Prevent h5 failing

src/nomad_catalysis/schema_packages/catalysis.py

@@ -172,8 +172,11 @@ def map_and_assign_attributes(self, logger, mapping, target, obj=None) -> None:
                 )
 
 
+threshold_conc = 1.1
+
+
 def check_if_concentration_in_percentage(self, conc_array, logger) -> None:
-    if conc_array is not None and any(y > 1.0 for y in conc_array):
+    if conc_array is not None and any(y > threshold_conc for y in conc_array):
         logger.error(
             f'Gas concentration for reagent "{self.name}" is above 1, '
             f'but should be given as fraction.'
@@ -748,15 +751,21 @@ def normalize(self, archive, logger):
         check_if_concentration_in_percentage(self, self.fraction_in, logger)
         try:
             if (
-                not self.fraction_in
-                and self.flow_rate
-                and self.m_parent
-                and getattr(self.m_parent, 'set_total_flow_rate', None)
+                self.fraction_in is None
+                and self.flow_rate is not None
+                and self.m_parent is not None
+                and getattr(self.m_parent, 'set_total_flow_rate', None) is not None
             ):
                 total_flow = getattr(self.m_parent, 'set_total_flow_rate', None)
                 self.fraction_in = self.flow_rate / total_flow
-        except (TypeError, ValueError):  # because truth value of array is ambiguous
-            pass
+        except (
+            TypeError,
+            ValueError,
+        ) as e:  # because truth value of array is ambiguous
+            logger.info(
+                f'Could not calculate fraction_in for reagent {self.name} '
+                f'from flow rate and total flow rate. Error: {e}'
+            )
         if self.name is None:
             return
         if self.name in ['C5-1', 'C6-1', 'nC5', 'nC6', 'Unknown', 'inert', 'P>=5C']:
@@ -1108,7 +1117,7 @@ class ReagentBatch(Reagent):
     m_def = Section(
         label_quantity='name',
         description='A reagent in a batch reaction.',
-        a_eln={'hide': ['fraction_in', 'flow_rate']},
+        a_eln={'hide': ['flow_rate']},
     )
 
     amount = Quantity(
@@ -1817,7 +1826,7 @@ def read_haber_data(self, archive, logger):  # noqa: PLR0912, PLR0915
 
     def check_and_read_data_file(self, archive, logger):
         """This functions checks the format of the data file and assigns the right
-        reader function to read the data file or logs an error if the format is not
+        reader function to read the data file or logs a warning if the format is not
         supported.
         """
         if self.data_file is None:
@@ -1830,14 +1839,23 @@ def check_and_read_data_file(self, archive, logger):
             if self.data_file.endswith('NH3_Decomposition.h5'):
                 self.read_haber_data(archive, logger)
             else:
-                logger.info("""This h5 file format might currently not be supported.
-                Pleasecontact the plugin developers if you want to add support for this.
-                            """)
-                self.read_haber_data(archive, logger)
+                try:
+                    self.read_haber_data(archive, logger)
+                except KeyError:
+                    logger.warning(
+                        """No data is extracted from this h5 data file as the file is
+                        either missing or the format is not (yet) supported.
+                        This file contains a different data
+                        structure or object names from currently supported h5 files for
+                        catalysis. Please check if you can modify the structure or
+                        contact the plugin developers if you want to add support for
+                        this."""
+                    )
         else:
-            logger.error(
-                """Data file format not supported. Please provide a
-                .csv, .xlsx or .h5 file."""
+            logger.warning(
+                """Data file format not supported. No data is extracted from the
+                provided file. Please provide a standadized .csv, .xlsx or .h5 file,
+                if you want direct data extraction into the schema."""
             )
             return
 
@@ -2470,7 +2488,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
 
         if self.data_file is not None:
             self.check_and_read_data_file(archive, logger)
-            logger.info('Data file read successfully.')
+            logger.info('Data file processed.')
 
         self.normalize_reaction_conditions(archive, logger)
         if self.pretreatment is not None: