def is_votable(source):
"""
Reads the header of a file to determine if it is a VOTable file.
Parameters
----------
source : str or readable file-like object
Path or file object containing a VOTABLE_ xml file.
Returns
-------
is_votable : bool
Returns `True` if the given file is a VOTable file.
"""
try:
with iterparser.get_xml_iterator(source) as iterator:
for start, tag, d, pos in iterator:
if tag != 'xml':
return False
break
for start, tag, d, pos in iterator:
if tag != 'VOTABLE':
return False
break
return True
except ValueError:
return False
def is_votable(source):
"""
Reads the header of a file to determine if it is a VOTable file.
Parameters
----------
source : str or readable file-like object
Path or file object containing a VOTABLE_ xml file.
Returns
-------
is_votable : bool
Returns `True` if the given file is a VOTable file.
"""
try:
with iterparser.get_xml_iterator(source) as iterator:
for start, tag, d, pos in iterator:
if tag != 'xml':
return False
break
for start, tag, d, pos in iterator:
if tag != 'VOTABLE':
return False
break
return True
except ValueError:
return False
def parse_for_object(
source, object_type, pedantic=None, filename=None,
_debug_python_based_parser=False
):
"""
Parses an xml file (or file-like object), and returns a
object of specified object_type. object_type must be a subtype of
`~pyvo.utils.xml.elements.Element` type
Parameters
----------
source : str or readable file-like object
Path or file object containing a tableset xml file.
object : object type to return (subtype `~pyvo.utils.xml.elements.Element`)
pedantic : bool, optional
When `True`, raise an error when the file violates the spec,
otherwise issue a warning. Warnings may be controlled using
the standard Python mechanisms. See the `warnings`
module in the Python standard library for more information.
Defaults to False.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
Returns
-------
object : `~pyvo.utils.xml.elements.Element` object or None
See also
--------
pyvo.io.vosi.exceptions : The exceptions this function may raise.
"""
config = {
'pedantic': pedantic,
'filename': filename
}
if filename is None and isinstance(source, str):
config['filename'] = source
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser
) as iterator:
return object_type(
config=config, pos=(1, 1)).parse(iterator, config)
def _votableparse(source,
columns=None,
invalid='mask',
pedantic=False,
table_number=None,
filename=None,
version="1.1"):
try:
import astropy.io.votable.tree as votabletree
import astropy.io.votable.table as votabletable
from astropy.utils.xml import iterparser
#from astropy.io.votable.exceptions import W22
from astropy.io.votable.exceptions import W03, W06, W20, W21, W42, W46, W47, W49, E10
for warning in (W03, W06, W20, W21, W42, W46, W47, W49, E10):
warnings.simplefilter("ignore", warning)
# MJG : 021913 - commented out to get CDS responses to work
# warnings.simplefilter("error", W22)
except ImportError:
raise RuntimeError("astropy votable not available")
invalid = invalid.lower()
assert invalid in ('exception', 'mask')
chunk_size = votabletree.DEFAULT_CHUNK_SIZE
if pedantic is None:
pedantic = votabletable.PEDANTIC()
config = {
'columns': columns,
'invalid': invalid,
'pedantic': pedantic,
'chunk_size': chunk_size,
'table_number': table_number,
'filename': filename,
'version_1_1_or_later': True
}
if filename is None and isinstance(source, basestring):
config['filename'] = source
if filename is None:
config['filename'] = 'dal_query'
with iterparser.get_xml_iterator(source) as iterator:
return votabletree.VOTableFile(config=config,
pos=(1, 1),
version=version).parse(
iterator, config)
def parse_job(
source, pedantic=None, filename=None, _debug_python_based_parser=False
):
"""
Parses a job xml file (or file-like object), and returns a
`~pyvo.io.uws.tree.JobFile` object.
Parameters
----------
source : str or readable file-like object
Path or file object containing a tableset xml file.
pedantic : bool, optional
When `True`, raise an error when the file violates the spec,
otherwise issue a warning. Warnings may be controlled using
the standard Python mechanisms. See the `warnings`
module in the Python standard library for more information.
Defaults to False.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
Returns
-------
votable : `~pyvo.io.vosi.endpoint.TableSetFile` object
See also
--------
pyvo.io.vosi.exceptions : The exceptions this function may raise.
"""
config = {
'pedantic': pedantic,
'filename': filename
}
if filename is None and isinstance(source, six.string_types):
config['filename'] = source
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser
) as iterator:
return JobFile(
config=config, pos=(1, 1)).parse(iterator, config)
def parse_availability(source,
pedantic=None,
filename=None,
_debug_python_based_parser=False):
"""
Parses a availability xml file (or file-like object), and returns a
`~pyvo.io.vosi.endpoint.AvailabilityFile` object.
