aiida.tools.importexport.common package

Common utility functions, classes, and exceptions

class aiida.tools.importexport.common.Archive(filepath)

Bases: object

Utility class to operate on exported archive files or directories.

The main usage should be to construct the class with the filepath of the export archive as an argument. The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance within a context and which will be automatically cleaned upon leaving that context. Example:

with Archive('/some/path/archive.aiida') as archive:
    archive.version

FILENAME_DATA = 'data.json'

FILENAME_METADATA = 'metadata.json'

__dict__ = mappingproxy({'__module__': 'aiida.tools.importexport.common.archive', '__doc__': "Utility class to operate on exported archive files or directories.\n\n The main usage should be to construct the class with the filepath of the export archive as an argument.\n The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance\n within a context and which will be automatically cleaned upon leaving that context. Example::\n\n with Archive('/some/path/archive.aiida') as archive:\n archive.version\n\n ", 'FILENAME_DATA': 'data.json', 'FILENAME_METADATA': 'metadata.json', '__init__': <function Archive.__init__>, '__enter__': <function Archive.__enter__>, '__exit__': <function Archive.__exit__>, 'ensure_within_context': <AdapterWrapper at 0x7fef14fbb180 for function>, 'ensure_unpacked': <AdapterWrapper at 0x7fef14fbb1e8 for function>, 'unpack': <FunctionWrapper at 0x7fef14fbb250 for function>, 'filepath': <property object>, 'folder': <property object>, 'data': <property object>, 'meta_data': <property object>, 'unpacked': <property object>, 'get_info': <FunctionWrapper at 0x7fef14fbb3f0 for function>, 'get_data_statistics': <FunctionWrapper at 0x7fef14fbb458 for function>, 'version_aiida': <property object>, 'version_format': <property object>, 'conversion_info': <property object>, '_read_json_file': <FunctionWrapper at 0x7fef14fbb798 for FunctionWrapper>, '__dict__': <attribute '__dict__' of 'Archive' objects>, '__weakref__': <attribute '__weakref__' of 'Archive' objects>})

__enter__()

Instantiate a SandboxFolder into which the archive can be lazily unpacked.

__exit__(exc_type, exc_value, traceback)

Clean the sandbox folder if it was instatiated.

__init__(filepath)

Initialize self. See help(type(self)) for accurate signature.

__module__ = 'aiida.tools.importexport.common.archive'

__weakref__

list of weak references to the object (if defined)

_read_json_file(filename)

Read the contents of a JSON file from the unpacked archive contents.

Parameters

filename – the filename relative to the sandbox folder

Returns

a dictionary with the loaded JSON content

property conversion_info

Return information about migration events that were applied to this archive.

Returns

list of conversion notifications

property data

Return the loaded content of the data file

Returns

dictionary with contents of data file

ensure_unpacked(instance, args, kwargs)

Decorator to ensure that the archive is unpacked before entering the decorated function.

ensure_within_context(instance, args, kwargs)

Decorator to ensure that the instance is called within a context manager.

property filepath

Return the filepath of the archive

Returns

the archive filepath

property folder

Return the sandbox folder

Returns

sandbox folder aiida.common.folders.SandboxFolder

get_data_statistics()

Return dictionary with statistics about data content, i.e. how many entries of each entity type it contains.

Returns

a dictionary with basic details

get_info()

Return a dictionary with basic information about the archive.

Returns

a dictionary with basic details

property meta_data

Return the loaded content of the meta data file

Returns

dictionary with contents of meta data file

unpack()

Unpack the archive and store the contents in a sandbox.

property unpacked

Return whether the archive has been unpacked into the sandbox folder.

property version_aiida

Return the version of AiiDA the archive was created with.

Returns

version number

property version_format

Return the version of the archive format.

Returns

version number

aiida.tools.importexport.common.extract_zip(infile, folder, nodes_export_subfolder=None, silent=False)

Extract the nodes to be imported from a zip file.

Parameters

• infile (str) – file path

• folder (SandboxFolder) – a temporary folder used to extract the file tree

• nodes_export_subfolder (str) – name of the subfolder for AiiDA nodes

• silent (bool) – suppress debug print

Raises

• TypeError – if parameter types are not respected

• CorruptArchive – if the archive misses files or files have incorrect formats

aiida.tools.importexport.common.extract_tar(infile, folder, nodes_export_subfolder=None, silent=False)

Extract the nodes to be imported from a (possibly zipped) tar file.

Parameters

• infile (str) – file path

• folder (SandboxFolder) – a temporary fodler used to extract the file tree

• nodes_export_subfolder (str) – name of the subfolder for AiiDA nodes

• silent (bool) – suppress debug print

Raises

• TypeError – if parameter types are not respected

• CorruptArchive – if the archive misses files or files have incorrect formats

aiida.tools.importexport.common.extract_tree(infile, folder)

Prepare to import nodes from plain file system tree by copying in the given sandbox folder.

