Transmission modify sample (#167)

* Order quantities; revert modification of basesection quantities

* Modify description of quantities

* Populate elements and components based on chemical_composition

* Add overwrite_quantity in merge_sections

* Include merge section capability to allow GUI interaction in `components`

* Restrict component class to `PureSubstanceComponent`

* Move material system as sub-section in TransmissionSample

* Add module for material_system and classes for Solid Solution

* Create TransmissionSampleReference class and use it in samples subsection

* Make SolidSolution as an entry class; reference it in TransmissionSample

* Bugfix: logic of adjusting composition

* Rearrange imports

* Add physical properties classes

* Refactor Transmission sample to be a section containing reference and physical props; refactor normalize

* Fixing rebase

* Changing warn to warning

* Move Physical properties to schema

* Rename section names; add docstring for naming convention

* Add crystal, polycrystal, mixed crystal, mixed polycrystal sections

* Ruff

* Add material system entry point; rename dopant as impurity

* Refine the ELN properties of sample related schemas

* Refine ELN properties for material system; make atomic percentage in to atomic fraction

* Remove materials_system: they will be moved to nomad-material-processing

* Align TransmissionSampleReference with CompositeSystemReference

* Compose a Sample class based on composite system

* Refactor extinction coefficient calc and plot

* Temporary bugfix for extinction coeff calc; minor changes in schema

* Update nomad

* Bugfix schema import; ignore search when in client context

* Add caplog conftest

* Bugfix: updating schema in search_quantities

* Add aliases

* Add previous archives to test for backward compatibility

* Add test for backward compatibility

* Add fixes for backward compatibility

* Move RawFileTransmissionData to schema

Author: ka-sarthak

transmission/transmission_plugin/uv_vis_nir_transmission_plugin/pyproject.toml

@@ -19,13 +19,15 @@ classifiers = [
     "License :: OSI Approved :: Apache Software License",
 ]
 dependencies = [
-    "nomad-lab>=1.2.2dev578",
+    "nomad-lab>=1.3.4dev",
+    "nomad-material-processing"
 ]
 [project.optional-dependencies]
 dev = [
     "ruff",
     "pytest",
     "structlog",
+    "nomad-lab[infrastructure]>=1.3.4dev",
 ]
 
 [project.license]

transmission/transmission_plugin/uv_vis_nir_transmission_plugin/src/transmission/__init__.py

@@ -46,6 +46,7 @@ def load(self):
     description='Schema for data from Transmission Spectrophotometry.',
 )
 
+
 parser = TransmissionParserEntryPoint(
     name='Transmission Parser',
     description='Parser for data from Transmission Spectrophotometry.',

transmission/transmission_plugin/uv_vis_nir_transmission_plugin/src/transmission/parser.py

@@ -17,18 +17,9 @@
 #
 from typing import TYPE_CHECKING
 
-from nomad.datamodel.data import (
-    EntryData,
-)
-from nomad.datamodel.metainfo.annotations import (
-    ELNAnnotation,
-)
-from nomad.metainfo import (
-    Quantity,
-)
 from nomad.parsing import MatchingParser
 
-from transmission.schema import ELNUVVisTransmission
+from transmission.schema import ELNUVVisNirTransmission, RawFileTransmissionData
 from transmission.utils import create_archive
 
 if TYPE_CHECKING:
@@ -37,19 +28,6 @@
     )
 
 
-class RawFileTransmissionData(EntryData):
-    """
-    Section for a Transmission Spectrophotometry data file.
-    """
-
-    measurement = Quantity(
-        type=ELNUVVisTransmission,
-        a_eln=ELNAnnotation(
-            component='ReferenceEditQuantity',
-        ),
-    )
-
-
 class TransmissionParser(MatchingParser):
     """
     Parser for matching files from Transmission Spectrophotometry and
@@ -60,7 +38,9 @@ def parse(
         self, mainfile: str, archive: 'EntryArchive', logger=None, child_archives=None
     ) -> None:
         data_file = mainfile.split('/')[-1]
-        entry = ELNUVVisTransmission.m_from_dict(ELNUVVisTransmission.m_def.a_template)
+        entry = ELNUVVisNirTransmission.m_from_dict(
+            ELNUVVisNirTransmission.m_def.a_template
+        )
         entry.data_file = data_file
         file_name = f'{".".join(data_file.split(".")[:-1])}.archive.json'
         archive.data = RawFileTransmissionData(