# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
A module for walking through the query response of VO data access layer
(DAL) queries and general VOTable-based datasets.
Most data queries in the VO return a table as a result, usually
formatted as a VOTable. Each row of the table describes a single
physical or virtual dataset which can be retrieved. For uniformity,
datasets are described via standard metadata defined by a data model
specific to the type of data being queried. The fields of the data
model are identified most generally by their VOClient alias as defined
in this interface, or at a lower level by the Utype or UCD of the
specific standard and version of the standard being queried. While
the data model differs depending upon the type of data being queried,
the form of the query response is the same for all classes of data,
allowing a common query response interface to be used.
An exception to this occurs when querying an astronomical catalog or
other externally defined table. In this case there is no VO defined
standard data model. Usually the field names are used to uniquely
identify table columns.
"""
__all__ = ["DALService", "DALQuery", "DALResults", "Record"]
import os
import shutil
import re
import requests
from collections.abc import Mapping
import collections
from warnings import warn
from astropy.table import Table, QTable
from astropy.io.votable import parse as votableparse
from astropy.io.votable.ucd import parse_ucd
from astropy.utils.exceptions import AstropyDeprecationWarning
from .mimetype import mime_object_maker
from .exceptions import (DALFormatError, DALServiceError, DALQueryError,
DALOverflowWarning)
from .. import samp
from ..utils.decorators import stream_decode_content
from ..utils.http import use_session
[docs]class DALService:
"""
an abstract base class representing a DAL service located a particular
endpoint.
"""
def __init__(self, baseurl, *, session=None, capability_description=None,):
"""
instantiate the service connecting it to a base URL
Parameters
----------
baseurl : str
the base URL that should be used for forming queries to the service.
session : object
optional session to use for network requests
description : str, optional
the description of the service.
"""
self._baseurl = baseurl
self._capability_description = capability_description
self._session = use_session(session)
@property
def baseurl(self):
"""
the base URL identifying the location of the service and where
queries are submitted (read-only)
"""
return self._baseurl
@property
def capability_description(self):
"""
The service description.
"""
return self._capability_description
def __repr__(self) -> str:
return (f"{type(self).__name__}(baseurl : '{self.baseurl}',"
f" description : '{self.capability_description}')")
[docs] def search(self, **keywords):
"""
send a search query to this service.
This implementation has no knowledge of the type of service being
queried. The query parameters are given as arbitrary keywords which
will be assumed to be understood by the service (i.e. there is no
argument checking). The response is a generic DALResults object.
Raises
------
DALServiceError
for errors connecting to or communicating with the service
DALQueryError
for errors either in the input query syntax or other user errors
detected by the service
DALFormatError
for errors parsing the VOTable response
"""
q = self.create_query(**keywords)
return q.execute()
[docs] def create_query(self, **keywords):
"""
create a query object that constraints can be added to and then
executed.
Returns
-------
DALQuery
a generic query object
"""
q = DALQuery(self.baseurl, session=self._session, **keywords)
return q
[docs] def describe(self):
"""
describe the general information about the DAL service
"""
print('DAL Service at {}'.format(self.baseurl))
[docs]class DALQuery(dict):
"""
a class for preparing a query to a particular service. Query constraints
are added via its service type-specific methods. The various execute()
functions will submit the query and return the results.
The base URL for the query can be changed via the baseurl property.
A session can also optionally be passed in that will be used for
network transactions made by this object to remote services.
"""
_ex = None
def __init__(self, baseurl, *, session=None, **keywords):
"""
initialize the query object with a baseurl
"""
if isinstance(baseurl, bytes):
baseurl = baseurl.decode("utf-8")
self._baseurl = baseurl.rstrip("?")
self._session = use_session(session)
self.update({key.upper(): value for key, value in keywords.items()})
@property
def baseurl(self):
"""
the base URL that this query will be sent to when one of the
execute functions is called.
"""
return self._baseurl
[docs] def execute(self):
"""
submit the query and return the results as a Results subclass instance
Raises
------
DALServiceError
for errors connecting to or communicating with the service
DALQueryError
for errors either in the input query syntax or
other user errors detected by the service
DALFormatError
for errors parsing the VOTable response
"""
return DALResults(self.execute_votable(), url=self.queryurl, session=self._session)
[docs] def execute_raw(self):
"""
submit the query and return the raw response as a string.
