Simbad: refactor to use TAP

CHANGES.rst

@@ -42,6 +42,51 @@ vizier
 - Change the type of raised error when the catalog is not found in ``Vizier.get_catalog_metadata``
   from ``IndexError`` to ``EmptyResponseError`` [#2980]
 
+simbad
+^^^^^^
+
+- The ``ROW_LIMIT`` value to have the maximum number of rows is now -1.
+  Use ``ROW_LIMIT = 0`` to retrieve the output's meta-data. [#2954]
+
+- ``ROW_LIMIT`` can now be set at instantiation
+  (e.g.: ``simbad = Simbad(ROW_LIMIT=10))``). [#2954]
+
+- ``list_votable_fields`` now return an astropy Table with added fields
+  information instead of a list of strings. [#2954]
+
+- ``list_votable_fields`` is now queried directly from SIMBAD instead of reading
+  a file in astroquery. This prevents it from being outdated. [#2954]
+
+- ``get_votable_fields`` now prints the table name and column name instead of
+  just the column name. [#2954]
+
+- The ``verbose`` and ``cache`` kwargs have been deprecated from all methods
+  as they have no effect with with the new query interface. [#2954]
+
+- ``get_adql`` is deprecated and replaced by ``get_query_payload`` in
+  ``list_columns`` and ``list_table``.
+  The payload output contains the ADQL under the ``QUERY`` key. [#2954]
+
+- all query methods except ``query_tap`` and ``query_criteria`` now accept a
+  ``criteria`` argument to restrict the results with custom criteria. [#2954]
+
+- ``query_objects`` outputs now have an additional column ``user_specified_id``
+  containing the objects' name as specified by the user.
+  The ``votable_field`` option ``typed_id`` is removed. [#2954]
+
+- The ``equinox`` and ``epoch`` kwargs are deprecated in ``query_region``,
+  use astropy.coordinates.SkyCoord directly instead. [#2954]
+
+- ``query_bibcode`` has a new option ``abstract`` that allows to also
+  retrieve the article's abstract. [#2954]
+
+- ``query_bibcode`` output is now in an astropy Table with distinct columns
+  instead of a single one in which all the information was a string. [#2954]
+
+- ``query_criteria`` is now deprecated and should be replaced by either custom
+  TAP queries or by the ``criteria`` argument added in the other query methods.
+  A helper method was added ``astroquery.simbad.utils.CriteriaTranslator`` to
+  translate between the sim-script syntax and the TAP/ADQL syntax. [#2954]
 
 skyview
 ^^^^^^^

README.rst

@@ -35,9 +35,10 @@ website <https://simbad.cds.unistra.fr/simbad/>`_, use the ``simbad`` sub-packag
     >>> from astroquery.simbad import Simbad
     >>> theta1c = Simbad.query_object('tet01 Ori C')
     >>> theta1c.pprint()
-       MAIN_ID          RA           DEC      ... COO_QUAL COO_WAVELENGTH     COO_BIBCODE
-    ------------- ------------- ------------- ... -------- -------------- -------------------
-    * tet01 Ori C 05 35 16.4637 -05 23 22.848 ...        A              O 2007A&A...474..653V
+       main_id          ra           dec      ... coo_wavelength     coo_bibcode       matched_id 
+                       deg           deg      ...                                                 
+    ------------- ------------- ------------- ... -------------- ------------------- -------------
+    * tet01 Ori C 83.8186095697 -5.3897005033 ...              O 2020yCat.1350....0G * tet01 Ori C
 
 Installation and Requirements
 -----------------------------

astroquery/esa/jwst/core.py

@@ -571,9 +571,12 @@ def resolve_target_coordinates(self, target_name, target_resolver):
         if target_resolver == "ALL" or target_resolver == "SIMBAD":
             try:
                 result_table = Simbad.query_object(target_name)
-                return SkyCoord((f'{result_table["RA"][0]} '
-                                 f'{result_table["DEC"][0]}'),
-                                unit=(units.hourangle,
+                # new simbad behavior does not return None but an empty table
+                if len(result_table) == 0:
+                    result_table = None
+                return SkyCoord((f'{result_table["ra"][0]} '
+                                 f'{result_table["dec"][0]}'),
+                                unit=(units.deg,
                                       units.deg), frame="icrs")
             except (KeyError, TypeError, ConnectionError):
                 log.info("SIMBAD could not resolve this target")

