add tool to retrieve whole molecule cat, add check for known

malformatted catalogs, improve LUT, refactor and significantly robustify
CDMS data table handling.  Also, update cached metadata files

add more regression tests

whitespace

whitespace

setup for data file

almost there ... unicode bad

col name

recode unicode raised minus (character 96) as simple dash

try replacing the text before ascii-reading it

oops

dashes

try a different approach...

try a different approach... part 2

super minor

remove unnecessary test that I just added

allow lookuptable to skip regex searching for exact matches

no single-char variables

looks like my fixes didn't work, and of course I made a bunch of stupid errors.  I might have to give up for the night

hooray!  got a different error this time.  Now just guesswork though....

Entry column

changelog

CI: ignoring a Deprecation we don't directly use but trigger somewhere in the stack

finish test

update docstr, inline comment

Author: keflavich

CHANGES.rst

@@ -8,6 +8,17 @@ New Tools and Services
 Service fixes and enhancements
 ------------------------------
 
+linelists.cdms
+^^^^^^^^^^^^^^
+
+- Add whole catalog retrieval, improve error messaging for unparseable lines,
+  improve metadata catalog, and improve lookuptable behavior [#3173,#2901]
+
+jplspec
+^^^^^^^
+
+- minor improvement to lookuptable behavior [#3173,#2901]
+
 
 Infrastructure, Utility and Other Changes and Additions
 -------------------------------------------------------

astroquery/jplspec/lookup_table.py

@@ -4,13 +4,13 @@
 
 class Lookuptable(dict):
 
-    def find(self, s, flags):
+    def find(self, st, flags):
         """
         Search dictionary keys for a regex match to string s
 
         Parameters
         ----------
-        s : str
+        st : str
             String to compile as a regular expression
             Can be entered non-specific for broader results
             ('H2O' yields 'H2O' but will also yield 'HCCCH2OD')
@@ -22,17 +22,20 @@ def find(self, s, flags):
 
         Returns
         -------
-        The list of values corresponding to the matches
+        The dictionary containing only values whose keys match the regex
 
         """
 
-        R = re.compile(s, flags)
+        if st in self:
+            return {st: self[st]}
+
+        R = re.compile(st, flags)
 
         out = {}
 
-        for k, v in self.items():
-            match = R.search(str(k))
+        for key, val in self.items():
+            match = R.search(str(key))
             if match:
-                out[k] = v
+                out[key] = val
 
         return out

astroquery/linelists/cdms/__init__.py

@@ -14,13 +14,25 @@ class Conf(_config.ConfigNamespace):
     Configuration parameters for `astroquery.linelists.cdms`.
     """
     server = _config.ConfigItem(
+        'https://cdms.astro.uni-koeln.de/',
+        'CDMS Search and Conversion Form URL.')
+
+    search = _config.ConfigItem(
         'https://cdms.astro.uni-koeln.de/cgi-bin/cdmssearch',
         'CDMS Search and Conversion Form URL.')
 
     catfile_url = _config.ConfigItem(
         'https://cdms.astro.uni-koeln.de/classic/entries/partition_function.html',
         'CDMS partition function table listing all available molecules.')
 
+    catfile_url2 = _config.ConfigItem(
+        'https://cdms.astro.uni-koeln.de/classic/predictions/catalog/catdir.html',
+        'CDMS catalog table listing all available molecules (with different names from partition function).')
+
+    classic_server = _config.ConfigItem(
+        'https://cdms.astro.uni-koeln.de/classic',
+        'CDMS Classic Molecule List server.')
+
     timeout = _config.ConfigItem(
         60,
         'Time limit for connecting to the CDMS server.')