No exceptions are raised here because non-2xx responses might still
contain payload. They can be raised later by calling ``raise_if_error``
"""
f = self.execute_stream()
out = None
try:
out = f.read()
finally:
f.close()
return out
[docs] @stream_decode_content
def execute_stream(self, *, post=False):
"""
Submit the query and return the raw response as a file stream.
No exceptions are raised here because non-2xx responses might still
contain payload. They can be raised later by calling ``raise_if_error``
"""
response = self.submit(post=post)
try:
response.raise_for_status()
except requests.RequestException as ex:
# save for later use
self._ex = ex
finally:
return response.raw
[docs] def submit(self, *, post=False):
"""
does the actual request
"""
url = self.queryurl
params = {k: v for k, v in self.items()}
if post:
response = self._session.post(url, data=params, stream=True,
allow_redirects=True)
else:
response = self._session.get(url, params=params, stream=True,
allow_redirects=True)
return response
[docs] def execute_votable(self, *, post=False):
"""
Submit the query and return the results as an AstroPy votable instance.
As this is the level where qualified error messages are available,
they are raised here instead of in the underlying execute_stream.
Returns
-------
astropy.io.votable.tree.VOTableFile
an Astropy votable object
Raises
------
DALServiceError
for errors connecting to or communicating with the service
DALFormatError
for errors parsing the VOTable response
See Also
--------
astropy.io.votable
DALServiceError
DALFormatError
DALQueryError
"""
try:
return votableparse(self.execute_stream(post=post).read)
except Exception as e:
self.raise_if_error()
raise DALFormatError(e, self.queryurl)
[docs] def raise_if_error(self):
"""
Raise if there was an error on http level.
"""
if self._ex:
e = self._ex
raise DALServiceError.from_except(e, self.queryurl)
@property
def queryurl(self):
"""
The URL that encodes the current query. This is the
URL that the execute functions will use if called next.
"""
return self.baseurl
[docs]class DALResults:
"""
Results from a DAL query. It provides random access to records in
the response. Alternatively, it can provide results via a Cursor
(compliant with the Python Database API) or an iterable.
"""
@classmethod
@stream_decode_content
def _from_result_url(cls, result_url, session):
return session.get(result_url, stream=True).raw
[docs] @classmethod
def from_result_url(cls, result_url, *, session=None):
"""
Create a result object from a url.
Uses the optional session to make the request.
"""
session = use_session(session)
return cls(
votableparse(cls._from_result_url(result_url, session).read),
url=result_url,
session=session)
def __init__(self, votable, *, url=None, session=None):
"""
initialize the cursor. This constructor is not typically called
by directly applications; rather an instance is obtained from calling
a DALQuery's execute().
Parameters
----------
votable : str
the service response parsed into an
astropy.io.votable.tree.VOTableFile instance.
url : str
the URL that produced the response
session : object
optional session to use for network requests
Raises
------
DALFormatError
if the response VOTable does not contain a response table
See Also
--------
pyvo.dal.DALFormatError
"""
self._votable = votable
self._url = url
self._session = use_session(session)
self._status = self._findstatus(votable)
if self._status[0].lower() not in ("ok", "overflow"):
raise DALQueryError(self._status[1], self._status[0], url)
if self._status[0].lower() == "overflow":
warn("Partial result set. Potential causes MAXREC, async storage space, etc.",
category=DALOverflowWarning)
self._resultstable = self._findresultstable(votable)
if not self._resultstable:
raise DALFormatError(
reason="VOTable response missing results table", url=url)
self._fldnames = tuple(
field.name for field in self._resultstable.fields)
if not self._fldnames:
raise DALFormatError(
reason="response table missing column descriptions.", url=url)
self._infos = self._findinfos(votable)
def _findresultstable(self, votable):
# this can be overridden to specialize for a particular DAL protocol
res = self._findresultsresource(votable)
if not res or len(res.tables) < 1:
return None
return res.tables[0]
def _findresultsresource(self, votable):
# this can be overridden to specialize for a particular DAL protocol
if len(votable.resources) < 1:
return None
for res in votable.resources:
if res.type.lower() == "results":
return res
return votable.resources[0]
def _findstatus(self, votable):
# this can be overridden to specialize for a particular DAL protocol
# look first in the result resource
res = self._findresultsresource(votable)
if res:
# should be a RESOURCE/INFO
info = self._findstatusinfo(res.infos)
if info:
return (info.value, info.content)
# if not there, check inside first table
if len(res.tables) > 0:
info = self._findstatusinfo(res.tables[0].infos)
if info:
return (info.value, info.content)
# otherwise, look just below the root element
info = self._findstatusinfo(votable.infos)
if info:
return (info.value, info.content)
# assume it's okay
return ("OK", "QUERY_STATUS not specified")
def _findstatusinfo(self, infos):
