UID of a collection from a path.

Returns the UID of the collection or a new UID if it can't be determined.

Arguments:
Index.sync_collection(self, uid, path=None, *, force_all=False) -> None

Sync the table with the file system.

Iterates through the simulations in the collection and updates the metadata and parameters if the HDF5 file has been modified.

Arguments:
  • uid:str

    UID of the collection

  • path:typing.Optional=None

    Path of the collection

  • force_all:bool=False
Index.collection(self, uid) -> CollectionORM | None

Return a collection from the index.

Arguments:
  • uid:str

    UID of the collection

Index.simulation(self, collection_uid, name) -> SimulationORM | None

Return a simulation from the index.

Arguments:
  • collection_uid:str

    UID of the collection

  • name:str

    Name of the simulation

Index.upsert_collection(self, uid, path) -> None

Cache a collection in the index.

Arguments:
  • uid:str

    UID of the collection

  • path:pathlib.Path

    Path of the collection

Index.upsert_simulation(self, collection_uid, simulation_name, parameters=None, metadata=None, *, collection_path=None) -> None

Cache a simulation from a collection.

Arguments:
  • collection_uid:str

    UID of the collection

  • simulation_name:str

    Name of the simulation

  • parameters:typing.Optional[typing.Mapping[typing.Any, typing.Any]]=None
  • metadata:typing.Optional[typing.Mapping[typing.Any, typing.Any]]=None
  • collection_path:typing.Optional=None

    Path of the collection

Index.update_simulation_metadata(self, collection_uid, simulation_name, data) -> None

Update the metadata of a simulation by passing it as a dict.

Arguments:
  • collection_uid:str
  • simulation_name:str
  • data:typing.Mapping

    Dictionary with new data

Index.update_simulation_parameters(self, collection_uid, simulation_name, parameters) -> None

Update the parameters of a simulation by passing it as a dict.

Arguments:
Index._initialize_root_process(self, url) -> None
Arguments:
  • url:str
Index._drop_collection(self, uid) -> None

Drop a collection from the cache.

Arguments:
  • uid:str

    UID of the collection

Index._drop_simulation(self, collection_uid, simulation_name) -> None

Drop a simulation from the cache.

Arguments:
  • collection_uid:str

    UID of the collection

  • simulation_name:str

    Name of the simulation

Index._get_collection_path(self, uid) -> Optional[Path]
Arguments:
  • uid:str
Index._get_collections(self) -> Sequence[CollectionORM]
Index._get_simulation(self, collection_uid, simulation_name) -> SimulationORM | None
Arguments:

_filtering

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SQLAlchemy ORM models for the bamboost index database.

On this page

Attributes
Functions
simulation_metadata_from_h5
create_identifier_file
get_identifier_filename
_sql_transaction
_validate_path
_find_uid_from_path
_find_collection
_find_files
_scan_directory_for_collections
Classes
CollectionUID
__new__
generate_uid
LazyDefaultIndex
__delete__
__set__
__get__
Index
sql_transaction
scan_for_collections
check_integrity
resolve_path
resolve_uid
sync_collection
collection
simulation
upsert_collection
upsert_simulation
update_simulation_metadata
update_simulation_parameters
_initialize_root_process
_drop_collection
_drop_simulation
_get_collection_path
_get_collections
_get_simulation