Add sputterparser and process base section to schema

pyproject.toml

@@ -113,8 +113,10 @@ where = ["src"]
 
 [project.entry-points.'nomad.plugin']
 # schema
-xrfschema = "nomad_uibk_plugin.schema_packages:xrfschema"
-sputtering = "nomad_uibk_plugin.schema_packages:sputtering"
+basesections = "nomad_uibk_plugin.schema_packages:basesections"
 sample = "nomad_uibk_plugin.schema_packages:sample"
+sputtering = "nomad_uibk_plugin.schema_packages:sputtering"
+xrfschema = "nomad_uibk_plugin.schema_packages:xrfschema"
 # parser
+sputterparser = "nomad_uibk_plugin.parsers:sputterparser"
 xrfparser = "nomad_uibk_plugin.parsers:xrfparser"

src/nomad_uibk_plugin/parsers/__init__.py

@@ -19,3 +19,23 @@ def load(self):
     mainfile_name_re=r'.*\.txt',
     mainfile_content_re=r'PositionType\s+Application\s+Sample\s+name\s+Date\s+\n[A-Z0-9-]+\s+Quant\s+analysis',
 )
+
+
+class SputterParserEntryPoint(ParserEntryPoint):
+    """
+    Sputter Parser plugin entry point.
+    """
+
+    def load(self):
+        # lazy import to avoid circular dependencies
+        from nomad_uibk_plugin.parsers.sputterparser import SputterParser
+
+        return SputterParser(**self.dict())
+
+
+sputterparser = SputterParserEntryPoint(
+    name='SputterParser',
+    description='Parser for UIBK Sputterdeposition .csv log files.',
+    mainfile_name_re=r'.*\.csv',
+    # mainfile_content_re=r'',
+)

src/nomad_uibk_plugin/parsers/sputterparser.py

@@ -0,0 +1,59 @@
+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.parser import MatchingParser
+from nomad_measurements.utils import (
+    create_archive,
+    get_entry_id_from_file_name,
+    get_reference,
+)
+
+from nomad_uibk_plugin.schema_packages.sputtering import UIBKSputterDeposition
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import EntryArchive
+    from structlog.stdlib import BoundLogger
+
+
+class RawFileSputterData(EntryData):
+    """
+    Section for a sputter deposition data file.
+    """
+
+    measurement = Quantity(
+        type=UIBKSputterDeposition,
+        a_eln=ELNAnnotation(
+            component='ReferenceEditQuantity',
+        ),
+    )
+
+
+class SputterParser(MatchingParser):
+    """
+    Parser for matching sputter deposition files and creating instances of
+    SputterDeposition.
+    """
+
+    def parse(
+        self,
+        mainfile: str,
+        archive: 'EntryArchive',
+        logger: 'BoundLogger',
+        child_archives: dict[str, 'EntryArchive'] = None,
+    ) -> None:
+        logger.info('SputterParser.parse')
+        data_file = mainfile.split('/')[-1]
+        entry = UIBKSputterDeposition.m_from_dict(
+            UIBKSputterDeposition.m_def.a_template
+        )
+        entry.data_file = data_file
+        file_name = f'{"".join(data_file.split(".")[:-1])}.archive.json'
+        archive.data = RawFileSputterData(
+            measurement=get_reference(
+                archive.metadata.upload_id,
+                get_entry_id_from_file_name(file_name, archive),
+            )
+        )
+        create_archive(entry, archive, file_name)

src/nomad_uibk_plugin/schema_packages/XRFschema.py

@@ -68,7 +68,7 @@
     'nomad_uibk_plugin.schema_packages:xrfschema'
 )
 
-m_package = SchemaPackage(name='nomad_xrf')
+m_package = SchemaPackage()
 
 
 class XRFElementalComposition(ElementalComposition):

src/nomad_uibk_plugin/schema_packages/__init__.py

@@ -12,6 +12,19 @@ class UIBKCategory(EntryDataCategory):
     m_def = Category(label='UIBK', categories=[EntryDataCategory])
 