Parameters
----------
source : str or readable file-like object
Path or file object containing a availability xml file.
pedantic : bool, optional
When `True`, raise an error when the file violates the spec,
otherwise issue a warning. Warnings may be controlled using
the standard Python mechanisms. See the `warnings`
module in the Python standard library for more information.
Defaults to False.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
Returns
-------
votable : `~pyvo.io.vosi.endpoint.AvailabilityFile` object
See also
--------
pyvo.io.vosi.exceptions : The exceptions this function may raise.
"""
config = _pedantic_settings(pedantic)
if filename is None and isinstance(source, six.string_types):
config['filename'] = source
else:
config['filename'] = filename
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser) as iterator:
return AvailabilityFile(config=config,
pos=(1, 1)).parse(iterator, config)
def _votableparse(source, columns=None, invalid='mask', pedantic=False,
table_number=None, filename=None, version="1.1"):
try:
import astropy.io.votable.tree as votabletree
import astropy.io.votable.table as votabletable
from astropy.utils.xml import iterparser
#from astropy.io.votable.exceptions import W22
from astropy.io.votable.exceptions import W03,W06,W20,W21,W42,W46,W47,W49,E10
for warning in (W03, W06, W20, W21, W42, W46, W47, W49, E10):
warnings.simplefilter("ignore", warning)
# MJG : 021913 - commented out to get CDS responses to work
# warnings.simplefilter("error", W22)
except ImportError:
raise RuntimeError("astropy votable not available")
invalid = invalid.lower()
assert invalid in ('exception', 'mask')
chunk_size=votabletree.DEFAULT_CHUNK_SIZE
if pedantic is None:
pedantic = votabletable.PEDANTIC()
config = {
'columns' : columns,
'invalid' : invalid,
'pedantic' : pedantic,
'chunk_size' : chunk_size,
'table_number' : table_number,
'filename' : filename,
'version_1_1_or_later': True }
if filename is None and isinstance(source, basestring):
config['filename'] = source
if filename is None:
config['filename'] = 'dal_query'
with iterparser.get_xml_iterator(source) as iterator:
return votabletree.VOTableFile(
config=config, pos=(1, 1), version=version).parse(iterator, config)
def parse(source, columns=None, invalid='exception', pedantic=None,
chunk_size=tree.DEFAULT_CHUNK_SIZE, table_number=None,
table_id=None, filename=None, unit_format=None,
datatype_mapping=None, _debug_python_based_parser=False):
"""
Parses a VOTABLE_ xml file (or file-like object), and returns a
`~astropy.io.votable.tree.VOTableFile` object.
Parameters
----------
source : str or readable file-like object
Path or file object containing a VOTABLE_ xml file.
columns : sequence of str, optional
List of field names to include in the output. The default is
to include all fields.
invalid : str, optional
One of the following values:
- 'exception': throw an exception when an invalid value is
encountered (default)
- 'mask': mask out invalid values
pedantic : bool, optional
When `True`, raise an error when the file violates the spec,
otherwise issue a warning. Warnings may be controlled using
the standard Python mechanisms. See the `warnings`
module in the Python standard library for more information.
When not provided, uses the configuration setting
``astropy.io.votable.pedantic``, which defaults to False.
chunk_size : int, optional
The number of rows to read before converting to an array.
Higher numbers are likely to be faster, but will consume more
memory.
table_number : int, optional
The number of table in the file to read in. If `None`, all
tables will be read. If a number, 0 refers to the first table
in the file, and only that numbered table will be parsed and
read in. Should not be used with ``table_id``.
table_id : str, optional
The ID of the table in the file to read in. Should not be
used with ``table_number``.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
unit_format : str, astropy.units.format.Base instance or None, optional
The unit format to use when parsing unit attributes. If a
string, must be the name of a unit formatter. The built-in
formats include ``generic``, ``fits``, ``cds``, and
``vounit``. A custom formatter may be provided by passing a
`~astropy.units.UnitBase` instance. If `None` (default),
the unit format to use will be the one specified by the
VOTable specification (which is ``cds`` up to version 1.2 of
VOTable, and (probably) ``vounit`` in future versions of the
spec).
datatype_mapping : dict of str to str, optional
A mapping of datatype names to valid VOTable datatype names.
For example, if the file being read contains the datatype
"unsignedInt" (an invalid datatype in VOTable), include the
mapping ``{"unsignedInt": "long"}``.
