Implement credentials

docs/source/usage.rst

@@ -24,13 +24,13 @@ Lists
 Lists are accepted only by the :python:`calibrator`, :python:`converter`, and :python:`generator`. These lists have to correspond to a list of source IDs. Both lists of strings and lists of long are accepted.
 
 When a list is passed to one of the tools, the function will internally request the required data for the given sources from the Gaia Archive (currently geapre), ask for
-credentials (username and password), execute the function, and return the results.
+Cosmos credentials (username and password), execute the function, and return the results.
 
 ADQL queries
 ------------
 ADQL queries are accepted only by the :python:`calibrator`, :python:`converter`, and :python:`generator`. Queries need to be passed as strings (e.g.: :python:`"select TOP 100 source_id from user_dr3int6.gaia_source where has_xp_continuous = 'True'"`).
 
-Queries are sent to the Gaia Archive (geapre), and executed after requesting credentials (username and password).
+Queries are sent to the Gaia Archive (geapre), and executed after requesting Cosmos credentials (username and password).
 
 DataFrames
 ----------

gaiaxpy/calibrator/calibrator.py

@@ -31,7 +31,9 @@ def calibrate(
         output_path='.',
         output_file='output_spectra',
         output_format=None,
-        save_file=True):
+        save_file=True,
+        username=None,
+        password=None):
     """
     Calibration utility: calibrates the input internally-calibrated
     continuously-represented mean spectra to the absolute system. An absolute
@@ -55,6 +57,8 @@ def calibrate(
             input file.
         save_file (bool): Whether to save the output in a file. If false, output_format
             and output_file are ignored.
+        username (str): Cosmos username.
+        password (str): Cosmos password.
 
     Returns:
         (tuple): tuple containing:
@@ -70,7 +74,9 @@ def calibrate(
         output_path,
         output_file,
         output_format,
-        save_file)
+        save_file,
+        username=username,
+        password=password)
 
 
 def _calibrate(
@@ -82,7 +88,9 @@ def _calibrate(
         output_format=None,
         save_file=True,
         bp_model='v375wi',
-        rp_model='v142r'):
+        rp_model='v142r',
+        username=None,
+        password=None):
     """
     Internal method of the calibration utility. Refer to "calibrate".
 
@@ -99,7 +107,7 @@ def _calibrate(
     """
     _validate_wl_sampling(sampling)
     _validate_arguments(_calibrate.__defaults__[3], output_file, save_file)
-    parsed_input_data, extension = InputReader(input_object, _calibrate)._read()
+    parsed_input_data, extension = InputReader(input_object, _calibrate, username, password)._read()
     label = 'calibrator'
 
     xp_design_matrices, xp_merge = _generate_xp_matrices_and_merge(label, sampling, bp_model, rp_model)

gaiaxpy/converter/converter.py

@@ -34,7 +34,9 @@ def convert(
         output_path='.',
         output_file='output_spectra',
         output_format=None,
-        save_file=True):
+        save_file=True,
+        username=None,
+        password=None):
     """
     Conversion utility: converts the input internally calibrated mean
     spectra from the continuous representation to a sampled form. The
@@ -60,6 +62,8 @@ def convert(
             input file.
         save_file (bool): Whether to save the output in a file. If false, output_format
             and output_file are ignored.
+        username (str): Cosmos username.
+        password (str): Cosmos password.
 
     Returns:
         (tuple): tuple containing:
@@ -72,7 +76,7 @@ def convert(
     # Check sampling
     _validate_pwl_sampling(sampling)
     _validate_arguments(convert.__defaults__[3], output_file, save_file)
-    parsed_input_data, extension = InputReader(input_object, convert)._read()
+    parsed_input_data, extension = InputReader(input_object, convert, username, password)._read()
     config_df = load_config(config_file)
     # Union of unique ids as sets
     unique_bases_ids = get_unique_basis_ids(parsed_input_data)

gaiaxpy/file_parser/parse_generic.py

@@ -81,7 +81,7 @@ def parse(self, file_path):
 
