# Licensed under a 3-clause BSD style license - see LICENSE.rst
# TODO: Test FITS parsing
# STDLIB
import io
import re
import gzip
import base64
import codecs
import urllib.request
import warnings
# THIRD-PARTY
import numpy as np
from numpy import ma
# LOCAL
from astropy.io import fits
from astropy import __version__ as astropy_version
from astropy.utils.collections import HomogeneousList
from astropy.utils.xml.writer import XMLWriter
from astropy.utils.exceptions import AstropyDeprecationWarning
from . import converters
from .exceptions import (warn_or_raise, vo_warn, vo_raise, vo_reraise,
warn_unknown_attrs, W06, W07, W08, W09, W10, W11, W12,
W13, W15, W17, W18, W19, W20, W21, W22, W26, W27, W28,
W29, W32, W33, W35, W36, W37, W38, W40, W41, W42, W43,
W44, W45, W50, W52, W53, W54, E06, E08, E09, E10, E11,
E12, E13, E15, E16, E17, E18, E19, E20, E21, E22, E23,
E25)
from . import ucd as ucd_mod
from . import util
from . import xmlutil
try:
from . import tablewriter
_has_c_tabledata_writer = True
except ImportError:
_has_c_tabledata_writer = False
__all__ = [
'Link', 'Info', 'Values', 'Field', 'Param', 'CooSys', 'TimeSys',
'FieldRef', 'ParamRef', 'Group', 'Table', 'Resource',
'VOTableFile', 'Element'
]
# The default number of rows to read in each chunk before converting
# to an array.
DEFAULT_CHUNK_SIZE = 256
RESIZE_AMOUNT = 1.5
######################################################################
# FACTORY FUNCTIONS
def _resize(masked, new_size):
"""
Masked arrays can not be resized inplace, and `np.resize` and
`ma.resize` are both incompatible with structured arrays.
Therefore, we do all this.
"""
new_array = ma.zeros((new_size,), dtype=masked.dtype)
length = min(len(masked), new_size)
new_array[:length] = masked[:length]
return new_array
def _lookup_by_attr_factory(attr, unique, iterator, element_name, doc):
"""
Creates a function useful for looking up an element by a given
attribute.
Parameters
----------
attr : str
The attribute name
unique : bool
Should be `True` if the attribute is unique and therefore this
should return only one value. Otherwise, returns a list of
values.
iterator : generator
A generator that iterates over some arbitrary set of elements
element_name : str
The XML element name of the elements being iterated over (used
for error messages only).
doc : str
A docstring to apply to the generated function.
Returns
-------
factory : function
A function that looks up an element by the given attribute.
"""
def lookup_by_attr(self, ref, before=None):
"""
Given a string *ref*, finds the first element in the iterator
where the given attribute == *ref*. If *before* is provided,
will stop searching at the object *before*. This is
important, since "forward references" are not allowed in the
VOTABLE format.
"""
for element in getattr(self, iterator)():
if element is before:
if getattr(element, attr, None) == ref:
vo_raise(
f"{element_name} references itself",
element._config, element._pos, KeyError)
break
if getattr(element, attr, None) == ref:
yield element
def lookup_by_attr_unique(self, ref, before=None):
for element in lookup_by_attr(self, ref, before=before):
return element
raise KeyError(
"No {} with {} '{}' found before the referencing {}".format(
element_name, attr, ref, element_name))
if unique:
lookup_by_attr_unique.__doc__ = doc
return lookup_by_attr_unique
else:
lookup_by_attr.__doc__ = doc
return lookup_by_attr
def _lookup_by_id_or_name_factory(iterator, element_name, doc):
"""
Like `_lookup_by_attr_factory`, but looks in both the "ID" and
"name" attributes.
"""
def lookup_by_id_or_name(self, ref, before=None):
"""
Given an key *ref*, finds the first element in the iterator
with the attribute ID == *ref* or name == *ref*. If *before*
is provided, will stop searching at the object *before*. This
is important, since "forward references" are not allowed in
the VOTABLE format.
"""
for element in getattr(self, iterator)():
if element is before:
if ref in (element.ID, element.name):
vo_raise(
f"{element_name} references itself",
element._config, element._pos, KeyError)
break
if ref in (element.ID, element.name):
return element
raise KeyError(
"No {} with ID or name '{}' found before the referencing {}".format(
element_name, ref, element_name))
lookup_by_id_or_name.__doc__ = doc
return lookup_by_id_or_name
def _get_default_unit_format(config):
"""
Get the default unit format as specified in the VOTable spec.
"""
# The unit format changed between VOTable versions 1.3 and 1.4,
# see issue #10791.
if config['version_1_4_or_later']:
return 'vounit'
else:
return 'cds'
def _get_unit_format(config):
"""
Get the unit format based on the configuration.
"""
if config.get('unit_format') is None:
format = _get_default_unit_format(config)
else:
format = config['unit_format']
return format
######################################################################
# ATTRIBUTE CHECKERS
def check_astroyear(year, field, config=None, pos=None):
"""
Raises a `~astropy.io.votable.exceptions.VOTableSpecError` if
*year* is not a valid astronomical year as defined by the VOTABLE
standard.
Parameters
----------
year : str
An astronomical year string
field : str
The name of the field this year was found in (used for error
message)
config, pos : optional
Information about the source of the value
"""
if (year is not None and
re.match(r"^[JB]?[0-9]+([.][0-9]*)?$", year) is None):
warn_or_raise(W07, W07, (field, year), config, pos)
return False
return True
def check_string(string, attr_name, config=None, pos=None):
"""
Raises a `~astropy.io.votable.exceptions.VOTableSpecError` if
*string* is not a string or Unicode string.
Parameters
----------
string : str
An astronomical year string
attr_name : str
The name of the field this year was found in (used for error
message)
config, pos : optional
Information about the source of the value
"""
if string is not None and not isinstance(string, str):
warn_or_raise(W08, W08, attr_name, config, pos)
return False
return True
def resolve_id(ID, id, config=None, pos=None):
if ID is None and id is not None:
warn_or_raise(W09, W09, (), config, pos)
return id
return ID
def check_ucd(ucd, config=None, pos=None):
"""
Warns or raises a
`~astropy.io.votable.exceptions.VOTableSpecError` if *ucd* is not
a valid `unified content descriptor`_ string as defined by the
VOTABLE standard.
Parameters
----------
ucd : str
A UCD string.
config, pos : optional
Information about the source of the value
"""
if config is None:
config = {}
if config.get('version_1_1_or_later'):
try:
ucd_mod.parse_ucd(
ucd,
check_controlled_vocabulary=config.get(
'version_1_2_or_later', False),
has_colon=config.get('version_1_2_or_later', False))
except ValueError as e:
# This weird construction is for Python 3 compatibility
if config.get('verify', 'ignore') == 'exception':
vo_raise(W06, (ucd, str(e)), config, pos)
elif config.get('verify', 'ignore') == 'warn':
vo_warn(W06, (ucd, str(e)), config, pos)
return False
else:
return False
return True
######################################################################
# PROPERTY MIXINS
class _IDProperty:
@property
def ID(self):
"""
The XML ID_ of the element. May be `None` or a string
conforming to XML ID_ syntax.
"""
return self._ID
@ID.setter
def ID(self, ID):
xmlutil.check_id(ID, 'ID', self._config, self._pos)
self._ID = ID
@ID.deleter
def ID(self):
self._ID = None
class _NameProperty:
@property
def name(self):
"""An optional name for the element."""
return self._name
@name.setter
def name(self, name):
xmlutil.check_token(name, 'name', self._config, self._pos)
self._name = name
@name.deleter
def name(self):
self._name = None
class _XtypeProperty:
@property
def xtype(self):
"""Extended data type information."""
return self._xtype
@xtype.setter
def xtype(self, xtype):
if xtype is not None and not self._config.get('version_1_2_or_later'):
warn_or_raise(
W28, W28, ('xtype', self._element_name, '1.2'),
self._config, self._pos)
check_string(xtype, 'xtype', self._config, self._pos)
self._xtype = xtype
@xtype.deleter
def xtype(self):
self._xtype = None
class _UtypeProperty:
_utype_in_v1_2 = False
@property
def utype(self):
"""The usage-specific or `unique type`_ of the element."""
return self._utype
@utype.setter
def utype(self, utype):
if (self._utype_in_v1_2 and
utype is not None and
not self._config.get('version_1_2_or_later')):
warn_or_raise(
W28, W28, ('utype', self._element_name, '1.2'),
self._config, self._pos)
check_string(utype, 'utype', self._config, self._pos)
self._utype = utype
@utype.deleter
def utype(self):
self._utype = None
class _UcdProperty:
_ucd_in_v1_2 = False
@property
def ucd(self):
"""The `unified content descriptor`_ for the element."""
return self._ucd
@ucd.setter
def ucd(self, ucd):
if ucd is not None and ucd.strip() == '':
ucd = None
if ucd is not None:
if (self._ucd_in_v1_2 and
not self._config.get('version_1_2_or_later')):
warn_or_raise(
W28, W28, ('ucd', self._element_name, '1.2'),
self._config, self._pos)
check_ucd(ucd, self._config, self._pos)
self._ucd = ucd
@ucd.deleter
def ucd(self):
self._ucd = None
class _DescriptionProperty:
@property
def description(self):
"""
An optional string describing the element. Corresponds to the
DESCRIPTION_ element.
"""
return self._description
@description.setter
def description(self, description):
self._description = description
@description.deleter
def description(self):
self._description = None
######################################################################
# ELEMENT CLASSES
class Element:
"""
A base class for all classes that represent XML elements in the
VOTABLE file.
"""
_element_name = ''
_attr_list = []
def _add_unknown_tag(self, iterator, tag, data, config, pos):
warn_or_raise(W10, W10, tag, config, pos)
def _ignore_add(self, iterator, tag, data, config, pos):
warn_unknown_attrs(tag, data.keys(), config, pos)
def _add_definitions(self, iterator, tag, data, config, pos):
if config.get('version_1_1_or_later'):
warn_or_raise(W22, W22, (), config, pos)
warn_unknown_attrs(tag, data.keys(), config, pos)
def parse(self, iterator, config):
"""
For internal use. Parse the XML content of the children of the
element.
Parameters
----------
iterator : xml iterable
An iterator over XML elements as returned by
`~astropy.utils.xml.iterparser.get_xml_iterator`.
config : dict
The configuration dictionary that affects how certain
elements are read.
Returns
-------
self : `~astropy.io.votable.tree.Element`
Returns self as a convenience.
"""
raise NotImplementedError()
def to_xml(self, w, **kwargs):
"""
For internal use. Output the element to XML.
Parameters
----------
w : astropy.utils.xml.writer.XMLWriter object
An XML writer to write to.
**kwargs : dict
Any configuration parameters to control the output.
"""
raise NotImplementedError()
class SimpleElement(Element):
"""
A base class for simple elements, such as FIELD, PARAM and INFO
that don't require any special parsing or outputting machinery.
"""
def __init__(self):
Element.__init__(self)
def __repr__(self):
buff = io.StringIO()
SimpleElement.to_xml(self, XMLWriter(buff))
return buff.getvalue().strip()
def parse(self, iterator, config):
for start, tag, data, pos in iterator:
if start and tag != self._element_name:
self._add_unknown_tag(iterator, tag, data, config, pos)
elif tag == self._element_name:
break
return self
def to_xml(self, w, **kwargs):
w.element(self._element_name,
attrib=w.object_attrs(self, self._attr_list))
class SimpleElementWithContent(SimpleElement):
"""
A base class for simple elements, such as FIELD, PARAM and INFO
that don't require any special parsing or outputting machinery.
