expand test coverage and resolve some problems discovered as a result

Author: keflavich

astroquery/linelists/cdms/core.py

@@ -12,6 +12,7 @@
 # import configurable items declared in __init__.py
 from astroquery.linelists.cdms import conf
 from astroquery.exceptions import InvalidQueryError, EmptyResponseError
+from astroquery import log
 
 import re
 import string
@@ -409,7 +410,7 @@ def tryfloat(x):
 
         return result
 
-    def get_molecule(self, molecule_id, *, cache=True):
+    def get_molecule(self, molecule_id, *, cache=True, return_response=False):
         """
         Retrieve the whole molecule table for a given molecule id
         """
@@ -418,6 +419,8 @@ def get_molecule(self, molecule_id, *, cache=True):
         url = f'{self.CLASSIC_URL}/entries/c{molecule_id}.cat'
         response = self._request(method='GET', url=url,
                                  timeout=self.TIMEOUT, cache=cache)
+        if return_response:
+            return response
         result = self._parse_cat(response)
 
         species_table = self.get_species_table()
@@ -449,7 +452,7 @@ def _parse_cat(self, response, *, verbose=False):
                   'GUP': 42,
                   'TAG': 44,
                   'QNFMT': 52,
-                  'Q1': 56,
+                  'Q1': 55,
                   'Q2': 58,
                   'Q3': 60,
                   'Q4': 62,
@@ -472,7 +475,7 @@ def _parse_cat(self, response, *, verbose=False):
                             format='fixed_width', fast_reader=False)
 
         # int truncates - which is what we want
-        result['MOLWT'] = [int(x/1e4) for x in result['TAG']]
+        result['MOLWT'] = [int(x/1e3) for x in result['TAG']]
 
         result['FREQ'].unit = u.MHz
         result['ERR'].unit = u.MHz
@@ -482,15 +485,18 @@ def _parse_cat(self, response, *, verbose=False):
         result['MOLWT'].unit = u.Da
 
         fix_keys = ['GUP']
-        for suf in '':
-            for qn in (f'Q{ii}' for ii in range(1, 15)):
-                qnind = qn+suf
-                fix_keys.append(qnind)
+        for qn in (f'Q{ii}' for ii in range(1, 15)):
+            fix_keys.append(qn)
+        log.debug(f"fix_keys: {fix_keys} should include Q1, Q2, ..., Q14 and GUP")
         for key in fix_keys:
             if not np.issubdtype(result[key].dtype, np.integer):
                 intcol = np.array(list(map(parse_letternumber, result[key])),
                                   dtype=int)
+                if any(intcol == -999999):
+                    intcol = np.ma.masked_where(intcol == -999999, intcol)
                 result[key] = intcol
+                if not np.issubdtype(result[key].dtype, np.integer):
+                    raise ValueError(f"Failed to parse {key} as integer")
 
         result['LGINT'].unit = u.nm**2 * u.MHz
         result['ELO'].unit = u.cm**(-1)
@@ -508,9 +514,12 @@ def parse_letternumber(st):
     From the CDMS docs:
     "Exactly two characters are available for each quantum number. Therefore, half
     integer quanta are rounded up ! In addition, capital letters are used to
-    indicate quantum numbers larger than 99. E. g. A0 is 100, Z9 is 359. Lower case characters 
+    indicate quantum numbers larger than 99. E. g. A0 is 100, Z9 is 359. Lower case characters
     are used similarly to signal negative quantum numbers smaller than –9. e. g., a0 is –10, b0 is –20, etc."
     """
+    if np.ma.is_masked(st):
+        return -999999
+
     asc = string.ascii_lowercase
     ASC = string.ascii_uppercase
     newst = ''.join(['-' + str((asc.index(x)+1)) if x in asc else

astroquery/linelists/cdms/tests/test_cdms.py

@@ -83,6 +83,7 @@ def test_query(patch_post):
     assert tbl['LGINT'][0] == -7.1425
     assert tbl['GUP'][0] == 3
     assert tbl['GUP'][7] == 17
+    assert tbl['MOLWT'][0] == 28
 
 
 def test_parseletternumber():
@@ -103,6 +104,8 @@ def test_parseletternumber():
     assert parse_letternumber("b0") == -20
     assert parse_letternumber("ZZ") == 3535
 
+    assert parse_letternumber(np.ma.masked) == -999999
+
 
 def test_hc7s(patch_post):
     """

astroquery/linelists/cdms/tests/test_cdms_remote.py

@@ -38,6 +38,24 @@ def test_remote_300K():
     assert tbl['FREQ'][0] == 505366.7875
     assert tbl['ERR'][0] == 49.13
     assert tbl['LGINT'][0] == -4.2182
+    assert tbl['MOLWT'][0] == 18
+
+
+@pytest.mark.remote_data
+def test_propanediol():
+    tbl1 = CDMS.get_molecule('076513')
+    assert 'int' in tbl1['Q2'].dtype.name
+
+    tbl = CDMS.query_lines(min_frequency=100.3 * u.GHz,
+                           max_frequency=100.5 * u.GHz,
+                           molecule='076513',
+    )
+    assert isinstance(tbl, Table)
+    assert len(tbl) >= 1
+    assert 'aG\'g-1,2-Propanediol' in tbl['name']
+    # check that the parser worked - this will be string or obj otherwise
+    assert 'int' in tbl['Ku'].dtype.name
+    assert tbl['MOLWT'][0] == 76
 
 
 @pytest.mark.remote_data