         Returns:
             DataFrame: Pandas DataFrame representing the file.
-            str: File extension ('.avro', '.csv', '.fits', or '.xml').
+            str: File extension ('.csv', '.fits', or '.xml').
         """
         extension = _get_file_extension(file_path)
         parser = self.get_parser(extension)

gaiaxpy/generator/generator.py

@@ -14,7 +14,9 @@ def generate(
         output_file='output_synthetic_photometry',
         output_format=None,
         save_file=True,
-        error_correction=False):
+        error_correction=False,
+        username=None,
+        password=None):
     """
     Synthetic photometry utility: generates synthetic photometry in a set of
     available systems from the input internally-calibrated
@@ -39,6 +41,8 @@ def generate(
         error_correction (bool): Whether to apply to the photometric errors the tabulated
             factors to mitigate underestimated errors (see Montegriffo et al., 2022, for
             more details).
+        username (str): Cosmos username.
+        password (str): Cosmos password.
 
     Returns:
         DataFrame: A DataFrame of all synthetic photometry results.
@@ -56,7 +60,7 @@ def generate(
     else:
         raise ValueError('Parameter photometric_system must be either a PhotometricSystem or a list.')
     # Load data
-    parsed_input_data, extension = InputReader(input_object, generate)._read()
+    parsed_input_data, extension = InputReader(input_object, generate, username, password)._read()
     gaia_system = PhotometricSystem.Gaia_DR3_Vega
     # Create multi generator
     gaia_initially_in_systems = bool(gaia_system in int_photometric_system)

gaiaxpy/input_reader/archive_reader.py

@@ -0,0 +1,16 @@
+from astroquery.gaia import GaiaClass
+
+class ArchiveReader(object):
+
+    def __init__(self, function, user, password):
+        self.function = function
+        self.user = user
+        self.password = password
+
+    def _login(self, gaia):
+        user = self.user
+        password = self.password
+        if user and password:
+            gaia.login(user=user, password=password)
+        else:
+            gaia.login()

gaiaxpy/input_reader/dataframe_reader.py

@@ -1,7 +1,7 @@
 from numpy import ndarray
+from pandas import isnull
 from .dataframe_numpy_array_reader import DataFrameNumPyArrayReader
 from .dataframe_string_array_reader import DataFrameStringArrayReader
-# TODO: move this function to core as it's now used by more than one subpackage
 from gaiaxpy.core import array_to_symmetric_matrix
 
 matrix_columns = [('bp_n_parameters', 'bp_coefficient_correlations'),
@@ -48,6 +48,10 @@ def _read_df(self):
         if needs_matrix_conversion(array_columns):
             for index, row in data.iterrows():
                 for size_column, values_column in matrix_columns:
-                    data[values_column][index] = array_to_symmetric_matrix(
-                        data[size_column][index].astype(int), row[values_column])
+                    try:
+                        data[values_column][index] = array_to_symmetric_matrix(
+                            data[size_column][index].astype(int), row[values_column])
+                    except AttributeError as err:
+                        if isnull(data[size_column][index]):
+                            continue
         return data, None  # No extension for dataframes

gaiaxpy/input_reader/dataframe_string_array_reader.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pandas as pd
+from math import isnan
 
 # Avoid warning, false positive
 pd.options.mode.chained_assignment = None
@@ -17,8 +18,13 @@ def _parse_parenthesis_arrays(self):
         for column in array_columns:
             # String column to NumPy array
             for index, row in df.iterrows():
-                df[column][index] = np.fromstring(
-                    row[column][1:-1], sep=',')
+                current_element = row[column]
+                try:
+                    df[column][index] = np.fromstring(
+                        current_element[1:-1], sep=',')
+                except TypeError:
+                    if isinstance(current_element, float) and isnan(current_element):
+                        continue
         return df
 
     def _parse_brackets_arrays(self):

gaiaxpy/input_reader/input_reader.py

@@ -5,41 +5,48 @@
 from .list_reader import ListReader
 from .query_reader import QueryReader
 
