FileDatastore¶

class lsst.daf.butler.datastores.fileDatastore.FileDatastore(config: Union[DatastoreConfig, str], bridgeManager: DatastoreRegistryBridgeManager, butlerRoot: str = None)¶

Bases: lsst.daf.butler.datastores.genericDatastore.GenericBaseDatastore

Generic Datastore for file-based implementations.

Should always be sub-classed since key abstract methods are missing.

Parameters:	config : `DatastoreConfig` or `str` Configuration as either a `Config` object or URI to file. bridgeManager : `DatastoreRegistryBridgeManager` Object that manages the interface between `Registry` and datastores. butlerRoot : `str`, optional New datastore root to use to override the configuration value.
Raises:	ValueError If root location does not exist and `create` is `False` in the configuration.

Attributes Summary

`bridge`	Object that manages the interface between this `Datastore` and the `Registry` (`DatastoreRegistryBridge`).
`containerKey`
`defaultConfigFile`	Path to configuration defaults.
`isEphemeral`
`names`	Names associated with this datastore returned as a list.

Methods Summary

`addStoredItemInfo`(refs, infos)	Record internal storage information associated with one or more datasets.
`computeChecksum`(uri, algorithm, block_size)	Compute the checksum of the supplied file.
`emptyTrash`(ignore_errors)	Remove all datasets from the trash.
`exists`(ref)	Check if the dataset exists in the datastore.
`export`(refs, *, directory, str, …)	Export datasets for transfer to another data repository.
`forget`(refs)	Indicate to the Datastore that it should remove all records of the given datasets, without actually deleting them.
`fromConfig`(config, bridgeManager, …)	Create datastore from type specified in config file.
`get`(ref, parameters, Any]] = None)	Load an InMemoryDataset from the store.
`getLookupKeys`()	Return all the lookup keys relevant to this datastore.
`getStoredItemsInfo`(ref)	Retrieve information associated with files stored in this `Datastore` associated with this dataset ref.
`getURI`(ref, predict)	URI to the Dataset.
`getURIs`(ref, predict)	Return URIs associated with dataset.
`ingest`(*datasets, transfer)	Ingest one or more files into the datastore.
`knows`(ref)	Check if the dataset is known to the datastore.
`makeTableSpec`(datasetIdColumnType)
`needs_expanded_data_ids`(transfer, entity, …)	Test whether this datastore needs expanded data IDs to ingest.
`put`(inMemoryDataset, ref)	Write a InMemoryDataset with a given `DatasetRef` to the store.
`remove`(ref)	Indicate to the Datastore that a dataset can be removed.
`removeStoredItemInfo`(ref)	Remove information about the file associated with this dataset.
`retrieveArtifacts`(refs, destination, …)	Retrieve the file artifacts associated with the supplied refs.
`setConfigRoot`(root, config, full, overwrite)	Set any filesystem-dependent config options for this Datastore to be appropriate for a new empty repository with the given root.
`transaction`()	Context manager supporting `Datastore` transactions.
`transfer`(inputDatastore, ref)	Retrieve a dataset from an input `Datastore`, and store the result in this `Datastore`.
`transfer_from`(source_datastore, refs, …)	Transfer dataset artifacts from another datastore to this one.
`trash`(ref, …)	Indicate to the Datastore that a Dataset can be moved to the trash.
`validateConfiguration`(entities, …)	Validate some of the configuration for this datastore.
`validateKey`(lookupKey, entity, DatasetType, …)	Validate a specific look up key with supplied entity.

Attributes Documentation

bridge¶: Object that manages the interface between this Datastore and the Registry (DatastoreRegistryBridge).

containerKey = None¶

defaultConfigFile = 'datastores/fileDatastore.yaml'¶: Path to configuration defaults. Accessed within the config resource or relative to a search path. Can be None if no defaults specified.

isEphemeral = False¶

names¶

Names associated with this datastore returned as a list.