"""
def __init__(self):
SimpleElement.__init__(self)
self._content = None
def parse(self, iterator, config):
for start, tag, data, pos in iterator:
if start and tag != self._element_name:
self._add_unknown_tag(iterator, tag, data, config, pos)
elif tag == self._element_name:
if data:
self.content = data
break
return self
def to_xml(self, w, **kwargs):
w.element(self._element_name, self._content,
attrib=w.object_attrs(self, self._attr_list))
@property
def content(self):
"""The content of the element."""
return self._content
@content.setter
def content(self, content):
check_string(content, 'content', self._config, self._pos)
self._content = content
@content.deleter
def content(self):
self._content = None
class Link(SimpleElement, _IDProperty):
"""
LINK_ elements: used to reference external documents and servers through a URI.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
_attr_list = ['ID', 'content_role', 'content_type', 'title', 'value',
'href', 'action']
_element_name = 'LINK'
def __init__(self, ID=None, title=None, value=None, href=None, action=None,
id=None, config=None, pos=None, **kwargs):
if config is None:
config = {}
self._config = config
self._pos = pos
SimpleElement.__init__(self)
content_role = kwargs.get('content-role') or kwargs.get('content_role')
content_type = kwargs.get('content-type') or kwargs.get('content_type')
if 'gref' in kwargs:
warn_or_raise(W11, W11, (), config, pos)
self.ID = resolve_id(ID, id, config, pos)
self.content_role = content_role
self.content_type = content_type
self.title = title
self.value = value
self.href = href
self.action = action
warn_unknown_attrs(
'LINK', kwargs.keys(), config, pos,
['content-role', 'content_role', 'content-type', 'content_type',
'gref'])
@property
def content_role(self):
"""
Defines the MIME role of the referenced object. Must be one of:
None, 'query', 'hints', 'doc', 'location' or 'type'
"""
return self._content_role
@content_role.setter
def content_role(self, content_role):
if ((content_role == 'type' and
not self._config['version_1_3_or_later']) or
content_role not in
(None, 'query', 'hints', 'doc', 'location')):
vo_warn(W45, (content_role,), self._config, self._pos)
self._content_role = content_role
@content_role.deleter
def content_role(self):
self._content_role = None
@property
def content_type(self):
"""Defines the MIME content type of the referenced object."""
return self._content_type
@content_type.setter
def content_type(self, content_type):
xmlutil.check_mime_content_type(content_type, self._config, self._pos)
self._content_type = content_type
@content_type.deleter
def content_type(self):
self._content_type = None
@property
def href(self):
"""
A URI to an arbitrary protocol. The vo package only supports
http and anonymous ftp.
"""
return self._href
@href.setter
def href(self, href):
xmlutil.check_anyuri(href, self._config, self._pos)
self._href = href
@href.deleter
def href(self):
self._href = None
def to_table_column(self, column):
meta = {}
for key in self._attr_list:
val = getattr(self, key, None)
if val is not None:
meta[key] = val
column.meta.setdefault('links', [])
column.meta['links'].append(meta)
@classmethod
def from_table_column(cls, d):
return cls(**d)
class Info(SimpleElementWithContent, _IDProperty, _XtypeProperty,
_UtypeProperty):
"""
INFO_ elements: arbitrary key-value pairs for extensions to the standard.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
_element_name = 'INFO'
_attr_list_11 = ['ID', 'name', 'value']
_attr_list_12 = _attr_list_11 + ['xtype', 'ref', 'unit', 'ucd', 'utype']
_utype_in_v1_2 = True
def __init__(self, ID=None, name=None, value=None, id=None, xtype=None,
ref=None, unit=None, ucd=None, utype=None,
config=None, pos=None, **extra):
if config is None:
config = {}
self._config = config
self._pos = pos
SimpleElementWithContent.__init__(self)
self.ID = (resolve_id(ID, id, config, pos) or
xmlutil.fix_id(name, config, pos))
self.name = name
self.value = value
self.xtype = xtype
self.ref = ref
self.unit = unit
self.ucd = ucd
self.utype = utype
if config.get('version_1_2_or_later'):
self._attr_list = self._attr_list_12
else:
self._attr_list = self._attr_list_11
if xtype is not None:
warn_unknown_attrs('INFO', ['xtype'], config, pos)
if ref is not None:
warn_unknown_attrs('INFO', ['ref'], config, pos)
if unit is not None:
warn_unknown_attrs('INFO', ['unit'], config, pos)
if ucd is not None:
warn_unknown_attrs('INFO', ['ucd'], config, pos)
if utype is not None:
warn_unknown_attrs('INFO', ['utype'], config, pos)
warn_unknown_attrs('INFO', extra.keys(), config, pos)
@property
def name(self):
"""[*required*] The key of the key-value pair."""
return self._name
@name.setter
def name(self, name):
if name is None:
warn_or_raise(W35, W35, ('name'), self._config, self._pos)
xmlutil.check_token(name, 'name', self._config, self._pos)
self._name = name
@property
def value(self):
"""
[*required*] The value of the key-value pair. (Always stored
as a string or unicode string).
"""
return self._value
@value.setter
def value(self, value):
if value is None:
warn_or_raise(W35, W35, ('value'), self._config, self._pos)
check_string(value, 'value', self._config, self._pos)
self._value = value
@property
def content(self):
"""The content inside the INFO element."""
return self._content
@content.setter
def content(self, content):
check_string(content, 'content', self._config, self._pos)
self._content = content
@content.deleter
def content(self):
self._content = None
@property
def ref(self):
"""
Refer to another INFO_ element by ID_, defined previously in
the document.
"""
return self._ref
@ref.setter
def ref(self, ref):
if ref is not None and not self._config.get('version_1_2_or_later'):
warn_or_raise(W28, W28, ('ref', 'INFO', '1.2'),
self._config, self._pos)
xmlutil.check_id(ref, 'ref', self._config, self._pos)
# TODO: actually apply the reference
# if ref is not None:
# try:
# other = self._votable.get_values_by_id(ref, before=self)
# except KeyError:
# vo_raise(
# "VALUES ref='%s', which has not already been defined." %
# self.ref, self._config, self._pos, KeyError)
# self.null = other.null
# self.type = other.type
# self.min = other.min
# self.min_inclusive = other.min_inclusive
# self.max = other.max
# self.max_inclusive = other.max_inclusive
# self._options[:] = other.options
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
@property
def unit(self):
"""A string specifying the units_ for the INFO_."""
return self._unit
@unit.setter
def unit(self, unit):
if unit is None:
self._unit = None
return
from astropy import units as u
if not self._config.get('version_1_2_or_later'):
warn_or_raise(W28, W28, ('unit', 'INFO', '1.2'),
self._config, self._pos)
# First, parse the unit in the default way, so that we can
# still emit a warning if the unit is not to spec.
default_format = _get_default_unit_format(self._config)
unit_obj = u.Unit(
unit, format=default_format, parse_strict='silent')
if isinstance(unit_obj, u.UnrecognizedUnit):
warn_or_raise(W50, W50, (unit,),
self._config, self._pos)
format = _get_unit_format(self._config)
if format != default_format:
unit_obj = u.Unit(
unit, format=format, parse_strict='silent')
self._unit = unit_obj
@unit.deleter
def unit(self):
self._unit = None
def to_xml(self, w, **kwargs):
attrib = w.object_attrs(self, self._attr_list)
if 'unit' in attrib:
attrib['unit'] = self.unit.to_string('cds')
w.element(self._element_name, self._content,
attrib=attrib)
class Values(Element, _IDProperty):
"""
VALUES_ element: used within FIELD_ and PARAM_ elements to define the domain of values.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
def __init__(self, votable, field, ID=None, null=None, ref=None,
type="legal", id=None, config=None, pos=None, **extras):
if config is None:
config = {}
self._config = config
self._pos = pos
Element.__init__(self)
self._votable = votable
self._field = field
self.ID = resolve_id(ID, id, config, pos)
self.null = null
self._ref = ref
self.type = type
self.min = None
self.max = None
self.min_inclusive = True
self.max_inclusive = True
self._options = []
warn_unknown_attrs('VALUES', extras.keys(), config, pos)
def __repr__(self):
buff = io.StringIO()
self.to_xml(XMLWriter(buff))
return buff.getvalue().strip()
@property
def null(self):
"""
For integral datatypes, *null* is used to define the value
used for missing values.
"""
return self._null
@null.setter
def null(self, null):
if null is not None and isinstance(null, str):
try:
null_val = self._field.converter.parse_scalar(
null, self._config, self._pos)[0]
except Exception:
warn_or_raise(W36, W36, null, self._config, self._pos)
null_val = self._field.converter.parse_scalar(
'0', self._config, self._pos)[0]
else:
null_val = null
self._null = null_val
@null.deleter
def null(self):
self._null = None
@property
def type(self):
"""
[*required*] Defines the applicability of the domain defined
by this VALUES_ element. Must be one of the following
strings:
- 'legal': The domain of this column applies in general to
this datatype. (default)
- 'actual': The domain of this column applies only to the
data enclosed in the parent table.
"""
return self._type
@type.setter
def type(self, type):
if type not in ('legal', 'actual'):
vo_raise(E08, type, self._config, self._pos)
self._type = type
@property
def ref(self):
"""
Refer to another VALUES_ element by ID_, defined previously in
the document, for MIN/MAX/OPTION information.
"""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
if ref is not None:
try:
other = self._votable.get_values_by_id(ref, before=self)
except KeyError:
warn_or_raise(W43, W43, ('VALUES', self.ref), self._config,
self._pos)
ref = None
else:
self.null = other.null
self.type = other.type
self.min = other.min
self.min_inclusive = other.min_inclusive
self.max = other.max
self.max_inclusive = other.max_inclusive
self._options[:] = other.options
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
@property
def min(self):
"""
The minimum value of the domain. See :attr:`min_inclusive`.
"""
return self._min
@min.setter
def min(self, min):
if hasattr(self._field, 'converter') and min is not None:
self._min = self._field.converter.parse(min)[0]
else:
self._min = min
@min.deleter
def min(self):
self._min = None
@property
def min_inclusive(self):
"""When `True`, the domain includes the minimum value."""
return self._min_inclusive
@min_inclusive.setter
def min_inclusive(self, inclusive):
if inclusive == 'yes':
self._min_inclusive = True
elif inclusive == 'no':
self._min_inclusive = False
else:
self._min_inclusive = bool(inclusive)
@min_inclusive.deleter
def min_inclusive(self):
self._min_inclusive = True
@property
def max(self):
"""
The maximum value of the domain. See :attr:`max_inclusive`.
"""
return self._max
@max.setter
def max(self, max):
if hasattr(self._field, 'converter') and max is not None:
self._max = self._field.converter.parse(max)[0]
else:
self._max = max
@max.deleter
def max(self):
self._max = None
@property
def max_inclusive(self):
"""When `True`, the domain includes the maximum value."""
return self._max_inclusive
@max_inclusive.setter
def max_inclusive(self, inclusive):
if inclusive == 'yes':
self._max_inclusive = True
elif inclusive == 'no':
self._max_inclusive = False
else:
self._max_inclusive = bool(inclusive)
@max_inclusive.deleter
def max_inclusive(self):
self._max_inclusive = True
@property
def options(self):
"""
A list of string key-value tuples defining other OPTION
elements for the domain. All options are ignored -- they are
stored for round-tripping purposes only.
"""
return self._options
def parse(self, iterator, config):
if self.ref is not None:
for start, tag, data, pos in iterator:
if start:
warn_or_raise(W44, W44, tag, config, pos)
else:
if tag != 'VALUES':
warn_or_raise(W44, W44, tag, config, pos)
break
else:
for start, tag, data, pos in iterator:
if start:
if tag == 'MIN':
if 'value' not in data:
vo_raise(E09, 'MIN', config, pos)
self.min = data['value']
self.min_inclusive = data.get('inclusive', 'yes')
warn_unknown_attrs(
'MIN', data.keys(), config, pos,
['value', 'inclusive'])
elif tag == 'MAX':
if 'value' not in data:
vo_raise(E09, 'MAX', config, pos)
self.max = data['value']
self.max_inclusive = data.get('inclusive', 'yes')
warn_unknown_attrs(
'MAX', data.keys(), config, pos,
['value', 'inclusive'])
elif tag == 'OPTION':
if 'value' not in data:
vo_raise(E09, 'OPTION', config, pos)
xmlutil.check_token(
data.get('name'), 'name', config, pos)
self.options.append(
(data.get('name'), data.get('value')))
warn_unknown_attrs(
'OPTION', data.keys(), config, pos,
['value', 'name'])
elif tag == 'VALUES':
break
return self
def is_defaults(self):
"""
Are the settings on this ``VALUE`` element all the same as the
XML defaults?