astroquery/linelists/cdms/core.py

@@ -5,6 +5,7 @@
 
 from bs4 import BeautifulSoup
 import astropy.units as u
+from astropy import table
 from astropy.io import ascii
 from astroquery.query import BaseQuery
 from astroquery.utils import async_to_sync
@@ -26,8 +27,11 @@ def data_path(filename):
 @async_to_sync
 class CDMSClass(BaseQuery):
     # use the Configuration Items imported from __init__.py
-    URL = conf.server
+    URL = conf.search
+    SERVER = conf.server
+    CLASSIC_URL = conf.classic_server
     TIMEOUT = conf.timeout
+    MALFORMATTED_MOLECULE_LIST = ['017506 NH3-wHFS', '028582 H2NC', '058501 H2C2S', '064527 HC3HCN']
 
     def query_lines_async(self, min_frequency, max_frequency, *,
                           min_strength=-500, molecule='All',
@@ -143,8 +147,6 @@ def query_lines_async(self, min_frequency, max_frequency, *,
             else:
                 payload['Molecules'] = molecule
 
-        payload = list(payload.items())
-
         if get_query_payload:
             return payload
         # BaseQuery classes come with a _request method that includes a
@@ -170,6 +172,13 @@ def query_lines_async(self, min_frequency, max_frequency, *,
         response2 = self._request(method='GET', url=fullurl,
                                   timeout=self.TIMEOUT, cache=cache)
 
+        # accounts for three formats, e.g.: '058501' or 'H2C2S' or '058501 H2C2S'
+        badlist = (self.MALFORMATTED_MOLECULE_LIST +  # noqa
+                   [y for x in self.MALFORMATTED_MOLECULE_LIST for y in x.split()])
+        if payload['Molecules'] in badlist:
+            raise ValueError(f"Molecule {payload['Molecules']} is known not to comply with standard CDMS format.  "
+                             f"Try get_molecule({payload['Molecules']}) instead.")
+
         return response2
 
     def _parse_result(self, response, *, verbose=False):
@@ -278,8 +287,9 @@ def _parse_result(self, response, *, verbose=False):
 
         return result
 
-    def get_species_table(self, *, catfile='catdir.cat', use_cached=True,
-                          catfile_url=conf.catfile_url):
+    def get_species_table(self, *, catfile='partfunc.cat', use_cached=True,
+                          catfile_url=conf.catfile_url,
+                          catfile2='catdir.cat', catfile_url2=conf.catfile_url2):
         """
         A directory of the catalog is found in a file called 'catdir.cat.'
 
@@ -302,9 +312,35 @@ def get_species_table(self, *, catfile='catdir.cat', use_cached=True,
         """
 
         if use_cached:
-            result = ascii.read(data_path(catfile), format='fixed_width', delimiter='|')
+            try:
+                result = ascii.read(data_path(catfile), format='fixed_width', delimiter='|')
+                result2 = ascii.read(data_path(catfile2), format='fixed_width', delimiter='|')
+            except UnicodeDecodeError:
+                with open(data_path(catfile), 'rb') as fh:
+                    content = fh.read()
+                text = content.decode('ascii', errors='replace')
+                result = ascii.read(text, format='basic', delimiter='|')
+                with open(data_path(catfile2), 'rb') as fh:
+                    content = fh.read()
+                text = content.decode('ascii', errors='replace')
+                result2 = ascii.read(text, format='basic', delimiter='|')
         else:
             result = retrieve_catfile(catfile_url)
+            result2 = retrieve_catfile2(catfile_url2)
+            result.write(data_path(catfile), format='ascii.fixed_width', delimiter='|', overwrite=True)
+            result2.write(data_path(catfile2), format='ascii.fixed_width', delimiter='|', overwrite=True)
+
+        merged = table.join(result, result2, keys=['tag'])
+        if not all(merged['#lines'] == merged['# lines']):
+            raise ValueError("Inconsistent table of molecules from CDMS.")
+        del merged['# lines']
+
+        # reorder columns
+        result = merged[['tag', 'molecule', 'Name', '#lines', 'lg(Q(1000))',
+                         'lg(Q(500))', 'lg(Q(300))', 'lg(Q(225))', 'lg(Q(150))', 'lg(Q(75))',
+                         'lg(Q(37.5))', 'lg(Q(18.75))', 'lg(Q(9.375))', 'lg(Q(5.000))',
+                         'lg(Q(2.725))',
+                         'Ver.', 'Documentation', 'Date of entry', 'Entry']]
 
         meta = {'lg(Q(1000))': 1000.0,
                 'lg(Q(500))': 500.0,
@@ -331,6 +367,96 @@ def tryfloat(x):
         result.meta = {'Temperature (K)': [1000., 500., 300., 225., 150., 75.,
                                            37.5, 18.75, 9.375, 5., 2.725]}
 
