# TODO: Test FITS parsing
from __future__ import division, absolute_import
from .util import IS_PY3K
# STDLIB
import codecs
import io
import re
if IS_PY3K:
string_types = (str, bytes)
else:
string_types = (str, unicode)
# THIRD-PARTY
import numpy as np
from numpy import ma
# LOCAL
from .. import fits
from ... import __version__ as astropy_version
from ...utils.collections import HomogeneousList
from ...utils.xml.writer import XMLWriter
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, E06, E08, E09, E10, E11, E12, E13,
E14, E15, E16, E17, E18, E19, E20, E21)
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',
'FieldRef', 'ParamRef', 'Group', 'Table', 'Resource',
'VOTableFile'
]
# 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.data[:length] = masked.data[:length]
if length != 0:
new_array.mask[:length] = masked.mask[:length]
return new_array
def _lookup_by_id_factory(iterator, element_name, doc):
"""
Creates a function useful for looking up an element by ID.
Parameters
----------
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 ID
"""
def lookup_by_id(self, ref, before=None):
"""
Given an XML id *ref*, finds the first element in the iterator
with the attribute ID == *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 element.ID == ref:
vo_raise(
"%s references itself" % element_name,
element._config, element._pos, KeyError)
break
if element.ID == ref:
return element
raise KeyError(
"No %s with ID '%s' found before the referencing %s" %
(element_name, ref, element_name))
lookup_by_id.__doc__ = doc
return lookup_by_id
def _lookup_by_id_or_name_factory(iterator, element_name, doc):
"""
Like `_lookup_by_id_factory`, but also looks in the "name" attribute.
"""
def lookup_by_id(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(
"%s references itself" % element_name,
element._config, element._pos, KeyError)
break
if ref in (element.ID, element.name):
return element
raise KeyError(
"No %s with ID or name '%s' found before the referencing %s" %
(element_name, ref, element_name))
lookup_by_id.__doc__ = doc
return lookup_by_id
######################################################################
# ATTRIBUTE CHECKERS
def check_astroyear(year, field, config={}, 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(ur"^[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={}, 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
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 string is not None and not isinstance(string, string_types):
warn_or_raise(W08, W08, attr_name, config, pos)
return False
return True
def resolve_id(ID, id, config={}, 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={}, 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.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('pedantic'):
vo_raise(W06, (ucd, unicode(e)), config, pos)
else:
vo_warn(W06, (ucd, unicode(e)), config, pos)
return False
return True
######################################################################
# PROPERTY MIXINS
class _IDProperty(object):
@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(object):
@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(object):
@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(object):
_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(object):
_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(object):
@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(object):
"""
A base class for all classes that represent XML elements in the
VOTABLE file.
"""
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.iterkeys(), 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.iterkeys(), config, pos)
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 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
[docs]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={}, pos=None, **kwargs):
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.iterkeys(), 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' or 'location'
"""
return self._content_role
@content_role.setter
def content_role(self, content_role):
if 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
[docs] 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
[docs] 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
[docs] def href(self):
self._href = None
[docs] 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
[docs] def from_table_column(cls, d):
return cls(**d)
[docs]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={}, pos=None, **extra):
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.iterkeys(), config, pos)
@property
def name(self):
"""[*required*] The key of the key-value pair."""
return self._name
@name.setter
[docs] 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
[docs] 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
[docs] 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
[docs] 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 ... 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)
unit = u.Unit(unit, format='cds', parse_strict='silent')
if isinstance(unit, u.UnrecognizedUnit):
warn_or_raise(W50, W50, (unit.to_string(),),
self._config, self._pos)
self._unit = unit
@unit.deleter
[docs] def unit(self):
self._unit = None
[docs] 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)
[docs]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={}, pos=None, **extras):
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.iterkeys(), config, pos)
@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, string_types):
try:
null_val = self._field.converter.parse_scalar(
null, self._config, self._pos)[0]
except:
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
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] def max_inclusive(self):
self._max_inclusive = True
@property
[docs] 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
[docs] 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.iterkeys(), 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.iterkeys(), 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.iterkeys(), config, pos,
['data', 'name'])
elif tag == 'VALUES':
break
return self
[docs] def is_defaults(self):
# 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 == [])
[docs] def to_xml(self, w, **kwargs):
def yes_no(value):
if value:
return u'yes'
return u'no'
if self.is_defaults():
return
if self.ref is not None:
w.element(u'VALUES', attrib=w.object_attrs(self, [u'ref']))
else:
with w.tag(u'VALUES',
attrib=w.object_attrs(
self, [u'ID', u'null', u'ref'])):
if self.min is not None:
w.element(
u'MIN',
value=self._field.converter.output(self.min, False),
inclusive=yes_no(self.min_inclusive))
if self.max is not None:
w.element(
u'MAX',
value=self._field.converter.output(self.max, False),
inclusive=yes_no(self.max_inclusive))
for name, value in self.options:
w.element(
u'OPTION',
name=name,
value=value)
[docs] def to_table_column(self, column):
# Have the ref filled in here
ref = self.ref
meta = {}
for key in [u'ID', u'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
[docs] def from_table_column(self, column):
if not 'values' in column.meta:
return
meta = column.meta['values']
for key in [u'ID', u'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 = meta['options'].items()
[docs]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={}, pos=None, **extra):
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 archive.noao.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 (not config.get('pedantic') 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'}
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.iterkeys(), config, pos)
@classmethod
[docs] 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 + "_%d" % i
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 + " %d" % i
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
[docs] 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(ur"^[FE]?[0-9]+$", precision):
vo_raise(E11, precision, self._config, self._pos)
self._precision = precision
@precision.deleter
[docs] 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
[docs] 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_ element.
