Source code for astroquery.nrao.core

# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import print_function

import re
import os
import warnings
import functools
import keyring

import numpy as np
import astropy.units as u
import astropy.io.votable as votable
from astropy import coordinates
import six
from astropy.table import Table
from astropy import log
from bs4 import BeautifulSoup

from ..query import QueryWithLogin
from ..utils import commons, async_to_sync, prepend_docstr_nosections
from ..exceptions import TableParseError, LoginError

from . import conf

__all__ = ["Nrao", "NraoClass"]


def _validate_params(func):
    @functools.wraps(func)
    def wrapper(*args, **kwargs):
        telescope = kwargs.get('telescope', 'all')
        telescope_config = kwargs.get('telescope_config', 'all')
        obs_band = kwargs.get('obs_band', 'all')
        sub_array = kwargs.get('sub_array', 'all')
        if not isinstance(telescope, (list, tuple)):
            telescope = [telescope]
        for tel in telescope:
            if tel not in Nrao.telescope_code:
                raise ValueError("'telescope must be one of {!s}"
                                 .format(Nrao.telescope_code.keys()))
        if not isinstance(telescope_config, (list, tuple)):
            telescope_config = [telescope_config]
        for tconf in telescope_config:
            if tconf.upper() not in Nrao.telescope_config:
                raise ValueError("'telescope_config' must be one of {!s}"
                                 .format(Nrao.telescope_config))
        if isinstance(obs_band, (list, tuple)):
            for ob in obs_band:
                if ob.upper() not in Nrao.obs_bands:
                    raise ValueError("'obs_band' must be one of {!s}"
                                     .format(Nrao.obs_bands))
        elif obs_band.upper() not in Nrao.obs_bands:
            raise ValueError("'obs_band' must be one of {!s}"
                             .format(Nrao.obs_bands))
        if sub_array not in Nrao.subarrays and sub_array != 'all':
            raise ValueError("'sub_array' must be one of {!s}"
                             .format(Nrao.subarrays))
        return func(*args, **kwargs)
    return wrapper


