aiida.tools.archive.implementations.sqlite_zip package

SQLite implementations of an archive file format.

Submodules

The file format implementation

class aiida.tools.archive.implementations.sqlite_zip.main.ArchiveFormatSqlZip

Bases: aiida.tools.archive.abstract.ArchiveFormatAbstract

Archive format, which uses a zip file, containing an SQLite database.

The content of the zip file is:

|- archive.zip
    |- metadata.json
    |- db.sqlite3
    |- repo/
        |- hashkey

Repository files are named by their SHA256 content hash.

__abstractmethods__ = frozenset({})

__module__ = 'aiida.tools.archive.implementations.sqlite_zip.main'

_abc_impl = <_abc_data object>

property key_format: str

Return the format of repository keys.

property latest_version: str

Return the latest schema version of the archive format.

migrate(inpath: Union[str, pathlib.Path], outpath: Union[str, pathlib.Path], version: str, *, force: bool = False, compression: int = 6) → None

Migrate an archive to a specific version.

Parameters

path – archive path

open(path: Union[str, pathlib.Path], mode: Literal['r'], *, compression: int = '6', **kwargs: Any) → aiida.tools.archive.implementations.sqlite_zip.reader.ArchiveReaderSqlZip

open(path: Union[str, pathlib.Path], mode: Literal['x', 'w'], *, compression: int = '6', **kwargs: Any) → aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveWriterSqlZip

open(path: Union[str, pathlib.Path], mode: Literal['a'], *, compression: int = '6', **kwargs: Any) → aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveAppenderSqlZip

Open an archive (latest version only).

Parameters

• path – archive path

• mode – open mode: ‘r’ (read), ‘x’ (exclusive write), ‘w’ (write) or ‘a’ (append)

• compression – default level of compression to use for writing (integer from 0 to 9)

Note, in write mode, the writer is responsible for writing the format version.

read_version(path: Union[str, pathlib.Path]) → str

Read the version of the archive from a file.

This method should account for reading all versions of the archive format.

Parameters

path – archive path

Raises

UnreachableStorage if the file does not exist

Raises

CorruptStorage if a version cannot be read from the archive

AiiDA archive reader implementation.

class aiida.tools.archive.implementations.sqlite_zip.reader.ArchiveReaderSqlZip(path: Union[str, pathlib.Path], **kwargs: Any)

Bases: aiida.tools.archive.abstract.ArchiveReaderAbstract

An archive reader for the SQLite format.

__abstractmethods__ = frozenset({})

__enter__() → aiida.tools.archive.implementations.sqlite_zip.reader.ArchiveReaderSqlZip

Start reading from the archive.

__exit__(*args, **kwargs) → None

Close the archive backend.

__init__(path: Union[str, pathlib.Path], **kwargs: Any)

Initialise the reader.

Parameters

path – archive path

__module__ = 'aiida.tools.archive.implementations.sqlite_zip.reader'

_abc_impl = <_abc_data object>

get_backend() → aiida.storage.sqlite_zip.backend.SqliteZipBackend

Return a ‘read-only’ backend for the archive.

get_metadata() → Dict[str, Any]

Return the top-level metadata.

Raises

CorruptStorage if the top-level metadata cannot be read from the archive

AiiDA archive writer implementation.

class aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveAppenderSqlZip(path: Union[str, pathlib.Path], fmt: aiida.tools.archive.abstract.ArchiveFormatAbstract, *, mode: Literal['x', 'w', 'a'] = 'x', compression: int = 6, work_dir: Optional[pathlib.Path] = None, _debug: bool = False, _enforce_foreign_keys: bool = True)

Bases: aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveWriterSqlZip

AiiDA archive appender implementation.

__abstractmethods__ = frozenset({})

__enter__() → aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveAppenderSqlZip

Start appending to the archive

__exit__(*args, **kwargs)

Finalise the archive

__module__ = 'aiida.tools.archive.implementations.sqlite_zip.writer'

_abc_impl = <_abc_data object>

_copy_old_zip_files()

Copy the old archive content to the new one (omitting any amended or deleted files)

delete_object(key: str) → None

Delete the object from the archive.

Parameters

key – fully qualified identifier for the object within the repository.

Raises

IOError – if the file could not be deleted.

class aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveWriterSqlZip(path: Union[str, pathlib.Path], fmt: aiida.tools.archive.abstract.ArchiveFormatAbstract, *, mode: Literal['x', 'w', 'a'] = 'x', compression: int = 6, work_dir: Optional[pathlib.Path] = None, _debug: bool = False, _enforce_foreign_keys: bool = True)

Bases: aiida.tools.archive.abstract.ArchiveWriterAbstract

AiiDA archive writer implementation.

__abstractmethods__ = frozenset({})

__enter__() → aiida.tools.archive.implementations.sqlite_zip.writer.ArchiveWriterSqlZip

Start writing to the archive

__exit__(*args, **kwargs)

Finalise the archive

__init__(path: Union[str, pathlib.Path], fmt: aiida.tools.archive.abstract.ArchiveFormatAbstract, *, mode: Literal['x', 'w', 'a'] = 'x', compression: int = 6, work_dir: Optional[pathlib.Path] = None, _debug: bool = False, _enforce_foreign_keys: bool = True)

Initialise the writer.

Parameters

• path – archive path

• mode – mode to open the archive in: ‘x’ (exclusive), ‘w’ (write) or ‘a’ (append)

• compression – default level of compression to use (integer from 0 to 9)

__module__ = 'aiida.tools.archive.implementations.sqlite_zip.writer'

_abc_impl = <_abc_data object>

_assert_in_context()

_stream_binary(name: str, handle: BinaryIO, *, buffer_size: Optional[int] = None, compression: Optional[int] = None, comment: Optional[bytes] = None) → None

Add a binary stream to the archive.

Parameters

• buffer_size – Number of bytes to buffer

• compression – Override global compression level

• comment – A binary meta comment about the object

bulk_insert(entity_type: aiida.orm.entities.EntityTypes, rows: List[Dict[str, Any]], allow_defaults: bool = False) → None

Add multiple rows of entity data to the archive.

Parameters

• entity_type – The type of the entity

• data – A list of dictionaries, containing all fields of the backend model, except the id field (a.k.a primary key), which will be generated dynamically

• allow_defaults – If False, assert that each row contains all fields, otherwise, allow default values for missing fields.

Raises

IntegrityError if the keys in a row are not a subset of the columns in the table

db_name = 'db.sqlite3'

delete_object(key: str) → None

Delete the object from the archive.

Parameters

key – fully qualified identifier for the object within the repository.

Raises

IOError – if the file could not be deleted.

meta_name = 'metadata.json'

put_object(stream: BinaryIO, *, buffer_size: Optional[int] = None, key: Optional[str] = None) → str

Add an object to the archive.

Parameters

• stream – byte stream to read the object from

• buffer_size – Number of bytes to buffer when read/writing

• key – key to use for the object (if None will be auto-generated)

Returns

the key of the object

update_metadata(data: Dict[str, Any], overwrite: bool = False) → None

Add key, values to the top-level metadata.

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