Note

the contents of the unpacked archive directory are copied into the sandbox folder, because the files will anyway haven to be copied to the repository at some point. By copying the contents of the source directory now and continuing operation only on the sandbox folder, we do not risk to modify the source files accidentally. During import then, the node files from the sandbox can be moved to the repository, so they won’t have to be copied again in any case.

Parameters

• infile (str) – absolute filepath point to the unpacked archive directory

• folder (SandboxFolder) – a temporary folder to which the archive contents are copied

exception aiida.tools.importexport.common.ExportImportException

Bases: aiida.common.exceptions.AiidaException

Base class for all AiiDA export/import module exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ArchiveExportError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA export exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ArchiveImportError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA import exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.CorruptArchive

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Raised when an operation is applied to a corrupt export archive, e.g. missing files or invalid formats.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.IncompatibleArchiveVersionError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Raised when trying to import an export archive with an incompatible schema version.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ExportValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveExportError

Raised when validation fails during export, e.g. for non-sealed ProcessNode s.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ImportUniquenessError

Bases: aiida.tools.importexport.common.exceptions.ArchiveImportError

Raised when the user tries to violate a uniqueness constraint.

Similar to UniquenessError.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ImportValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveImportError

Raised when validation fails during import, e.g. for parameter types and values.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.ArchiveMigrationError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA export archive migration exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.MigrationValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveMigrationError

Raised when validation fails during migration of export archives.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.DanglingLinkError

Bases: aiida.tools.importexport.common.exceptions.MigrationValidationError

Raised when an export archive is detected to contain dangling links when importing.

__module__ = 'aiida.tools.importexport.common.exceptions'

Submodules

Utility functions and classes to interact with AiiDA export archives.

class aiida.tools.importexport.common.archive.Archive(filepath)

Bases: object

Utility class to operate on exported archive files or directories.

The main usage should be to construct the class with the filepath of the export archive as an argument. The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance within a context and which will be automatically cleaned upon leaving that context. Example:

with Archive('/some/path/archive.aiida') as archive:
    archive.version

FILENAME_DATA = 'data.json'

FILENAME_METADATA = 'metadata.json'

__dict__ = mappingproxy({'__module__': 'aiida.tools.importexport.common.archive', '__doc__': "Utility class to operate on exported archive files or directories.\n\n The main usage should be to construct the class with the filepath of the export archive as an argument.\n The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance\n within a context and which will be automatically cleaned upon leaving that context. Example::\n\n with Archive('/some/path/archive.aiida') as archive:\n archive.version\n\n ", 'FILENAME_DATA': 'data.json', 'FILENAME_METADATA': 'metadata.json', '__init__': <function Archive.__init__>, '__enter__': <function Archive.__enter__>, '__exit__': <function Archive.__exit__>, 'ensure_within_context': <AdapterWrapper at 0x7fef14fbb180 for function>, 'ensure_unpacked': <AdapterWrapper at 0x7fef14fbb1e8 for function>, 'unpack': <FunctionWrapper at 0x7fef14fbb250 for function>, 'filepath': <property object>, 'folder': <property object>, 'data': <property object>, 'meta_data': <property object>, 'unpacked': <property object>, 'get_info': <FunctionWrapper at 0x7fef14fbb3f0 for function>, 'get_data_statistics': <FunctionWrapper at 0x7fef14fbb458 for function>, 'version_aiida': <property object>, 'version_format': <property object>, 'conversion_info': <property object>, '_read_json_file': <FunctionWrapper at 0x7fef14fbb798 for FunctionWrapper>, '__dict__': <attribute '__dict__' of 'Archive' objects>, '__weakref__': <attribute '__weakref__' of 'Archive' objects>})

__enter__()

Instantiate a SandboxFolder into which the archive can be lazily unpacked.

__exit__(exc_type, exc_value, traceback)

Clean the sandbox folder if it was instatiated.

__init__(filepath)

Initialize self. See help(type(self)) for accurate signature.

__module__ = 'aiida.tools.importexport.common.archive'

__weakref__

list of weak references to the object (if defined)

_read_json_file(filename)

Read the contents of a JSON file from the unpacked archive contents.

Parameters

filename – the filename relative to the sandbox folder

Returns

a dictionary with the loaded JSON content

property conversion_info

Return information about migration events that were applied to this archive.

Returns

list of conversion notifications

property data

Return the loaded content of the data file

Returns

dictionary with contents of data file

ensure_unpacked(instance, args, kwargs)

Decorator to ensure that the archive is unpacked before entering the decorated function.

ensure_within_context(instance, args, kwargs)

Decorator to ensure that the instance is called within a context manager.

property filepath

Return the filepath of the archive

Returns

the archive filepath

property folder

Return the sandbox folder

Returns

sandbox folder aiida.common.folders.SandboxFolder

get_data_statistics()

Return dictionary with statistics about data content, i.e. how many entries of each entity type it contains.

Returns

a dictionary with basic details

get_info()

Return a dictionary with basic information about the archive.

