Refactor parsing of Cleaning and add CleaningStep class

FAIRmat-NFDI · Nov 7, 2024 · f025c6c · f025c6c
1 parent f67b73b
commit f025c6c
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Showing 2 changed files with 45 additions and 35 deletions.
diff --git a/src/perovskite_tandem_database/parsers/tandemparser.py b/src/perovskite_tandem_database/parsers/tandemparser.py
@@ -18,6 +18,7 @@
     ChalcopyriteAlkaliMetalDoping,
     ChalcopyriteLayer,
     Cleaning,
+    CleaningStep,
     GasPhaseSynthesis,
     General,
     Ion,
@@ -285,6 +286,25 @@ def exact_get(data, label, default=None, default_unit=None):
         return default
 
 
+def extract_cleaning(data_frame):
+    """
+    Extracts the cleaning steps from the data subframe.
+    """
+
+    df_cleaning = data_frame[data_frame.index.str.contains('Cleaning')]
+    if df_cleaning.empty:
+        return None
+    else:
+        df_cleaning = split_data(df_cleaning, delimiter='|')  # probably not necessary
+        df_cleaning = split_data(df_cleaning, delimiter='>>')
+        cleaning_steps = []
+        for syn_step in df_cleaning.columns:
+            cleaning_steps.append(
+                CleaningStep(name=partial_get(df_cleaning[syn_step], 'procedure'))
+            )
+        return Cleaning(steps=cleaning_steps)
+
+
 def extract_additives(data_frame):
     """
     Extracts the additives from the data subframe.
@@ -521,17 +541,7 @@ def extract_layer_stack(data_frame):
             continue
 
         # Cleaning
-        cleaning_steps = []
-        df_cleaning = df_layer[df_layer.index.str.contains('Cleaning')]
-        if not df_cleaning.empty:
-            df_cleaning = split_data(
-                df_cleaning, delimiter='|'
-            )  # probably not necessary
-            df_cleaning = split_data(df_cleaning, delimiter='>>')
-            for syn_step in df_cleaning.columns:
-                cleaning_steps.append(
-                    Cleaning(procedure=partial_get(df_cleaning[syn_step], 'Procedure'))
-                )
+        cleaning = extract_cleaning(df_layer)
 
         # Deposition
         df_sublayers = split_data(df_layer, delimiter='|')
@@ -611,7 +621,7 @@ def extract_layer_stack(data_frame):
                     layer_stack.append(
                         Substrate(
                             **sublayer_properties,
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                         )
@@ -620,7 +630,7 @@ def extract_layer_stack(data_frame):
                     layer_stack.append(
                         NonAbsorbingLayer(
                             **sublayer_properties,
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                             additives=additives,
@@ -667,7 +677,7 @@ def extract_layer_stack(data_frame):
                             **sublayer_properties,
                             **perovskite_properties,
                             composition=extract_perovskite_composition(df_sublayer),
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                             additives=additives,
@@ -685,7 +695,7 @@ def extract_layer_stack(data_frame):
                             **sublayer_properties,
                             **silicon_properties,
                             perovskite_inspired=None,
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                             additives=additives,
@@ -698,7 +708,7 @@ def extract_layer_stack(data_frame):
                             composition=extract_chalcopyrite_composition(df_sublayer),
                             alkali_metal_doping=extract_alkali_doping(df_sublayer),
                             perovskite_inspired=None,
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                             additives=additives,
@@ -709,7 +719,7 @@ def extract_layer_stack(data_frame):
                         PhotoAbsorber(
                             **sublayer_properties,
                             perovskite_inspired=None,
-                            cleaning=cleaning_steps,
+                            cleaning=cleaning,
                             synthesis=synthesis,
                             storage=storage,
                             additives=additives,

diff --git a/src/perovskite_tandem_database/schema_packages/tandem.py b/src/perovskite_tandem_database/schema_packages/tandem.py
@@ -3,6 +3,7 @@
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
 from nomad.datamodel.metainfo.basesections import (
     Activity,
+    ActivityStep,
     ElementalComposition,
     Process,
 )
@@ -250,26 +251,25 @@ class SynthesisStep(Activity, ArchiveSection):
     )
 
 
-class Cleaning(Activity, ArchiveSection):
+class CleaningStep(ActivityStep):
     """
-    A section describing a cleaning step. Typically before a subsequent synthesis step.
+    A cleaning procedure step.
     """
 
-    # TODO: Make repeatable if possible
-    procedure = Quantity(
-        type=Enum(
-            [
-                'Soap',
-                'Ultrasonic Bath',
-                'Ethanol',
-                'Acetone',
-                'UV-ozone',
-                'Piranha solutionion',
-                'Unknown',
-            ]
-        ),
-        description='',
-        shape=[],
+    pass
+
+
+class Cleaning(Activity):
+    """
+    A section describing a cleaning procedure. Typically before a subsequent synthesis step.
+    """
+
+    steps = SubSection(
+        section_def=CleaningStep,
+        description="""
+        An ordered list of all the cleaning steps that make up this activity.
+        """,
+        repeats=True,
     )
 
 
@@ -410,7 +410,7 @@ class Layer(ArchiveSection):
         shape=[],
         description='The specific brand name of a commercially purchased layer',
     )
-    cleaning = SubSection(section_def=Cleaning, repeats=True)
+    cleaning = SubSection(section_def=Cleaning)
     synthesis = SubSection(section_def=Synthesis)
 
     # Storage