Returns
-------
votable : `~astropy.io.votable.tree.VOTableFile` object
See also
--------
astropy.io.votable.exceptions : The exceptions this function may raise.
"""
from . import conf
invalid = invalid.lower()
if invalid not in ('exception', 'mask'):
raise ValueError("accepted values of ``invalid`` are: "
"``'exception'`` or ``'mask'``.")
if pedantic is None:
pedantic = conf.pedantic
if datatype_mapping is None:
datatype_mapping = {}
config = {
'columns': columns,
'invalid': invalid,
'pedantic': pedantic,
'chunk_size': chunk_size,
'table_number': table_number,
'filename': filename,
'unit_format': unit_format,
'datatype_mapping': datatype_mapping
}
if filename is None and isinstance(source, str):
config['filename'] = source
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser) as iterator:
return tree.VOTableFile(
config=config, pos=(1, 1)).parse(iterator, config)
def parse(source,
columns=None,
invalid='exception',
verify=None,
chunk_size=tree.DEFAULT_CHUNK_SIZE,
table_number=None,
table_id=None,
filename=None,
unit_format=None,
datatype_mapping=None,
_debug_python_based_parser=False):
"""
Parses a VOTABLE_ xml file (or file-like object), and returns a
`~astropy.io.votable.tree.VOTableFile` object.
Parameters
----------
source : str or readable file-like object
Path or file object containing a VOTABLE_ xml file.
columns : sequence of str, optional
List of field names to include in the output. The default is
to include all fields.
invalid : str, optional
One of the following values:
- 'exception': throw an exception when an invalid value is
encountered (default)
- 'mask': mask out invalid values
verify : {'ignore', 'warn', 'exception'}, optional
When ``'exception'``, raise an error when the file violates the spec,
otherwise either issue a warning (``'warn'``) or silently continue
(``'ignore'``). Warnings may be controlled using the standard Python
mechanisms. See the `warnings` module in the Python standard library
for more information. When not provided, uses the configuration setting
``astropy.io.votable.verify``, which defaults to 'ignore'.
.. versionchanged:: 4.0
``verify`` replaces the ``pedantic`` argument, which will be
deprecated in future.
chunk_size : int, optional
The number of rows to read before converting to an array.
Higher numbers are likely to be faster, but will consume more
memory.
table_number : int, optional
The number of table in the file to read in. If `None`, all
tables will be read. If a number, 0 refers to the first table
in the file, and only that numbered table will be parsed and
read in. Should not be used with ``table_id``.
table_id : str, optional
The ID of the table in the file to read in. Should not be
used with ``table_number``.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
unit_format : str, astropy.units.format.Base instance or None, optional
The unit format to use when parsing unit attributes. If a
string, must be the name of a unit formatter. The built-in
formats include ``generic``, ``fits``, ``cds``, and
``vounit``. A custom formatter may be provided by passing a
`~astropy.units.UnitBase` instance. If `None` (default),
the unit format to use will be the one specified by the
VOTable specification (which is ``cds`` up to version 1.2 of
VOTable, and (probably) ``vounit`` in future versions of the
spec).
datatype_mapping : dict of str to str, optional
A mapping of datatype names to valid VOTable datatype names.
For example, if the file being read contains the datatype
"unsignedInt" (an invalid datatype in VOTable), include the
mapping ``{"unsignedInt": "long"}``.
Returns
-------
votable : `~astropy.io.votable.tree.VOTableFile` object
See also
--------
astropy.io.votable.exceptions : The exceptions this function may raise.
"""
from . import conf
invalid = invalid.lower()
if invalid not in ('exception', 'mask'):
raise ValueError("accepted values of ``invalid`` are: "
"``'exception'`` or ``'mask'``.")
if verify is None:
# NOTE: since the pedantic argument isn't fully deprecated yet, we need
# to catch the deprecation warning that occurs when accessing the
# configuration item, but only if it is for the pedantic option in the
# [io.votable] section.
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
r"Config parameter \'pedantic\' in section \[io.votable\]",
AstropyDeprecationWarning)
conf_verify_lowercase = conf.verify.lower()
