Renamings.

pyproject.toml

@@ -74,7 +74,7 @@ select = [
     "UP",
     # isort
     "I",
-    # pylint 
+    # pylint
     "PL",
 ]
 
@@ -108,7 +108,6 @@ package-dir = { "" = "src" }
 where = ["src"]
 
 [project.entry-points.'nomad.plugin']
-myparser = "nomad_tadf_molecules.parsers:myparser"
-mypackage = "nomad_tadf_molecules.schema_packages:mypackage"
-
-myapp = "nomad_tadf_molecules.apps:myapp"
+parser = "nomad_tadf_molecules.parsers:tadf_molecules"
+package = "nomad_tadf_molecules.schema_packages:tadf_molecules"
+app = "nomad_tadf_molecules.apps:tadf_molecules"

src/nomad_tadf_molecules/apps/__init__.py

@@ -1,24 +1,9 @@
 from nomad.config.models.plugins import AppEntryPoint
-from nomad.config.models.ui import App, Column, Columns, FilterMenu, FilterMenus
 
+from nomad_tadf_molecules.apps.tadf_molecules import tadf_molecules_app
 
-myapp = AppEntryPoint(
-    name='MyApp',
-    description='App defined using the new plugin mechanism.',
-    app=App(
-        label='MyApp',
-        path='myapp',
-        category='simulation',
-        columns=Columns(
-            selected=['entry_id'],
-            options={
-                'entry_id': Column(),
-            },
-        ),
-        filter_menus=FilterMenus(
-            options={
-                'material': FilterMenu(label='Material'),
-            }
-        ),
-    ),
+tadf_molecules = AppEntryPoint(
+    name='TADF Molecules',
+    description='Search information about thermally activated delayed fluorescent (TADF) molecules.',
+    app=tadf_molecules_app,
 )

src/nomad_tadf_molecules/apps/tadf_molecules.py

@@ -0,0 +1,88 @@
+from nomad.config.models.ui import (
+    App,
+    Axis,
+    Column,
+    Columns,
+    Dashboard,
+    FilterMenu,
+    FilterMenus,
+    Filters,
+    Layout,
+    WidgetPeriodicTable,
+    WidgetHistogram,
+    WidgetScatterPlot,
+    WidgetTerms,
+)
+
+schema = 'nomad_tadf_molecules.schema_packages.tadf.TADFMolecule'
+tadf_molecules_app = App(
+        label='Fluorescent Molecules',
+        path='fluorescent-molecules',
+        description='Search for fluorescent molecule data',
+        category='Experiment',
+        filters=Filters(include=[f'*#{schema}'],),
+        filters_locked={'section_defs.definition_qualified_name': schema},
+        columns=Columns(
+            selected=[
+                'results.material.chemical_formula_hill',
+                f'data.photoluminescence_quantum_yield#{schema}',
+                f'data.peak_emission_wavelength#{schema}',
+                f'data.delayed_lifetime#{schema}',
+                f'data.singlet_triplet_energy_splitting#{schema}',
+                f'data.DOI_number#{schema}',
+            ],
+            options={
+                'results.material.chemical_formula_hill': Column(),
+                f'data.photoluminescence_quantum_yield#{schema}': Column(),
+                f'data.peak_emission_wavelength#{schema}': Column(),
+                f'data.delayed_lifetime#{schema}': Column(),
+                f'data.singlet_triplet_energy_splitting#{schema}': Column(),
+                f'data.DOI_number#{schema}': Column(),
+            }
+        ),
+        filter_menus=FilterMenus(
+            options={
+                'material': FilterMenu(label='Material'),
+                'elements': FilterMenu(label='Elements / Formula', level=1, size='xl'),
+                'custom_quantities': FilterMenu(label='Custom Quantities', size='l'),
+            }
+        ),
+        dashboard=Dashboard(
+          widgets=[
+            WidgetPeriodicTable(
+              type='periodictable',
+              scale='linear',
+              quantity='results.material.elements',
+              layout={'lg': Layout(w=11, h=7, x=0, y=0)},
+            ),
+            WidgetScatterPlot(
+              type='scatterplot',
+              layout={'lg':Layout(w=7, h=7, x=11, y=0)},
+              x=Axis(quantity=f'data.peak_emission_wavelength#{schema}', unit='nm'),
+              y=Axis(quantity=f'data.photoluminescence_quantum_yield#{schema}'),
+            ),
+            WidgetTerms(
+              type='terms',
+              layout={'lg': Layout(w=6, h=7, x=18, y=0)},
+              quantity='results.material.chemical_fomula_fill',
+              scale='linear',
+            ),
+            WidgetHistogram(
+              type='histogram',
+              layout={'lg': Layout(w=12, h=4, x=12, y=7)},
+              autorange=True,
+              nbins=30,
+              scale='linear',
+              quantity=f'data.delayed_lifetime#{schema}',
+            ),
+            WidgetHistogram(
+              type='histogram',
+              layout={'lg': Layout(w=12, h=4, x=12, y=7)},
+              autorange=True,
+              nbins=30,
+              scale='linear',
+              quantity=f'data.singlet_triplet_energy_splitting#{schema}',
+            )
+        ]
+    )
+)