"""
# If there's nothing meaningful or non-default to write,
# don't write anything.
return (self.ref is None and self.null is None and self.ID is None and
self.max is None and self.min is None and self.options == [])
def to_xml(self, w, **kwargs):
def yes_no(value):
if value:
return 'yes'
return 'no'
if self.is_defaults():
return
if self.ref is not None:
w.element('VALUES', attrib=w.object_attrs(self, ['ref']))
else:
with w.tag('VALUES',
attrib=w.object_attrs(
self, ['ID', 'null', 'ref'])):
if self.min is not None:
w.element(
'MIN',
value=self._field.converter.output(self.min, False),
inclusive=yes_no(self.min_inclusive))
if self.max is not None:
w.element(
'MAX',
value=self._field.converter.output(self.max, False),
inclusive=yes_no(self.max_inclusive))
for name, value in self.options:
w.element(
'OPTION',
name=name,
value=value)
def to_table_column(self, column):
# Have the ref filled in here
meta = {}
for key in ['ID', 'null']:
val = getattr(self, key, None)
if val is not None:
meta[key] = val
if self.min is not None:
meta['min'] = {
'value': self.min,
'inclusive': self.min_inclusive}
if self.max is not None:
meta['max'] = {
'value': self.max,
'inclusive': self.max_inclusive}
if len(self.options):
meta['options'] = dict(self.options)
column.meta['values'] = meta
def from_table_column(self, column):
if column.info.meta is None or 'values' not in column.info.meta:
return
meta = column.info.meta['values']
for key in ['ID', 'null']:
val = meta.get(key, None)
if val is not None:
setattr(self, key, val)
if 'min' in meta:
self.min = meta['min']['value']
self.min_inclusive = meta['min']['inclusive']
if 'max' in meta:
self.max = meta['max']['value']
self.max_inclusive = meta['max']['inclusive']
if 'options' in meta:
self._options = list(meta['options'].items())
class Field(SimpleElement, _IDProperty, _NameProperty, _XtypeProperty,
_UtypeProperty, _UcdProperty):
"""
FIELD_ element: describes the datatype of a particular column of data.
The keyword arguments correspond to setting members of the same
name, documented below.
If *ID* is provided, it is used for the column name in the
resulting recarray of the table. If no *ID* is provided, *name*
is used instead. If neither is provided, an exception will be
raised.
"""
_attr_list_11 = ['ID', 'name', 'datatype', 'arraysize', 'ucd',
'unit', 'width', 'precision', 'utype', 'ref']
_attr_list_12 = _attr_list_11 + ['xtype']
_element_name = 'FIELD'
def __init__(self, votable, ID=None, name=None, datatype=None,
arraysize=None, ucd=None, unit=None, width=None,
precision=None, utype=None, ref=None, type=None, id=None,
xtype=None,
config=None, pos=None, **extra):
if config is None:
if hasattr(votable, '_get_version_checks'):
config = votable._get_version_checks()
else:
config = {}
self._config = config
self._pos = pos
SimpleElement.__init__(self)
if config.get('version_1_2_or_later'):
self._attr_list = self._attr_list_12
else:
self._attr_list = self._attr_list_11
if xtype is not None:
warn_unknown_attrs(self._element_name, ['xtype'], config, pos)
# TODO: REMOVE ME ----------------------------------------
# This is a terrible hack to support Simple Image Access
# Protocol results from https://astroarchive.noirlab.edu/ . It creates a field
# for the coordinate projection type of type "double", which
# actually contains character data. We have to hack the field
# to store character data, or we can't read it in. A warning
# will be raised when this happens.
if (config.get('verify', 'ignore') != 'exception' and name == 'cprojection' and
ID == 'cprojection' and ucd == 'VOX:WCS_CoordProjection' and
datatype == 'double'):
datatype = 'char'
arraysize = '3'
vo_warn(W40, (), config, pos)
# ----------------------------------------
self.description = None
self._votable = votable
self.ID = (resolve_id(ID, id, config, pos) or
xmlutil.fix_id(name, config, pos))
self.name = name
if name is None:
if (self._element_name == 'PARAM' and
not config.get('version_1_1_or_later')):
pass
else:
warn_or_raise(W15, W15, self._element_name, config, pos)
self.name = self.ID
if self._ID is None and name is None:
vo_raise(W12, self._element_name, config, pos)
datatype_mapping = {
'string': 'char',
'unicodeString': 'unicodeChar',
'int16': 'short',
'int32': 'int',
'int64': 'long',
'float32': 'float',
'float64': 'double',
# The following appear in some Vizier tables
'unsignedInt': 'long',
'unsignedShort': 'int'
}
datatype_mapping.update(config.get('datatype_mapping', {}))
if datatype in datatype_mapping:
warn_or_raise(W13, W13, (datatype, datatype_mapping[datatype]),
config, pos)
datatype = datatype_mapping[datatype]
self.ref = ref
self.datatype = datatype
self.arraysize = arraysize
self.ucd = ucd
self.unit = unit
self.width = width
self.precision = precision
self.utype = utype
self.type = type
self._links = HomogeneousList(Link)
self.title = self.name
self.values = Values(self._votable, self)
self.xtype = xtype
self._setup(config, pos)
warn_unknown_attrs(self._element_name, extra.keys(), config, pos)
@classmethod
def uniqify_names(cls, fields):
"""
Make sure that all names and titles in a list of fields are
unique, by appending numbers if necessary.
"""
unique = {}
for field in fields:
i = 2
new_id = field.ID
while new_id in unique:
new_id = field.ID + f"_{i:d}"
i += 1
if new_id != field.ID:
vo_warn(W32, (field.ID, new_id), field._config, field._pos)
field.ID = new_id
unique[new_id] = field.ID
for field in fields:
i = 2
if field.name is None:
new_name = field.ID
implicit = True
else:
new_name = field.name
implicit = False
if new_name != field.ID:
while new_name in unique:
new_name = field.name + f" {i:d}"
i += 1
if (not implicit and
new_name != field.name):
vo_warn(W33, (field.name, new_name), field._config, field._pos)
field._unique_name = new_name
unique[new_name] = field.name
def _setup(self, config, pos):
if self.values._ref is not None:
self.values.ref = self.values._ref
self.converter = converters.get_converter(self, config, pos)
@property
def datatype(self):
"""
[*required*] The datatype of the column. Valid values (as
defined by the spec) are:
'boolean', 'bit', 'unsignedByte', 'short', 'int', 'long',
'char', 'unicodeChar', 'float', 'double', 'floatComplex', or
'doubleComplex'
Many VOTABLE files in the wild use 'string' instead of 'char',
so that is also a valid option, though 'string' will always be
converted to 'char' when writing the file back out.
"""
return self._datatype
@datatype.setter
def datatype(self, datatype):
if datatype is None:
if self._config.get('version_1_1_or_later'):
warn_or_raise(E10, E10, self._element_name, self._config,
self._pos)
datatype = 'char'
if datatype not in converters.converter_mapping:
vo_raise(E06, (datatype, self.ID), self._config, self._pos)
self._datatype = datatype
@property
def precision(self):
"""
Along with :attr:`width`, defines the `numerical accuracy`_
associated with the data. These values are used to limit the
precision when writing floating point values back to the XML
file. Otherwise, it is purely informational -- the Numpy
recarray containing the data itself does not use this
information.
"""
return self._precision
@precision.setter
def precision(self, precision):
if precision is not None and not re.match(r"^[FE]?[0-9]+$", precision):
vo_raise(E11, precision, self._config, self._pos)
self._precision = precision
@precision.deleter
def precision(self):
self._precision = None
@property
def width(self):
"""
Along with :attr:`precision`, defines the `numerical
accuracy`_ associated with the data. These values are used to
limit the precision when writing floating point values back to
the XML file. Otherwise, it is purely informational -- the
Numpy recarray containing the data itself does not use this
information.
"""
return self._width
@width.setter
def width(self, width):
if width is not None:
width = int(width)
if width <= 0:
vo_raise(E12, width, self._config, self._pos)
self._width = width
@width.deleter
def width(self):
self._width = None
# ref on FIELD and PARAM behave differently than elsewhere -- here
# they're just informational, such as to refer to a coordinate
# system.
@property
def ref(self):
"""
On FIELD_ elements, ref is used only for informational
purposes, for example to refer to a COOSYS_ or TIMESYS_ element.
"""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
@property
def unit(self):
"""A string specifying the units_ for the FIELD_."""
return self._unit
@unit.setter
def unit(self, unit):
if unit is None:
self._unit = None
return
from astropy import units as u
# First, parse the unit in the default way, so that we can
# still emit a warning if the unit is not to spec.
default_format = _get_default_unit_format(self._config)
unit_obj = u.Unit(
unit, format=default_format, parse_strict='silent')
if isinstance(unit_obj, u.UnrecognizedUnit):
warn_or_raise(W50, W50, (unit,),
self._config, self._pos)
format = _get_unit_format(self._config)
if format != default_format:
unit_obj = u.Unit(
unit, format=format, parse_strict='silent')
self._unit = unit_obj
@unit.deleter
def unit(self):
self._unit = None
@property
def arraysize(self):
"""
Specifies the size of the multidimensional array if this
FIELD_ contains more than a single value.
See `multidimensional arrays`_.
"""
return self._arraysize
@arraysize.setter
def arraysize(self, arraysize):
if (arraysize is not None and
not re.match(r"^([0-9]+x)*[0-9]*[*]?(s\W)?$", arraysize)):
vo_raise(E13, arraysize, self._config, self._pos)
self._arraysize = arraysize
@arraysize.deleter
def arraysize(self):
self._arraysize = None
@property
def type(self):
"""
The type attribute on FIELD_ elements is reserved for future
extensions.
"""
return self._type
@type.setter
def type(self, type):
self._type = type
@type.deleter
def type(self):
self._type = None
@property
def values(self):
"""
A :class:`Values` instance (or `None`) defining the domain
of the column.
"""
return self._values
@values.setter
def values(self, values):
assert values is None or isinstance(values, Values)
self._values = values
@values.deleter
def values(self):
self._values = None
@property
def links(self):
"""
A list of :class:`Link` instances used to reference more
details about the meaning of the FIELD_. This is purely
informational and is not used by the `astropy.io.votable`
package.
"""
return self._links
def parse(self, iterator, config):
for start, tag, data, pos in iterator:
if start:
if tag == 'VALUES':
self.values.__init__(
self._votable, self, config=config, pos=pos, **data)
self.values.parse(iterator, config)
elif tag == 'LINK':
link = Link(config=config, pos=pos, **data)
self.links.append(link)
link.parse(iterator, config)
elif tag == 'DESCRIPTION':
warn_unknown_attrs(
'DESCRIPTION', data.keys(), config, pos)
elif tag != self._element_name:
self._add_unknown_tag(iterator, tag, data, config, pos)
else:
if tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(
W17, W17, self._element_name, config, pos)
self.description = data or None
elif tag == self._element_name:
break
if self.description is not None:
self.title = " ".join(x.strip() for x in
self.description.splitlines())
else:
self.title = self.name
self._setup(config, pos)
return self
def to_xml(self, w, **kwargs):
attrib = w.object_attrs(self, self._attr_list)
if 'unit' in attrib:
attrib['unit'] = self.unit.to_string('cds')
with w.tag(self._element_name, attrib=attrib):
if self.description is not None:
w.element('DESCRIPTION', self.description, wrap=True)
if not self.values.is_defaults():
self.values.to_xml(w, **kwargs)
for link in self.links:
link.to_xml(w, **kwargs)
def to_table_column(self, column):
"""
Sets the attributes of a given `astropy.table.Column` instance
to match the information in this `Field`.
"""
for key in ['ucd', 'width', 'precision', 'utype', 'xtype']:
val = getattr(self, key, None)
if val is not None:
column.meta[key] = val
if not self.values.is_defaults():
self.values.to_table_column(column)
for link in self.links:
link.to_table_column(column)
if self.description is not None:
column.description = self.description
if self.unit is not None:
# TODO: Use units framework when it's available
column.unit = self.unit
if (isinstance(self.converter, converters.FloatingPoint) and
self.converter.output_format != '{!r:>}'):
column.format = self.converter.output_format
elif isinstance(self.converter, converters.Char):
column.info.meta['_votable_string_dtype'] = 'char'
elif isinstance(self.converter, converters.UnicodeChar):
column.info.meta['_votable_string_dtype'] = 'unicodeChar'
@classmethod
def from_table_column(cls, votable, column):
"""
Restores a `Field` instance from a given
`astropy.table.Column` instance.