Can be different to name for a chaining datastore.

Methods Documentation

addStoredItemInfo(refs: Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef], infos: Iterable[lsst.daf.butler.core.storedFileInfo.StoredFileInfo]) → None¶

Record internal storage information associated with one or more datasets.

Parameters:	refs : sequence of `DatasetRef` The datasets that have been stored. infos : sequence of `StoredDatastoreItemInfo` Metadata associated with the stored datasets.

static computeChecksum(uri: lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI, algorithm: str = 'blake2b', block_size: int = 8192) → Optional[str]¶

Compute the checksum of the supplied file.

Parameters:	uri : `ButlerURI` Name of resource to calculate checksum from. algorithm : `str`, optional Name of algorithm to use. Must be one of the algorithms supported by :py:class`hashlib`. block_size : `int` Number of bytes to read from file at one time.
Returns:	hexdigest : `str` Hex digest of the file.

Notes

Currently returns None if the URI is for a remote resource.

emptyTrash(ignore_errors: bool = True) → None¶

Remove all datasets from the trash.

Parameters:	ignore_errors : `bool` If `True` return without error even if something went wrong. Problems could occur if another process is simultaneously trying to delete.

exists(ref: lsst.daf.butler.core.datasets.ref.DatasetRef) → bool¶

Check if the dataset exists in the datastore.

Parameters:	ref : `DatasetRef` Reference to the required dataset.
Returns:	exists : `bool` `True` if the entity exists in the `Datastore`.

export(refs: Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef], *, directory: Union[lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI, str, None] = None, transfer: Optional[str] = 'auto') → Iterable[lsst.daf.butler.core.fileDataset.FileDataset]¶

Export datasets for transfer to another data repository.

Parameters:	refs : iterable of `DatasetRef` Dataset references to be exported. directory : `str`, optional Path to a directory that should contain files corresponding to output datasets. Ignored if `transfer` is `None`. transfer : `str`, optional Mode that should be used to move datasets out of the repository. Valid options are the same as those of the `transfer` argument to `ingest`, and datastores may similarly signal that a transfer mode is not supported by raising `NotImplementedError`.
Returns:	dataset : iterable of `DatasetTransfer` Structs containing information about the exported datasets, in the same order as `refs`.
Raises:	NotImplementedError Raised if the given transfer mode is not supported.

forget(refs: Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef]) → None¶

Indicate to the Datastore that it should remove all records of the given datasets, without actually deleting them.

Parameters:	refs : `Iterable` [ `DatasetRef` ] References to the datasets being forgotten.

Notes

Asking a datastore to forget a DatasetRef it does not hold should be a silent no-op, not an error.

static fromConfig(config: Config, bridgeManager: DatastoreRegistryBridgeManager, butlerRoot: Optional[Union[str, ButlerURI]] = None) → 'Datastore'¶

Create datastore from type specified in config file.

Parameters:	config : `Config` Configuration instance. bridgeManager : `DatastoreRegistryBridgeManager` Object that manages the interface between `Registry` and datastores. butlerRoot : `str`, optional Butler root directory.

get(ref: lsst.daf.butler.core.datasets.ref.DatasetRef, parameters: Optional[Mapping[str, Any]] = None) → Any¶

Load an InMemoryDataset from the store.

Parameters:	ref : `DatasetRef` Reference to the required Dataset. parameters : `dict` `StorageClass`-specific parameters that specify, for example, a slice of the dataset to be loaded.
Returns:	inMemoryDataset : `object` Requested dataset or slice thereof as an InMemoryDataset.
Raises:	FileNotFoundError Requested dataset can not be retrieved. TypeError Return value from formatter has unexpected type. ValueError Formatter failed to process the dataset.

getLookupKeys() → Set[LookupKey]¶

Return all the lookup keys relevant to this datastore.