+        result.add_index('tag')
+
+        return result
+
+    def get_molecule(self, molecule_id, *, cache=True):
+        """
+        Retrieve the whole molecule table for a given molecule id
+        """
+        if not isinstance(molecule_id, str) or len(molecule_id) != 6:
+            raise ValueError("molecule_id should be a length-6 string of numbers")
+        url = f'{self.CLASSIC_URL}/entries/c{molecule_id}.cat'
+        response = self._request(method='GET', url=url,
+                                 timeout=self.TIMEOUT, cache=cache)
+        result = self._parse_cat(response)
+
+        species_table = self.get_species_table()
+        result.meta = dict(species_table.loc[int(molecule_id)])
+
+        return result
+
+    def _parse_cat(self, response, *, verbose=False):
+        """
+        Parse a catalog response into an `~astropy.table.Table`
+
+        See details in _parse_response; this is a very similar function,
+        but the catalog responses have a slightly different format.
+        """
+
+        if 'Zero lines were found' in response.text:
+            raise EmptyResponseError(f"Response was empty; message was '{response.text}'.")
+
+        text = response.text
+
+        # notes about the format
+        # [F13.4, 2F8.4, I2, F10.4, I3, I7, I4, 12I2]: FREQ, ERR, LGINT, DR, ELO, GUP, TAG, QNFMT, QN  noqa
+        #      13 21 29  31     41  44  51  55  57 59 61 63 65 67  69 71 73 75 77 79                   noqa
+        starts = {'FREQ': 0,
+                  'ERR': 14,
+                  'LGINT': 22,
+                  'DR': 30,
+                  'ELO': 32,
+                  'GUP': 42,
+                  'TAG': 45,
+                  'QNFMT': 52,
+                  'Q1': 56,
+                  'Q2': 58,
+                  'Q3': 60,
+                  'Q4': 62,
+                  'Q5': 64,
+                  'Q6': 66,
+                  'Q7': 68,
+                  'Q8': 70,
+                  'Q9': 72,
+                  'Q10': 74,
+                  'Q11': 76,
+                  'Q12': 78,
+                  'Q13': 80,
+                  'Q14': 82,
+                  }
+
+        result = ascii.read(text, header_start=None, data_start=0,
+                            comment=r'THIS|^\s{12,14}\d{4,6}.*',
+                            names=list(starts.keys()),
+                            col_starts=list(starts.values()),
+                            format='fixed_width', fast_reader=False)
+
+        # int truncates - which is what we want
+        result['MOLWT'] = [int(x/1e4) for x in result['TAG']]
+
+        result['FREQ'].unit = u.MHz
+        result['ERR'].unit = u.MHz
+
+        result['Lab'] = result['MOLWT'] < 0
+        result['MOLWT'] = np.abs(result['MOLWT'])
+        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 key in fix_keys:
+            if not np.issubdtype(result[key].dtype, np.integer):
+                intcol = np.array(list(map(parse_letternumber, result[key])),
+                                  dtype=int)
+                result[key] = intcol
+
+        result['LGINT'].unit = u.nm**2 * u.MHz
+        result['ELO'].unit = u.cm**(-1)
+
         return result
 
 
@@ -375,10 +501,13 @@ def find(self, st, flags):
 
         Returns
         -------
-        The list of values corresponding to the matches
+        The dictionary containing only values whose keys match the regex
 
         """
 
+        if st in self:
+            return {st: self[st]}
+
         out = {}
 
         for kk, vv in self.items():
@@ -394,24 +523,89 @@ def find(self, st, flags):
 def build_lookup():
 
     result = CDMS.get_species_table()
+
+    # start with the 'molecule' column
     keys = list(result['molecule'][:])  # convert NAME column to list
     values = list(result['tag'][:])  # convert TAG column to list
     dictionary = dict(zip(keys, values))  # make k,v dictionary
+
+    # repeat with the Name column
+    keys = list(result['Name'][:])
+    values = list(result['tag'][:])
+    dictionary2 = dict(zip(keys, values))
+    dictionary.update(dictionary2)
+
     lookuptable = Lookuptable(dictionary)  # apply the class above
 