"""
kwargs = {}
meta = column.info.meta
if meta:
for key in ['ucd', 'width', 'precision', 'utype', 'xtype']:
val = meta.get(key, None)
if val is not None:
kwargs[key] = val
# TODO: Use the unit framework when available
if column.info.unit is not None:
kwargs['unit'] = column.info.unit
kwargs['name'] = column.info.name
result = converters.table_column_to_votable_datatype(column)
kwargs.update(result)
field = cls(votable, **kwargs)
if column.info.description is not None:
field.description = column.info.description
field.values.from_table_column(column)
if meta and 'links' in meta:
for link in meta['links']:
field.links.append(Link.from_table_column(link))
# TODO: Parse format into precision and width
return field
class Param(Field):
"""
PARAM_ element: constant-valued columns in the data.
:class:`Param` objects are a subclass of :class:`Field`, and have
all of its methods and members. Additionally, it defines :attr:`value`.
"""
_attr_list_11 = Field._attr_list_11 + ['value']
_attr_list_12 = Field._attr_list_12 + ['value']
_element_name = 'PARAM'
def __init__(self, votable, ID=None, name=None, value=None, datatype=None,
arraysize=None, ucd=None, unit=None, width=None,
precision=None, utype=None, type=None, id=None, config=None,
pos=None, **extra):
self._value = value
Field.__init__(self, votable, ID=ID, name=name, datatype=datatype,
arraysize=arraysize, ucd=ucd, unit=unit,
precision=precision, utype=utype, type=type,
id=id, config=config, pos=pos, **extra)
@property
def value(self):
"""
[*required*] The constant value of the parameter. Its type is
determined by the :attr:`~Field.datatype` member.
"""
return self._value
@value.setter
def value(self, value):
if value is None:
value = ""
if isinstance(value, str):
self._value = self.converter.parse(
value, self._config, self._pos)[0]
else:
self._value = value
def _setup(self, config, pos):
Field._setup(self, config, pos)
self.value = self._value
def to_xml(self, w, **kwargs):
tmp_value = self._value
self._value = self.converter.output(tmp_value, False)
# We must always have a value
if self._value is None:
self._value = ""
Field.to_xml(self, w, **kwargs)
self._value = tmp_value
class CooSys(SimpleElement):
"""
COOSYS_ element: defines a coordinate system.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
_attr_list = ['ID', 'equinox', 'epoch', 'system']
_element_name = 'COOSYS'
def __init__(self, ID=None, equinox=None, epoch=None, system=None, id=None,
config=None, pos=None, **extra):
if config is None:
config = {}
self._config = config
self._pos = pos
# COOSYS was deprecated in 1.2 but then re-instated in 1.3
if (config.get('version_1_2_or_later') and
not config.get('version_1_3_or_later')):
warn_or_raise(W27, W27, (), config, pos)
SimpleElement.__init__(self)
self.ID = resolve_id(ID, id, config, pos)
self.equinox = equinox
self.epoch = epoch
self.system = system
warn_unknown_attrs('COOSYS', extra.keys(), config, pos)
@property
def ID(self):
"""
[*required*] The XML ID of the COOSYS_ element, used for
cross-referencing. May be `None` or a string conforming to
XML ID_ syntax.
"""
return self._ID
@ID.setter
def ID(self, ID):
if self._config.get('version_1_1_or_later'):
if ID is None:
vo_raise(E15, (), self._config, self._pos)
xmlutil.check_id(ID, 'ID', self._config, self._pos)
self._ID = ID
@property
def system(self):
"""
Specifies the type of coordinate system. Valid choices are:
'eq_FK4', 'eq_FK5', 'ICRS', 'ecl_FK4', 'ecl_FK5', 'galactic',
'supergalactic', 'xy', 'barycentric', or 'geo_app'
"""
return self._system
@system.setter
def system(self, system):
if system not in ('eq_FK4', 'eq_FK5', 'ICRS', 'ecl_FK4', 'ecl_FK5',
'galactic', 'supergalactic', 'xy', 'barycentric',
'geo_app'):
warn_or_raise(E16, E16, system, self._config, self._pos)
self._system = system
@system.deleter
def system(self):
self._system = None
@property
def equinox(self):
"""
A parameter required to fix the equatorial or ecliptic systems
(as e.g. "J2000" as the default "eq_FK5" or "B1950" as the
default "eq_FK4").
"""
return self._equinox
@equinox.setter
def equinox(self, equinox):
check_astroyear(equinox, 'equinox', self._config, self._pos)
self._equinox = equinox
@equinox.deleter
def equinox(self):
self._equinox = None
@property
def epoch(self):
"""
Specifies the epoch of the positions. It must be a string
specifying an astronomical year.
"""
return self._epoch
@epoch.setter
def epoch(self, epoch):
check_astroyear(epoch, 'epoch', self._config, self._pos)
self._epoch = epoch
@epoch.deleter
def epoch(self):
self._epoch = None
class TimeSys(SimpleElement):
"""
TIMESYS_ element: defines a time system.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
_attr_list = ['ID', 'timeorigin', 'timescale', 'refposition']
_element_name = 'TIMESYS'
def __init__(self, ID=None, timeorigin=None, timescale=None, refposition=None, id=None,
config=None, pos=None, **extra):
if config is None:
config = {}
self._config = config
self._pos = pos
# TIMESYS is supported starting in version 1.4
if not config['version_1_4_or_later']:
warn_or_raise(
W54, W54, config['version'], config, pos)
SimpleElement.__init__(self)
self.ID = resolve_id(ID, id, config, pos)
self.timeorigin = timeorigin
self.timescale = timescale
self.refposition = refposition
warn_unknown_attrs('TIMESYS', extra.keys(), config, pos,
['ID', 'timeorigin', 'timescale', 'refposition'])
@property
def ID(self):
"""
[*required*] The XML ID of the TIMESYS_ element, used for
cross-referencing. Must be a string conforming to
XML ID_ syntax.
"""
return self._ID
@ID.setter
def ID(self, ID):
if ID is None:
vo_raise(E22, (), self._config, self._pos)
xmlutil.check_id(ID, 'ID', self._config, self._pos)
self._ID = ID
@property
def timeorigin(self):
"""
Specifies the time origin of the time coordinate,
given as a Julian Date for the the time scale and
reference point defined. It is usually given as a
floating point literal; for convenience, the magic
strings "MJD-origin" (standing for 2400000.5) and
"JD-origin" (standing for 0) are also allowed.
The timeorigin attribute MUST be given unless the
time’s representation contains a year of a calendar
era, in which case it MUST NOT be present. In VOTables,
these representations currently are Gregorian calendar
years with xtype="timestamp", or years in the Julian
or Besselian calendar when a column has yr, a, or Ba as
its unit and no time origin is given.
"""
return self._timeorigin
@timeorigin.setter
def timeorigin(self, timeorigin):
if (timeorigin is not None and
timeorigin != 'MJD-origin' and timeorigin != 'JD-origin'):
try:
timeorigin = float(timeorigin)
except ValueError:
warn_or_raise(E23, E23, timeorigin, self._config, self._pos)
self._timeorigin = timeorigin
@timeorigin.deleter
def timeorigin(self):
self._timeorigin = None
@property
def timescale(self):
"""
[*required*] String specifying the time scale used. Values
should be taken from the IVOA timescale vocabulary (documented
at http://www.ivoa.net/rdf/timescale).
"""
return self._timescale
@timescale.setter
def timescale(self, timescale):
self._timescale = timescale
@timescale.deleter
def timescale(self):
self._timescale = None
@property
def refposition(self):
"""
[*required*] String specifying the reference position. Values
should be taken from the IVOA refposition vocabulary (documented
at http://www.ivoa.net/rdf/refposition).
"""
return self._refposition
@refposition.setter
def refposition(self, refposition):
self._refposition = refposition
@refposition.deleter
def refposition(self):
self._refposition = None
class FieldRef(SimpleElement, _UtypeProperty, _UcdProperty):
"""
FIELDref_ element: used inside of GROUP_ elements to refer to remote FIELD_ elements.
"""
_attr_list_11 = ['ref']
_attr_list_12 = _attr_list_11 + ['ucd', 'utype']
_element_name = "FIELDref"
_utype_in_v1_2 = True
_ucd_in_v1_2 = True
def __init__(self, table, ref, ucd=None, utype=None, config=None, pos=None,
**extra):
"""
*table* is the :class:`Table` object that this :class:`FieldRef`
is a member of.
*ref* is the ID to reference a :class:`Field` object defined
elsewhere.
"""
if config is None:
config = {}
self._config = config
self._pos = pos
SimpleElement.__init__(self)
self._table = table
self.ref = ref
self.ucd = ucd
self.utype = utype
if config.get('version_1_2_or_later'):
self._attr_list = self._attr_list_12
else:
self._attr_list = self._attr_list_11
if ucd is not None:
warn_unknown_attrs(self._element_name, ['ucd'], config, pos)
if utype is not None:
warn_unknown_attrs(self._element_name, ['utype'], config, pos)
@property
def ref(self):
"""The ID_ of the FIELD_ that this FIELDref_ references."""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
def get_ref(self):
"""
Lookup the :class:`Field` instance that this :class:`FieldRef`
references.
"""
for field in self._table._votable.iter_fields_and_params():
if isinstance(field, Field) and field.ID == self.ref:
return field
vo_raise(
f"No field named '{self.ref}'",
self._config, self._pos, KeyError)
class ParamRef(SimpleElement, _UtypeProperty, _UcdProperty):
"""
PARAMref_ element: used inside of GROUP_ elements to refer to remote PARAM_ elements.
The keyword arguments correspond to setting members of the same
name, documented below.
It contains the following publicly-accessible members:
*ref*: An XML ID referring to a element.
"""
_attr_list_11 = ['ref']
_attr_list_12 = _attr_list_11 + ['ucd', 'utype']
_element_name = "PARAMref"
_utype_in_v1_2 = True
_ucd_in_v1_2 = True
def __init__(self, table, ref, ucd=None, utype=None, config=None, pos=None):
if config is None:
config = {}
self._config = config
self._pos = pos
Element.__init__(self)
self._table = table
self.ref = ref
self.ucd = ucd
self.utype = utype
if config.get('version_1_2_or_later'):
self._attr_list = self._attr_list_12
else:
self._attr_list = self._attr_list_11
if ucd is not None:
warn_unknown_attrs(self._element_name, ['ucd'], config, pos)
if utype is not None:
warn_unknown_attrs(self._element_name, ['utype'], config, pos)
@property
def ref(self):
"""The ID_ of the PARAM_ that this PARAMref_ references."""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
def get_ref(self):
"""
Lookup the :class:`Param` instance that this :class:``PARAMref``
references.
"""
for param in self._table._votable.iter_fields_and_params():
if isinstance(param, Param) and param.ID == self.ref:
return param
vo_raise(
f"No params named '{self.ref}'",
self._config, self._pos, KeyError)
class Group(Element, _IDProperty, _NameProperty, _UtypeProperty,
_UcdProperty, _DescriptionProperty):
"""
GROUP_ element: groups FIELD_ and PARAM_ elements.
This information is currently ignored by the vo package---that is
the columns in the recarray are always flat---but the grouping
information is stored so that it can be written out again to the
XML file.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
def __init__(self, table, ID=None, name=None, ref=None, ucd=None,
utype=None, id=None, config=None, pos=None, **extra):
if config is None:
config = {}
self._config = config
self._pos = pos
Element.__init__(self)
self._table = table
self.ID = (resolve_id(ID, id, config, pos)
or xmlutil.fix_id(name, config, pos))
self.name = name
self.ref = ref
self.ucd = ucd
self.utype = utype
self.description = None
self._entries = HomogeneousList(
(FieldRef, ParamRef, Group, Param))
warn_unknown_attrs('GROUP', extra.keys(), config, pos)
def __repr__(self):
return f'... {len(self._entries)} entries ...'