astroquery/esa/jwst/tests/data/simbad_M1.vot

@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Produced with astropy.io.votable version 6.0.0
+     http://www.astropy.org/ -->
+<VOTABLE version="1.3" xmlns="http://www.ivoa.net/xml/VOTable/v1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.ivoa.net/xml/VOTable/v1.3 http://www.ivoa.net/xml/VOTable/VOTable-1.3.xsd">
+ <RESOURCE type="results">
+  <INFO ID="QUERY_STATUS" name="QUERY_STATUS" value="OK"/>
+  <INFO ID="PROVIDER" name="PROVIDER" value="CDS">SIMBAD TAP Service</INFO>
+  <INFO ID="QUERY" name="QUERY" value="SELECT basic.&quot;main_id&quot;, basic.&quot;ra&quot;, basic.&quot;dec&quot;, basic.&quot;coo_err_maj&quot;, basic.&quot;coo_err_min&quot;, basic.&quot;coo_err_angle&quot;, basic.&quot;coo_wavelength&quot;, basic.&quot;coo_bibcode&quot;, ident.&quot;id&quot; AS matched_id FROM basic JOIN ident ON basic.&quot;oid&quot; = ident.&quot;oidref&quot; WHERE id = &apos;M1&apos;"/>
+  <TABLE ID="result_S1708521282485" name="result_S1708521282485">
+   <FIELD ID="main_id" arraysize="*" datatype="char" name="main_id" ucd="meta.id;meta.main">
+    <DESCRIPTION>
+     Main identifier for an object
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="ra" datatype="double" name="ra" ucd="pos.eq.ra;meta.main" unit="deg">
+    <DESCRIPTION>
+     Right ascension
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="dec" datatype="double" name="dec" ucd="pos.eq.dec;meta.main" unit="deg">
+    <DESCRIPTION>
+     Declination
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_maj" datatype="float" name="coo_err_maj" ucd="phys.angSize.smajAxis;pos.errorEllipse;pos.eq" unit="mas">
+    <DESCRIPTION>
+     Coordinate error major axis
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_min" datatype="float" name="coo_err_min" ucd="phys.angSize.sminAxis;pos.errorEllipse;pos.eq" unit="mas">
+    <DESCRIPTION>
+     Coordinate error minor axis
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_angle" datatype="short" name="coo_err_angle" ucd="pos.posAng;pos.errorEllipse;pos.eq" unit="deg">
+    <DESCRIPTION>
+     Coordinate error angle
+    </DESCRIPTION>
+    <VALUES null="-32768"/>
+   </FIELD>
+   <FIELD ID="coo_wavelength" arraysize="1" datatype="char" name="coo_wavelength" ucd="instr.bandpass;pos.eq">
+    <DESCRIPTION>
+     Wavelength class for the origin of the coordinates (R,I,V,U,X,G)
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_bibcode" arraysize="*" datatype="char" name="coo_bibcode" ucd="meta.bib.bibcode;pos.eq">
+    <DESCRIPTION>
+     Coordinate reference
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="matched_id" arraysize="*" datatype="char" name="matched_id" ucd="meta.id">
+    <DESCRIPTION>
+     Identifier
+    </DESCRIPTION>
+   </FIELD>
+   <DATA>
+    <TABLEDATA>
+     <TR>
+      <TD>M   1</TD>
+      <TD>83.6287</TD>
+      <TD>22.0147</TD>
+      <TD>18500</TD>
+      <TD>18500</TD>
+      <TD>0</TD>
+      <TD>R</TD>
+      <TD>1995AuJPh..48..143S</TD>
+      <TD>M   1</TD>
+     </TR>
+    </TABLEDATA>
+   </DATA>
+  </TABLE>
+ </RESOURCE>
+</VOTABLE>