# this can be overridden to specialize for a particular DAL protocol
status = None
# return the last status to catch potential overflow or error sent
# after the results.
for info in infos:
if info.name.lower() == 'query_status':
status = info
return status
def _findinfos(self, votable):
# this can be overridden to specialize for a particular DAL protocol
infos = {}
res = self._findresultsresource(votable)
for info in res.infos:
infos[info.name] = info.value
for info in votable.infos:
infos[info.name] = info.value
return infos
def __repr__(self):
return f"<DALResults{repr(self.to_table())[1:]}"
@property
def queryurl(self):
"""
the URL query that produced these results. None is returned if unknown
"""
return self._url
@property
def votable(self):
"""
The complete votable XML Document `astropy.io.votable.tree.VOTableFile`
"""
return self._votable
@property
def resultstable(self):
"""
The votable XML element `astropy.io.votable.tree.TableElement`
"""
return self._resultstable
[docs] def to_table(self):
"""
Returns a astropy Table object.
Returns
-------
`astropy.table.Table`
"""
return self.resultstable.to_table(use_names_over_ids=True)
[docs] def to_qtable(self):
"""
Returns a astropy QTable object containing quantities instead of simple
values
Returns
-------
`astropy.table.QTable`
"""
return QTable(self.resultstable.to_table(use_names_over_ids=True))
@property
def table(self):
warn(AstropyDeprecationWarning(
'Using the table property is deprecated. '
'Please use the to_table() instead.'
))
return self.to_table()
def __len__(self):
"""
return the record count
"""
return len(self.resultstable.array)
def __getitem__(self, indx):
"""
if indx is a string, r[indx] will return the field with the name of
indx; if indx is an integer, r[indx] will return the indx-th record.
"""
if isinstance(indx, int):
return self.getrecord(indx)
elif isinstance(indx, tuple):
return self.getvalue(*indx)
else:
return self.getcolumn(indx)
@property
def fieldnames(self):
"""
return the names of the columns. These are the names that are used
to access values from the dictionaries returned by getrecord(). They
correspond to the column name.
"""
return self._fldnames
@property
def fielddescs(self):
"""
return the full metadata the columns as a list of Field instances,
a simple object with attributes corresponding the the VOTable FIELD
attributes, namely: name, id, type, ucd, utype, arraysize, description
"""
return self.resultstable.fields
@property
def status(self):
"""
The query status as a 2-element tuple e.g. ('OK', 'Everythings fine')
"""
return self._status
[docs] def fieldname_with_ucd(self, ucd):
"""
return the field name that has a given UCD value or None if the UCD
is not found.
"""
search_ucds = set(parse_ucd(ucd, has_colon=True))
for field in (field for field in self.fielddescs if field.ucd):
field_ucds = set(parse_ucd(field.ucd, has_colon=True))
if search_ucds & field_ucds:
return field.name
return None
[docs] def fieldname_with_utype(self, utype):
"""
return the field name that has a given UType value or None if the UType
is not found.