@property
def ref(self):
"""
Currently ignored, as it's not clear from the spec how this is
meant to work.
"""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
@property
def entries(self):
"""
[read-only] A list of members of the GROUP_. This list may
only contain objects of type :class:`Param`, :class:`Group`,
:class:`ParamRef` and :class:`FieldRef`.
"""
return self._entries
def _add_fieldref(self, iterator, tag, data, config, pos):
fieldref = FieldRef(self._table, config=config, pos=pos, **data)
self.entries.append(fieldref)
def _add_paramref(self, iterator, tag, data, config, pos):
paramref = ParamRef(self._table, config=config, pos=pos, **data)
self.entries.append(paramref)
def _add_param(self, iterator, tag, data, config, pos):
if isinstance(self._table, VOTableFile):
votable = self._table
else:
votable = self._table._votable
param = Param(votable, config=config, pos=pos, **data)
self.entries.append(param)
param.parse(iterator, config)
def _add_group(self, iterator, tag, data, config, pos):
group = Group(self._table, config=config, pos=pos, **data)
self.entries.append(group)
group.parse(iterator, config)
def parse(self, iterator, config):
tag_mapping = {
'FIELDref': self._add_fieldref,
'PARAMref': self._add_paramref,
'PARAM': self._add_param,
'GROUP': self._add_group,
'DESCRIPTION': self._ignore_add}
for start, tag, data, pos in iterator:
if start:
tag_mapping.get(tag, self._add_unknown_tag)(
iterator, tag, data, config, pos)
else:
if tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(W17, W17, 'GROUP', config, pos)
self.description = data or None
elif tag == 'GROUP':
break
return self
def to_xml(self, w, **kwargs):
with w.tag(
'GROUP',
attrib=w.object_attrs(
self, ['ID', 'name', 'ref', 'ucd', 'utype'])):
if self.description is not None:
w.element("DESCRIPTION", self.description, wrap=True)
for entry in self.entries:
entry.to_xml(w, **kwargs)
def iter_fields_and_params(self):
"""
Recursively iterate over all :class:`Param` elements in this
:class:`Group`.
"""
for entry in self.entries:
if isinstance(entry, Param):
yield entry
elif isinstance(entry, Group):
for field in entry.iter_fields_and_params():
yield field
def iter_groups(self):
"""
Recursively iterate over all sub-:class:`Group` instances in
this :class:`Group`.
"""
for entry in self.entries:
if isinstance(entry, Group):
yield entry
for group in entry.iter_groups():
yield group
class Table(Element, _IDProperty, _NameProperty, _UcdProperty,
_DescriptionProperty):
"""
TABLE_ element: optionally contains data.
It contains the following publicly-accessible and mutable
attribute:
*array*: A Numpy masked array of the data itself, where each
row is a row of votable data, and columns are named and typed
based on the elements of the table. The mask is
parallel to the data array, except for variable-length fields.
For those fields, the numpy array's column type is "object"
(``"O"``), and another masked array is stored there.
If the Table contains no data, (for example, its enclosing
:class:`Resource` has :attr:`~Resource.type` == 'meta') *array*
will have zero-length.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
def __init__(self, votable, ID=None, name=None, ref=None, ucd=None,
utype=None, nrows=None, id=None, config=None, pos=None,
**extra):
if config is None:
config = {}
self._config = config
self._pos = pos
self._empty = False
Element.__init__(self)
self._votable = votable
self.ID = (resolve_id(ID, id, config, pos)
or xmlutil.fix_id(name, config, pos))
self.name = name
xmlutil.check_id(ref, 'ref', config, pos)
self._ref = ref
self.ucd = ucd
self.utype = utype
if nrows is not None:
nrows = int(nrows)
if nrows < 0:
raise ValueError("'nrows' cannot be negative.")
self._nrows = nrows
self.description = None
self.format = 'tabledata'
self._fields = HomogeneousList(Field)
self._params = HomogeneousList(Param)
self._groups = HomogeneousList(Group)
self._links = HomogeneousList(Link)
self._infos = HomogeneousList(Info)
self.array = ma.array([])
warn_unknown_attrs('TABLE', extra.keys(), config, pos)
def __repr__(self):
return repr(self.to_table())
def __bytes__(self):
return bytes(self.to_table())
def __str__(self):
return str(self.to_table())
@property
def ref(self):
return self._ref
@ref.setter
def ref(self, ref):
"""
Refer to another TABLE, previously defined, by the *ref* ID_
for all metadata (FIELD_, PARAM_ etc.) information.
"""
# When the ref changes, we want to verify that it will work
# by actually going and looking for the referenced table.
# If found, set a bunch of properties in this table based
# on the other one.
xmlutil.check_id(ref, 'ref', self._config, self._pos)
if ref is not None:
try:
table = self._votable.get_table_by_id(ref, before=self)
except KeyError:
warn_or_raise(
W43, W43, ('TABLE', self.ref), self._config, self._pos)
ref = None
else:
self._fields = table.fields
self._params = table.params
self._groups = table.groups
self._links = table.links
else:
del self._fields[:]
del self._params[:]
del self._groups[:]
del self._links[:]
self._ref = ref
@ref.deleter
def ref(self):
self._ref = None
@property
def format(self):
"""
[*required*] The serialization format of the table. Must be
one of:
'tabledata' (TABLEDATA_), 'binary' (BINARY_), 'binary2' (BINARY2_)
'fits' (FITS_).
Note that the 'fits' format, since it requires an external
file, can not be written out. Any file read in with 'fits'
format will be read out, by default, in 'tabledata' format.
See :ref:`astropy:votable-serialization`.
"""
return self._format
@format.setter
def format(self, format):
format = format.lower()
if format == 'fits':
vo_raise("fits format can not be written out, only read.",
self._config, self._pos, NotImplementedError)
if format == 'binary2':
if not self._config['version_1_3_or_later']:
vo_raise(
"binary2 only supported in votable 1.3 or later",
self._config, self._pos)
elif format not in ('tabledata', 'binary'):
vo_raise(f"Invalid format '{format}'",
self._config, self._pos)
self._format = format
@property
def nrows(self):
"""
[*immutable*] The number of rows in the table, as specified in
the XML file.
"""
return self._nrows
@property
def fields(self):
"""
A list of :class:`Field` objects describing the types of each
of the data columns.
"""
return self._fields
@property
def params(self):
"""
A list of parameters (constant-valued columns) for the
table. Must contain only :class:`Param` objects.
"""
return self._params
@property
def groups(self):
"""
A list of :class:`Group` objects describing how the columns
and parameters are grouped. Currently this information is
only kept around for round-tripping and informational
purposes.
"""
return self._groups
@property
def links(self):
"""
A list of :class:`Link` objects (pointers to other documents
or servers through a URI) for the table.
"""
return self._links
@property
def infos(self):
"""
A list of :class:`Info` objects for the table. Allows for
post-operational diagnostics.
"""
return self._infos
def is_empty(self):
"""
Returns True if this table doesn't contain any real data
because it was skipped over by the parser (through use of the
``table_number`` kwarg).
"""
return self._empty
def create_arrays(self, nrows=0, config=None):
"""
Create a new array to hold the data based on the current set
of fields, and store them in the *array* and member variable.
Any data in the existing array will be lost.
*nrows*, if provided, is the number of rows to allocate.
"""
if nrows is None:
nrows = 0
fields = self.fields
if len(fields) == 0:
array = np.recarray((nrows,), dtype='O')
mask = np.zeros((nrows,), dtype='b')
else:
# for field in fields: field._setup(config)
Field.uniqify_names(fields)
dtype = []
for x in fields:
if x._unique_name == x.ID:
id = x.ID
else:
id = (x._unique_name, x.ID)
dtype.append((id, x.converter.format))
array = np.recarray((nrows,), dtype=np.dtype(dtype))
descr_mask = []
for d in array.dtype.descr:
new_type = (d[1][1] == 'O' and 'O') or 'bool'
if len(d) == 2:
descr_mask.append((d[0], new_type))
elif len(d) == 3:
descr_mask.append((d[0], new_type, d[2]))
mask = np.zeros((nrows,), dtype=descr_mask)
self.array = ma.array(array, mask=mask)
def _resize_strategy(self, size):
"""
Return a new (larger) size based on size, used for
reallocating an array when it fills up. This is in its own
function so the resizing strategy can be easily replaced.
"""
# Once we go beyond 0, make a big step -- after that use a
# factor of 1.5 to help keep memory usage compact
if size == 0:
return 512
return int(np.ceil(size * RESIZE_AMOUNT))
def _add_field(self, iterator, tag, data, config, pos):
field = Field(self._votable, config=config, pos=pos, **data)
self.fields.append(field)
field.parse(iterator, config)
def _add_param(self, iterator, tag, data, config, pos):
param = Param(self._votable, config=config, pos=pos, **data)
self.params.append(param)
param.parse(iterator, config)
def _add_group(self, iterator, tag, data, config, pos):
group = Group(self, config=config, pos=pos, **data)
self.groups.append(group)
group.parse(iterator, config)
def _add_link(self, iterator, tag, data, config, pos):
link = Link(config=config, pos=pos, **data)
self.links.append(link)
link.parse(iterator, config)
def _add_info(self, iterator, tag, data, config, pos):
if not config.get('version_1_2_or_later'):
warn_or_raise(W26, W26, ('INFO', 'TABLE', '1.2'), config, pos)
info = Info(config=config, pos=pos, **data)
self.infos.append(info)
info.parse(iterator, config)
def parse(self, iterator, config):
columns = config.get('columns')
# If we've requested to read in only a specific table, skip
# all others
table_number = config.get('table_number')
current_table_number = config.get('_current_table_number')
skip_table = False
if current_table_number is not None:
config['_current_table_number'] += 1
if (table_number is not None and
table_number != current_table_number):
skip_table = True
self._empty = True
table_id = config.get('table_id')
if table_id is not None:
if table_id != self.ID:
skip_table = True
self._empty = True
if self.ref is not None:
# This table doesn't have its own datatype descriptors, it
# just references those from another table.
# This is to call the property setter to go and get the
# referenced information
self.ref = self.ref
for start, tag, data, pos in iterator:
if start:
if tag == 'DATA':
warn_unknown_attrs(
'DATA', data.keys(), config, pos)
break
else:
if tag == 'TABLE':
return self
elif tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(W17, W17, 'RESOURCE', config, pos)
self.description = data or None
else:
tag_mapping = {
'FIELD': self._add_field,
'PARAM': self._add_param,
'GROUP': self._add_group,
'LINK': self._add_link,
'INFO': self._add_info,
'DESCRIPTION': self._ignore_add}
for start, tag, data, pos in iterator:
if start:
if tag == 'DATA':
if len(self.fields) == 0:
warn_or_raise(E25, E25, None, config, pos)
warn_unknown_attrs(
'DATA', data.keys(), config, pos)
break
tag_mapping.get(tag, self._add_unknown_tag)(
iterator, tag, data, config, pos)
else:
if tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(W17, W17, 'RESOURCE', config, pos)
self.description = data or None
elif tag == 'TABLE':
# For error checking purposes
Field.uniqify_names(self.fields)
# We still need to create arrays, even if the file
# contains no DATA section
self.create_arrays(nrows=0, config=config)
return self
self.create_arrays(nrows=self._nrows, config=config)
fields = self.fields
names = [x.ID for x in fields]
# Deal with a subset of the columns, if requested.
if not columns:
colnumbers = list(range(len(fields)))
else:
if isinstance(columns, str):
columns = [columns]
columns = np.asarray(columns)
if issubclass(columns.dtype.type, np.integer):
if np.any(columns < 0) or np.any(columns > len(fields)):
raise ValueError(
"Some specified column numbers out of range")
colnumbers = columns
elif issubclass(columns.dtype.type, np.character):
try:
colnumbers = [names.index(x) for x in columns]
except ValueError:
raise ValueError(
f"Columns '{columns}' not found in fields list")
else:
raise TypeError("Invalid columns list")
if (not skip_table) and (len(fields) > 0):
for start, tag, data, pos in iterator:
if start:
if tag == 'TABLEDATA':
warn_unknown_attrs(
'TABLEDATA', data.keys(), config, pos)
self.array = self._parse_tabledata(
iterator, colnumbers, fields, config)
break
elif tag == 'BINARY':
warn_unknown_attrs(
'BINARY', data.keys(), config, pos)
self.array = self._parse_binary(
1, iterator, colnumbers, fields, config, pos)
break
elif tag == 'BINARY2':
if not config['version_1_3_or_later']:
warn_or_raise(
W52, W52, config['version'], config, pos)
self.array = self._parse_binary(
2, iterator, colnumbers, fields, config, pos)
break
elif tag == 'FITS':
warn_unknown_attrs(
'FITS', data.keys(), config, pos, ['extnum'])
try:
extnum = int(data.get('extnum', 0))
if extnum < 0:
raise ValueError("'extnum' cannot be negative.")