+
 default_extension = 'csv'
 
 
 class InputReader(object):
 
-    def __init__(self, content, function):
+    def __init__(self, content, function, user=None, password=None):
         self.content = content
         self.function = function
+        self.user = user
+        self.password = password
 
     def _string_reader(self):
         content = self.content
         function = self.function
+        user = self.user
+        password = self.password
         # Check whether content is path
         if path.isfile(content) or path.isabs(content):
             selector = FileReader(function)
             parser = selector._select()  # Select type of parser required
             parsed_input_data, extension = parser.parse(content)
         # Query should start with select
         elif content.lower().startswith('select'):
-            parsed_input_data, extension = QueryReader(content, function)._read()
+            parsed_input_data, extension = QueryReader(content, function, user, password)._read()
         else:
             raise ValueError('Input string does not correspond to an existing file and it is not an ADQL query.')
         return parsed_input_data, extension
 
     def _read(self):
         content = self.content
         function = self.function
+        user = self.user
+        password = self.password
         # DataFrame reader
         if isinstance(content, pd.DataFrame):
             # Call Dataframe reader
             parsed_data, extension = DataFrameReader(content)._read_df()
         # List reader for query
         elif isinstance(content, list):
             # Construct query from list
-            parsed_data, extension = ListReader(content, function)._read()
+            parsed_data, extension = ListReader(content, function, user, password)._read()
         # String can be either query or file path
         elif isinstance(content, str):
             parsed_data, extension = self._string_reader()

gaiaxpy/input_reader/list_reader.py

@@ -1,5 +1,6 @@
 from astroquery.gaia import GaiaClass
 from .dataframe_reader import DataFrameReader
+from .archive_reader import ArchiveReader
 
 not_supported_functions = ['apply_colour_equation']
 
@@ -13,14 +14,14 @@ def extremes_are_enclosing(first_row, column):
         return False
 
 
-class ListReader(object):
+class ListReader(ArchiveReader):
 
-    def __init__(self, content, function):
+    def __init__(self, content, function, user, password):
+        super(ListReader, self).__init__(function, user, password)
         if content != []:
             self.content = content
         else:
             raise ValueError('Input list cannot be empty.')
-        self.function = function
 
     def _read(self):
         sources = self.content
@@ -29,7 +30,7 @@ def _read(self):
             raise ValueError(f'Function {function_name} does not support receiving a list as input.')
         # Connect to geapre
         gaia = GaiaClass(gaia_tap_server='https://geapre.esac.esa.int/', gaia_data_server='https://geapre.esac.esa.int/')
-        gaia.login()
+        self._login(gaia)
         # ADQL query
         result = gaia.load_data(ids=sources, format='csv', data_release='Gaia DR3_INT6', data_structure='raw',
                                 retrieval_type='XP_CONTINUOUS', avoid_datatype_check=True)

gaiaxpy/input_reader/query_reader.py

@@ -1,14 +1,15 @@
 from astroquery.gaia import GaiaClass
 from .dataframe_reader import DataFrameReader
+from .archive_reader import ArchiveReader
 
 not_supported_functions = ['apply_colour_equation']
 
 
-class QueryReader(object):
+class QueryReader(ArchiveReader):
 
-    def __init__(self, content, function):
+    def __init__(self, content, function, user=None, password=None):
         self.content = content
-        self.function = function
+        super(QueryReader, self).__init__(function, user, password)
 
     def _read(self, data_release='Gaia DR3_INT6'):
         query = self.content
@@ -17,7 +18,7 @@ def _read(self, data_release='Gaia DR3_INT6'):
             raise ValueError(f'Function {function_name} does not support receiving a query as input.')
         # Connect to geapre
         gaia = GaiaClass(gaia_tap_server='https://geapre.esac.esa.int/', gaia_data_server='https://geapre.esac.esa.int/')
-        gaia.login()
+        self._login(gaia)
         # ADQL query
         job = gaia.launch_job_async(query, dump_to_file=False)
         ids = job.get_results()