"""
try:
iterchain = (
self.getdesc(fieldname) for fieldname in self.fieldnames)
iterchain = (field for field in iterchain if field.utype == utype)
return next(iterchain).name
except StopIteration:
return None
[docs] def getcolumn(self, name):
"""
return a numpy array containing the values for the column with the
given name
"""
try:
if name not in self.fieldnames:
name = self.resultstable.get_field_by_id(name).name
return self.resultstable.array[name]
except KeyError:
raise KeyError("No such column: {}".format(name))
[docs] def getrecord(self, index):
"""
return a representation of a result record that follows dictionary
semantics. The keys of the dictionary are those returned by this
instance's fieldnames attribute.The returned record may have additional
accessor methods for getting at stardard DAL response metadata
(e.g. ra, dec).
Parameters
----------
index : int
the integer index of the desired record where 0 returns the first
record
Returns
-------
Record
a dictionary-like wrapper containing the result record metadata.
Raises
------
IndexError
if index is negative or equal or larger than the number of rows in
the result table.
See Also
--------
Record
"""
return Record(self, index, session=self._session)
[docs] def getvalue(self, name, index):
"""
return the value of a record attribute--a value from a column and row.
Parameters
----------
name : str
the name of the attribute (column)
index : int
the zero-based index of the record
Raises
------
IndexError
if index is negative or equal or larger than the
number of rows in the result table.
KeyError
if name is not a recognized column name
"""
return self.getrecord(index)[name]
[docs] def getdesc(self, name):
"""
return the field description for the record attribute (column) with
the given name
Parameters
----------
name : str
the name of the attribute (column)
Returns
-------
object
with attributes (name, id, datatype, unit, ucd, utype, arraysize)
which describe the column
"""
if name not in self._fldnames:
raise KeyError(name)
return self.resultstable.get_field_by_id_or_name(name)
def __iter__(self):
"""
return a python iterable for stepping through the records in this
result
"""
pos = 0
while True:
try:
out = self.getrecord(pos)
except IndexError:
break
yield out
pos += 1
[docs] def broadcast_samp(self, *, client_name=None):
"""
Broadcast the table to ``client_name`` via SAMP
"""
with samp.connection() as conn:
samp.send_table_to(
conn, self.to_table(),
client_name=client_name, name=self.queryurl)
[docs] def cursor(self):
"""
return a cursor that is compliant with the Python Database API's
``Cursor`` interface. See PEP 249 for details.
"""
from .dbapi2 import Cursor
return Cursor(self)
[docs]class Record(Mapping):
"""
one record from a DAL query result. The column values are accessible
as dictionary items. It also provides special added functions for
accessing the dataset the record corresponds to. Subclasses may provide
additional functions for access to service type-specific data.
"""
def __init__(self, results, index, *, session=None):
self._results = results
self._index = index
self._session = use_session(session)
self._mapping = collections.OrderedDict(
zip(
results.fieldnames,
results.resultstable.array.data[index]
)
)
def __getitem__(self, key):
try:
if key not in self._mapping:
key = self._results.resultstable.get_field_by_id(key).name
return self._mapping[key]
except KeyError:
raise KeyError("No such column: {}".format(key))
def __iter__(self):
return iter(self._mapping)
def __len__(self):
return len(self._mapping)
def __repr__(self):
return repr(tuple(self.values()))
[docs] def get(self, key, default=None, decode=False):
"""
This method mimics the dict get method and adds a decode parameter
to allow decoding of binary strings.
"""
out = self._mapping.get(key, default)
if decode and isinstance(out, bytes):
out = out.decode('ascii')
return out
[docs] def getbyucd(self, ucd, default=None, decode=False):
"""
return the column with the given ucd.
"""
return self.get(
self._results.fieldname_with_ucd(ucd), default, decode)
[docs] def getbyutype(self, utype, default=None, decode=False):
"""
return the column with the given utype.
Raises
------
KeyError
if theres no column with the given utype.
"""
return self.get(
self._results.fieldname_with_utype(utype), default, decode)
[docs] def getdataurl(self):
"""
return the URL contained in the access URL column which can be used
to retrieve the dataset described by this record. None is returned
if no such column exists.
"""
for fieldname in self._results.fieldnames:
field = self._results.getdesc(fieldname)
if (field.utype and "access.reference" in field.utype.lower()) or (
field.ucd and "meta.dataset" in field.ucd
and "meta.ref.url" in field.ucd
):
out = self[fieldname]
if isinstance(out, bytes):
out = out.decode('utf-8')
return out
return None
[docs] def getdataobj(self):
"""
return the appropriate data object suitable for the data content behind
this record.