[docs]@async_to_sync class NraoClass(QueryWithLogin): DATA_URL = conf.server TIMEOUT = conf.timeout USERNAME = conf.username # dicts and lists for data archive queries telescope_code = { "all": "ALL", "jansky_vla": "EVLA", "historical_vla": "VLA", "vlba": "VLBA", "gbt": "GBT", } telescope_config = ['ALL', 'A', 'AB', 'BnA', 'B', 'BC', 'CnB', 'C', 'CD', 'DnC', 'D', 'DA'] obs_bands = ['ALL', 'all', '4', 'P', 'L', 'S', 'C', 'X', 'U', 'K', 'Ka', 'Q', 'W'] # we only ever use uppercase versions telescope_config = [x.upper() for x in telescope_config] obs_bands = [x.upper() for x in obs_bands] subarrays = ['ALL', 1, 2, 3, 4, 5] @_validate_params def _args_to_payload(self, **kwargs): """ Queries the NRAO data archive and fetches table of observation summaries. Parameters ---------- coordinates : str or `astropy.coordinates` object The target around which to search. It may be specified as a string in which case it is resolved using online services or as the appropriate `astropy.coordinates` object. ICRS coordinates may also be entered as a string. radius : str or `~astropy.units.Quantity` object, optional The string must be parsable by `astropy.coordinates.Angle`. The appropriate `~astropy.units.Quantity` object may also be used. Defaults to 1 arcminute. equinox : str, optional One of 'J2000' or 'B1950'. Defaults to 'J2000'. telescope : str, optional The telescope that produced the data. Defaults to 'all'. Valid values are: ['gbt', 'all', 'historical_vla', 'vlba', 'jansky_vla'] start_date : str, optional The starting date and time of the observations , e.g. 2010-06-21 14:20:30 Decimal seconds are not allowed. Defaults to `None` for no constraints. end_date : str, optional The ending date and time of the observations , e.g. 2010-06-21 14:20:30 Decimal seconds are not allowed. Defaults to `None` for no constraints. freq_low : `~astropy.units.Quantity` object, optional The lower frequency of the observations in proper units of frequency via `astropy.units`. Defaults to `None` for no constraints. freq_up : `~astropy.units.Quantity` object, optional The upper frequency of the observations in proper units of frequency via `astropy.units`. Defaults to `None` for no constraints. telescope_config : str, optional Select the telescope configuration (only valid for VLA array). Defaults to 'all'. Valid values are ['all', 'A', 'AB', 'BnA', 'B', 'BC', 'CnB', 'C', 'CD', 'DnC', 'D', 'DA'] obs_band : str, optional The frequency bands for the observation. Defaults to 'all'. Valid values are ['all', '4', 'P', 'L', 'S', 'C', 'X', 'U', 'K', 'Ka', 'Q', 'W']. sub_array : str, number, optional VLA subarray designations, may be set to an integer from 1 to 5. Defaults to 'all'. project_code : str, optional A string indicating the project code. Examples:: * GBT: AGBT12A_055 * JVLA: 12A-256 querytype : str The type of query to perform. "OBSSUMMARY" is the default, but it is only valid for VLA/VLBA observations. ARCHIVE will give the list of files available for download. OBSERVATION will provide full details of the sources observed and under what configurations. source_id : str, optional A source name (to be parsed by SIMBAD or NED) protocol : 'VOTable-XML' or 'HTML' The type of table to return. In theory, this should not matter, but in practice the different table types actually have different content. For ``querytype='ARCHIVE'``, the protocol will be force to HTML because the archive doesn't support votable returns for archive queries. get_query_payload : bool, optional if set to `True` then returns the dictionary sent as the HTTP request. Defaults to `False` cache : bool Cache the query results retry : bool or int The number of times to retry querying the server if it doesn't raise an exception but returns a null result (this sort of behavior seems unique to the NRAO archive) Returns ------- request_payload : dict The dictionary of parameters to send via HTTP GET request. """ lower_frequency = kwargs.get('freq_low', None) upper_frequency = kwargs.get('freq_up', None) if lower_frequency is not None and upper_frequency is not None: freq_str = (str(lower_frequency.to(u.MHz).value) + '-' + str(upper_frequency.to(u.MHz).value)) else: freq_str = "" obs_bands = kwargs.get('obs_band', 'all') if isinstance(obs_bands, six.string_types): obs_bands = obs_bands.upper() elif isinstance(obs_bands, (list, tuple)): obs_bands = [x.upper() for x in obs_bands] telescope_config = kwargs.get('telescope_config', 'all') if isinstance(telescope_config, six.string_types): telescope_config = telescope_config.upper() elif isinstance(telescope_config, (list, tuple)): telescope_config = [x.upper() for x in telescope_config] telescope_ = kwargs.get('telescope', 'all') if isinstance(telescope_, six.string_types): telescope = Nrao.telescope_code[telescope_] elif isinstance(telescope, (list, tuple)): telescope = [Nrao.telescope_code[telescope_] for x in telescope_] request_payload = dict( QUERYTYPE=kwargs.get('querytype', "OBSSUMMARY"), PROTOCOL=kwargs.get('protocol', "VOTable-XML"), MAX_ROWS="NO LIMIT", SORT_PARM="Starttime", SORT_ORDER="Asc", SORT_PARM2="Starttime", SORT_ORDER2="Asc", QUERY_ID=9999, QUERY_MODE="AAT_TOOL", LOCKMODE="PROJECT", SITE_CODE="AOC", DBHOST="CHEWBACCA", WRITELOG=0, TELESCOPE=telescope, PROJECT_CODE=kwargs.get('project_code', ''), SEGMENT="", MIN_EXPOSURE='', TIMERANGE1=kwargs.get('start_date', ''), OBSERVER="", ARCHIVE_VOLUME="", TIMERANGE2=kwargs.get('end_date', ''), EQUINOX=kwargs.get('equinox', 'J2000'), CENTER_RA='', CENTER_DEC='', SRAD=str( coordinates.Angle(kwargs.get('radius', "1.0m")).deg) + 'd', TELESCOPE_CONFIG=telescope_config, OBS_BANDS=obs_bands, SUBARRAY=kwargs.get('subarray', 'all').upper(), SOURCE_ID=kwargs.get('source_id', ''), SRC_SEARCH_TYPE='SIMBAD or NED', OBSFREQ1=freq_str, OBS_POLAR="ALL", RECEIVER_ID="ALL", BACKEND_ID="ALL", DATATYPE="ALL", PASSWD="", # TODO: implement login... SUBMIT="Submit Query") if ((request_payload['QUERYTYPE'] == "ARCHIVE" and request_payload['PROTOCOL'] != 'HTML')): warnings.warn("Changing protocol to HTML: ARCHIVE queries do not" " support votable returns") request_payload['PROTOCOL'] = 'HTML' if request_payload['PROTOCOL'] not in ('HTML', 'VOTable-XML'): raise ValueError("Only HTML and VOTable-XML returns are supported") if request_payload['QUERYTYPE'] not in ('ARCHIVE', 'OBSSUMMARY', 'OBSERVATION'): raise ValueError("Only ARCHIVE, OBSSUMMARY, and OBSERVATION " "querytypes are supported") if 'coordinates' in kwargs: c = commons.parse_coordinates( kwargs['coordinates']).transform_to(coordinates.ICRS) request_payload['CENTER_RA'] = str(c.ra.degree) + 'd' request_payload['CENTER_DEC'] = str(c.dec.degree) + 'd' return request_payload def _login(self, username=None, store_password=False, reenter_password=False): """ Login to the NRAO archive Parameters ---------- username : str, optional Username to the NRAO archive. If not given, it should be specified in the config file. store_password : bool, optional Stores the password securely in your keyring. Default is False. reenter_password : bool, optional Asks for the password even if it is already stored in the keyring. This is the way to overwrite an already stored passwork on the keyring. Default is False. """ # Developer notes: # Login via https://my.nrao.edu/cas/login # # this can be added to auto-redirect back to the query tool: # ?service=https://archive.nrao.edu/archive/advquery.jsp if username is None: if not self.USERNAME: raise LoginError("If you do not pass a username to login(), " "you should configure a default one!") else: username = self.USERNAME # Check if already logged in loginpage = self._request("GET", "https://my.nrao.edu/cas/login", cache=False) root = BeautifulSoup(loginpage.content, 'html5lib') if root.find('div', class_='success'): log.info("Already logged in.") return True # Get password from keyring or prompt password, password_from_keyring = self._get_password( "astroquery:my.nrao.edu", username, reenter=reenter_password) # Authenticate log.info("Authenticating {0} on my.nrao.edu ...".format(username)) # Do not cache pieces of the login process data = {kw: root.find('input', {'name': kw})['value'] for kw in ('lt', '_eventId', 'execution')} data['username'] = username data['password'] = password data['execution'] = 'e1s1' # not sure if needed data['_eventId'] = 'submit' data['submit'] = 'LOGIN' login_response = self._request("POST", "https://my.nrao.edu/cas/login", data=data, cache=False) authenticated = ('You have successfully logged in' in login_response.text) if authenticated: log.info("Authentication successful!") self.USERNAME = username else: log.exception("Authentication failed!") # When authenticated, save password in keyring if needed if authenticated and password_from_keyring is None and store_password: keyring.set_password("astroquery:my.nrao.edu", username, password) return authenticated