src/nomad_tadf_molecules/parsers/__init__.py

@@ -1,18 +1,15 @@
 from nomad.config.models.plugins import ParserEntryPoint
-from pydantic import Field
 
 
-class MyParserEntryPoint(ParserEntryPoint):
-    parameter: int = Field(0, description='Custom configuration parameter')
-
+class TADFMoleculesParserEntryPoint(ParserEntryPoint):
     def load(self):
-        from nomad_tadf_molecules.parsers.myparser import MyParser
+        from nomad_tadf_molecules.parsers.tadf_molecules import TADFMoleculesParser
 
-        return MyParser(**self.dict())
+        return TADFMoleculesParser(**self.dict())
 
 
-myparser = MyParserEntryPoint(
-    name='MyParser',
-    description='Parser defined using the new plugin mechanism.',
-    mainfile_name_re='.*\.myparser',
+tadf_molecules = TADFMoleculesParserEntryPoint(
+    name='TADFMoleculesParser',
+    description='Used to parse information about thermally activated fluorescent molecules from JSON files.',
+    mainfile_name_re='.*molecule\d+.json',
 )

src/nomad_tadf_molecules/parsers/tadf_molecules.py

@@ -0,0 +1,41 @@
+import json
+
+from nomad.datamodel.datamodel import EntryArchive
+from nomad.parsing.parser import MatchingParser
+from nomad.units import ureg
+from structlog.stdlib import BoundLogger
+
+from nomad_tadf_molecules.schema_packages.tadf_molecules import TADFMolecule
+
+
+class TADFMoleculesParser(MatchingParser):
+    def parse(
+        self,
+        mainfile: str,
+        archive: EntryArchive,
+        logger: BoundLogger,
+    ) -> None:
+        # Extract file contents
+        with open(mainfile) as file:
+            raw = json.load(file)
+
+        # Fill information about the chemical composition
+        schema_instance = TADFMolecule()
+        schema_instance.DOI_number = raw['doi']
+        schema_instance.name = raw['abbreviated_name']
+        schema_instance.iupac_name = raw['iupac_name']
+        schema_instance.smile = raw['smiles']
+
+        # Extract the four measured properties
+        for name in [
+            'photoluminescence_quantum_yield',
+            'peak_emission_wavelength',
+            'delayed_lifetime',
+            'singlet_triplet_energy_splitting',
+        ]:
+            value = raw.get(f'{name}_value')
+            if value is not None:
+                setattr(schema_instance, name, value * ureg(raw[f'{name}_unit']))
+
+        # Save schema instance into archive.data
+        archive.data = schema_instance

src/nomad_tadf_molecules/schema_packages/__init__.py

@@ -1,17 +1,14 @@
 from nomad.config.models.plugins import SchemaPackageEntryPoint
-from pydantic import Field
 
 
-class MySchemaPackageEntryPoint(SchemaPackageEntryPoint):
-    parameter: int = Field(0, description='Custom configuration parameter')
-
+class TADFMoleculesSchemaPackageEntryPoint(SchemaPackageEntryPoint):
     def load(self):
-        from nomad_tadf_molecules.schema_packages.mypackage import m_package
- 
+        from nomad_tadf_molecules.schema_packages.tadf_molecules import m_package
+
         return m_package
 
 
-mypackage = MySchemaPackageEntryPoint(
-    name='MyPackage',
-    description='Schema package defined using the new plugin mechanism.',
+tadf_molecules = TADFMoleculesSchemaPackageEntryPoint(
+    name='TADF molecules',
+    description='Schema package for thermally activated delayed fluorescent (TADF) molecules.',
 )