Merge pull request #2264 from rickynilsson/fix_issue_2239

bsipocz · web-flow · commit 334288817e7d · 2022-03-03T16:50:29.000-08:00
Fix_issue_2239: Nasa Exoplanet Archive query_object method suddenly produces InvalidTableError
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -41,6 +41,11 @@ gaia
   the name provided by the user for the output file when the results are
   returned by the TAP in compressed format. [#2077]
 
+ipac.nexsci.nasa_exoplanet_archive
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Fixes to alias query, and regularize keyword removed from deprecated query_star() method. [#2264]
+
 mast
 ^^^^
 
@@ -1163,4 +1168,4 @@ Infrastructure, Utility and Other Changes and Additions
 0.1 (2013-09-19)
 ================
 
-- Initial release.  Includes features!
+- Initial release.  Includes features!
diff --git a/astroquery/ipac/nexsci/nasa_exoplanet_archive/__init__.py b/astroquery/ipac/nexsci/nasa_exoplanet_archive/__init__.py
@@ -21,6 +21,9 @@ class Conf(_config.ConfigNamespace):
     url_tap = _config.ConfigItem(
         "https://exoplanetarchive.ipac.caltech.edu/TAP/",
         "URL for the NASA Exoplanet Archive TAP")
+    url_aliaslookup = _config.ConfigItem(
+        "https://exoplanetarchive.ipac.caltech.edu/cgi-bin/Lookup/nph-aliaslookup.py?objname=",
+        "URL for the NASA Exoplanet Archive aliaslookup")
     timeout = _config.ConfigItem(
         600, "Time limit for requests from the NASA Exoplanet Archive servers")
     cache = _config.ConfigItem(False, "Should the requests be cached?")
diff --git a/astroquery/ipac/nexsci/nasa_exoplanet_archive/core.py b/astroquery/ipac/nexsci/nasa_exoplanet_archive/core.py
@@ -5,6 +5,8 @@
 import io
 import re
 import warnings
+import requests
+import json
 
 # Import various astropy modules
 import astropy.coordinates as coord
@@ -105,6 +107,8 @@ def get_access_url(service='tap'):
         url = conf.url_tap
     elif service == 'api':
         url = conf.url_api
+    elif service == 'aliaslookup':
+        url = conf.url_aliaslookup
     return url
 
 
@@ -138,7 +142,7 @@ class NasaExoplanetArchiveClass(BaseQuery):
     """
 
     # When module us imported, __init__.py runs and loads a configuration object,
-    # setting the configuration parameters con.url, conf.timeout and conf.cache
+    # setting the configuration parameters conf.url, conf.timeout and conf.cache
     URL_API = conf.url_api
     URL_TAP = conf.url_tap
     TIMEOUT = conf.timeout
@@ -377,7 +381,7 @@ def query_aliases(self, object_name, *, cache=None):
         Parameters
         ----------
         object_name : str
-            The name of a planet or star to regularize using the ``aliastable`` table.
+            The name of a planet or star to regularize using the ``aliaslookup`` service.
         cache : bool, optional
             Should the request result be cached? This can be useful for large repeated queries,
             but since the data in the archive is updated regularly, this defaults to ``False``.
@@ -387,24 +391,47 @@ def query_aliases(self, object_name, *, cache=None):
         response : list
             A list of aliases found for the object name. The default name will be listed first.
         """
-        return list(
-            self.query_criteria(
-                "aliastable", objname=object_name.strip(), cache=cache, format="csv"
-            )["aliasdis"]
-        )
+        data = self._request_query_aliases(object_name)
+
+        try:
+            objname_split = object_name.split()
+            if len(objname_split) > 1 and len(objname_split[-1]) == 1 and objname_split[-1].isalpha():
+                pl_letter = object_name.split()[-1]
+            else:
+                pl_letter = ''
+
+            default_objname = [data['system']['system_info']['alias_set']['default_name']]
+            other_objnames = list(set(data['system']['objects']['stellar_set']['stars'][default_objname[0]]['alias_set']['aliases']) - set(default_objname))
+            other_objnames.sort()
+            aliases = default_objname + other_objnames
+
+            if pl_letter:
+                aliases = [a + ' ' + pl_letter for a in aliases]
+
+        except KeyError:
+            aliases = []
+            warnings.warn("No aliases found for name: '{0}'".format(object_name), NoResultsWarning)
+
+        return aliases
 
     @class_or_instance
     def _regularize_object_name(self, object_name):
-        """Regularize the name of a planet or planet host using the ``aliastable`` table"""
+        """Regularize the name of a planet or planet host using the ``aliaslookup`` service"""
         try:
             aliases = self.query_aliases(object_name, cache=False)
-        except RemoteServiceError:
+        except KeyError:
             aliases = []
         if aliases:
             return aliases[0]
         warnings.warn("No aliases found for name: '{0}'".format(object_name), NoResultsWarning)
         return object_name
 