Returns:	keys : `set` of `LookupKey` The keys stored internally for looking up information based on `DatasetType` name or `StorageClass`.

getStoredItemsInfo(ref: DatasetIdRef) → List[StoredFileInfo]¶

Retrieve information associated with files stored in this Datastore associated with this dataset ref.

Parameters:	ref : `DatasetRef` The dataset that is to be queried.
Returns:	items : `list` [`StoredDatastoreItemInfo`] Stored information about the files and associated formatters associated with this dataset. Only one file will be returned if the dataset has not been disassembled. Can return an empty list if no matching datasets can be found.

getURI(ref: lsst.daf.butler.core.datasets.ref.DatasetRef, predict: bool = False) → lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI¶

URI to the Dataset.

Parameters:	ref : `DatasetRef` Reference to the required Dataset. predict : `bool` If `True`, allow URIs to be returned of datasets that have not been written.
Returns:	uri : `str` URI pointing to the dataset within the datastore. If the dataset does not exist in the datastore, and if `predict` is `True`, the URI will be a prediction and will include a URI fragment “#predicted”. If the datastore does not have entities that relate well to the concept of a URI the returned URI will be descriptive. The returned URI is not guaranteed to be obtainable.
Raises:	FileNotFoundError Raised if a URI has been requested for a dataset that does not exist and guessing is not allowed. RuntimeError Raised if a request is made for a single URI but multiple URIs are associated with this dataset.

Notes

When a predicted URI is requested an attempt will be made to form a reasonable URI based on file templates and the expected formatter.

getURIs(ref: lsst.daf.butler.core.datasets.ref.DatasetRef, predict: bool = False) → Tuple[Optional[lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI], Dict[str, lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI]]¶

Return URIs associated with dataset.

Parameters:	ref : `DatasetRef` Reference to the required dataset. predict : `bool`, optional If the datastore does not know about the dataset, should it return a predicted URI or not?
Returns:	primary : `ButlerURI` The URI to the primary artifact associated with this dataset. If the dataset was disassembled within the datastore this may be `None`. components : `dict` URIs to any components associated with the dataset artifact. Can be empty if there are no components.

ingest(*datasets, transfer: Optional[str] = None) → None¶

Ingest one or more files into the datastore.

Parameters:

datasets : FileDataset: Each positional argument is a struct containing information about a file to be ingested, including its path (either absolute or relative to the datastore root, if applicable), a complete DatasetRef (with dataset_id not None), and optionally a formatter class or its fully-qualified string name. If a formatter is not provided, the one the datastore would use for put on that dataset is assumed.
transfer : str, optional: How (and whether) the dataset should be added to the datastore. If None (default), the file must already be in a location appropriate for the datastore (e.g. within its root directory), and will not be modified. Other choices include “move”, “copy”, “link”, “symlink”, “relsymlink”, and “hardlink”. “link” is a special transfer mode that will first try to make a hardlink and if that fails a symlink will be used instead. “relsymlink” creates a relative symlink rather than use an absolute path. Most datastores do not support all transfer modes. “auto” is a special option that will let the data store choose the most natural option for itself.

Raises:

NotImplementedError: Raised if the datastore does not support the given transfer mode (including the case where ingest is not supported at all).
DatasetTypeNotSupportedError: Raised if one or more files to be ingested have a dataset type that is not supported by the datastore.
FileNotFoundError: Raised if one of the given files does not exist.
FileExistsError: Raised if transfer is not None but the (internal) location the file would be moved to is already occupied.

Notes

Subclasses should implement _prepIngest and _finishIngest instead of implementing ingest directly. Datastores that hold and delegate to child datastores may want to call those methods as well.

Subclasses are encouraged to document their supported transfer modes in their class documentation.

knows(ref: lsst.daf.butler.core.datasets.ref.DatasetRef) → bool¶

Check if the dataset is known to the datastore.

Does not check for existence of any artifact.

