aiida.tools.dbimporters package#

Module for plugins to import data from external databases into an AiiDA database.

Submodules#

Base class implementation for an external database importer.

class aiida.tools.dbimporters.baseclasses.CifEntry(db_name=None, db_uri=None, id=None, version=None, extras=None, uri=None)[source]#

Bases: aiida.tools.dbimporters.baseclasses.DbEntry

Represents an entry from the structure database (COD, ICSD, …).

__module__ = 'aiida.tools.dbimporters.baseclasses'#
property cif#

Returns raw contents of a CIF file as string.

get_aiida_structure(converter='pymatgen', store=False, **kwargs)[source]#
Returns

AiiDA structure corresponding to the CIF file.

get_ase_structure()[source]#

Returns ASE representation of the CIF.

Note

To be removed, as it is duplicated in aiida.orm.nodes.data.cif.CifData.

get_cif_node(store=False, parse_policy='lazy')[source]#

Creates a CIF node, that can be used in AiiDA workflow.

Returns

aiida.orm.nodes.data.cif.CifData object

get_parsed_cif()[source]#

Returns data structure, representing the CIF file. Can be created using PyCIFRW or any other open-source parser.

Returns

list of lists

get_raw_cif()[source]#

Returns raw contents of a CIF file as string.

Returns

contents of a file as string

class aiida.tools.dbimporters.baseclasses.DbEntry(db_name=None, db_uri=None, id=None, version=None, extras=None, uri=None)[source]#

Bases: object

Represents an entry from external database.

__dict__ = mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n    Represents an entry from external database.\n    ', '_license': None, '__init__': <function DbEntry.__init__>, '__repr__': <function DbEntry.__repr__>, 'contents': <property object>, '__dict__': <attribute '__dict__' of 'DbEntry' objects>, '__weakref__': <attribute '__weakref__' of 'DbEntry' objects>, '__annotations__': {}})#
__init__(db_name=None, db_uri=None, id=None, version=None, extras=None, uri=None)[source]#

Sets the basic parameters for the database entry:

Parameters

  • db_name – name of the source database

  • db_uri – URI of the source database

  • id – structure identifyer in the database

  • version – version of the database

  • extras – a dictionary with some extra parameters (e.g. database ID number)

  • uri – URI of the structure (should be permanent)

__module__ = 'aiida.tools.dbimporters.baseclasses'#
__repr__()[source]#

Return repr(self).

__weakref__#

list of weak references to the object (if defined)

_license = None#
property contents#

Returns raw contents of a file as string.

class aiida.tools.dbimporters.baseclasses.DbImporter[source]#

Bases: object

Base class implementation for an external database importer.

__dict__ = mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': 'Base class implementation for an external database importer.', 'query': <function DbImporter.query>, 'setup_db': <function DbImporter.setup_db>, 'get_supported_keywords': <function DbImporter.get_supported_keywords>, '__dict__': <attribute '__dict__' of 'DbImporter' objects>, '__weakref__': <attribute '__weakref__' of 'DbImporter' objects>, '__annotations__': {}})#
__module__ = 'aiida.tools.dbimporters.baseclasses'#
__weakref__#

list of weak references to the object (if defined)

get_supported_keywords()[source]#

Returns the list of all supported query keywords.

Returns

list of strings

query(**kwargs)[source]#

Method to query the database.

Parameters

  • id – database-specific entry identificator

  • element – element name from periodic table of elements

  • number_of_elements – number of different elements

  • mineral_name – name of mineral

  • chemical_name – chemical name of substance

  • formula – chemical formula

  • volume – volume of the unit cell in cubic angstroms

  • spacegroup – symmetry space group symbol in Hermann-Mauguin notation

  • spacegroup_hall – symmetry space group symbol in Hall notation

  • a – length of lattice vector in angstroms

  • b – length of lattice vector in angstroms

  • c – length of lattice vector in angstroms

  • alpha – angles between lattice vectors in degrees

  • beta – angles between lattice vectors in degrees

  • gamma – angles between lattice vectors in degrees

  • z – number of the formula units in the unit cell

  • measurement_temp – temperature in kelvins at which the unit-cell parameters were measured

  • measurement_pressure – pressure in kPa at which the unit-cell parameters were measured