except ValueError:
vo_raise(E17, (), config, pos)
self.array = self._parse_fits(
iterator, extnum, config)
break
else:
warn_or_raise(W37, W37, tag, config, pos)
break
for start, tag, data, pos in iterator:
if not start and tag == 'DATA':
break
for start, tag, data, pos in iterator:
if start and tag == 'INFO':
if not config.get('version_1_2_or_later'):
warn_or_raise(
W26, W26, ('INFO', 'TABLE', '1.2'), config, pos)
info = Info(config=config, pos=pos, **data)
self.infos.append(info)
info.parse(iterator, config)
elif not start and tag == 'TABLE':
break
return self
def _parse_tabledata(self, iterator, colnumbers, fields, config):
# Since we don't know the number of rows up front, we'll
# reallocate the record array to make room as we go. This
# prevents the need to scan through the XML twice. The
# allocation is by factors of 1.5.
invalid = config.get('invalid', 'exception')
# Need to have only one reference so that we can resize the
# array
array = self.array
del self.array
parsers = [field.converter.parse for field in fields]
binparsers = [field.converter.binparse for field in fields]
numrows = 0
alloc_rows = len(array)
colnumbers_bits = [i in colnumbers for i in range(len(fields))]
row_default = [x.converter.default for x in fields]
mask_default = [True] * len(fields)
array_chunk = []
mask_chunk = []
chunk_size = config.get('chunk_size', DEFAULT_CHUNK_SIZE)
for start, tag, data, pos in iterator:
if tag == 'TR':
# Now parse one row
row = row_default[:]
row_mask = mask_default[:]
i = 0
for start, tag, data, pos in iterator:
if start:
binary = (data.get('encoding', None) == 'base64')
warn_unknown_attrs(
tag, data.keys(), config, pos, ['encoding'])
else:
if tag == 'TD':
if i >= len(fields):
vo_raise(E20, len(fields), config, pos)
if colnumbers_bits[i]:
try:
if binary:
rawdata = base64.b64decode(
data.encode('ascii'))
buf = io.BytesIO(rawdata)
buf.seek(0)
try:
value, mask_value = binparsers[i](
buf.read)
except Exception as e:
vo_reraise(
e, config, pos,
"(in row {:d}, col '{}')".format(
len(array_chunk),
fields[i].ID))
else:
try:
value, mask_value = parsers[i](
data, config, pos)
except Exception as e:
vo_reraise(
e, config, pos,
"(in row {:d}, col '{}')".format(
len(array_chunk),
fields[i].ID))
except Exception as e:
if invalid == 'exception':
vo_reraise(e, config, pos)
else:
row[i] = value
row_mask[i] = mask_value
elif tag == 'TR':
break
else:
self._add_unknown_tag(
iterator, tag, data, config, pos)
i += 1
if i < len(fields):
vo_raise(E21, (i, len(fields)), config, pos)
array_chunk.append(tuple(row))
mask_chunk.append(tuple(row_mask))
if len(array_chunk) == chunk_size:
while numrows + chunk_size > alloc_rows:
alloc_rows = self._resize_strategy(alloc_rows)
if alloc_rows != len(array):
array = _resize(array, alloc_rows)
array[numrows:numrows + chunk_size] = array_chunk
array.mask[numrows:numrows + chunk_size] = mask_chunk
numrows += chunk_size
array_chunk = []
mask_chunk = []
elif not start and tag == 'TABLEDATA':
break
# Now, resize the array to the exact number of rows we need and
# put the last chunk values in there.
alloc_rows = numrows + len(array_chunk)
array = _resize(array, alloc_rows)
array[numrows:] = array_chunk
if alloc_rows != 0:
array.mask[numrows:] = mask_chunk
numrows += len(array_chunk)
if (self.nrows is not None and
self.nrows >= 0 and
self.nrows != numrows):
warn_or_raise(W18, W18, (self.nrows, numrows), config, pos)
self._nrows = numrows
return array
def _get_binary_data_stream(self, iterator, config):
have_local_stream = False
for start, tag, data, pos in iterator:
if tag == 'STREAM':
if start:
warn_unknown_attrs(
'STREAM', data.keys(), config, pos,
['type', 'href', 'actuate', 'encoding', 'expires',
'rights'])
if 'href' not in data:
have_local_stream = True
if data.get('encoding', None) != 'base64':
warn_or_raise(
W38, W38, data.get('encoding', None),
config, pos)
else:
href = data['href']
xmlutil.check_anyuri(href, config, pos)
encoding = data.get('encoding', None)
else:
buffer = data
break
if have_local_stream:
buffer = base64.b64decode(buffer.encode('ascii'))
string_io = io.BytesIO(buffer)
string_io.seek(0)
read = string_io.read
else:
if not href.startswith(('http', 'ftp', 'file')):
vo_raise(
"The vo package only supports remote data through http, " +
"ftp or file",
self._config, self._pos, NotImplementedError)
fd = urllib.request.urlopen(href)
if encoding is not None:
if encoding == 'gzip':
fd = gzip.GzipFile(href, 'rb', fileobj=fd)
elif encoding == 'base64':
fd = codecs.EncodedFile(fd, 'base64')
else:
vo_raise(
f"Unknown encoding type '{encoding}'",
self._config, self._pos, NotImplementedError)
read = fd.read
def careful_read(length):
result = read(length)
if len(result) != length:
raise EOFError
return result
return careful_read
def _parse_binary(self, mode, iterator, colnumbers, fields, config, pos):
fields = self.fields
careful_read = self._get_binary_data_stream(iterator, config)
# Need to have only one reference so that we can resize the
# array
array = self.array
del self.array
binparsers = [field.converter.binparse for field in fields]
numrows = 0
alloc_rows = len(array)
while True:
# Resize result arrays if necessary
if numrows >= alloc_rows:
alloc_rows = self._resize_strategy(alloc_rows)
array = _resize(array, alloc_rows)
row_data = []
row_mask_data = []
try:
if mode == 2:
mask_bits = careful_read(int((len(fields) + 7) / 8))
row_mask_data = list(converters.bitarray_to_bool(
mask_bits, len(fields)))
# Ignore the mask for string columns (see issue 8995)
for i, f in enumerate(fields):
if row_mask_data[i] and (f.datatype == 'char' or f.datatype == 'unicodeChar'):
row_mask_data[i] = False
for i, binparse in enumerate(binparsers):
try:
value, value_mask = binparse(careful_read)
except EOFError:
raise
except Exception as e:
vo_reraise(
e, config, pos, "(in row {:d}, col '{}')".format(
numrows, fields[i].ID))
row_data.append(value)
if mode == 1:
row_mask_data.append(value_mask)
else:
row_mask_data[i] = row_mask_data[i] or value_mask
except EOFError:
break
row = [x.converter.default for x in fields]
row_mask = [False] * len(fields)
for i in colnumbers:
row[i] = row_data[i]
row_mask[i] = row_mask_data[i]
array[numrows] = tuple(row)
array.mask[numrows] = tuple(row_mask)
numrows += 1
array = _resize(array, numrows)
return array
def _parse_fits(self, iterator, extnum, config):
for start, tag, data, pos in iterator:
if tag == 'STREAM':
if start:
warn_unknown_attrs(
'STREAM', data.keys(), config, pos,
['type', 'href', 'actuate', 'encoding', 'expires',
'rights'])
href = data['href']
encoding = data.get('encoding', None)
else:
break
if not href.startswith(('http', 'ftp', 'file')):
vo_raise(
"The vo package only supports remote data through http, "
"ftp or file",
self._config, self._pos, NotImplementedError)
fd = urllib.request.urlopen(href)
if encoding is not None:
if encoding == 'gzip':
fd = gzip.GzipFile(href, 'r', fileobj=fd)
elif encoding == 'base64':
fd = codecs.EncodedFile(fd, 'base64')
else:
vo_raise(
f"Unknown encoding type '{encoding}'",
self._config, self._pos, NotImplementedError)
hdulist = fits.open(fd)
array = hdulist[int(extnum)].data
if array.dtype != self.array.dtype:
warn_or_raise(W19, W19, (), self._config, self._pos)
return array
def to_xml(self, w, **kwargs):
specified_format = kwargs.get('tabledata_format')
if specified_format is not None:
format = specified_format
else:
format = self.format
if format == 'fits':
format = 'tabledata'
with w.tag(
'TABLE',
attrib=w.object_attrs(
self,
('ID', 'name', 'ref', 'ucd', 'utype', 'nrows'))):
if self.description is not None:
w.element("DESCRIPTION", self.description, wrap=True)
for element_set in (self.fields, self.params):
for element in element_set:
element._setup({}, None)
if self.ref is None:
for element_set in (self.fields, self.params, self.groups,
self.links):
for element in element_set:
element.to_xml(w, **kwargs)
elif kwargs['version_1_2_or_later']:
index = list(self._votable.iter_tables()).index(self)
group = Group(self, ID=f"_g{index}")
group.to_xml(w, **kwargs)
if len(self.array):
with w.tag('DATA'):
if format == 'tabledata':
self._write_tabledata(w, **kwargs)
elif format == 'binary':
self._write_binary(1, w, **kwargs)
elif format == 'binary2':
self._write_binary(2, w, **kwargs)
if kwargs['version_1_2_or_later']:
for element in self._infos:
element.to_xml(w, **kwargs)
def _write_tabledata(self, w, **kwargs):
fields = self.fields
array = self.array
with w.tag('TABLEDATA'):
w._flush()
if (_has_c_tabledata_writer and
not kwargs.get('_debug_python_based_parser')):
supports_empty_values = [
field.converter.supports_empty_values(kwargs)
for field in fields]
fields = [field.converter.output for field in fields]
indent = len(w._tags) - 1
tablewriter.write_tabledata(
w.write, array.data, array.mask, fields,
supports_empty_values, indent, 1 << 8)
else:
write = w.write
indent_spaces = w.get_indentation_spaces()
tr_start = indent_spaces + "\n"
tr_end = indent_spaces + "
\n"
td = indent_spaces + " {} | \n"
td_empty = indent_spaces + " | \n"
fields = [(i, field.converter.output,
field.converter.supports_empty_values(kwargs))
for i, field in enumerate(fields)]
for row in range(len(array)):
write(tr_start)
array_row = array.data[row]
mask_row = array.mask[row]
for i, output, supports_empty_values in fields:
data = array_row[i]
masked = mask_row[i]
if supports_empty_values and np.all(masked):
write(td_empty)
else:
try:
val = output(data, masked)
except Exception as e:
vo_reraise(
e,
additional="(in row {:d}, col '{}')".format(
row, self.fields[i].ID))
if len(val):
write(td.format(val))
else:
write(td_empty)
write(tr_end)
def _write_binary(self, mode, w, **kwargs):
fields = self.fields
array = self.array
if mode == 1:
tag_name = 'BINARY'
else:
tag_name = 'BINARY2'
with w.tag(tag_name):
with w.tag('STREAM', encoding='base64'):
fields_basic = [(i, field.converter.binoutput)
for (i, field) in enumerate(fields)]
data = io.BytesIO()
for row in range(len(array)):
array_row = array.data[row]
array_mask = array.mask[row]
if mode == 2:
flattened = np.array([np.all(x) for x in array_mask])
data.write(converters.bool_to_bitarray(flattened))
for i, converter in fields_basic:
try:
chunk = converter(array_row[i], array_mask[i])
assert type(chunk) == bytes
except Exception as e:
vo_reraise(
e, additional=f"(in row {row:d}, col '{fields[i].ID}')")
data.write(chunk)
w._flush()
w.write(base64.b64encode(data.getvalue()).decode('ascii'))
def to_table(self, use_names_over_ids=False):
"""
Convert this VO Table to an `astropy.table.Table` instance.
