Merge pull request #18 from IKZ-Berlin/fixes-for-transmission

Fixes for transmission

pyproject.toml

@@ -35,11 +35,16 @@ dependencies = [
     'nomad-analysis', # develop branch
     'lakeshore-nomad-plugin @ git+https://github.com/IKZ-Berlin/lakeshore-nomad-plugin.git@69a6deb3f0e99d7b0dc66714105dd62a56f157e9',
     'laytec_epitt_plugin @ git+https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin.git@f4953ac4ecb55b7003dee323d7d7f473e49ab4e3',
-    # 'transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@de012ac8820dbb514f5dd73aafdf46bf2a879481#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin',
+    'transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@3b05b9e0f8fa842e928768506ed4ba64aab83a46#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin',
 ]
 
 [project.optional-dependencies]
-dev = ["ruff", "pytest", "structlog"]
+dev = [
+    "ruff",
+    "pytest",
+    "structlog",
+    "python-logstash>=0.4.6",
+]
 
 [project.urls]
 "Homepage" = "https://github.com/IKZ-Berlin/nomad-ikz-plugin"
@@ -139,6 +144,7 @@ where = ["src"]
 [project.entry-points.'nomad.plugin']
 general_schema = "nomad_ikz_plugin.general:schema"
 characterization_schema = "nomad_ikz_plugin.characterization:schema"
+characterization_transmission_parser = "nomad_ikz_plugin.characterization:transmission_parser"
 pld_schema = "nomad_ikz_plugin.pld:schema"
 movpe_schema = "nomad_ikz_plugin.movpe:schema"
 movpe2_growth_excel_parser = "nomad_ikz_plugin.movpe.movpe2.growth_excel:parser"

src/nomad_ikz_plugin/characterization/__init__.py

@@ -15,8 +15,7 @@
 # limitations under the License.
 #
 
-from nomad.config.models.plugins import SchemaPackageEntryPoint
-from pydantic import Field
+from nomad.config.models.plugins import ParserEntryPoint, SchemaPackageEntryPoint
 
 
 class CharacterizationEntryPoint(SchemaPackageEntryPoint):
@@ -26,7 +25,25 @@ def load(self):
         return m_package
 
 
+class TransmissionParserEntryPoint(ParserEntryPoint):
+    """
+    Entry point for lazy loading of the TransmissionParser.
+    """
+
+    def load(self):
+        from nomad_ikz_plugin.characterization.parser import TransmissionParser
+
+        return TransmissionParser(**self.dict())
+
+
 schema = CharacterizationEntryPoint(
     name='CharacterizationSchema',
     description='Schema package for general characterization methods used at IKZ.',
 )
+
+transmission_parser = TransmissionParserEntryPoint(
+    name='Transmission Parser',
+    description='Parser for data from Transmission Spectrophotometry.',
+    mainfile_mime_re='text/.*|application/zip',
+    mainfile_name_re='^.*\.asc$',
+)

src/nomad_ikz_plugin/characterization/parser.py

@@ -0,0 +1,50 @@
+#
+# 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 transmission.schema import RawFileTransmissionData
+from transmission.utils import create_archive
+
+from nomad_ikz_plugin.characterization.schema import IKZELNUVVisNirTransmission
+
+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 = IKZELNUVVisNirTransmission.m_from_dict(
+            IKZELNUVVisNirTransmission.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'