Modifications for None and numpy passes at Dictionaries and MetaInfoStorage

parser/parser-amber/AMBERDictionary.py

@@ -1013,46 +1013,46 @@ def get_updateDictionary(self, defname):
             value=self.minConverged
             ),
         'number_of_conserved_quantity_evaluations_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
                     {'frame_sequence_conserved_quantity_frames' : None}
-                    )['frame_sequence_conserved_quantity_frames']
-                ])
+                    )['frame_sequence_conserved_quantity_frames']['val']
+                )
             ),
         'number_of_frames_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
                     {'frame_sequence_potential_energy_frames' : None}
-                    )['frame_sequence_potential_energy_frames']
-                ])
+                    )['frame_sequence_potential_energy_frames']['val']
+                )
             ),
         'number_of_kinetic_energies_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
                     {'frame_sequence_kinetic_energy_frames' : None}
-                    )['frame_sequence_kinetic_energy_frames']
-                ])
+                    )['frame_sequence_kinetic_energy_frames']['val']
+                )
             ),
         'number_of_potential_energies_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
                     {'frame_sequence_potential_energy_frames' : None}
-                    )['frame_sequence_potential_energy_frames']
-                ])
+                    )['frame_sequence_potential_energy_frames']['val']
+                )
             ),
         'number_of_pressure_evaluations_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
-                    {'frame_sequence_pressure_frames' : None}
-                    )['frame_sequence_pressure_frames']
-                ])
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
+                {'frame_sequence_pressure_frames' : None}
+                )['frame_sequence_pressure_frames']['val']
+                )
             ),
         'number_of_temperatures_in_sequence' : MetaInfoMap(startpage,
-            value=len([
-                item for item in self.metaStorage.fetchAttr(
+            value=(lambda x: np.array(x).flatten().shape[0] if x is not None else None)(
+                self.metaStorage.fetchAttr(
                     {'frame_sequence_temperature_frames' : None}
-                    )['frame_sequence_temperature_frames']
-                ])
+                    )['frame_sequence_temperature_frames']['val']
+                )
             ),
         #'previous_sequence_ref' : MetaInfoMap(startpage)
         }

parser/parser-amber/MetaInfoStorage.py

@@ -16,6 +16,8 @@ PUBLIC_META_INFO_PATH = os.path.normpath(os.path.join(
     os.path.dirname(os.path.abspath(__file__)), 
     "../../../../nomad-meta-info/meta_info/nomad_meta_info/public.nomadmetainfo.json"))
 
+NOTEXCEPT = re.compile(r'[^a-cf-zA-CF-Z!\.?,]')
+
 class Container(object):
     """The container class for nested data storage
     """
@@ -316,6 +318,7 @@ class Container(object):
         newunit = newunit.replace('-','*').replace(' ', '*').replace('^', "**")
         for key,value in unitdict.items():
             newunit = newunit.replace(str(key), str(value))
+        NOTEXCEPT.sub('', newunit)
         return float(eval(newunit))
 
     def checkTestsDicts(self, item, localdict):
@@ -393,6 +396,8 @@ class Container(object):
                     backend.addArrayValues(itemk, value)
                 elif isinstance(value, (list, tuple)):
                     backend.addArrayValues(itemk, np.asarray(value))
+                elif value is None:
+                    pass
                 else:
                     backend.addValue(itemk, value)