+    def _request_query_aliases(self, object_name):
+        """Service request for query_aliases()"""
+        url = requests.get(get_access_url('aliaslookup')+object_name)
+        response = json.loads(url.text)
+        return response
+
     # Look for response errors. This might need to be updated for TAP
     def _handle_error(self, text):
         """
@@ -653,7 +680,7 @@ def _request_to_sql(self, request_payload):
     @deprecated(since="v0.4.1", alternative="query_object")
     @deprecated_renamed_argument(["show_progress", "table_path"],
                                  [None, None], "v0.4.1", arg_in_kwargs=True)
-    def query_planet(self, planet_name, cache=None, regularize=True, **criteria):
+    def query_planet(self, planet_name, cache=None, **criteria):
         """
         Search the ``exoplanets`` table for a confirmed planet
 
@@ -665,22 +692,18 @@ def query_planet(self, planet_name, cache=None, regularize=True, **criteria):
         cache : bool, optional
             Should the request result be cached? This can be useful for large repeated queries,
             but since the data in the archive is updated regularly, this defaults to ``False``.
-        regularize : bool, optional
-            If ``True``, the ``aliastable`` will be used to regularize the target name.
         **criteria
             Any other filtering criteria to apply. Values provided using the ``where`` keyword will
             be ignored.
         """
-        if regularize:
-            planet_name = self._regularize_object_name(planet_name)
         criteria = self._handle_all_columns_argument(**criteria)
         criteria["where"] = "pl_name='{0}'".format(planet_name.strip())
         return self.query_criteria("exoplanets", cache=cache, **criteria)
 
     @deprecated(since="v0.4.1", alternative="query_object")
     @deprecated_renamed_argument(["show_progress", "table_path"],
                                  [None, None], "v0.4.1", arg_in_kwargs=True)
-    def query_star(self, host_name, cache=None, regularize=True, **criteria):
+    def query_star(self, host_name, cache=None, **criteria):
         """
         Search the ``exoplanets`` table for a confirmed planet host
 
@@ -692,14 +715,10 @@ def query_star(self, host_name, cache=None, regularize=True, **criteria):
         cache : bool, optional
             Should the request result be cached? This can be useful for large repeated queries,
             but since the data in the archive is updated regularly, this defaults to ``False``.
-        regularize : bool, optional
-            If ``True``, the ``aliastable`` will be used to regularize the target name.
         **criteria
             Any other filtering criteria to apply. Values provided using the ``where`` keyword will
             be ignored.
         """
-        if regularize:
-            host_name = self._regularize_object_name(host_name)
         criteria = self._handle_all_columns_argument(**criteria)
         criteria["where"] = "pl_hostname='{0}'".format(host_name.strip())
         return self.query_criteria("exoplanets", cache=cache, **criteria)
diff --git a/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/data/bpic_aliaslookup.json b/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/data/bpic_aliaslookup.json
@@ -0,0 +1,99 @@
+{
+    "manifest": {
+        "requested_name": "bet pic",
+        "resolved_name": "bet Pic",
+        "lookup_status": "OK",
+        "compilation_date": "2022-01-28 14:31:40.254838",
+        "system_snapshot": {
+            "number_of_stars": 1,
+            "number_of_planets": 2
+        }
+    },
+    "system": {
+        "system_info": {
+            "id": "bet Pic",
+            "alias_set": {
+                "item_count": 1,
+                "default_name": "bet Pic",
+                "aliases": [
+                    "bet Pic"
+                ]
+            }
+        },
+        "objects": {
+            "stellar_set": {
+                "item_count": 1,
+                "stars": {
+                    "bet Pic": {
+                        "alias_set": {
+                            "item_count": 14,
+                            "aliases": [
+                                "TIC 270577175",
+                                "Gaia DR2 4792774797545105664",
+                                "GJ 219",
+                                "HR 2020",
+                                "bet Pic",
+                                "HD 39060",
+                                "HIP 27321",
+                                "SAO 234134",
+                                "CD-51 1620",
+                                "CPD-51 774",
+                                "IRAS 05460-5104",
+                                "TYC 8099-01392-1",
+                                "2MASS J05471708-5103594",
+                                "WISE J054717.10-510358.4"
+                            ]
+                        }
+                    }
+                }
+            },
+            "planet_set": {
+                "item_count": 2,
+                "planets": {
+                    "bet Pic b": {
+                        "alias_set": {
+                            "item_count": 14,
+                            "aliases": [
+                                "GJ 219 b",
+                                "HR 2020 b",
+                                "bet Pic b",
+                                "HD 39060 b",
+                                "HIP 27321 b",
+                                "SAO 234134 b",
+                                "CD-51 1620 b",
+                                "CPD-51 774 b",
+                                "IRAS 05460-5104 b",
+                                "TYC 8099-01392-1 b",
+                                "2MASS J05471708-5103594 b",
+                                "WISE J054717.10-510358.4 b",
+                                "TIC 270577175 b",
+                                "Gaia DR2 4792774797545105664 b"
+                            ]
+                        }
+                    },
+                    "bet Pic c": {
+                        "alias_set": {
+                            "item_count": 14,
+                            "aliases": [
+                                "GJ 219 c",
+                                "HR 2020 c",
+                                "bet Pic c",
+                                "HD 39060 c",
+                                "HIP 27321 c",
+                                "SAO 234134 c",
+                                "CD-51 1620 c",
+                                "CPD-51 774 c",
+                                "IRAS 05460-5104 c",
+                                "TYC 8099-1392-1 c",
+                                "2MASS J05471708-5103594 c",
+                                "WISE J054717.10-510358.4 c",
+                                "TIC 270577175 c",
+                                "Gaia DR2 4792774797545105664 c"
+                            ]
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/test_nasa_exoplanet_archive.py b/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/test_nasa_exoplanet_archive.py
@@ -14,7 +14,7 @@
 