Parameters
----------
use_names_over_ids : bool, optional
When `True` use the ``name`` attributes of columns as the
names of columns in the `astropy.table.Table` instance.
Since names are not guaranteed to be unique, this may cause
some columns to be renamed by appending numbers to the end.
Otherwise (default), use the ID attributes as the column
names.
.. warning::
Variable-length array fields may not be restored
identically when round-tripping through the
`astropy.table.Table` instance.
"""
from astropy.table import Table
meta = {}
for key in ['ID', 'name', 'ref', 'ucd', 'utype', 'description']:
val = getattr(self, key, None)
if val is not None:
meta[key] = val
if use_names_over_ids:
names = [field.name for field in self.fields]
unique_names = []
for i, name in enumerate(names):
new_name = name
i = 2
while new_name in unique_names:
new_name = f'{name}{i}'
i += 1
unique_names.append(new_name)
names = unique_names
else:
names = [field.ID for field in self.fields]
table = Table(self.array, names=names, meta=meta)
for name, field in zip(names, self.fields):
column = table[name]
field.to_table_column(column)
return table
@classmethod
def from_table(cls, votable, table):
"""
Create a `Table` instance from a given `astropy.table.Table`
instance.
"""
kwargs = {}
for key in ['ID', 'name', 'ref', 'ucd', 'utype']:
val = table.meta.get(key)
if val is not None:
kwargs[key] = val
new_table = cls(votable, **kwargs)
if 'description' in table.meta:
new_table.description = table.meta['description']
for colname in table.colnames:
column = table[colname]
new_table.fields.append(Field.from_table_column(votable, column))
if table.mask is None:
new_table.array = ma.array(np.asarray(table))
else:
new_table.array = ma.array(np.asarray(table),
mask=np.asarray(table.mask))
return new_table
def iter_fields_and_params(self):
"""
Recursively iterate over all FIELD and PARAM elements in the
TABLE.
"""
for param in self.params:
yield param
for field in self.fields:
yield field
for group in self.groups:
for field in group.iter_fields_and_params():
yield field
get_field_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_fields_and_params', 'FIELD or PARAM',
"""
Looks up a FIELD or PARAM element by the given ID.
""")
get_field_by_id_or_name = _lookup_by_id_or_name_factory(
'iter_fields_and_params', 'FIELD or PARAM',
"""
Looks up a FIELD or PARAM element by the given ID or name.
""")
get_fields_by_utype = _lookup_by_attr_factory(
'utype', False, 'iter_fields_and_params', 'FIELD or PARAM',
"""
Looks up a FIELD or PARAM element by the given utype and
returns an iterator emitting all matches.
""")
def iter_groups(self):
"""
Recursively iterate over all GROUP elements in the TABLE.
"""
for group in self.groups:
yield group
for g in group.iter_groups():
yield g
get_group_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_groups', 'GROUP',
"""
Looks up a GROUP element by the given ID. Used by the group's
"ref" attribute
""")
get_groups_by_utype = _lookup_by_attr_factory(
'utype', False, 'iter_groups', 'GROUP',
"""
Looks up a GROUP element by the given utype and returns an
iterator emitting all matches.
""")
def iter_info(self):
for info in self.infos:
yield info
class Resource(Element, _IDProperty, _NameProperty, _UtypeProperty,
_DescriptionProperty):
"""
RESOURCE_ element: Groups TABLE_ and RESOURCE_ elements.
The keyword arguments correspond to setting members of the same
name, documented below.
"""
def __init__(self, name=None, ID=None, utype=None, type='results',
id=None, config=None, pos=None, **kwargs):
if config is None:
config = {}
self._config = config
self._pos = pos
Element.__init__(self)
self.name = name
self.ID = resolve_id(ID, id, config, pos)
self.utype = utype
self.type = type
self._extra_attributes = kwargs
self.description = None
self._coordinate_systems = HomogeneousList(CooSys)
self._time_systems = HomogeneousList(TimeSys)
self._groups = HomogeneousList(Group)
self._params = HomogeneousList(Param)
self._infos = HomogeneousList(Info)
self._links = HomogeneousList(Link)
self._tables = HomogeneousList(Table)
self._resources = HomogeneousList(Resource)
warn_unknown_attrs('RESOURCE', kwargs.keys(), config, pos)
def __repr__(self):
buff = io.StringIO()
w = XMLWriter(buff)
w.element(
self._element_name,
attrib=w.object_attrs(self, self._attr_list))
return buff.getvalue().strip()
@property
def type(self):
"""
[*required*] The type of the resource. Must be either:
- 'results': This resource contains actual result values
(default)
- 'meta': This resource contains only datatype descriptions
(FIELD_ elements), but no actual data.
"""
return self._type
@type.setter
def type(self, type):
if type not in ('results', 'meta'):
vo_raise(E18, type, self._config, self._pos)
self._type = type
@property
def extra_attributes(self):
"""
A dictionary of string keys to string values containing any
extra attributes of the RESOURCE_ element that are not defined
in the specification. (The specification explicitly allows
for extra attributes here, but nowhere else.)
"""
return self._extra_attributes
@property
def coordinate_systems(self):
"""
A list of coordinate system definitions (COOSYS_ elements) for
the RESOURCE_. Must contain only `CooSys` objects.
"""
return self._coordinate_systems
@property
def time_systems(self):
"""
A list of time system definitions (TIMESYS_ elements) for
the RESOURCE_. Must contain only `TimeSys` objects.
"""
return self._time_systems
@property
def infos(self):
"""
A list of informational parameters (key-value pairs) for the
resource. Must only contain `Info` objects.
"""
return self._infos
@property
def groups(self):
"""
A list of groups
"""
return self._groups
@property
def params(self):
"""
A list of parameters (constant-valued columns) for the
resource. Must contain only `Param` objects.
"""
return self._params
@property
def links(self):
"""
A list of links (pointers to other documents or servers
through a URI) for the resource. Must contain only `Link`
objects.
"""
return self._links
@property
def tables(self):
"""
A list of tables in the resource. Must contain only
`Table` objects.
"""
return self._tables
@property
def resources(self):
"""
A list of nested resources inside this resource. Must contain
only `Resource` objects.
"""
return self._resources
def _add_table(self, iterator, tag, data, config, pos):
table = Table(self._votable, config=config, pos=pos, **data)
self.tables.append(table)
table.parse(iterator, config)
def _add_info(self, iterator, tag, data, config, pos):
info = Info(config=config, pos=pos, **data)
self.infos.append(info)
info.parse(iterator, config)
def _add_group(self, iterator, tag, data, config, pos):
group = Group(self, config=config, pos=pos, **data)
self.groups.append(group)
group.parse(iterator, config)
def _add_param(self, iterator, tag, data, config, pos):
param = Param(self._votable, config=config, pos=pos, **data)
self.params.append(param)
param.parse(iterator, config)
def _add_coosys(self, iterator, tag, data, config, pos):
coosys = CooSys(config=config, pos=pos, **data)
self.coordinate_systems.append(coosys)
coosys.parse(iterator, config)
def _add_timesys(self, iterator, tag, data, config, pos):
timesys = TimeSys(config=config, pos=pos, **data)
self.time_systems.append(timesys)
timesys.parse(iterator, config)
def _add_resource(self, iterator, tag, data, config, pos):
resource = Resource(config=config, pos=pos, **data)
self.resources.append(resource)
resource.parse(self._votable, iterator, config)
def _add_link(self, iterator, tag, data, config, pos):
link = Link(config=config, pos=pos, **data)
self.links.append(link)
link.parse(iterator, config)
def parse(self, votable, iterator, config):
self._votable = votable
tag_mapping = {
'TABLE': self._add_table,
'INFO': self._add_info,
'PARAM': self._add_param,
'GROUP': self._add_group,
'COOSYS': self._add_coosys,
'TIMESYS': self._add_timesys,
'RESOURCE': self._add_resource,
'LINK': self._add_link,
'DESCRIPTION': self._ignore_add
}
for start, tag, data, pos in iterator:
if start:
tag_mapping.get(tag, self._add_unknown_tag)(
iterator, tag, data, config, pos)
elif tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(W17, W17, 'RESOURCE', config, pos)
self.description = data or None
elif tag == 'RESOURCE':
break
del self._votable
return self
def to_xml(self, w, **kwargs):
attrs = w.object_attrs(self, ('ID', 'type', 'utype'))
attrs.update(self.extra_attributes)
with w.tag('RESOURCE', attrib=attrs):
if self.description is not None:
w.element("DESCRIPTION", self.description, wrap=True)
for element_set in (self.coordinate_systems, self.time_systems,
self.params, self.infos, self.links,
self.tables, self.resources):
for element in element_set:
element.to_xml(w, **kwargs)
def iter_tables(self):
"""
Recursively iterates over all tables in the resource and
nested resources.
"""
for table in self.tables:
yield table
for resource in self.resources:
for table in resource.iter_tables():
yield table
def iter_fields_and_params(self):
"""
Recursively iterates over all FIELD_ and PARAM_ elements in
the resource, its tables and nested resources.
"""
for param in self.params:
yield param
for table in self.tables:
for param in table.iter_fields_and_params():
yield param
for resource in self.resources:
for param in resource.iter_fields_and_params():
yield param
def iter_coosys(self):
"""
Recursively iterates over all the COOSYS_ elements in the
resource and nested resources.
"""
for coosys in self.coordinate_systems:
yield coosys
for resource in self.resources:
for coosys in resource.iter_coosys():
yield coosys
def iter_timesys(self):
"""
Recursively iterates over all the TIMESYS_ elements in the
resource and nested resources.
"""
for timesys in self.time_systems:
yield timesys
for resource in self.resources:
for timesys in resource.iter_timesys():
yield timesys
def iter_info(self):
"""
Recursively iterates over all the INFO_ elements in the
resource and nested resources.
"""
for info in self.infos:
yield info
for table in self.tables:
for info in table.iter_info():
yield info
for resource in self.resources:
for info in resource.iter_info():
yield info
class VOTableFile(Element, _IDProperty, _DescriptionProperty):
"""
VOTABLE_ element: represents an entire file.
The keyword arguments correspond to setting members of the same
name, documented below.
*version* is settable at construction time only, since conformance
tests for building the rest of the structure depend on it.
"""
def __init__(self, ID=None, id=None, config=None, pos=None, version="1.4"):
if config is None:
config = {}
self._config = config
self._pos = pos
Element.__init__(self)
self.ID = resolve_id(ID, id, config, pos)
self.description = None
self._coordinate_systems = HomogeneousList(CooSys)
self._time_systems = HomogeneousList(TimeSys)
self._params = HomogeneousList(Param)
self._infos = HomogeneousList(Info)
self._resources = HomogeneousList(Resource)
self._groups = HomogeneousList(Group)
version = str(version)
if version == '1.0':
warnings.warn('VOTable 1.0 support is deprecated in astropy 4.3 and will be '
'removed in a future release', AstropyDeprecationWarning)
elif (version != '1.0') and (version not in self._version_namespace_map):
allowed_from_map = "', '".join(self._version_namespace_map)
raise ValueError(f"'version' should be in ('1.0', '{allowed_from_map}').")
self._version = version
def __repr__(self):
n_tables = len(list(self.iter_tables()))
return f'... {n_tables} tables ...'
@property
def version(self):
"""
The version of the VOTable specification that the file uses.
"""
return self._version
@version.setter
def version(self, version):
version = str(version)
if version not in self._version_namespace_map:
allowed_from_map = "', '".join(self._version_namespace_map)
raise ValueError(
f"astropy.io.votable only supports VOTable versions '{allowed_from_map}'")
self._version = version
@property
def coordinate_systems(self):
"""
A list of coordinate system descriptions for the file. Must
contain only `CooSys` objects.
"""
return self._coordinate_systems
@property
def time_systems(self):
"""
A list of time system descriptions for the file. Must
contain only `TimeSys` objects.
"""
return self._time_systems
@property
def params(self):
"""
A list of parameters (constant-valued columns) that apply to
the entire file. Must contain only `Param` objects.
