update to add boolean in methods to determine which SSIP description to use.

Described in issue #3. This is just for the processing of a phase information csv file, CLI update to follow.

phasecalculator/io/phasecsvconverter.py

@@ -34,16 +34,18 @@ LOGGER = logging.getLogger(__name__)
 LOGGER.setLevel(logging.WARN)
 
 NAME_INCHIKEY_MAP = pureinf.get_name_inchikey_mapping()
-INCHIKEY_SSIP_FILE_DICT = pureinf.get_ssip_file_dict()
+INCHIKEY_POLARISED_SSIP_FILE_DICT = pureinf.get_ssip_file_dict()
+INCHIKEY_UNPOLARISED_SSIP_FILE_DICT = pureinf.get_unpolarised_ssip_file_dict()
 
-
-def convert_csv_file_to_phases(csv_filename):
+def convert_csv_file_to_phases(csv_filename, unpolarised_ssips):
     """Read CSV file and convert contents to Phases.
 
     Parameters
     ----------
     csv_filename : str
         CSV filename.
+    unpolarised_ssips : boolean
+        True if unpolarised SSIP descriptions are to be used.
 
     Returns
     -------
@@ -52,7 +54,7 @@ def convert_csv_file_to_phases(csv_filename):
 
     """
     csv_file_contents = read_csv_file(csv_filename)
-    return create_phases(csv_file_contents)
+    return create_phases(csv_file_contents, unpolarised_ssips)
 
 
 def read_csv_file(csv_filename):
@@ -74,13 +76,15 @@ def read_csv_file(csv_filename):
         return [row for row in csv_reader]
 
 
-def create_phases(csv_file_contents):
+def create_phases(csv_file_contents, unpolarised_ssips):
     """Create Phases for csv file contents
 
     Parameters
     ----------
     csv_file_contents : list of lists
         List of CSV file lines.
+    unpolarised_ssips : boolean
+        True if unpolarised SSIP descriptions are to be used.
 
     Returns
     -------
@@ -90,11 +94,11 @@ def create_phases(csv_file_contents):
     """
     phase_list = []
     for csv_file_line in csv_file_contents:
-        phase_list.append(create_phase(csv_file_line))
+        phase_list.append(create_phase(csv_file_line, unpolarised_ssips))
     return Phases(phase_list)
 
 
-def create_phase(csv_file_line):
+def create_phase(csv_file_line, unpolarised_ssips):
     """Create Phase from information list.
     
 
@@ -102,6 +106,8 @@ def create_phase(csv_file_line):
     ----------
     csv_file_line : list of str
         line from CSV file.
+    unpolarised_ssips : boolean
+        True if unpolarised SSIP descriptions are to be used.
 
     Returns
     -------
@@ -114,11 +120,11 @@ def create_phase(csv_file_line):
     for i in range(1, len(csv_file_line), 2):
         name = csv_file_line[i]
         molefraction = float(csv_file_line[i + 1])
-        molecule_list.append(create_molecule(name, molefraction))
+        molecule_list.append(create_molecule(name, molefraction, unpolarised_ssips))
     return Phase(molecule_list, temperature)
 
 
-def create_molecule(name, molefraction):
+def create_molecule(name, molefraction, unpolarised_ssips):
     """Create Molecule.
 
     Parameters
@@ -127,6 +133,8 @@ def create_molecule(name, molefraction):
         Molecule name.
     molefraction : float
         mole fraction of molecule in phase.
+    unpolarised_ssips : boolean
+        True if unpolarised SSIP descriptions are to be used.
 
     Raises
     ------
@@ -141,7 +149,10 @@ def create_molecule(name, molefraction):
     """
     try:
         inchikey = NAME_INCHIKEY_MAP[name]
-        ssip_file_loc = INCHIKEY_SSIP_FILE_DICT[inchikey]
+        if unpolarised_ssips:
+            ssip_file_loc = INCHIKEY_UNPOLARISED_SSIP_FILE_DICT[inchikey]
+        else:
+            ssip_file_loc = INCHIKEY_POLARISED_SSIP_FILE_DICT[inchikey]
         return Molecule(name, inchikey, ssip_file_loc, molefraction)
     except KeyError as keyerr:
         LOGGER.error("Invalid entry: %s Not found.", name)

phasecalculator/test/iotest/phasecsvconvertertest.py

@@ -54,7 +54,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
         self.molecule = Molecule(
             "water",
             "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
-            phasecsv.INCHIKEY_SSIP_FILE_DICT["XLYOFNOQVPJJNP-UHFFFAOYSA-N"],
+            phasecsv.INCHIKEY_POLARISED_SSIP_FILE_DICT["XLYOFNOQVPJJNP-UHFFFAOYSA-N"],
             1.0,
         )
         self.phase = Phase([self.molecule], self.temperature)
@@ -77,7 +77,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
         None.
 
         """
-        actual_phases = phasecsv.convert_csv_file_to_phases(self.example_csv)
+        actual_phases = phasecsv.convert_csv_file_to_phases(self.example_csv,False)
         self.assertEqual(self.phases, actual_phases)
 
     def test_read_csv_file(self):
@@ -99,7 +99,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
         None.
 
         """
-        actual_phases = phasecsv.create_phases(self.csv_file_contents)
+        actual_phases = phasecsv.create_phases(self.csv_file_contents, False)
         self.assertEqual(self.phases, actual_phases)
 
     def test_create_phase(self):
@@ -110,7 +110,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
         None.
 
         """
-        actual_phase = phasecsv.create_phase(["298.0", "water", "1.0"])
+        actual_phase = phasecsv.create_phase(["298.0", "water", "1.0"], False)
         self.assertEqual(self.phase, actual_phase)
 
     def test_create_molecule(self):
@@ -121,7 +121,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
         None.
 
         """
-        actual_molecule = phasecsv.create_molecule("water", 1.0)
+        actual_molecule = phasecsv.create_molecule("water", 1.0, False)
         self.assertEqual(self.molecule, actual_molecule)
 
     def test_create_temperature(self):