 from astroquery.exceptions import NoResultsWarning
 from astroquery.utils.mocks import MockResponse
-from astroquery.ipac.nexsci.nasa_exoplanet_archive.core import NasaExoplanetArchiveClass, conf, InvalidTableError
+from astroquery.ipac.nexsci.nasa_exoplanet_archive.core import NasaExoplanetArchiveClass, conf, InvalidTableError, get_access_url
 try:
     from unittest.mock import Mock, patch, PropertyMock
 except ImportError:
@@ -119,16 +119,53 @@ def patch_get(request):  # pragma: nocover
     return mp
 
 
-def test_regularize_object_name(patch_get):
-    NasaExoplanetArchiveMock = NasaExoplanetArchiveClass()
+# aliaslookup file in data/
+LOOKUP_DATA_FILE = 'bpic_aliaslookup.json'
+
+
+def data_path(filename):
+    data_dir = os.path.join(os.path.dirname(__file__), 'data')
+    return os.path.join(data_dir, filename)
+
+
+# monkeypatch replacement request function
+def query_aliases_mock(self, *args, **kwargs):
+    with open(data_path(LOOKUP_DATA_FILE), 'rb') as f:
+        response = json.load(f)
+    return response
+
+
+# use a pytest fixture to create a dummy 'requests.get' function,
+# that mocks(monkeypatches) the actual 'requests.get' function:
+@pytest.fixture
+def query_aliases_request(request):
+    mp = request.getfixturevalue("monkeypatch")
+    mp.setattr(NasaExoplanetArchiveClass, '_request_query_aliases', query_aliases_mock)
+    return mp
+
+
+def test_query_aliases(query_aliases_request):
+    nasa_exoplanet_archive = NasaExoplanetArchiveClass()
+    result = nasa_exoplanet_archive.query_aliases(object_name='bet Pic')
+    assert len(result) > 10
+    assert 'GJ 219' in result
+    assert 'bet Pic' in result
+    assert '2MASS J05471708-5103594' in result
+
+
+def test_query_aliases_planet(query_aliases_request):
+    nasa_exoplanet_archive = NasaExoplanetArchiveClass()
+    result = nasa_exoplanet_archive.query_aliases('bet Pic b')
+    assert len(result) > 10
+    assert 'GJ 219 b' in result
+    assert 'bet Pic b' in result
+    assert '2MASS J05471708-5103594 b' in result
 
-    NasaExoplanetArchiveMock._tap_tables = ['list']
-    assert NasaExoplanetArchiveMock._regularize_object_name("kepler 2") == "HAT-P-7"
-    assert NasaExoplanetArchiveMock._regularize_object_name("kepler 1 b") == "TrES-2 b"
 
-    with pytest.warns(NoResultsWarning) as warning:
-        NasaExoplanetArchiveMock._regularize_object_name("not a planet")
-    assert "No aliases found for name: 'not a planet'" == str(warning[0].message)
+def test_get_access_url():
+    assert get_access_url('tap') == conf.url_tap
+    assert get_access_url('api') == conf.url_api
+    assert get_access_url('aliaslookup') == conf.url_aliaslookup
 
 
 def test_backwards_compat(patch_get):
diff --git a/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/test_nasa_exoplanet_archive_remote.py b/astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/test_nasa_exoplanet_archive_remote.py
@@ -159,7 +159,7 @@ def test_query_region():
 def test_query_aliases():
     name = "bet Pic"
     aliases = NasaExoplanetArchive.query_aliases(name)
-    assert len(aliases) == 12
+    assert len(aliases) > 10
     assert "HD 39060" in aliases
 
 
diff --git a/docs/ipac/nexsci/nasa_exoplanet_archive.rst b/docs/ipac/nexsci/nasa_exoplanet_archive.rst
