122 move the transmission code from areaa repo (#123)

* Add parser and schema

* Add init file containing transmission entry points

* Add deps and entry points to pyproject

* Bugfix: name of the file reader

* Add transmission raw files

* Add parser test

* Reference any composite system in the sample reference

* Rename to path_length

* Copy latest changes from AreaA repo

* Integrate suggestions from AreaA TF: sample path lenght and orientation

* Rename to detector_gain, detector_integration_time

* Reordering settings sections

* Fix

* Rename attenuator settings class

* Plural names

* Use common utils

* Use composite system for sample reference

* Move transmission test file

* Refactor test file

* Add schema config

* Test normalized data for one file

* Regex for matching raw file content

* Review: from sourcery

* Review: from Hampus

pyproject.toml

@@ -38,6 +38,8 @@ dependencies = [
     "nomad-lab>=1.3.6", 
     "xmltodict==0.13.0",
     "fairmat-readers-xrd>=0.0.3",
+    "nomad-material-processing",
+    "fairmat-readers-transmission",
 ]
 [project.urls]
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-measurements"
@@ -137,5 +139,7 @@ xrd_parser = "nomad_measurements.xrd:parser"
 ppms_schema = "nomad_measurements.ppms:ppms_schema"
 ppms_data_parser = "nomad_measurements.ppms:ppms_data_parser"
 ppms_sequence_parser = "nomad_measurements.ppms:ppms_sequence_parser"
+transmission_schema = "nomad_measurements.transmission:schema"
+transmission_parser = "nomad_measurements.transmission:parser"
 
 [tool.setuptools_scm]

src/nomad_measurements/transmission/__init__.py

@@ -0,0 +1,59 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from nomad.config.models.plugins import ParserEntryPoint, SchemaPackageEntryPoint
+
+
+class TransmissionSchemaEntryPoint(SchemaPackageEntryPoint):
+    """
+    Entry point for lazy loading of the Transmission schemas.
+    """
+
+    def load(self):
+        from nomad_measurements.transmission.schema import m_package
+
+        return m_package
+
+
+class TransmissionParserEntryPoint(ParserEntryPoint):
+    """
+    Entry point for lazy loading of the TransmissionParser.
+    """
+
+    def load(self):
+        from nomad_measurements.transmission.parser import TransmissionParser
+
+        return TransmissionParser(**self.dict())
+
+
+schema = TransmissionSchemaEntryPoint(
+    name='Transmission Schema',
+    description='Schema for data from Transmission Spectrophotometry.',
+)
+
+
+parser = TransmissionParserEntryPoint(
+    name='Transmission Parser',
+    description="""
+    Parser for data from Transmission Spectrophotometry measurements. Currently 
+    supports `.asc` files generated by Perkin Elmer UV WinLab software.
+    """,
+    mainfile_mime_re=r'text/.*|application/zip',
+    mainfile_name_re=r'^.*\.asc$',
+    mainfile_contents_re=r'^PE UV',
+)

src/nomad_measurements/transmission/parser.py

@@ -0,0 +1,52 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+from typing import TYPE_CHECKING
+
+from nomad.parsing import MatchingParser
+
+from nomad_measurements.transmission.schema import (
+    ELNUVVisNirTransmission,
+    RawFileTransmissionData,
+)
+from nomad_measurements.utils import create_archive
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import (
+        EntryArchive,
+    )
+
+
+class TransmissionParser(MatchingParser):
+    """
+    Parser for matching files from Transmission Spectrophotometry and
+    creating instances of ELN.
+    """
+
+    def parse(
+        self, mainfile: str, archive: 'EntryArchive', logger=None, child_archives=None
+    ) -> None:
+        data_file = mainfile.split('/')[-1]
+        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(
+            measurement=create_archive(entry, archive, file_name)
+        )
+        archive.metadata.entry_name = f'{data_file} data file'