"""
return self._params
@property
def infos(self):
"""
A list of informational parameters (key-value pairs) for the
entire file. Must only contain `Info` objects.
"""
return self._infos
@property
def resources(self):
"""
A list of resources, in the order they appear in the file.
Must only contain `Resource` objects.
"""
return self._resources
@property
def groups(self):
"""
A list of groups, in the order they appear in the file. Only
supported as a child of the VOTABLE element in VOTable 1.2 or
later.
"""
return self._groups
def _add_param(self, iterator, tag, data, config, pos):
param = Param(self, config=config, pos=pos, **data)
self.params.append(param)
param.parse(iterator, config)
def _add_resource(self, iterator, tag, data, config, pos):
resource = Resource(config=config, pos=pos, **data)
self.resources.append(resource)
resource.parse(self, iterator, config)
def _add_coosys(self, iterator, tag, data, config, pos):
coosys = CooSys(config=config, pos=pos, **data)
self.coordinate_systems.append(coosys)
coosys.parse(iterator, config)
def _add_timesys(self, iterator, tag, data, config, pos):
timesys = TimeSys(config=config, pos=pos, **data)
self.time_systems.append(timesys)
timesys.parse(iterator, config)
def _add_info(self, iterator, tag, data, config, pos):
info = Info(config=config, pos=pos, **data)
self.infos.append(info)
info.parse(iterator, config)
def _add_group(self, iterator, tag, data, config, pos):
if not config.get('version_1_2_or_later'):
warn_or_raise(W26, W26, ('GROUP', 'VOTABLE', '1.2'), config, pos)
group = Group(self, config=config, pos=pos, **data)
self.groups.append(group)
group.parse(iterator, config)
def _get_version_checks(self):
config = {}
config['version_1_1_or_later'] = \
util.version_compare(self.version, '1.1') >= 0
config['version_1_2_or_later'] = \
util.version_compare(self.version, '1.2') >= 0
config['version_1_3_or_later'] = \
util.version_compare(self.version, '1.3') >= 0
config['version_1_4_or_later'] = \
util.version_compare(self.version, '1.4') >= 0
return config
# Map VOTable version numbers to namespace URIs and schema information.
_version_namespace_map = {
# Version 1.0 isn't well-supported, but is allowed on parse (with a warning).
# It used DTD rather than schema, so this information would not be useful.
# By omitting 1.0 from this dict we can use the keys as the list of versions
# that are allowed in various other checks.
"1.1": {
"namespace_uri": "http://www.ivoa.net/xml/VOTable/v1.1",
"schema_location_attr": "xsi:noNamespaceSchemaLocation",
"schema_location_value": "http://www.ivoa.net/xml/VOTable/v1.1"
},
"1.2": {
"namespace_uri": "http://www.ivoa.net/xml/VOTable/v1.2",
"schema_location_attr": "xsi:noNamespaceSchemaLocation",
"schema_location_value": "http://www.ivoa.net/xml/VOTable/v1.2"
},
# With 1.3 we'll be more explicit with the schema location.
# - xsi:schemaLocation uses the namespace name along with the URL
# to reference it.
# - For convenience, but somewhat confusingly, the namespace URIs
# are also usable URLs for accessing an applicable schema.
# However to avoid confusion, we'll use the explicit schema URL.
"1.3": {
"namespace_uri": "http://www.ivoa.net/xml/VOTable/v1.3",
"schema_location_attr": "xsi:schemaLocation",
"schema_location_value":
"http://www.ivoa.net/xml/VOTable/v1.3 http://www.ivoa.net/xml/VOTable/VOTable-1.3.xsd"
},
# With 1.4 namespace URIs stopped incrementing with minor version changes
# so we use the same URI as with 1.3. See this IVOA note for more info:
# http://www.ivoa.net/documents/Notes/XMLVers/20180529/
"1.4": {
"namespace_uri": "http://www.ivoa.net/xml/VOTable/v1.3",
"schema_location_attr": "xsi:schemaLocation",
"schema_location_value":
"http://www.ivoa.net/xml/VOTable/v1.3 http://www.ivoa.net/xml/VOTable/VOTable-1.4.xsd"
}
}
def parse(self, iterator, config):
config['_current_table_number'] = 0
for start, tag, data, pos in iterator:
if start:
if tag == 'xml':
pass
elif tag == 'VOTABLE':
if 'version' not in data:
warn_or_raise(W20, W20, self.version, config, pos)
config['version'] = self.version
else:
config['version'] = self._version = data['version']
if config['version'].lower().startswith('v'):
warn_or_raise(
W29, W29, config['version'], config, pos)
self._version = config['version'] = \
config['version'][1:]
if config['version'] not in self._version_namespace_map:
vo_warn(W21, config['version'], config, pos)
if 'xmlns' in data:
ns_info = self._version_namespace_map.get(config['version'], {})
correct_ns = ns_info.get('namespace_uri')
if data['xmlns'] != correct_ns:
vo_warn(W41, (correct_ns, data['xmlns']), config, pos)
else:
vo_warn(W42, (), config, pos)
break
else:
vo_raise(E19, (), config, pos)
config.update(self._get_version_checks())
tag_mapping = {
'PARAM': self._add_param,
'RESOURCE': self._add_resource,
'COOSYS': self._add_coosys,
'TIMESYS': self._add_timesys,
'INFO': self._add_info,
'DEFINITIONS': self._add_definitions,
'DESCRIPTION': self._ignore_add,
'GROUP': self._add_group}
for start, tag, data, pos in iterator:
if start:
tag_mapping.get(tag, self._add_unknown_tag)(
iterator, tag, data, config, pos)
elif tag == 'DESCRIPTION':
if self.description is not None:
warn_or_raise(W17, W17, 'VOTABLE', config, pos)
self.description = data or None
if not len(self.resources) and config['version_1_2_or_later']:
warn_or_raise(W53, W53, (), config, pos)
return self
def to_xml(self, fd, compressed=False, tabledata_format=None,
_debug_python_based_parser=False, _astropy_version=None):
"""
Write to an XML file.
Parameters
----------
fd : str or file-like
Where to write the file. If a file-like object, must be writable.
compressed : bool, optional
When `True`, write to a gzip-compressed file. (Default:
`False`)
tabledata_format : str, optional
Override the format of the table(s) data to write. Must
be one of ``tabledata`` (text representation), ``binary`` or
``binary2``. By default, use the format that was specified
in each `Table` object as it was created or read in. See
:ref:`astropy:votable-serialization`.
"""
if tabledata_format is not None:
if tabledata_format.lower() not in (
'tabledata', 'binary', 'binary2'):
raise ValueError(f"Unknown format type '{format}'")
kwargs = {
'version': self.version,
'tabledata_format':
tabledata_format,
'_debug_python_based_parser': _debug_python_based_parser,
'_group_number': 1}
kwargs.update(self._get_version_checks())
with util.convert_to_writable_filelike(
fd, compressed=compressed) as fd:
w = XMLWriter(fd)
version = self.version
if _astropy_version is None:
lib_version = astropy_version
else:
lib_version = _astropy_version
xml_header = """
\n"""
w.write(xml_header.lstrip().format(**locals()))
# Build the VOTABLE tag attributes.
votable_attr = {
'version': version,
'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instance"
}
ns_info = self._version_namespace_map.get(version, {})
namespace_uri = ns_info.get('namespace_uri')
if namespace_uri:
votable_attr['xmlns'] = namespace_uri
schema_location_attr = ns_info.get('schema_location_attr')
schema_location_value = ns_info.get('schema_location_value')
if schema_location_attr and schema_location_value:
votable_attr[schema_location_attr] = schema_location_value
with w.tag('VOTABLE', votable_attr):
if self.description is not None:
w.element("DESCRIPTION", self.description, wrap=True)
element_sets = [self.coordinate_systems, self.time_systems,
self.params, self.infos, self.resources]
if kwargs['version_1_2_or_later']:
element_sets[0] = self.groups
for element_set in element_sets:
for element in element_set:
element.to_xml(w, **kwargs)
def iter_tables(self):
"""
Iterates over all tables in the VOTable file in a "flat" way,
ignoring the nesting of resources etc.
"""
for resource in self.resources:
for table in resource.iter_tables():
yield table
def get_first_table(self):
"""
Often, you know there is only one table in the file, and
that's all you need. This method returns that first table.
"""
for table in self.iter_tables():
if not table.is_empty():
return table
raise IndexError("No table found in VOTABLE file.")
get_table_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_tables', 'TABLE',
"""
Looks up a TABLE_ element by the given ID. Used by the table
"ref" attribute.
""")
get_tables_by_utype = _lookup_by_attr_factory(
'utype', False, 'iter_tables', 'TABLE',
"""
Looks up a TABLE_ element by the given utype, and returns an
iterator emitting all matches.
""")
def get_table_by_index(self, idx):
"""
Get a table by its ordinal position in the file.
"""
for i, table in enumerate(self.iter_tables()):
if i == idx:
return table
raise IndexError(
f"No table at index {idx:d} found in VOTABLE file.")
def iter_fields_and_params(self):
"""
Recursively iterate over all FIELD_ and PARAM_ elements in the
VOTABLE_ file.
"""
for resource in self.resources:
for field in resource.iter_fields_and_params():
yield field
get_field_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_fields_and_params', 'FIELD',
"""
Looks up a FIELD_ element by the given ID_. Used by the field's
"ref" attribute.
""")
get_fields_by_utype = _lookup_by_attr_factory(
'utype', False, 'iter_fields_and_params', 'FIELD',
"""
Looks up a FIELD_ element by the given utype and returns an
iterator emitting all matches.
""")
get_field_by_id_or_name = _lookup_by_id_or_name_factory(
'iter_fields_and_params', 'FIELD',
"""
Looks up a FIELD_ element by the given ID_ or name.
""")
def iter_values(self):
"""
Recursively iterate over all VALUES_ elements in the VOTABLE_
file.
"""
for field in self.iter_fields_and_params():
yield field.values
get_values_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_values', 'VALUES',
"""
Looks up a VALUES_ element by the given ID. Used by the values
"ref" attribute.
""")
def iter_groups(self):
"""
Recursively iterate over all GROUP_ elements in the VOTABLE_
file.
"""
for table in self.iter_tables():
for group in table.iter_groups():
yield group
get_group_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_groups', 'GROUP',
"""
Looks up a GROUP_ element by the given ID. Used by the group's
"ref" attribute
""")
get_groups_by_utype = _lookup_by_attr_factory(
'utype', False, 'iter_groups', 'GROUP',
"""
Looks up a GROUP_ element by the given utype and returns an
iterator emitting all matches.
""")
def iter_coosys(self):
"""
Recursively iterate over all COOSYS_ elements in the VOTABLE_
file.
"""
for coosys in self.coordinate_systems:
yield coosys
for resource in self.resources:
for coosys in resource.iter_coosys():
yield coosys
get_coosys_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_coosys', 'COOSYS',
"""Looks up a COOSYS_ element by the given ID.""")
def iter_timesys(self):
"""
Recursively iterate over all TIMESYS_ elements in the VOTABLE_
file.
"""
for timesys in self.time_systems:
yield timesys
for resource in self.resources:
for timesys in resource.iter_timesys():
yield timesys
get_timesys_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_timesys', 'TIMESYS',
"""Looks up a TIMESYS_ element by the given ID.""")
def iter_info(self):
"""
Recursively iterate over all INFO_ elements in the VOTABLE_
file.
"""
for info in self.infos:
yield info
for resource in self.resources:
for info in resource.iter_info():
yield info
get_info_by_id = _lookup_by_attr_factory(
'ID', True, 'iter_info', 'INFO',
"""Looks up a INFO element by the given ID.""")
def set_all_tables_format(self, format):
"""
Set the output storage format of all tables in the file.
"""
for table in self.iter_tables():
table.format = format
@classmethod
def from_table(cls, table, table_id=None):
"""
Create a `VOTableFile` instance from a given
`astropy.table.Table` instance.
Parameters
----------
table_id : str, optional
Set the given ID attribute on the returned Table instance.
"""
votable_file = cls()
resource = Resource()
votable = Table.from_table(votable_file, table)
if table_id is not None:
votable.ID = table_id
resource.tables.append(votable)
votable_file.resources.append(resource)
return votable_file