     return lookuptable
 
 
-def retrieve_catfile(url='https://cdms.astro.uni-koeln.de/classic/entries/partition_function.html'):
+def retrieve_catfile(url=f'{conf.classic_server}/entries/partition_function.html'):
     """
     Simple retrieve index function
     """
     response = requests.get(url)
     response.raise_for_status()
-    tbl = ascii.read(response.text, header_start=None, data_start=15, data_end=-5,
-                     names=['tag', 'molecule', '#lines', 'lg(Q(1000))', 'lg(Q(500))', 'lg(Q(300))', 'lg(Q(225))',
-                            'lg(Q(150))', 'lg(Q(75))', 'lg(Q(37.5))', 'lg(Q(18.75))', 'lg(Q(9.375))', 'lg(Q(5.000))',
-                            'lg(Q(2.725))'],
-                     col_starts=(0, 7, 34, 41, 53, 66, 79, 92, 106, 117, 131, 145, 159, 173),
-                     format='fixed_width', delimiter=' ')
+    lines = response.text.split("\n")
+
+    # used to convert '---' to nan
+    def tryfloat(x):
+        try:
+            return float(x)
+        except ValueError:
+            return np.nan
+
+    # the 'fixed width' table reader fails because there are rows that violate fixed width
+    tbl_rows = []
+    for row in lines[15:-5]:
+        split = row.split()
+        tag = int(split[0])
+        molecule_and_lines = row[7:41]
+        molecule = " ".join(molecule_and_lines.split()[:-1])
+        nlines = int(molecule_and_lines.split()[-1])
+        partfunc = map(tryfloat, row[41:].split())
+        partfunc_dict = dict(zip(['lg(Q(1000))', 'lg(Q(500))', 'lg(Q(300))', 'lg(Q(225))',
+                                  'lg(Q(150))', 'lg(Q(75))', 'lg(Q(37.5))', 'lg(Q(18.75))',
+                                  'lg(Q(9.375))', 'lg(Q(5.000))', 'lg(Q(2.725))'], partfunc))
+        tbl_rows.append({'tag': tag,
+                         'molecule': molecule,
+                         '#lines': nlines,
+                         })
+        tbl_rows[-1].update(partfunc_dict)
+    tbl = table.Table(tbl_rows)
+    # tbl = ascii.read(response.text, header_start=None, data_start=15, data_end=-5,
+    #                  names=['tag', 'molecule', '#lines', 'lg(Q(1000))', 'lg(Q(500))', 'lg(Q(300))', 'lg(Q(225))',
+    #                         'lg(Q(150))', 'lg(Q(75))', 'lg(Q(37.5))', 'lg(Q(18.75))', 'lg(Q(9.375))', 'lg(Q(5.000))',
+    #                         'lg(Q(2.725))'],
+    #                  col_starts=(0, 7, 34, 41, 53, 66, 79, 92, 106, 117, 131, 145, 159, 173),
+    #                  format='fixed_width', delimiter=' ')
+    return tbl
+
+
+def retrieve_catfile2(url=f'{conf.classic_server}/predictions/catalog/catdir.html'):
+    """
+    Simple retrieve index function
+    """
+    response = requests.get(url)
+    response.raise_for_status()
+    try:
+        tbl = ascii.read(response.text, format='html')
+    except UnicodeDecodeError:
+        # based on https://github.com/astropy/astropy/issues/3826#issuecomment-256113937
+        # which suggests to start with the bytecode content and decode with 'replace errors'
+        text = response.content.decode('ascii', errors='replace')
+        tbl = ascii.read(text, format='html')
+
+    # delete a junk column (wastes space)
+    del tbl['Catalog']
+
+    # for joining - want same capitalization
+    tbl.rename_column("Tag", "tag")
+
+    # one of these is a unicode dash, the other is a normal dash.... in theory
+    if 'Entry in cm–1' in tbl.colnames:
+        tbl.rename_column('Entry in cm–1', 'Entry')
+    if 'Entry in cm-1' in tbl.colnames:
+        tbl.rename_column('Entry in cm-1', 'Entry')
+
     return tbl