dwca.classes package#

This module corresponds to the “class” type terms defined in the https://dwc.tdwg.org/list/#31-index-by-term-name “Classes” section, excluding the deprecated ones. These Python classes represent a complete file in a Darwin Core Archive.

This classes are the ones listed in the description of rowType in the Attributes section for a <core> or <extension> element. Presented below:

(…) For convenience the URIs for classes defined by the Darwin Core are: dwc:Occurrence: http://rs.tdwg.org/dwc/terms/Occurrence, dwc:Organism: http://rs.tdwg.org/dwc/terms/Organism, dwc:MaterialEntity: http://rs.tdwg.org/dwc/terms/MaterialEntity, dwc:MaterialSample: http://rs.tdwg.org/dwc/terms/MaterialSample, dwc:Event: http://rs.tdwg.org/dwc/terms/Event, dcterms:Location: http://purl.org/dc/terms/Location, dwc:GeologicalContext: http://purl.org/dc/terms/GeologicalContext, dwc:Identification: http://rs.tdwg.org/dwc/terms/Identification, dwc:Taxon: http://rs.tdwg.org/dwc/terms/Taxon, dwc:ResourceRelationship: http://rs.tdwg.org/dwc/terms/ResourceRelationship, dwc:MeasurementOrFact: http://rs.tdwg.org/dwc/terms/MeasurementOrFact, chrono:ChronometricAge: http://rs.tdwg.org/chrono/terms/ChronometricAge,

DataFile Class#

class dwca.classes.data_file.DataFile(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: XMLObject, ABC

Abstract class representing the class of data represented by each row in a data entity.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Number of lines to ignore at the start of document. Default 0 lines.

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

class Entry(**kwargs)#

Bases: object

Methods

to_dict

to_dict() → Dict#

URI = 'http://rs.tdwg.org/dwc/terms/'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

add_field(field: Field) → None#

Add a field to this Data File.

Parameters:

fieldField: A dwca.terms.field.Field object.

Returns:

None

as_pandas(_no_interaction: bool = False) → pd.DataFrame#

Convert information in this DataFile in a pandas.DataFrame.

Returns:

DataFrame: Information as a pandas.DataFrame.

as_polars(_no_interaction: bool = False) → pl.DataFrame#

Convert information in this DataFile in a polars DataFrame.

Returns:

DataFrame:: Information as a polars.DataFrame.

classmethod check_principal_tag(tag: str, nmap: Dict) → None#

Overwrite due to different possible tags.

Parameters:

tagstr: Actual tag.
nmapDict: Namespace.

close() → None#

property fields: List[str]#: List[str]: List of terms of this data file.

property filename: str#: str: Filename of the Data File entity.

generate_sql_table() → str#

Generate the CREATE TABLE statement for SQL database.

Returns:

str: CREATE TABLE statement.

classmethod get_term_class(element: Element) → Type[Field]#

Extract the Python class term from an XML element instance.

Parameters:

elementlxml.etree.Element: XML element instance.

Returns:

Type[Field]: The Python class representing the term name.

property id: int#: int: Column to be identified as primary key

property insert_sql: Generator[str, Tuple[Any]]#: Generate the INSERT INTO sql statement and the values to be inserted.

is_lazy() → bool#

Check if data file load its data as a Lazy Frame.

Returns:

bool: True when file read as a Lazy Frame, False otherwise.

merge(data_file: DataFile) → DataFile#

property name: str#: str: The name of the field.

property pandas: pd.DataFrame#: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.

classmethod parse(element: Element, nmap: Dict) → DataFile | None#

Parse an lxml.etree.Element into a concrete DataFile object.

Parameters:

elementlxml.etree.Element: An XML Element.
nmapDict: Dictionary of prefix:uri.

Returns:

DataFile: An instance of a concrete DataFile class.

classmethod parse_kwargs(element: Element, nmap: Dict) → Dict#

Parse an lxml.etree.Element into the DataFile parameters.

Parameters:

elementlxml.etree.Element: An XML Element.
nmapDict: Dictionary of prefix:uri.

Returns:

Dict: The Parameters of any DataFile.

property polars: pl.DataFrame#: polars.DataFrame: Data of this DataFile as polars.DataFrame.

read_file(content: str, source_file: BinaryIO = None, lazy: bool = False, _no_interaction: bool = False) → None#

Read the content of the file specified in files parameters (filename()).

Parameters:

contentstr: Content of the file
source_fileBinaryIO, optional: File to read in case of laziness.
lazybool, optional: Read the file in lazy evaluation mode. Default False.
_no_interactionbool, optional: Not to show progress bar if library tqdm is installed. Default False.

set_core_field(field: Field) → None#

Set the Core field in an Extension DataFile.

Parameters:

fieldField: Primary Key from the Core DataFile.

Returns:

None

set_primary_key(primary_key: str) → None#

Set the primary key in an Extension DataFile to be referenced on the new SQL table.