[docs] @prepend_docstr_nosections(_args_to_payload.__doc__) def query_async(self, get_query_payload=False, cache=True, retry=False, **kwargs): """ Returns ------- response : `~requests.Response` The HTTP response returned from the service. """ request_payload = self._args_to_payload(**kwargs) if get_query_payload: return request_payload response = self._request('POST', self.DATA_URL, params=request_payload, timeout=self.TIMEOUT, cache=cache) self._last_response = response response.raise_for_status() # fail if response is entirely whitespace or if it is empty if not response.content.strip(): if cache: last_pickle = self._last_query.hash()+".pickle" cache_fn = os.path.join(self.cache_location, last_pickle) os.remove(cache_fn) if retry > 0: log.warning("Query resulted in an empty result. Retrying {0}" " more times.".format(retry)) self.query_async(cache=cache, retry=retry-1, **kwargs) else: raise ValueError("Query resulted in an empty result but " "the server did not raise an error.") return response
[docs] @prepend_docstr_nosections(_args_to_payload.__doc__) def query_region_async(self, coordinates, radius=1 * u.arcmin, equinox='J2000', telescope='all', start_date="", end_date="", freq_low=None, freq_up=None, telescope_config='all', obs_band='all', querytype='OBSSUMMARY', sub_array='all', project_code=None, protocol='VOTable-XML', retry=False, get_query_payload=False, cache=True): """ Returns ------- response : `~requests.Response` The HTTP response returned from the service. """ return self.query_async(coordinates=coordinates, radius=radius, equinox=equinox, telescope=telescope, start_date=start_date, end_date=end_date, freq_low=freq_low, freq_up=freq_up, telescope_config=telescope_config, obs_band=obs_band, sub_array=sub_array, querytype=querytype, protocol=protocol, get_query_payload=get_query_payload, retry=retry, cache=cache)
def _parse_result(self, response, verbose=False): if '<?xml' in response.text[:5]: return self._parse_votable_result(response, verbose=verbose) elif '<html>' in response.text[:6]: return self._parse_html_result(response, verbose=verbose) else: raise ValueError("Unrecognized response type; it does not appear " "to be VO-XML or HTML") def _parse_votable_result(self, response, verbose=False): if not verbose: commons.suppress_vo_warnings() new_content = response.text # these are pretty bad hacks, but also needed... days_re = re.compile(r'unit="days" datatype="double"') new_content = days_re.sub(r'unit="days" datatype="char" ' 'arraysize="*"', new_content) degrees_re = re.compile(r'unit="degrees" datatype="double"') new_content = degrees_re.sub(r'unit="degrees" datatype="char" ' 'arraysize="*"', new_content) telconfig_re = re.compile(r'datatype="char" name="Telescope:config"') new_content = telconfig_re.sub(r'datatype="unicodeChar" ' 'name="Telescope:config" ' ' arraysize="*" ', new_content) datatype_mapping = {'integer': 'long'} try: tf = six.BytesIO(new_content.encode()) first_table = votable.parse( tf, pedantic=False, datatype_mapping=datatype_mapping).get_first_table() try: table = first_table.to_table(use_names_over_ids=True) except TypeError: warnings.warn("NRAO table parsing: astropy versions prior " "to 6558975c use the table column IDs instead " "of names.") table = first_table.to_table() return table except Exception as ex: self.response = response self.table_parse_error = ex raise TableParseError("Failed to parse NRAO votable result! The " "raw response can be found in self.response," " and the error in self.table_parse_error.") def _parse_html_result(self, response, verbose=False): # parse the HTML return... root = BeautifulSoup(response.content, 'html5lib') htmltable = root.findAll('table') # if len(htmltable) != 1: # raise ValueError("Found the wrong number of tables: {0}" # .format(len(htmltable))) string_to_parse = htmltable[-1].encode('ascii') if six.PY2: from astropy.io.ascii import html from astropy.io.ascii.core import convert_numpy htmlreader = html.HTML({'parser': 'html5lib'}) htmlreader.outputter.default_converters.append(convert_numpy(np.unicode)) table = htmlreader.read(string_to_parse) else: table = Table.read(string_to_parse.decode('utf-8'), format='ascii.html') return table
Nrao = NraoClass()