# We need to allow verify to be booleans as strings since the
# configuration framework doesn't make it easy/possible to have mixed
# types.
if conf_verify_lowercase in ['false', 'true']:
verify = conf_verify_lowercase == 'true'
else:
verify = conf_verify_lowercase
if isinstance(verify, bool):
verify = 'exception' if verify else 'warn'
elif verify not in VERIFY_OPTIONS:
raise ValueError('verify should be one of {0}'.format(
'/'.join(VERIFY_OPTIONS)))
if datatype_mapping is None:
datatype_mapping = {}
config = {
'columns': columns,
'invalid': invalid,
'verify': verify,
'chunk_size': chunk_size,
'table_number': table_number,
'filename': filename,
'unit_format': unit_format,
'datatype_mapping': datatype_mapping
}
if filename is None and isinstance(source, str):
config['filename'] = source
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser) as iterator:
return tree.VOTableFile(config=config,
pos=(1, 1)).parse(iterator, config)
def parse(source,
columns=None,
invalid='exception',
pedantic=None,
chunk_size=tree.DEFAULT_CHUNK_SIZE,
table_number=None,
table_id=None,
filename=None,
unit_format=None,
datatype_mapping=None,
_debug_python_based_parser=False):
"""
Parses a VOTABLE_ xml file (or file-like object), and returns a
`~astropy.io.votable.tree.VOTableFile` object.
Parameters
----------
source : str or readable file-like object
Path or file object containing a VOTABLE_ xml file.
columns : sequence of str, optional
List of field names to include in the output. The default is
to include all fields.
invalid : str, optional
One of the following values:
- 'exception': throw an exception when an invalid value is
encountered (default)
- 'mask': mask out invalid values
pedantic : bool, optional
When `True`, raise an error when the file violates the spec,
otherwise issue a warning. Warnings may be controlled using
the standard Python mechanisms. See the `warnings`
module in the Python standard library for more information.
When not provided, uses the configuration setting
``astropy.io.votable.pedantic``, which defaults to False.
chunk_size : int, optional
The number of rows to read before converting to an array.
Higher numbers are likely to be faster, but will consume more
memory.
table_number : int, optional
The number of table in the file to read in. If `None`, all
tables will be read. If a number, 0 refers to the first table
in the file, and only that numbered table will be parsed and
read in. Should not be used with ``table_id``.
table_id : str, optional
The ID of the table in the file to read in. Should not be
used with ``table_number``.
filename : str, optional
A filename, URL or other identifier to use in error messages.
If *filename* is None and *source* is a string (i.e. a path),
then *source* will be used as a filename for error messages.
Therefore, *filename* is only required when source is a
file-like object.
unit_format : str, astropy.units.format.Base instance or None, optional
The unit format to use when parsing unit attributes. If a
string, must be the name of a unit formatter. The built-in
formats include ``generic``, ``fits``, ``cds``, and
``vounit``. A custom formatter may be provided by passing a
`~astropy.units.UnitBase` instance. If `None` (default),
the unit format to use will be the one specified by the
VOTable specification (which is ``cds`` up to version 1.2 of
VOTable, and (probably) ``vounit`` in future versions of the
spec).
datatype_mapping : dict of str to str, optional
A mapping of datatype names to valid VOTable datatype names.
For example, if the file being read contains the datatype
"unsignedInt" (an invalid datatype in VOTable), include the
mapping ``{"unsignedInt": "long"}``.
Returns
-------
votable : `~astropy.io.votable.tree.VOTableFile` object
See also
--------
astropy.io.votable.exceptions : The exceptions this function may raise.
"""
from . import conf
invalid = invalid.lower()
if invalid not in ('exception', 'mask'):
raise ValueError("accepted values of ``invalid`` are: "
"``'exception'`` or ``'mask'``.")
if pedantic is None:
pedantic = conf.pedantic
if datatype_mapping is None:
datatype_mapping = {}
config = {
'columns': columns,
'invalid': invalid,
'pedantic': pedantic,
'chunk_size': chunk_size,
'table_number': table_number,
'filename': filename,
'unit_format': unit_format,
'datatype_mapping': datatype_mapping
}
if filename is None and isinstance(source, str):
config['filename'] = source
with iterparser.get_xml_iterator(
source,
_debug_python_based_parser=_debug_python_based_parser) as iterator:
return tree.VOTableFile(config=config,
pos=(1, 1)).parse(iterator, config)
invalid = invalid.lower()
assert invalid in ('exception', 'mask')
chunk_size=votabletree.DEFAULT_CHUNK_SIZE
if pedantic is None:
pedantic = votabletable.PEDANTIC()
config = {
'columns' : columns,
'invalid' : invalid,
'pedantic' : pedantic,
'chunk_size' : chunk_size,
'table_number' : table_number,
'filename' : filename,
'version_1_1_or_later': True }
if filename is None and isinstance(source, basestring):
config['filename'] = source
if filename is None:
config['filename'] = 'dal_query'
with iterparser.get_xml_iterator(source) as iterator:
return votabletree.VOTableFile(
config=config, pos=(1, 1), version=version).parse(iterator, config)