"""
return mime_object_maker(self.getdataurl(), self.getdataformat())
[docs] @stream_decode_content
def getdataset(self, timeout=None):
"""
Get the dataset described by this record from the server.
Parameters
----------
timeout : float
the time in seconds to allow for a successful
connection with server before failing with an
IOError (specifically, socket.timeout) exception
Returns
-------
A file-like object which may be read to retrieve the referenced
dataset.
Raises
------
KeyError
if no datast access URL is included in the record
URLError
if the dataset access URL is invalid (note: subclass of IOError)
HTTPError
if an HTTP error occurs while accessing the dataset
(note: subclass of IOError)
socket.timeout
if the timeout is exceeded before a connection is established.
(note: subclass of IOError)
IOError
if some other error occurs while establishing the data stream.
"""
url = self.getdataurl()
if not url:
raise KeyError("no dataset access URL recognized in record")
if timeout:
response = self._session.get(url, stream=True, timeout=timeout)
else:
response = self._session.get(url, stream=True)
try:
response.raise_for_status()
except requests.RequestException as ex:
raise DALServiceError.from_except(ex, url)
return response.raw
[docs] def cachedataset(self, *, filename=None, dir=".", timeout=None, bufsize=None):
"""
retrieve the dataset described by this record and write it out to
a file with the given name. If the file already exists, it will be
over-written.
Parameters
----------
filename : str
the name of the file to write dataset to. If the
value represents a relative path, it will be taken
to be relative to the value of the ``dir``
parameter. If None, a default name is attempted
based on the record title and format.
dir : str
the directory to write the file into. This value
will be ignored if filename is an absolute path.
timeout : int
the time in seconds to allow for a successful
connection with server before failing with an
IOError (specifically, socket.timeout) exception
bufsize : int
a buffer size in bytes for copying the data to disk
(default: 0.5 MB)
Raises
------
KeyError
if no datast access URL is included in the record
URLError
if the dataset access URL is invalid
HTTPError
if an HTTP error occurs while accessing the dataset
socket.timeout
if the timeout is exceeded before a connection is established.
(note: subclass of IOError)
IOError
if an error occurs while writing out the dataset
"""
if not bufsize:
bufsize = 524288
if not filename:
filename = self.make_dataset_filename(dir=dir)
inp = self.getdataset(timeout)
try:
with open(filename, 'wb') as out:
shutil.copyfileobj(inp, out)
finally:
inp.close()
_dsname_no = 0 # used by make_dataset_filename
[docs] def make_dataset_filename(self, *, dir=".", base=None, ext=None):
"""
create a viable pathname in a given directory for saving the dataset
available via getdataset(). The pathname that is returned is
guaranteed not to already exist (under single-threaded conditions).
This implementation will first try combining the base name with the
file extension (with a dot). If this file already exists in the
directory, a name that appends an integer suffix ("-#") to the base
before joining with the extension will be tried. The integer will
be incremented until a non-existent filename is created.
Parameters
----------
dir : str
the directory to save the dataset under. This must already exist.
base : str
a basename to use to as the base of the filename. If None, the
result of ``suggest_dataset_basename()`` will be used.
ext : str
the filename extension to use. If None, the result of
``suggest_extension()`` will be used.
"""
if not dir:
raise ValueError(
"make_dataset_filename(): no dir parameter provided")
if not os.path.exists(dir):
os.mkdir(dir)
if not os.path.isdir(dir):
raise ValueError("{}: not a directory".format(dir))
if not base:
base = self.suggest_dataset_basename()
if not ext:
ext = self.suggest_extension(default="dat")
# be efficient when writing a bunch of files into the same directory
# in succession
n = self._dsname_no
def mkpath(i):
return os.path.join(dir, "{}-{}.{}".format(base, i, ext))
if n > 0:
# find the last file written of the form, base-n.ext
while n > 0 and not os.path.exists(mkpath(n)):
n -= 1
if n > 0:
n += 1
if n == 0:
# never wrote a file of form, base-n.ext; try base.ext
path = os.path.join(dir, "{}.{}".format(base, ext))
if not os.path.exists(path):
return path
n += 1
# find next available name
while os.path.exists(mkpath(n)):
n += 1
self._dsname_no = n
return mkpath(n)
[docs] def suggest_dataset_basename(self):
"""
return a default base filename that the dataset available via
``getdataset()`` can be saved as. This function is
specialized for a particular service type this record originates from
so that it can be used by ``cachedataset()`` via
``make_dataset_filename()``.