"""
return self._ref
@ref.setter
def ref(self, ref):
xmlutil.check_id(ref, 'ref', self._config, self._pos)
self._ref = ref
@ref.deleter
[docs] 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 ... import units as u
unit = u.Unit(unit, format='cds', parse_strict='silent')
if isinstance(unit, u.UnrecognizedUnit):
warn_or_raise(
W50, W50, (unit.to_string(),),
self._config, self._pos)
self._unit = unit
@unit.deleter
[docs] 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(ur"^([0-9]+x)*[0-9]*[*]?(s\W)?$", arraysize)):
vo_raise(E13, arraysize, self._config, self._pos)
self._arraysize = arraysize
@arraysize.deleter
[docs] 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
[docs] 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
[docs] def values(self):
self._values = None
@property
[docs] 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
[docs] 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.iterkeys(), 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.split("\n"))
else:
self.title = self.name
self._setup(config, pos)
return self
[docs] 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(u'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)
[docs] 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.units = self.unit
if isinstance(self.converter, converters.FloatingPoint):
column.format = self.converter.output_format
@classmethod
[docs] def from_table_column(cls, votable, column):
"""
Restores a `Field` instance from a given
`astropy.table.Column` instance.
"""
kwargs = {}
for key in ['ucd', 'width', 'precision', 'utype', 'xtype']:
val = column.meta.get(key, None)
if val is not None:
kwargs[key] = val
# TODO: Use the unit framework when available
if column.units is not None:
kwargs['unit'] = column.units
kwargs['name'] = column.name
result = converters.table_column_to_votable_datatype(column)
kwargs.update(result)
field = cls(votable, **kwargs)
if column.description is not None:
field.description = column.description
field.values.from_table_column(column)
if 'links' in column.meta:
for link in column.meta['links']:
field.links.append(Link.from_table_column(link))
# TODO: Parse format into precision and width
return field
[docs]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={},
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
[docs] def value(self, value):
if value is None:
value = ""
if ((IS_PY3K and isinstance(value, unicode)) or
(not IS_PY3K and isinstance(value, string_types))):
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
[docs] 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 = u""
Field.to_xml(self, w, **kwargs)
self._value = tmp_value
[docs]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={}, pos=None, **extra):
self._config = config
self._pos = pos
if config.get('version_1_2_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.iterkeys(), 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
[docs] 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
[docs] 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
[docs] 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
[docs] def epoch(self):
self._epoch = None
[docs]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={}, 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.
"""
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
[docs] def ref(self):
self._ref = None
[docs] 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(
"No field named '%s'" % self.ref,
self._config, self._pos, KeyError)
[docs]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 refering to a <PARAM> 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={}, pos=None):
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
[docs] def ref(self):
self._ref = None
[docs] 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(
"No params named '%s'" % self.ref,
self._config, self._pos, KeyError)
[docs]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={}, pos=None, **extra):
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.iterkeys(), config, pos)
@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
[docs] def ref(self):
self._ref = None
@property
[docs] 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)
[docs] 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
[docs] def to_xml(self, w, **kwargs):
with w.tag(
u'GROUP',
attrib=w.object_attrs(
self, [u'ID', u'name', u'ref', u'ucd', u'utype'])):
if self.description is not None:
w.element(u"DESCRIPTION", self.description, wrap=True)
for entry in self.entries:
entry.to_xml(w, **kwargs)
[docs] 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
[docs] 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
[docs]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 <FIELD> 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={}, pos=None,
**extra):
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)
assert nrows >= 0
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.iterkeys(), config, pos)
@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
[docs] 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_), '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.