Parameters:	ref : `DatasetRef` Reference to the required dataset.
Returns:	exists : `bool` `True` if the dataset is known to the datastore.

classmethod makeTableSpec(datasetIdColumnType: type) → lsst.daf.butler.core.ddl.TableSpec¶

needs_expanded_data_ids(transfer: Optional[str], entity: Union[lsst.daf.butler.core.datasets.ref.DatasetRef, lsst.daf.butler.core.datasets.type.DatasetType, lsst.daf.butler.core.storageClass.StorageClass, None] = None) → bool¶

Test whether this datastore needs expanded data IDs to ingest.

Parameters:	transfer : `str` or `None` Transfer mode for ingest. entity, optional Object representing what will be ingested. If not provided (or not specific enough), `True` may be returned even if expanded data IDs aren’t necessary.
Returns:	needed : `bool` If `True`, expanded data IDs may be needed. `False` only if expansion definitely isn’t necessary.

put(inMemoryDataset: Any, ref: lsst.daf.butler.core.datasets.ref.DatasetRef) → None¶

Write a InMemoryDataset with a given DatasetRef to the store.

Parameters:	inMemoryDataset : `object` The dataset to store. ref : `DatasetRef` Reference to the associated Dataset.
Raises:	TypeError Supplied object and storage class are inconsistent. DatasetTypeNotSupportedError The associated `DatasetType` is not handled by this datastore.

Notes

If the datastore is configured to reject certain dataset types it is possible that the put will fail and raise a DatasetTypeNotSupportedError. The main use case for this is to allow ChainedDatastore to put to multiple datastores without requiring that every datastore accepts the dataset.

remove(ref: DatasetRef) → None¶

Indicate to the Datastore that a dataset can be removed.

Warning

This method deletes the artifact associated with this dataset and can not be reversed.

Parameters:	ref : `DatasetRef` Reference to the required Dataset.
Raises:	FileNotFoundError Attempt to remove a dataset that does not exist.

Notes

This method is used for immediate removal of a dataset and is generally reserved for internal testing of datastore APIs. It is implemented by calling trash() and then immediately calling emptyTrash(). This call is meant to be immediate so errors encountered during removal are not ignored.

removeStoredItemInfo(ref: DatasetIdRef) → None¶

Remove information about the file associated with this dataset.

Parameters:	ref : `DatasetRef` The dataset that has been removed.

retrieveArtifacts(refs: Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef], destination: lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI, transfer: str = 'auto', preserve_path: bool = True, overwrite: bool = False) → List[lsst.daf.butler.core._butlerUri._butlerUri.ButlerURI]¶

Retrieve the file artifacts associated with the supplied refs.

Parameters:

refs : iterable of DatasetRef: The datasets for which file artifacts are to be retrieved. A single ref can result in multiple files. The refs must be resolved.
destination : ButlerURI: Location to write the file artifacts.
transfer : str, optional: Method to use to transfer the artifacts. Must be one of the options supported by ButlerURI.transfer_from(). “move” is not allowed.
preserve_path : bool, optional: If True the full path of the file artifact within the datastore is preserved. If False the final file component of the path is used.
overwrite : bool, optional: If True allow transfers to overwrite existing files at the destination.

Returns:

targets : list of ButlerURI: URIs of file artifacts in destination location. Order is not preserved.

classmethod setConfigRoot(root: str, config: lsst.daf.butler.core.config.Config, full: lsst.daf.butler.core.config.Config, overwrite: bool = True) → None¶

Set any filesystem-dependent config options for this Datastore to be appropriate for a new empty repository with the given root.

Parameters:

root : str: URI to the root of the data repository.
config : Config: A Config to update. Only the subset understood by this component will be updated. Will not expand defaults.
full : Config: A complete config with all defaults expanded that can be converted to a DatastoreConfig. Read-only and will not be modified by this method. Repository-specific options that should not be obtained from defaults when Butler instances are constructed should be copied from full to config.
overwrite : bool, optional: If False, do not modify a value in config if the value already exists. Default is always to overwrite with the provided root.

