dwca package#

Package for reading Darwin Core Archive (DwCA) files.

Darwin Core Base Class#

class dwca.base.darwincore.DarwinCore#

Bases: ABC

Base class of this package.

Methods

`from_file`(path_to_archive)	Generate a Darwin Core Standard from a file.
`to_file`(path_to_archive[, encoding])	Generate a Darwin Core file using the information of this instance.

abstractmethod classmethod from_file(path_to_archive: str) → DarwinCore#

Generate a Darwin Core Standard from a file.

Parameters:

path_to_archivestr: Path of the archive file.

Returns:

DarwinCore: Instance of the Darwin Core Standard.

abstractmethod to_file(path_to_archive: str, encoding: str = 'utf-8') → None#

Generate a Darwin Core file using the information of this instance.

Parameters:

path_to_archivestr: Path of the archive to generate.
encodingstr, optional: Encoding of the corresponding files. Default “utf-8”.

Darwin Core Archive Class#

class dwca.base.darwincore_archive.DarwinCoreArchive(_id: str = None)#

Bases: DarwinCore

Represent a Darwin Core Archive file with all its elements.

Parameters:

_idstr, optional: A unique id for this Darwin Core Archive.

Attributes:

core: DataFile: The file with the core of the archive.
dataset_metadata: Dict[str, EML]: Metadata instances for each dataset present on DWC-A.
extensions: List[DataFile]: A list with the extension of the archive.
id: str: A unique identifier for this DarwinCoreArchive.
language: Language: Language of the Darwin Core Archive register on metadata.
metadata: EML: Metadata instance, currently supported EML.
metadata_filename: str: The filename of the metadata file.

Methods

`Metadata`([metadata])	Metadata class of the Darwin Core Archive storing the file name of the archive elements.
`from_file`(path_to_archive[, lazy, ...])	Generate a Darwin Core Archive instance from an archive file (.zip).
`generate_eml`([filename])	Generate an EML file on the archive.
`set_eml`(eml[, filename])	Set an EML file in the archive.
`to_file`(path_to_archive[, encoding, ...])	Generate a Darwin Core Archive file (.zip file) using the information of this instance.

merge

class Metadata(metadata: str = None)#

Bases: XMLObject

Metadata class of the Darwin Core Archive storing the file name of the archive elements.

Parameters:

metadatastr, optional: Name of the metadata file (e.g.: eml.xml)

Attributes:

NAMESPACE_TAG

Methods

`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`check_principal_tag`(tag, nmap)	Checks if the tag is the Principal tag of the object.
`from_string`(text)	Generates XML Object from a string of an XML file.
`from_xml`(file[, encoding])	Generates an XML Object from an XML file.
`get_dwc_class`(element)	Extract the row type from an XML element instance.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parses an lxml.etree.Element in a Metadata instance.
`to_element`()	Generate an element from a Metadata instance.
`to_xml`()	Generates text of an XML file.

PRINCIPAL_TAG = 'archive'#: str : The principal tag of the XML document.

classmethod get_dwc_class(element: Element) → Type[DataFile]#

Extract the row type from an XML element instance.

Parameters:

elementlxml.etree.Element: XML element instance.

Returns:

Type[DataFile]: The Python class representing the class term.

classmethod parse(element: Element, nmap: Dict) → Metadata#

Parses an lxml.etree.Element in a Metadata instance.

Parameters:

elementlxml.etree.Element: XML element to be parsed.
nmapDict: Namespace prefix:uri.

Returns:

Metadata: New Metadata instance with the data from the element.

to_element() → Element#

Generate an element from a Metadata instance.

Returns:

lxml.etree.Element: XML element from Metadata instance

xmlns = 'http://rs.tdwg.org/dwc/text/'#: str : Require tag of the metadata

property core: DataFile#: DataFile: The file with the core of the archive.

property dataset_metadata: Dict[str, EML]#: Dict[str, EML]: Metadata instances for each dataset present on DWC-A.

property extensions: List[DataFile]#: List[DataFile]: A list with the extension of the archive.

classmethod from_file(path_to_archive: str, lazy: bool = False, _no_interaction: bool = False) → DarwinCoreArchive#

Generate a Darwin Core Archive instance from an archive file (.zip).

Parameters:

path_to_archivestr: Path of the archive file.
lazybool, optional: Read the archive lazy. Default False.
_no_interactionbool, optional: Not to show progress bar if library tqdm is installed. Default False.

Returns:

DarwinCoreArchive: Instance of the Darwin Core Archive.

generate_eml(filename: str = 'eml.xml') → None#

Generate an EML file on the archive.

Parameters:

filenamestr: Filename for the EML file to be generated. Defaults to “eml.xml”.

property id: str#: str: A unique identifier for this DarwinCoreArchive.

property language: Language#: Language: Language of the Darwin Core Archive register on metadata.

classmethod merge(first_archive: DarwinCoreArchive, second_archive: DarwinCoreArchive, _id: str = None, eml: EML = None, eml_filename: str = 'eml.xml') → DarwinCoreArchive#

property metadata: EML#: EML: Metadata instance, currently supported EML.

property metadata_filename: str#: str: The filename of the metadata file.

set_eml(eml: EML, filename: str = 'eml.xml') → None#

Set an EML file in the archive.

Parameters:

emlEML: Metadata instance to set.
filenamestr, optional: Filename for the EML file. Defaults to “eml.xml”.

to_file(path_to_archive: str, encoding: str = 'utf-8', compression: int = 8, compression_level: int = 6, _no_interaction: bool = False) → None#

Generate a Darwin Core Archive file (.zip file) using the information of this instance.

Parameters:

path_to_archivestr: Path of the archive to generate.
encodingstr, optional: Encoding of the corresponding files. Default “utf-8”.
compressionint, optional: The ZIP compression method to use. Default zipfile.ZIP_DEFLATED.
compression_levelint, optional: Compression level to use when writing files to the archive. Default 6.
_no_interactionbool, optional: Not to show progress bar if library tqdm is installed. Default False.

Simple Darwin Core Class#

class dwca.base.simple_darwincore.SimpleDarwinCore#

Bases: DarwinCore

Class representing a Simple Darwin Core standard.

Methods

`from_file`(path_to_archive)	Generate a Darwin Core Standard from a file.
`to_file`(path_to_archive[, encoding])	Generate a Darwin Core file using the information of this instance.

classmethod from_file(path_to_archive: str) → SimpleDarwinCore#

Generate a Darwin Core Standard from a file.

Parameters:

path_to_archivestr: Path of the archive file.

Returns:

DarwinCore: Instance of the Darwin Core Standard.

to_file(path_to_archive: str, encoding: str = 'utf-8') → None#

Generate a Darwin Core file using the information of this instance.

Parameters:

path_to_archivestr: Path of the archive to generate.
encodingstr, optional: Encoding of the corresponding files. Default “utf-8”.

dwca package#

Darwin Core Base Class#

Darwin Core Archive Class#

Simple Darwin Core Class#

Subpackages#