"""
return self._format
@format.setter
@property
[docs] def nrows(self):
"""
[*immutable*] The number of rows in the table, as specified in
the XML file.
"""
return self._nrows
@property
[docs] def fields(self):
"""
A list of :class:`Field` objects describing the types of each
of the data columns.
"""
return self._fields
@property
[docs] def params(self):
"""
A list of parameters (constant-valued columns) for the
table. Must contain only :class:`Param` objects.
"""
return self._params
@property
[docs] 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
[docs] 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
[docs] def infos(self):
"""
A list of :class:`Info` objects for the table. Allows for
post-operational diagnostics.
"""
return self._infos
[docs] 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
[docs] def create_arrays(self, nrows=0, config={}):
"""
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 IS_PY3K:
if x._unique_name == x.ID:
id = x.ID
else:
id = (x._unique_name, x.ID)
else:
if x._unique_name == x.ID:
id = x.ID.encode('utf-8')
else:
id = (x._unique_name.encode('utf-8'),
x.ID.encode('utf-8'))
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)
[docs] 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.iterkeys(), 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,
'DESCRIPTION' : self._ignore_add}
for start, tag, data, pos in iterator:
if start:
if tag == 'DATA':
warn_unknown_attrs(
'DATA', data.iterkeys(), 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)
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 = range(len(fields))
else:
if isinstance(columns, string_types):
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(
"Columns '%s' not found in fields list" % columns)
else:
raise TypeError("Invalid columns list")
if not skip_table:
for start, tag, data, pos in iterator:
if start:
if tag == 'TABLEDATA':
warn_unknown_attrs(
'TABLEDATA', data.iterkeys(), config, pos)
self.array = self._parse_tabledata(
iterator, colnumbers, fields, config)
break
elif tag == 'BINARY':
warn_unknown_attrs(
'BINARY', data.iterkeys(), config, pos)
self.array = self._parse_binary(
iterator, colnumbers, fields, config)
break
elif tag == 'FITS':
warn_unknown_attrs(
'FITS', data.iterkeys(), config, pos, ['extnum'])
try:
extnum = int(data.get('extnum', 0))
if extnum < 0:
raise ValueError()
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.iterkeys(), 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:
import base64
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 '%s')" %
(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 '%s')" %
(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 _parse_binary(self, iterator, colnumbers, fields, config):
fields = self.fields
have_local_stream = False
for start, tag, data, pos in iterator:
if tag == 'STREAM':
if start:
warn_unknown_attrs(
'STREAM', data.iterkeys(), 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:
import base64
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') or
href.startswith('ftp') or
href.startswith('file')):
vo_raise(
"The vo package only supports remote data through http, " +
"ftp or file",
self._config, self._pos, NotImplementedError)
import urllib2
fd = urllib2.urlopen(href)
if encoding is not None:
if encoding == 'gzip':
from ...utils.compat import gzip
fd = gzip.GzipFile(href, 'rb', fileobj=fd)
elif encoding == 'base64':
fd = codecs.EncodedFile(fd, 'base64')
else:
vo_raise(
"Unknown encoding type '%s'" % encoding,
self._config, self._pos, NotImplementedError)
read = fd.read
def careful_read(length):
result = read(length)
if len(result) != length:
raise EOFError
return result
# 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:
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 '%s')" %
(numrows, fields[i].ID))
row_data.append(value)
row_mask_data.append(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.iterkeys(), config, pos,
['type', 'href', 'actuate', 'encoding', 'expires',
'rights'])
href = data['href']
encoding = data.get('encoding', None)
else:
break
if not (href.startswith('http') or
href.startswith('ftp') or
href.startswith('file')):
vo_raise(
"The vo package only supports remote data through http, "
"ftp or file",
self._config, self._pos, NotImplementedError)
import urllib2
fd = urllib2.urlopen(href)
if encoding is not None:
if encoding == 'gzip':
from ...utils.compat import gzip
fd = gzip.GzipFile(href, 'r', fileobj=fd)
elif encoding == 'base64':
fd = codecs.EncodedFile(fd, 'base64')
else:
vo_raise(
"Unknown encoding type '%s'" % 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