Parameters:

primary_keystr: Name of the Core Data File.

Returns:

None

property sql_table: str#: str: Data file as CREATE TABLE sql statement.

to_element() → Element#

Generate a XML Element instance

Returns:

lxml.etree.Element: XML Element instance

property uri: str#: str: Unified Resource Identifier (URI) for the term.

write_file(_no_interaction: bool = False) → str#

Write the content as a text using format information on this object.

Returns:

str: Data File as plain text.

class dwca.classes.data_file.DataFileType(value)#

Bases: Enum

Type of data file in the Darwin Core Archive.

CORE = 0#

EXTENSION = 1#

OutsideClass Class#

This is a special class, and its idea is to represent any data file that is not defined in the standard.

class dwca.classes.outside_class.OutsideClass(_id: int, uri: str, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

Classes defined outside the Darwin Core specifications.

Parameters:

_idint: Unique identifier for the core entity.
uristr: URI of the term.
filesstr: File location, in the archive, this is inside the zip file.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into an OutsideClass object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

classmethod get_term_class(element: Element) → Type[Field]#

Extract the Python class term from an XML element instance.

Parameters:

elementlxml.etree.Element: XML element instance.

Returns:

Type[Field]: The Python class representing the term name.

classmethod parse(element: Element, nmap: Dict) → OutsideClass | None#

Parse an lxml.etree.Element into an OutsideClass object.

Parameters:

elementlxml.etree.Element: An XML Element.
nmapDict: Dictionary of prefix:uri.

Returns:

OutsideClass: An instance of OutsideClass.

ChronometricAge Class#

This particular “class” term was extracted from http://rs.tdwg.org/dwc/doc/chrono/ (https://chrono.tdwg.org/list/#31-index-by-term-name “Classes” section).

class dwca.classes.chronometric_age.ChronometricAge(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

An approximation of a temporal position that is supported via evidence.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/chrono/terms/ChronometricAge'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Event Class#

class dwca.classes.event.Event(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

An action that occurs at some location during some time.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/Event'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

GeologicalContext Class#

class dwca.classes.geological_context.GeologicalContext(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

Geological information, such as stratigraphy, that qualifies a region or place.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/GeologicalContext'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Identification Class#

class dwca.classes.identification.Identification(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A taxonomic determination (e.g., the assignment to a dwc:Taxon).

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/Identification'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Location Class#

class dwca.classes.location.Location(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A spatial region or named place.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://purl.org/dc/terms/Location'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

MaterialEntity Class#

class dwca.classes.material_entity.MaterialEntity(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

An entity that can be identified, exists for some period of time, and consists of physical matter while it exists.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/MaterialEntity'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

MaterialSample Class#

class dwca.classes.material_sample.MaterialSample(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A material entity that represents an entity of interest in whole or in part.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/MaterialSample'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

MeasurementOrFact Class#

class dwca.classes.measurement_or_fact.MeasurementOrFact(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A measurement of or fact about a Resource.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/MeasurementOrFact'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Occurrence Class#

class dwca.classes.occurrence.Occurrence(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

An existence of an organism at a particular place at a particular time.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/Occurrence'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Organism Class#

class dwca.classes.organism.Organism(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A particular organism or defined group of organisms considered to be taxonomically homogeneous.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/Organism'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

ResourceRelationship Class#

class dwca.classes.resource_relationship.ResourceRelationship(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A relationship of one Resource to another.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/ResourceRelationship'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

Taxon Class#

class dwca.classes.taxon.Taxon(_id: int, files: str, fields: List[Field], data_file_type: DataFileType = DataFileType.CORE, encoding: str = 'utf-8', lines_terminated_by: str = '\n', fields_terminated_by: str = ',', fields_enclosed_by: str = '', ignore_header_lines: int = 0)#

Bases: DataFile

A group of organisms considered by taxonomists to form a homogeneous unit.

Parameters:

_idint: Unique identifier for the core entity.
filesstr: File location, in the archive, this is inside the zip file.
fieldsList[Field]: A list of the Field (columns) in the Core data entity.
data_file_type: DataFileType: The Data File Type in the Darwin Core Archive.
encodingstr, optional: Encoding of the file location (files parameter), default is “utf-8”.
lines_terminated_bystr, optional: Delimiter of lines on the file, default “\n”.
fields_terminated_bystr, optional: Delimiter of the file (cells) on the file, default “,”.
fields_enclosed_bystr, optional: Specifies the character used to enclose (mark the start and end of) each field, default empty “”.
ignore_header_linesint, optional: Ignore headers at the start of document, can be one line or a list of them, default 0 (first line).