  • diffraction_temp – mean temperature in kelvins at which the intensities were measured

  • diffraction_pressure – mean pressure in kPa at which the intensities were measured

  • authors – authors of the publication

  • journal – name of the journal

  • title – title of the publication

  • year – year of the publication

  • journal_volume – journal volume of the publication

  • journal_issue – journal issue of the publication

  • first_page – first page of the publication

  • last_page – last page of the publication

  • doi – digital object identifyer (DOI), refering to the publication

Raises

NotImplementedError – if search using given keyword is not implemented.

setup_db(**kwargs)[source]#

Sets the database parameters. The method should reconnect to the database using updated parameters, if already connected.

class aiida.tools.dbimporters.baseclasses.DbSearchResults(results)[source]#

Bases: object

Base class for database results.

All classes, inheriting this one and overriding at(), are able to benefit from having functions __iter__, __len__ and __getitem__.

class DbSearchResultsIterator(results, increment=1)[source]#

Bases: object

Iterator for search results.

__dict__ = mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': 'Iterator for search results.', '__init__': <function DbSearchResults.DbSearchResultsIterator.__init__>, '__next__': <function DbSearchResults.DbSearchResultsIterator.__next__>, '__dict__': <attribute '__dict__' of 'DbSearchResultsIterator' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResultsIterator' objects>, '__annotations__': {}})#
__init__(results, increment=1)[source]#
__module__ = 'aiida.tools.dbimporters.baseclasses'#
__next__()[source]#

Return the next entry in the iterator.

__weakref__#

list of weak references to the object (if defined)

__dict__ = mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n    Base class for database results.\n\n    All classes, inheriting this one and overriding ``at()``, are able to\n    benefit from having functions ``__iter__``, ``__len__`` and\n    ``__getitem__``.\n    ', '_return_class': None, '__init__': <function DbSearchResults.__init__>, 'DbSearchResultsIterator': <class 'aiida.tools.dbimporters.baseclasses.DbSearchResults.DbSearchResultsIterator'>, '__iter__': <function DbSearchResults.__iter__>, '__len__': <function DbSearchResults.__len__>, '__getitem__': <function DbSearchResults.__getitem__>, 'fetch_all': <function DbSearchResults.fetch_all>, 'next': <function DbSearchResults.next>, 'at': <function DbSearchResults.at>, '_get_source_dict': <function DbSearchResults._get_source_dict>, '_get_url': <function DbSearchResults._get_url>, '__dict__': <attribute '__dict__' of 'DbSearchResults' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResults' objects>, '__annotations__': {}})#
__getitem__(key)[source]#
__init__(results)[source]#
__iter__()[source]#

Instances of aiida.tools.dbimporters.baseclasses.DbSearchResults can be used as iterators.

__len__()[source]#
__module__ = 'aiida.tools.dbimporters.baseclasses'#
__weakref__#

list of weak references to the object (if defined)

_get_source_dict(result_dict)[source]#

Returns a dictionary, which is passed as kwargs to the created DbEntry instance, describing the source of the entry.

Parameters

result_dict – dictionary, describing an entry in the results.

_get_url(result_dict)[source]#

Returns an URL of an entry CIF file.

Parameters

result_dict – dictionary, describing an entry in the results.

_return_class = None#
at(position)[source]#

Returns position-th result as aiida.tools.dbimporters.baseclasses.DbEntry.

Parameters

position – zero-based index of a result.

Raises

IndexError – if position is out of bounds.

fetch_all()[source]#

Returns all query results as an array of aiida.tools.dbimporters.baseclasses.DbEntry.

next()[source]#

Returns the next result of the query (instance of aiida.tools.dbimporters.baseclasses.DbEntry).

Raises

StopIteration – when the end of result array is reached.

class aiida.tools.dbimporters.baseclasses.UpfEntry(db_name=None, db_uri=None, id=None, version=None, extras=None, uri=None)[source]#

Bases: aiida.tools.dbimporters.baseclasses.DbEntry

Represents an entry from the pseudopotential database.

__module__ = 'aiida.tools.dbimporters.baseclasses'#
get_upf_node(store=False)[source]#

Creates an UPF node, that can be used in AiiDA workflow.

Returns

aiida.orm.nodes.data.upf.UpfData object

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