astroquery/esa/jwst/tests/data/simbad_TEST.vot

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Produced with astropy.io.votable version 6.0.0
+     http://www.astropy.org/ -->
+<VOTABLE version="1.3" xmlns="http://www.ivoa.net/xml/VOTable/v1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.ivoa.net/xml/VOTable/v1.3 http://www.ivoa.net/xml/VOTable/VOTable-1.3.xsd">
+ <RESOURCE type="results">
+  <INFO ID="QUERY_STATUS" name="QUERY_STATUS" value="OK"/>
+  <INFO ID="PROVIDER" name="PROVIDER" value="CDS">SIMBAD TAP Service</INFO>
+  <INFO ID="QUERY" name="QUERY" value="SELECT basic.&quot;main_id&quot;, basic.&quot;ra&quot;, basic.&quot;dec&quot;, basic.&quot;coo_err_maj&quot;, basic.&quot;coo_err_min&quot;, basic.&quot;coo_err_angle&quot;, basic.&quot;coo_wavelength&quot;, basic.&quot;coo_bibcode&quot;, ident.&quot;id&quot; AS matched_id FROM basic JOIN ident ON basic.&quot;oid&quot; = ident.&quot;oidref&quot; WHERE id = &apos;TEST&apos;"/>
+  <TABLE ID="result_S1708521454265" name="result_S1708521454265">
+   <FIELD ID="main_id" arraysize="*" datatype="char" name="main_id" ucd="meta.id;meta.main">
+    <DESCRIPTION>
+     Main identifier for an object
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="ra" datatype="double" name="ra" ucd="pos.eq.ra;meta.main" unit="deg">
+    <DESCRIPTION>
+     Right ascension
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="dec" datatype="double" name="dec" ucd="pos.eq.dec;meta.main" unit="deg">
+    <DESCRIPTION>
+     Declination
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_maj" datatype="float" name="coo_err_maj" ucd="phys.angSize.smajAxis;pos.errorEllipse;pos.eq" unit="mas">
+    <DESCRIPTION>
+     Coordinate error major axis
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_min" datatype="float" name="coo_err_min" ucd="phys.angSize.sminAxis;pos.errorEllipse;pos.eq" unit="mas">
+    <DESCRIPTION>
+     Coordinate error minor axis
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_err_angle" datatype="short" name="coo_err_angle" ucd="pos.posAng;pos.errorEllipse;pos.eq" unit="deg">
+    <DESCRIPTION>
+     Coordinate error angle
+    </DESCRIPTION>
+    <VALUES null="-32768"/>
+   </FIELD>
+   <FIELD ID="coo_wavelength" arraysize="1" datatype="char" name="coo_wavelength" ucd="instr.bandpass;pos.eq">
+    <DESCRIPTION>
+     Wavelength class for the origin of the coordinates (R,I,V,U,X,G)
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="coo_bibcode" arraysize="*" datatype="char" name="coo_bibcode" ucd="meta.bib.bibcode;pos.eq">
+    <DESCRIPTION>
+     Coordinate reference
+    </DESCRIPTION>
+   </FIELD>
+   <FIELD ID="matched_id" arraysize="*" datatype="char" name="matched_id" ucd="meta.id">
+    <DESCRIPTION>
+     Identifier
+    </DESCRIPTION>
+   </FIELD>
+  </TABLE>
+ </RESOURCE>
+</VOTABLE>

astroquery/esa/jwst/tests/test_jwsttap.py

@@ -11,7 +11,7 @@
 import os
 import shutil
 from pathlib import Path
-from unittest.mock import MagicMock
+from unittest.mock import MagicMock, patch
 import sys
 import io
 
@@ -21,14 +21,15 @@
 from astropy import units
 from astropy.coordinates.name_resolve import NameResolveError
 from astropy.coordinates.sky_coordinate import SkyCoord
+from astropy.io.votable import parse_single_table
 from astropy.table import Table
 from astropy.units import Quantity
 from astroquery.exceptions import TableParseError
 
 from astroquery.esa.jwst import JwstClass
 from astroquery.esa.jwst.tests.DummyTapHandler import DummyTapHandler
 from astroquery.ipac.ned import Ned
-from astroquery.simbad import Simbad
+from astroquery.simbad import SimbadClass
 from astroquery.utils.tap.conn.tests.DummyConnHandler import DummyConnHandler
 from astroquery.utils.tap.conn.tests.DummyResponse import DummyResponse
 from astroquery.utils.tap.core import TapPlus
@@ -914,53 +915,58 @@ def __check_extracted_files(self, files_expected, files_returned):
                 raise ValueError(f"Not found expected file: {f}")
 