"""
# abstract; specialized for the different service types
return "dataset"
[docs] def suggest_extension(self, *, default=None):
"""
returns a recommended filename extension for the dataset described
by this record. Typically, this would look at the column describing
the format and choose an extension accordingly. This function is
specialized for a particular service type this record originates from
so that it can be used by ``cachedataset()`` via
``make_dataset_filename()``.
"""
# abstract; specialized for the different service types
return default
class Iter:
def __init__(self, res):
self.resultset = res
self.pos = 0
def __iter__(self):
return self
def __next__(self):
try:
out = self.resultset.getrecord(self.pos)
self.pos += 1
return out
except IndexError:
raise StopIteration()
next = __next__
class Upload:
"""
This class represents a DALI Upload as described in
http://www.ivoa.net/documents/DALI/20161101/PR-DALI-1.1-20161101.html#tth_sEc3.4.5
"""
def __init__(self, name, content):
"""
Initialise the Upload object with the given parameters
Parameters
----------
name : str
Tablename for use in queries
content : object
If its a file-like object, a string pointing to a local file,
a `DALResults` object or a astropy table, `is_inline` will be true
and it will expose a file-like object under `fileobj`
Otherwise it exposes a URI under `uri`
"""
try:
self._is_file = os.path.isfile(content)
except Exception:
self._is_file = False
self._is_fileobj = hasattr(content, "read")
self._is_table = isinstance(content, Table)
self._is_resultset = isinstance(content, DALResults)
self._inline = any((
self._is_file,
self._is_fileobj,
self._is_table,
self._is_resultset,
))
self._name = name
self._content = content
@property
def is_inline(self):
"""
True if the upload can be inlined
"""
return self._inline
@property
def name(self):
return self._name
def fileobj(self):
"""
A file-like object for a local resource
Raises
------
ValueError
if theres no valid local resource
"""
if not self.is_inline:
raise ValueError(
"Upload {name} doesn't refer to a local resource".format(
name=self.name))
# astropy table
if isinstance(self._content, Table):
from io import BytesIO
fileobj = BytesIO()
self._content.write(output=fileobj, format="votable")
fileobj.seek(0)
return fileobj
elif isinstance(self._content, DALResults):
from io import BytesIO
fileobj = BytesIO()
table = self._content.to_table()
table.write(output=fileobj, format="votable")
fileobj.seek(0)
return fileobj
fileobj = self._content
try:
fileobj = open(self._content)
finally:
return fileobj
def uri(self):
"""
The URI pointing to the result
"""
# TODO: use a async job base class instead of hasattr for inspection
if hasattr(self._content, "result_uri"):
self._content.raise_if_error()
uri = self._content.result_uri
else:
uri = str(self._content)
return uri
def query_part(self):
"""
The query part for use in DALI requests
"""
if self.is_inline:
value = "{name},param:{name}"
else:
value = "{name},{uri}"
return value.format(name=self.name, uri=self.uri())
class UploadList(list):
"""
This class extends the native python list with utility functions for
upload handling
"""
@classmethod
def fromdict(cls, dct):
"""
Constructs a upload list from a dictionary with table_name: content
"""
return cls(Upload(key, value) for key, value in dct.items())
def param(self):
"""
Returns a string suitable for use in UPLOAD parameters
"""
return ";".join(upload.query_part() for upload in self)
_image_mt_re = re.compile(r'^image/(\w+)')
_text_mt_re = re.compile(r'^text/(\w+)')
_votable_mt_re = re.compile(r'^(\w+)/(x-)?votable(\+\w+)?')