Notes

If a keyword is explicitly defined in the supplied config it will not be overridden by this method if overwrite is False. This allows explicit values set in external configs to be retained.

transaction() → Iterator[lsst.daf.butler.core.datastore.DatastoreTransaction]¶

Context manager supporting Datastore transactions.

Transactions can be nested, and are to be used in combination with Registry.transaction.

transfer(inputDatastore: Datastore, ref: DatasetRef) → None¶

Retrieve a dataset from an input Datastore, and store the result in this Datastore.

Parameters:	inputDatastore : `Datastore` The external `Datastore` from which to retreive the Dataset. ref : `DatasetRef` Reference to the required dataset in the input data store.

transfer_from(source_datastore: lsst.daf.butler.core.datastore.Datastore, refs: Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef], local_refs: Optional[Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef]] = None, transfer: str = 'auto') → None¶

Transfer dataset artifacts from another datastore to this one.

Parameters:

source_datastore : Datastore: The datastore from which to transfer artifacts. That datastore must be compatible with this datastore receiving the artifacts.
refs : iterable of DatasetRef: The datasets to transfer from the source datastore.
local_refs : iterable of DatasetRef, optional: The dataset refs associated with the registry associated with this datastore. Can be None if the source and target datastore are using UUIDs.
transfer : str, optional: How (and whether) the dataset should be added to the datastore. Choices include “move”, “copy”, “link”, “symlink”, “relsymlink”, and “hardlink”. “link” is a special transfer mode that will first try to make a hardlink and if that fails a symlink will be used instead. “relsymlink” creates a relative symlink rather than use an absolute path. Most datastores do not support all transfer modes. “auto” (the default) is a special option that will let the data store choose the most natural option for itself. If the source location and transfer location are identical the transfer mode will be ignored.

Raises:

TypeError: Raised if the two datastores are not compatible.

trash(ref: Union[lsst.daf.butler.core.datasets.ref.DatasetRef, Iterable[lsst.daf.butler.core.datasets.ref.DatasetRef]], ignore_errors: bool = True) → None¶

Indicate to the Datastore that a Dataset can be moved to the trash.

Parameters:	ref : `DatasetRef` or iterable thereof Reference(s) to the required Dataset. ignore_errors : `bool`, optional Determine whether errors should be ignored. When multiple refs are being trashed there will be no per-ref check.
Raises:	FileNotFoundError When Dataset does not exist and errors are not ignored. Only checked if a single ref is supplied (and not in a list).

Notes

Some Datastores may implement this method as a silent no-op to disable Dataset deletion through standard interfaces.

validateConfiguration(entities: Iterable[Union[lsst.daf.butler.core.datasets.ref.DatasetRef, lsst.daf.butler.core.datasets.type.DatasetType, lsst.daf.butler.core.storageClass.StorageClass]], logFailures: bool = False) → None¶

Validate some of the configuration for this datastore.

Parameters:	entities : iterable of `DatasetRef`, `DatasetType`, or `StorageClass` Entities to test against this configuration. Can be differing types. logFailures : `bool`, optional If `True`, output a log message for every validation error detected.
Raises:	DatastoreValidationError Raised if there is a validation problem with a configuration. All the problems are reported in a single exception.

Notes

This method checks that all the supplied entities have valid file templates and also have formatters defined.

validateKey(lookupKey: LookupKey, entity: Union[DatasetRef, DatasetType, StorageClass]) → None¶

Validate a specific look up key with supplied entity.

Parameters:	lookupKey : `LookupKey` Key to use to retrieve information from the datastore configuration. entity : `DatasetRef`, `DatasetType`, or `StorageClass` Entity to compare with configuration retrieved using the specified lookup key.
Raises:	DatastoreValidationError Raised if there is a problem with the combination of entity and lookup key.

Notes

Bypasses the normal selection priorities by allowing a key that would normally not be selected to be validated.

Navigation

FileDatastore¶