     def test_query_target_error(self):
-        jwst = JwstClass(show_messages=False)
-        simbad = Simbad()
-        ned = Ned()
-        vizier = Vizier()
-        # Testing default parameters
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target(target_name="M1", target_resolver="")
-        assert "This target resolver is not allowed" in err.value.args[0]
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target("TEST")
-        assert ('This target name cannot be determined with this '
-                'resolver: ALL' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target(target_name="M1", target_resolver="ALL")
-        assert err.value.args[0] in ["This target name cannot be determined "
-                                     "with this resolver: ALL", "Missing "
-                                     "required argument: 'width'"]
-
-        # Testing no valid coordinates from resolvers
-        simbad_file = data_path('test_query_by_target_name_simbad_ned_error.vot')
-        simbad_table = Table.read(simbad_file)
-        simbad.query_object = MagicMock(return_value=simbad_table)
-        ned_file = data_path('test_query_by_target_name_simbad_ned_error.vot')
-        ned_table = Table.read(ned_file)
-        ned.query_object = MagicMock(return_value=ned_table)
-        vizier_file = data_path('test_query_by_target_name_vizier_error.vot')
-        vizier_table = Table.read(vizier_file)
-        vizier.query_object = MagicMock(return_value=vizier_table)
-
-        # coordinate_error = 'coordinate must be either a string or astropy.coordinates'
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target(target_name="test", target_resolver="SIMBAD",
-                              radius=units.Quantity(5, units.deg))
-        assert ('This target name cannot be determined with this '
-                'resolver: SIMBAD' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
-
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target(target_name="test", target_resolver="NED",
-                              radius=units.Quantity(5, units.deg))
-        assert ('This target name cannot be determined with this '
-                'resolver: NED' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
-
-        with pytest.raises((ValueError, TableParseError)) as err:
-            jwst.query_target(target_name="test", target_resolver="VIZIER",
-                              radius=units.Quantity(5, units.deg))
-        assert ('This target name cannot be determined with this resolver: '
-                'VIZIER' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
+        # need to patch simbad query object here
+        with patch("astroquery.simbad.SimbadClass.query_object",
+                   side_effect=lambda object_name: parse_single_table(
+                       Path(__file__).parent / "data" / f"simbad_{object_name}.vot"
+                   ).to_table()):
+            jwst = JwstClass(show_messages=False)
+            simbad = SimbadClass()
+            ned = Ned()
+            vizier = Vizier()
+            # Testing default parameters
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target(target_name="M1", target_resolver="")
+                assert "This target resolver is not allowed" in err.value.args[0]
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target("TEST")
+                assert ('This target name cannot be determined with this '
+                        'resolver: ALL' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target(target_name="M1", target_resolver="ALL")
+                assert err.value.args[0] in ["This target name cannot be determined "
+                                             "with this resolver: ALL", "Missing "
+                                             "required argument: 'width'"]
+
+            # Testing no valid coordinates from resolvers
+            simbad_file = data_path('test_query_by_target_name_simbad_ned_error.vot')
+            simbad_table = Table.read(simbad_file)
+            simbad.query_object = MagicMock(return_value=simbad_table)
+            ned_file = data_path('test_query_by_target_name_simbad_ned_error.vot')
+            ned_table = Table.read(ned_file)
+            ned.query_object = MagicMock(return_value=ned_table)
+            vizier_file = data_path('test_query_by_target_name_vizier_error.vot')
+            vizier_table = Table.read(vizier_file)
+            vizier.query_object = MagicMock(return_value=vizier_table)
+
+            # coordinate_error = 'coordinate must be either a string or astropy.coordinates'
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target(target_name="TEST", target_resolver="SIMBAD",
+                                  radius=units.Quantity(5, units.deg))
+                assert ('This target name cannot be determined with this '
+                        'resolver: SIMBAD' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
+
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target(target_name="TEST", target_resolver="NED",
+                                  radius=units.Quantity(5, units.deg))
+                assert ('This target name cannot be determined with this '
+                        'resolver: NED' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
+
+            with pytest.raises((ValueError, TableParseError)) as err:
+                jwst.query_target(target_name="TEST", target_resolver="VIZIER",
+                                  radius=units.Quantity(5, units.deg))
+                assert ('This target name cannot be determined with this resolver: '
+                        'VIZIER' in err.value.args[0] or 'Failed to parse' in err.value.args[0])
 
     def test_remove_jobs(self):
         dummyTapHandler = DummyTapHandler()

astroquery/query.py

@@ -203,6 +203,10 @@ def __init__(self):
 
         self.name = self.__class__.__name__.split("Class")[0]
 
+    def __call__(self, *args, **kwargs):
+        """ init a fresh copy of self """
+        return self.__class__(*args, **kwargs)
+
 
 class BaseQuery(metaclass=LoginABCMeta):
     """

astroquery/simbad/__init__.py

@@ -3,10 +3,9 @@
 SIMBAD Query Tool
 =================
 
-The SIMBAD query tool creates a `script query
-<https://simbad.cds.unistra.fr/simbad/sim-fscript>`__ that returns VOtable XML
-data that is then parsed into a SimbadResult object.  This object then
-parses the data and returns a table parsed with `astropy.io.votable.parse`.
+The SIMBAD query tool creates `TAP ADQL queries
+<https://cds.unistra.fr/help/documentation/simbad-more/adql-simbad/>`__ that return VOtable XML
+data. This is then parsed into a `~astropy.table.Table` object.
 """
 from astropy import config as _config
 
@@ -27,16 +26,17 @@ class Conf(_config.ConfigNamespace):
         'Time limit for connecting to Simbad server.')
 
     row_limit = _config.ConfigItem(
-        # O defaults to the maximum limit
-        0,
+        # defaults to the maximum limit
+        -1,
         'Maximum number of rows that will be fetched from the result.')
 
+    # should be columns of 'basic'
+    default_columns = ["main_id", "ra", "dec", "coo_err_maj", "coo_err_min",
+                       "coo_err_angle", "coo_wavelength", "coo_bibcode"]
+
 
 conf = Conf()
 
-from .core import Simbad, SimbadClass, SimbadBaseQuery
+from .core import Simbad, SimbadClass
 
-__all__ = ['Simbad', 'SimbadClass',
-           'SimbadBaseQuery',
-           'Conf', 'conf',
-           ]
+__all__ = ['Simbad', 'SimbadClass', 'Conf', 'conf']