[docs] def to_xml(self, w, **kwargs):
with w.tag(
u'TABLE',
attrib=w.object_attrs(
self,
(u'ID', u'name', u'ref', u'ucd', u'utype', u'nrows'))):
if self.description is not None:
w.element(u"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)
if len(self.array):
with w.tag(u'DATA'):
if self.format == u'fits':
self.format = u'tabledata'
if self.format == u'tabledata':
self._write_tabledata(w, **kwargs)
elif self.format == u'binary':
self._write_binary(w, **kwargs)
if self.ref is None and 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
write_null_values = kwargs.get('write_null_values', False)
with w.tag(u'TABLEDATA'):
w._flush()
if (_has_c_tabledata_writer and
not kwargs.get('_debug_python_based_parser')):
fields = [field.converter.output for field in fields]
indent = len(w._tags) - 1
tablewriter.write_tabledata(
w.write, array.data, array.mask, fields, write_null_values,
indent, 1 << 8)
else:
write = w.write
indent_spaces = w.get_indentation_spaces()
tr_start = indent_spaces + u"<TR>\n"
tr_end = indent_spaces + u"</TR>\n"
td = indent_spaces + u" <TD>%s</TD>\n"
td_empty = indent_spaces + u" <TD/>\n"
fields = [(i, field.converter.output)
for i, field in enumerate(fields)]
for row in xrange(len(array)):
write(tr_start)
array_row = array.data[row]
mask_row = array.mask[row]
for i, output in fields:
data = array_row[i]
masked = mask_row[i]
if (not np.all(masked) or
write_null_values):
try:
val = output(data, masked)
except Exception as e:
vo_reraise(e,
additional="(in row %d, col '%s')" %
(row, self.fields[i].ID))
if len(val):
write(td % val)
else:
write(td_empty)
else:
write(td_empty)
write(tr_end)
def _write_binary(self, w, **kwargs):
import base64
fields = self.fields
array = self.array
with w.tag(u'BINARY'):
with w.tag(u'STREAM', encoding='base64'):
fields_basic = [(i, field.converter.binoutput)
for (i, field) in enumerate(fields)]
data = io.BytesIO()
for row in xrange(len(array)):
array_row = array.data[row]
array_mask = array.mask[row]
for i, converter in fields_basic:
try:
chunk = converter(array_row[i], array_mask[i])
assert type(chunk) == type(b'')
except Exception as e:
vo_reraise(e,
additional="(in row %d, col '%s')" %
(row, fields[i].ID))
data.write(chunk)
w._flush()
w.write(base64.b64encode(data.getvalue()).decode('ascii'))
[docs] def to_table(self):
"""
Convert this VO Table to an `astropy.table.Table` instance.
.. warning::
Variable-length array fields may not be restored
identically when round-tripping through the
`astropy.table.Table` instance.
"""
from ...table import Table
meta = {}
for key in [u'ID', u'name', u'ref', u'ucd', u'utype', u'description']:
val = getattr(self, key, None)
if val is not None:
meta[key] = val
table = Table(self.array, meta=meta)
for field in self.fields:
column = table[field.ID]
field.to_table_column(column)
return table
@classmethod
[docs] def from_table(cls, votable, table):
"""
Create a `Table` instance from a given `astropy.table.Table`
instance.
"""
kwargs = {}
for key in [u'ID', u'name', u'ref', u'ucd', u'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))
new_table.array = ma.array(np.asarray(table), mask=table.mask)
return new_table
[docs] 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_id_factory(
'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.
""")
[docs] 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_id_factory(
'iter_groups', 'GROUP',
"""
Looks up a GROUP element by the given ID. Used by the group's
"ref" attribute
""")
[docs]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={}, pos=None, **kwargs):
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._params = HomogeneousList(Param)
self._infos = HomogeneousList(Info)
self._links = HomogeneousList(Link)
self._tables = HomogeneousList(Table)
self._resources = HomogeneousList(Resource)
warn_unknown_attrs('RESOURCE', kwargs.iterkeys(), config, pos)
@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
[docs] def type(self, type):
if type not in ('results', 'meta'):
vo_raise(E18, type, self._config, self._pos)
self._type = type
@property
@property
[docs] 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
[docs] def infos(self):
"""
A list of informational parameters (key-value pairs) for the
resource. Must only contain `Info` objects.
"""
return self._infos
@property
[docs] def params(self):
"""
A list of parameters (constant-valued columns) for the
resource. Must contain only `Param` objects.
"""
return self._params
@property
[docs] 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
[docs] def tables(self):
"""
A list of tables in the resource. Must contain only
`Table` objects.
