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Merge pull request #2967 from esdc-esac-esa-int/ESA_gaia_read_votable…
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…s_columns_based_on_names_GAIAPCR-1313

Gaia:  Define new constant USE_NAMES_OVER_IDS that gives preference to ``name`` over ID attributes of columns as the names of   columns in the `astropy.table.Table` instance.
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@bsipocz
bsipocz authored May 3, 2024
2 parents 0c824a8 + 65a00ad commit d77dad2
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Showing 15 changed files with 2,879 additions and 350 deletions.
5 changes: 4 additions & 1 deletion CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,10 @@ gaia
- For the functions that return files in FITS/ECSV format, the files are now provided as uncompressed files.
[#2983]

- New parameter USE_NAMES_OVER_IDS that gives preference to ``name`` over ID attributes of columns as the names of
columns in the `astropy.table.Table` instance. By default, value True is set, that gives name preference. [#2967]

- Fix method search_async_jobs in the class TapPlus. [#2967]

jplhorizons
^^^^^^^^^^^
Expand Down Expand Up @@ -252,7 +256,6 @@ gaia

- Default Gaia catalog updated to DR3. [#2596]


heasarc
^^^^^^^

Expand Down
77 changes: 29 additions & 48 deletions astroquery/gaia/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,11 @@ class GaiaClass(TapPlus):
VALID_DATALINK_RETRIEVAL_TYPES = conf.VALID_DATALINK_RETRIEVAL_TYPES
VALID_LINKING_PARAMETERS = conf.VALID_LINKING_PARAMETERS
GAIA_MESSAGES = "notification?action=GetNotifications"
USE_NAMES_OVER_IDS = True
"""When `True` use the ``name`` attributes of columns as the names of columns in the `astropy.table.Table` instance.
Since names are not guaranteed to be unique, this may cause some columns to be renamed by appending numbers to
the end. Otherwise, use the ID attributes as the column names.
"""

def __init__(self, *, tap_plus_conn_handler=None,
datalink_handler=None,
Expand All @@ -64,7 +69,8 @@ def __init__(self, *, tap_plus_conn_handler=None,
data_context="data",
datalink_context="datalink",
connhandler=tap_plus_conn_handler,
verbose=verbose)
verbose=verbose,
use_names_over_ids=self.USE_NAMES_OVER_IDS)
# Data uses a different TapPlus connection
if datalink_handler is None:
self.__gaiadata = TapPlus(url=gaia_data_server,
Expand All @@ -74,16 +80,16 @@ def __init__(self, *, tap_plus_conn_handler=None,
table_edit_context="TableTool",
data_context="data",
datalink_context="datalink",
verbose=verbose)
verbose=verbose,
use_names_over_ids=self.USE_NAMES_OVER_IDS)
else:
self.__gaiadata = datalink_handler

# Enable notifications
if show_server_messages:
self.get_status_messages()

def login(self, *, user=None, password=None, credentials_file=None,
verbose=False):
def login(self, *, user=None, password=None, credentials_file=None, verbose=False):
"""Performs a login.
User and password arguments can be used or a file that contains
username and password
Expand All @@ -104,18 +110,15 @@ def login(self, *, user=None, password=None, credentials_file=None,
"""
try:
log.info("Login to gaia TAP server")
TapPlus.login(self, user=user, password=password,
credentials_file=credentials_file,
verbose=verbose)
TapPlus.login(self, user=user, password=password, credentials_file=credentials_file, verbose=verbose)
except HTTPError:
log.error("Error logging in TAP server")
return
new_user = self._TapPlus__user
new_password = self._TapPlus__pwd
try:
log.info("Login to gaia data server")
TapPlus.login(self.__gaiadata, user=new_user, password=new_password,
verbose=verbose)
TapPlus.login(self.__gaiadata, user=new_user, password=new_password, verbose=verbose)
except HTTPError:
log.error("Error logging in data server")
log.error("Logging out from TAP server")
Expand All @@ -139,8 +142,7 @@ def login_gui(self, *, verbose=False):
new_password = self._TapPlus__pwd
try:
log.info("Login to gaia data server")
TapPlus.login(self.__gaiadata, user=new_user, password=new_password,
verbose=verbose)
TapPlus.login(self.__gaiadata, user=new_user, password=new_password, verbose=verbose)
except HTTPError:
log.error("Error logging in data server")
log.error("Logging out from TAP server")
Expand Down Expand Up @@ -304,9 +306,7 @@ def load_data(self, ids, *, data_release=None, data_structure='INDIVIDUAL', retr
log.error("Creation of the directory %s failed" % path)

try:
self.__gaiadata.load_data(params_dict=params_dict,
output_file=output_file,
verbose=verbose)
self.__gaiadata.load_data(params_dict=params_dict, output_file=output_file, verbose=verbose)
files = Gaia.__get_data_files(output_file=output_file, path=path)
except Exception as err:
raise err
Expand Down Expand Up @@ -342,7 +342,6 @@ def __get_data_files(output_file, path):
if '.fits' in key:
tables = []
with fits.open(value) as hduList:
# print(hduList)
num_hdus = len(hduList)
for i in range(1, num_hdus):
table = Table.read(hduList[i], format='fits')
Expand All @@ -357,8 +356,7 @@ def __get_data_files(output_file, path):

elif '.csv' in key:
tables = []
table = Table.read(value, format='ascii.csv',
fast_reader=False)
table = Table.read(value, format='ascii.csv', fast_reader=False)
tables.append(table)
files[key] = tables