Returns

a dictionary with basic details

property meta_data

Return the loaded content of the meta data file

Returns

dictionary with contents of meta data file

unpack()

Unpack the archive and store the contents in a sandbox.

property unpacked

Return whether the archive has been unpacked into the sandbox folder.

property version_aiida

Return the version of AiiDA the archive was created with.

Returns

version number

property version_format

Return the version of the archive format.

Returns

version number

aiida.tools.importexport.common.archive.extract_zip(infile, folder, nodes_export_subfolder=None, silent=False)

Extract the nodes to be imported from a zip file.

Parameters

• infile (str) – file path

• folder (SandboxFolder) – a temporary folder used to extract the file tree

• nodes_export_subfolder (str) – name of the subfolder for AiiDA nodes

• silent (bool) – suppress debug print

Raises

• TypeError – if parameter types are not respected

• CorruptArchive – if the archive misses files or files have incorrect formats

aiida.tools.importexport.common.archive.extract_tar(infile, folder, nodes_export_subfolder=None, silent=False)

Extract the nodes to be imported from a (possibly zipped) tar file.

Parameters

• infile (str) – file path

• folder (SandboxFolder) – a temporary fodler used to extract the file tree

• nodes_export_subfolder (str) – name of the subfolder for AiiDA nodes

• silent (bool) – suppress debug print

Raises

• TypeError – if parameter types are not respected

• CorruptArchive – if the archive misses files or files have incorrect formats

aiida.tools.importexport.common.archive.extract_tree(infile, folder)

Prepare to import nodes from plain file system tree by copying in the given sandbox folder.

Note

the contents of the unpacked archive directory are copied into the sandbox folder, because the files will anyway haven to be copied to the repository at some point. By copying the contents of the source directory now and continuing operation only on the sandbox folder, we do not risk to modify the source files accidentally. During import then, the node files from the sandbox can be moved to the repository, so they won’t have to be copied again in any case.

Parameters

• infile (str) – absolute filepath point to the unpacked archive directory

• folder (SandboxFolder) – a temporary folder to which the archive contents are copied

Configuration file for AiiDA Import/Export module

Module that defines the exceptions thrown by AiiDA’s export/import module.

Note: In order to not override the built-in ImportError, both ImportError and ExportError are prefixed with

Archive.

exception aiida.tools.importexport.common.exceptions.ExportImportException

Bases: aiida.common.exceptions.AiidaException

Base class for all AiiDA export/import module exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ArchiveExportError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA export exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ArchiveImportError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA import exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.CorruptArchive

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Raised when an operation is applied to a corrupt export archive, e.g. missing files or invalid formats.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.IncompatibleArchiveVersionError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Raised when trying to import an export archive with an incompatible schema version.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ExportValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveExportError

Raised when validation fails during export, e.g. for non-sealed ProcessNode s.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ImportUniquenessError

Bases: aiida.tools.importexport.common.exceptions.ArchiveImportError

Raised when the user tries to violate a uniqueness constraint.

Similar to UniquenessError.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ImportValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveImportError

Raised when validation fails during import, e.g. for parameter types and values.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.ArchiveMigrationError

Bases: aiida.tools.importexport.common.exceptions.ExportImportException

Base class for all AiiDA export archive migration exceptions.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.MigrationValidationError

Bases: aiida.tools.importexport.common.exceptions.ArchiveMigrationError

Raised when validation fails during migration of export archives.

__module__ = 'aiida.tools.importexport.common.exceptions'

exception aiida.tools.importexport.common.exceptions.DanglingLinkError

Bases: aiida.tools.importexport.common.exceptions.MigrationValidationError

Raised when an export archive is detected to contain dangling links when importing.

__module__ = 'aiida.tools.importexport.common.exceptions'

Utility functions for import/export of AiiDA entities

class aiida.tools.importexport.common.utils.HTMLGetLinksParser(filter_extension=None)

Bases: html.parser.HTMLParser

If a filter_extension is passed, only links with extension matching the given one will be returned.

__init__(filter_extension=None)

Initialize and reset this instance.

If convert_charrefs is True (the default), all character references are automatically converted to the corresponding Unicode characters.

__module__ = 'aiida.tools.importexport.common.utils'

get_links()

Return the links that were found during the parsing phase.

handle_starttag(tag, attrs)

Store the urls encountered, if they match the request.

aiida.tools.importexport.common.utils.export_shard_uuid(uuid)

Sharding of the UUID for the import/export

Parameters

uuid (str) – UUID to be sharded (v4)

Returns

Sharded UUID as a subfolder path

Return type

str

aiida.tools.importexport.common.utils.get_valid_import_links(url)

Open the given URL, parse the HTML and return a list of valid links where the link file has a .aiida extension.

aiida.tools.importexport.common.utils.schema_to_entity_names(class_string)

Mapping from classes path to entity names (used by the SQLA import/export) This could have been written much simpler if it is only for SQLA but there is an attempt the SQLA import/export code to be used for Django too.