 
+class BaseSectionEntryPoint(SchemaPackageEntryPoint):
+    def load(self):
+        from nomad_uibk_plugin.schema_packages.basesections import m_package
+
+        return m_package
+
+
+basesections = BaseSectionEntryPoint(
+    name='Basesections',
+    description='Base sections for the UIBK plugin.',
+)
+
+
 class XRFSchemaPackageEntryPoint(SchemaPackageEntryPoint):
     parameter: int = Field(0, description='Custom configuration parameter')
 

src/nomad_uibk_plugin/schema_packages/basesections.py

@@ -0,0 +1,85 @@
+#
+# 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.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
+from nomad.datamodel.metainfo.basesections import (
+    Process,
+)
+from nomad.metainfo import Quantity, SchemaPackage, SubSection
+
+from nomad_uibk_plugin.schema_packages.sample import UIBKSampleReference
+
+# if TYPE_CHECKING:
+#     from nomad.datamodel.datamodel import EntryArchive
+#     from structlog.stdlib import BoundLogger
+
+m_package = SchemaPackage()
+
+
+class UIBKProcess(Process):
+    """Base class for UIBK processes which adds sample linking."""
+
+    samples = SubSection(
+        section_def=UIBKSampleReference,
+        description='Reference to the sample.',
+        repeats=True,
+    )
+
+    lab_id = Quantity(
+        type=str,
+        description='The lab ID of the process.',
+        a_eln=ELNAnnotation(component=ELNComponentEnum.StringEditQuantity),
+    )
+
+    # def normalize(self, archive: EntryArchive, logger: BoundLogger) -> None:
+
+    #     from nomad.datamodel.context import ServerContext
+
+    #     # TODO: check if statement
+    #     if self.samples is None or self.samples == []:
+
+    #         from nomad.search import MetadataPagination, search
+
+    #         query = {'results.eln.lab_ids': self.lab_id}
+    #         search_result = search(
+    #             owner='all',
+    #             query=query,
+    #             pagination=MetadataPagination(page_size=1),
+    #             user_id=archive.metadata.user_id, # TODO: check if this is correct
+    #         )
+
+    #         if search_result.pagination.total > 0:
+    #             entry_id = search_result.data[0]['entry_id']
+    #             upload_id = search_result.data[0]['upload_id']
+    #             self.system = f'../uploads/{upload_id}/archive/{entry_id}#data'
+    #             if search_result.pagination.total > 1:
+    #                 logger.warn(
+    #                     f'Found {search_result.pagination.total} entries with lab_id: '  # noqa: E501
+    #                     f'"{self.lab_id}". Will use the first one found.'
+    #                 )
+    #         else:
+    #             logger.warn(f'Found no entries with lab_id: "{self.lab_id}".')
+    #     elif self.lab_id is None and len(self.samples) > 0:
+    #         self.lab_id = self.samples[0].lab_id
+    #     if self.name is None:
+    #         self.name = self.lab_id
+
+
+m_package.__init_metainfo__()

src/nomad_uibk_plugin/schema_packages/sample.py

@@ -6,7 +6,8 @@
 )
 from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
 from nomad.datamodel.metainfo.basesections import (
-    CompositeSystem,  # CompositeSystemReference
+    CompositeSystem,
+    CompositeSystemReference,
 )
 from nomad.datamodel.metainfo.plot import PlotlyFigure, PlotSection
 from nomad.metainfo import Quantity, SchemaPackage, Section, SubSection
@@ -16,7 +17,7 @@
     from structlog.stdlib import BoundLogger
 
 
-m_package = SchemaPackage(name='nomad_uibk_sample')
+m_package = SchemaPackage()
 
 
 class MicroCell(CompositeSystem):
@@ -133,4 +134,19 @@ def normalize(self, archive, logger):
         self.plot(archive, logger)
 
 
+class UIBKSampleReference(CompositeSystemReference):
+    """
+    Reference section to an UIBK sample.
+    """
+
+    reference = Quantity(
+        type=UIBKSample,
+        description='Reference to an UIBK sample',
+        a_eln=ELNAnnotation(
+            component='ReferenceEditQuantity',
+            label='Link to Sample',
+        ),
+    )
+
+
 m_package.__init_metainfo__()

src/nomad_uibk_plugin/schema_packages/sputtering.py

@@ -27,7 +27,7 @@
 from nomad_uibk_plugin.schema_packages import UIBKCategory
 from nomad_uibk_plugin.schema_packages.sample import UIBKSample
 
-m_package = SchemaPackage(name='nomad_uibk_sputtering')
+m_package = SchemaPackage()
 
 
 class Target(PVDSource, EntryData):