Expand Down Expand Up @@ -492,8 +490,7 @@ def __query_object(self, coordinate, *, radius=None, width=None, height=None,
coord = self.__getCoordInput(coordinate, "coordinate")

if radius is not None:
job = self.__cone_search(coord, radius, async_job=async_job,
verbose=verbose, columns=columns)
job = self.__cone_search(coord, radius, async_job=async_job, verbose=verbose, columns=columns)
else:
raHours, dec = commons.coord_to_radec(coord)
ra = raHours * 15.0 # Converts to degrees
Expand Down Expand Up @@ -541,8 +538,7 @@ def __query_object(self, coordinate, *, radius=None, width=None, height=None,
job = self.launch_job(query, verbose=verbose)
return job.get_results()

def query_object(self, coordinate, *, radius=None, width=None, height=None,
verbose=False, columns=()):
def query_object(self, coordinate, *, radius=None, width=None, height=None, verbose=False, columns=()):
"""Launches a synchronous cone search for the input search radius or the box on the sky, sorted by angular
separation
TAP & TAP+
Expand All @@ -566,12 +562,10 @@ def query_object(self, coordinate, *, radius=None, width=None, height=None,
-------
The job results (astropy.table).
"""
return self.__query_object(coordinate, radius=radius,
width=width, height=height, async_job=False,
return self.__query_object(coordinate, radius=radius, width=width, height=height, async_job=False,
verbose=verbose, columns=columns)

def query_object_async(self, coordinate, *, radius=None, width=None,
height=None, verbose=False, columns=()):
def query_object_async(self, coordinate, *, radius=None, width=None, height=None, verbose=False, columns=()):
"""Launches an asynchronous cone search for the input search radius or the box on the sky, sorted by angular
separation
TAP & TAP+
Expand All @@ -595,9 +589,8 @@ def query_object_async(self, coordinate, *, radius=None, width=None,
-------
The job results (astropy.table).
"""
return self.__query_object(coordinate, radius=radius, width=width,
height=height, async_job=True, verbose=verbose,
columns=columns)
return self.__query_object(coordinate, radius=radius, width=width, height=height, async_job=True,
verbose=verbose, columns=columns)

def __cone_search(self, coordinate, radius, *, table_name=None,
ra_column_name=MAIN_GAIA_TABLE_RA,
Expand Down Expand Up @@ -680,17 +673,10 @@ def __cone_search(self, coordinate, radius, *, table_name=None,
'table_name': table_name or self.MAIN_GAIA_TABLE or conf.MAIN_GAIA_TABLE})

if async_job:
return self.launch_job_async(query=query,
output_file=output_file,
output_format=output_format,
verbose=verbose,
dump_to_file=dump_to_file,
background=background)
return self.launch_job_async(query=query, output_file=output_file, output_format=output_format,
verbose=verbose, dump_to_file=dump_to_file, background=background)
else:
return self.launch_job(query=query,
output_file=output_file,
output_format=output_format,
verbose=verbose,
return self.launch_job(query=query, output_file=output_file, output_format=output_format, verbose=verbose,
dump_to_file=dump_to_file)

def cone_search(self, coordinate, *, radius=None,
Expand Down Expand Up @@ -809,23 +795,19 @@ def __getQuantityInput(self, value, msg):
raise ValueError(f"{msg} must be either a string or astropy.coordinates")

if isinstance(value, str):
q = Quantity(value)
return q
return Quantity(value)
else:
return value

def __checkCoordInput(self, value, msg):
if not (isinstance(value, str) or isinstance(value,
commons.CoordClasses)):
if not (isinstance(value, str) or isinstance(value, commons.CoordClasses)):
raise ValueError(f"{msg} must be either a string or astropy.coordinates")

def __getCoordInput(self, value, msg):
if not (isinstance(value, str) or isinstance(value,
commons.CoordClasses)):
if not (isinstance(value, str) or isinstance(value, commons.CoordClasses)):
raise ValueError(f"{msg} must be either a string or astropy.coordinates")
if isinstance(value, str):
c = commons.parse_coordinates(value)
return c
return commons.parse_coordinates(value)
else:
return value

Expand Down Expand Up @@ -866,8 +848,7 @@ def load_user(self, user_id, *, verbose=False):
A user
"""

return self.is_valid_user(user_id=user_id,
verbose=verbose)
return self.is_valid_user(user_id=user_id, verbose=verbose)

def cross_match(self, *, full_qualified_table_name_a,
full_qualified_table_name_b,
Expand Down
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