"""
return self._tables
@property
[docs] 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_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_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)
[docs] def parse(self, votable, iterator, config):
self._votable = votable
tag_mapping = {
'TABLE' : self._add_table,
'INFO' : self._add_info,
'PARAM' : self._add_param,
'COOSYS' : self._add_coosys,
'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
del self._votable
return self
[docs] def to_xml(self, w, **kwargs):
attrs = w.object_attrs(self, (u'ID', u'type', u'utype'))
attrs.update(self.extra_attributes)
with w.tag(u'RESOURCE', attrib=attrs):
if self.description is not None:
w.element(u"DESCRIPTION", self.description, wrap=True)
for element_set in (self.coordinate_systems, self.params,
self.infos, self.links, self.tables,
self.resources):
for element in element_set:
element.to_xml(w, **kwargs)
[docs] 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
[docs] 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
[docs] 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
[docs]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={}, pos=None, version="1.2"):
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._params = HomogeneousList(Param)
self._infos = HomogeneousList(Info)
self._resources = HomogeneousList(Resource)
self._groups = HomogeneousList(Group)
version = str(version)
assert version in ("1.0", "1.1", "1.2")
self._version = version
@property
[docs] def version(self):
"""
The version of the VOTable specification that the file uses.
"""
return self._version
@property
[docs] def coordinate_systems(self):
"""
A list of coordinate system descriptions for the file. Must
contain only `CooSys` objects.
"""
return self._coordinate_systems
@property
[docs] 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
[docs] def infos(self):
"""
A list of informational parameters (key-value pairs) for the
entire file. Must only contain `Info` objects.
"""
return self._infos
@property
[docs] def resources(self):
"""
A list of resources, in the order they appear in the file.
Must only contain `Resource` objects.
"""
return self._resources
@property
[docs] 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_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)
[docs] 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 ('1.1', '1.2'):
vo_warn(W21, config['version'], config, pos)
if 'xmlns' in data:
correct_ns = ('http://www.ivoa.net/xml/VOTable/v%s' %
config['version'])
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['version_1_1_or_later'] = \
util.version_compare(config['version'], '1.1') >= 0
config['version_1_2_or_later'] = \
util.version_compare(config['version'], '1.2') >= 0
tag_mapping = {
'PARAM' : self._add_param,
'RESOURCE' : self._add_resource,
'COOSYS' : self._add_coosys,
'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
return self
[docs] def to_xml(self, fd, write_null_values=False,
compressed=False,
_debug_python_based_parser=False,
_astropy_version=None):
"""
Write to an XML file.
Parameters
----------
fd : str path or writable file-like object
Where to write the file.
write_null_values : bool, optional
When `True`, write the 'null' value (specified in the null
attribute of the VALUES element for each FIELD) for empty
values. When False (default), simply write no value.
compressed : bool, optional
When `True`, write to a gzip-compressed file. (Default:
`False`)
"""
kwargs = {
'write_null_values': write_null_values,
'version': self.version,
'version_1_1_or_later':
util.version_compare(self.version, u'1.1') >= 0,
'version_1_2_or_later':
util.version_compare(self.version, u'1.2') >= 0,
'_debug_python_based_parser': _debug_python_based_parser}
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 = u"""
<?xml version="1.0" encoding="utf-8"?>
<!-- Produced with astropy.io.votable version %(lib_version)s
http://www.astropy.org/ -->\n"""
w.write(xml_header.lstrip() % locals())
with w.tag(u'VOTABLE',
{u'version': version,
u'xmlns:xsi':
u"http://www.w3.org/2001/XMLSchema-instance",
u'xsi:noNamespaceSchemaLocation':
u"http://www.ivoa.net/xml/VOTable/v%s" % version,
u'xmlns':
u"http://www.ivoa.net/xml/VOTable/v%s" % version}):
if self.description is not None:
w.element(u"DESCRIPTION", self.description, wrap=True)
element_sets = [self.coordinate_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)
[docs] 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
[docs] 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_id_factory(
'iter_tables', 'TABLE',
"""
Looks up a TABLE_ element by the given ID. Used by the table
"ref" attribute.
""")
[docs] 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("No table at index %d found in VOTABLE file." % idx)
[docs] 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_id_factory(
'iter_fields_and_params', 'FIELD',
"""
Looks up a FIELD_ element by the given ID_. Used by the field's
"ref" attribute.
""")
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.
""")
[docs] 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_id_factory(
'iter_values', 'VALUES',
"""
Looks up a VALUES_ element by the given ID. Used by the values
"ref" attribute.
""")
[docs] 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_id_factory(
'iter_groups', 'GROUP',
"""
Looks up a GROUP_ element by the given ID. Used by the group's
"ref" attribute
""")
[docs] 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_id_factory(
'iter_coosys', 'COOSYS',
"""Looks up a COOSYS_ element by the given ID.""")
@classmethod
[docs] 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