Attributes:

NAMESPACE_TAG
fields: List[str]: List of terms of this data file.
filename: str: Filename of the Data File entity.
id: int: Column to be identified as primary key
insert_sql: Generate the INSERT INTO sql statement and the values to be inserted.
name: str: The name of the field.
pandas: pandas.DataFrame: Data of this DataFile as pandas.DataFrame.
polars: polars.DataFrame: Data of this DataFile as polars.DataFrame.
sql_table: str: Data file as CREATE TABLE sql statement.
uri: str: Unified Resource Identifier (URI) for the term.

Methods

`add_field`(field)	Add a field to this Data File.
`add_namespace`(prefix, uri)	Add a namespace to the XML object.
`all_synonyms`(taxa_id[, get_names])	Get a list of all valid names of a list of taxa.
`as_pandas`([_no_interaction])	Convert information in this DataFile in a pandas.DataFrame.
`as_polars`([_no_interaction])	Convert information in this DataFile in a polars DataFrame.
`check_principal_tag`(tag, nmap)	Overwrite due to different possible tags.
`filter_by_class`(classes[, fuzzy_threshold])	Filter data by a valid class.
`filter_by_family`(families[, fuzzy_threshold])	Filter data by a valid family.
`filter_by_genus`(genera[, fuzzy_threshold])	Filter data by a valid genus.
`filter_by_kingdom`(kingdoms[, fuzzy_threshold])	Filter data by a valid kingdoms.
`filter_by_order`(orders[, fuzzy_threshold])	Filter data by a valid order.
`filter_by_phylum`(phyla[, fuzzy_threshold])	Filter data by a valid phylum.
`filter_by_species`(species[, fuzzy_threshold])	Filer data by species or any rank taxonomy below (subspecies, variety, form, etc.).
`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.
`generate_sql_table`()	Generate the CREATE TABLE statement for SQL database.
`get_parents`(taxa_id)	Get a list of taxa ids of the parent of the list taxa id provided.
`get_principal_tag`()	Returns the principal tag with namespaces if it is present.
`get_term_class`(element)	Extract the Python `class` term from an XML element instance.
`is_lazy`()	Check if data file load its data as a Lazy Frame.
`object_to_element`(tag[, prefix])	Generates an element using tag, adding namespace tag.
`parse`(element, nmap)	Parse an lxml.etree.Element into a concrete DataFile object.
`parse_kwargs`(element, nmap)	Parse an lxml.etree.Element into the DataFile parameters.
`read_file`(content[, source_file, lazy, ...])	Read the content of the file specified in files parameters (`filename()`).
`set_core_field`(field)	Set the Core field in an Extension DataFile.
`set_primary_key`(primary_key)	Set the primary key in an Extension DataFile to be referenced on the new SQL table.
`to_element`()	Generate a XML Element instance
`to_xml`()	Generates text of an XML file.
`write_file`([_no_interaction])	Write the content as a text using format information on this object.

Entry
close
merge

URI = 'http://rs.tdwg.org/dwc/terms/Taxon'#: str: Unified Resource Identifier (URI) for the term identifying the class of data.

all_synonyms(taxa_id: Iterable[str], get_names: bool = False) → List[str]#

Get a list of all valid names of a list of taxa.

Parameters:

taxa_idIterable[str]: A list (or iterable) of dwca.terms.taxon.TaxonID value.
get_namesbool: Whether to get dwca.terms.taxon.ScientificName or dwca.terms.taxon.TaxonID.

Returns:

List[str]: A list of dwca.terms.taxon.TaxonID.

filter_by_class(classes: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid class.

Parameters:

classesList[str]: Class names to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_family(families: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid family.

Parameters:

familiesList[str]: Family names to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_genus(genera: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid genus.

Parameters:

generaList[str]: Class names to filter genus.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_kingdom(kingdoms: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid kingdoms.

Parameters:

kingdomsList[str]: Kingdom names to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_order(orders: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid order.

Parameters:

ordersList[str]: Order names to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_phylum(phyla: List[str], fuzzy_threshold: float = -1) → None#

Filter data by a valid phylum.

Parameters:

phylaList[str]: Phylum names to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

filter_by_species(species: List[str], fuzzy_threshold: float = -1) → None#

Filer data by species or any rank taxonomy below (subspecies, variety, form, etc.).

In contrast with the other filter_by_ taxonomy methods, this one filter the taxonomic data using the scientific name field dwca.terms.taxon.ScientificName.

Warning

Because of that, use this method with precautions. If a scientific name of a rank above species (genus, order, etc…) is used, it could result in unexpected behaviour.

Parameters:

speciesList[str]: Scientific Name of species (or rank below) to filter data.
fuzzy_thresholdfloat, optional: If given any value > 0 it will use Levenshtein Distance with that threshold instead of exact match.

get_parents(taxa_id: List[str]) → Set[str]#

Get a list of taxa ids of the parent of the list taxa id provided.

Parameters:

taxa_idList[str]: A list of dwca.terms.taxon.TaxonID to look for parents.

Returns:

Set[str]: Set of taxa ids.