First working parsing from log file

- minor bugfixes
- sorted reader in /filereader/
- improved labelling in parser

src/nomad_uibk_plugin/filereader/sputterreader.py

@@ -0,0 +1,83 @@
+#
+# 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
+
+# import numpy as np
+from nomad_uibk_plugin.schema_packages.sputtering import (
+    SputterParameters,
+    UIBKSputterDeposition,
+)
+
+if TYPE_CHECKING:
+    from structlog.stdlib import (
+        BoundLogger,
+    )
+
+
+def read_sputter_csv(
+    file_path: str, logger: 'BoundLogger' = None
+) -> UIBKSputterDeposition:
+    """
+    Read the sputter deposition data from a .csv file and return an instance of
+    UIBKSputterDeposition.
+    """
+
+    # with open(file_path, 'r') as file:
+    #     lines = file.readlines()
+
+    # # Split sections
+    # in_metadata = True
+    # metadata = {}
+    # time_series_lines = []
+    # for line in lines:
+    #     # skip commented lines
+    #     if line.startswith("%") or line.startswith("#"):
+    #         continue
+
+    #     line = line.strip()
+    #     # skip empty lines
+    #     if not line:
+    #         continue
+    #     if line == "END_OF_PARAMETERS":
+    #         in_metadata = False
+    #         continue
+
+    #     # Split metadata and time series
+    #     if in_metadata:
+    #         key, *values = line.split(';')
+    #         key = key.strip()
+    #         values = [v.strip() for v in values if v.strip()]
+    #         metadata[key] = values
+    #     else:
+    #         time_series_lines.append(line)
+
+    deposition = UIBKSputterDeposition(
+        name='TESTTESTTEST',
+    )
+
+    # Parse metadata
+    # TODO: Implement metadata parsing
+
+    # Parse time series
+    # TODO: Implement time series parsing
+
+    deposition.parameters = SputterParameters(test='HUHU!')
+    deposition.samples = []
+
+    return deposition

src/nomad_uibk_plugin/parsers/sputterparser.py

@@ -44,16 +44,17 @@ def parse(
         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'
+        filename = mainfile.split('/')[-1]
+        # entry = UIBKSputterDeposition.m_from_dict(
+        #     UIBKSputterDeposition.m_def.a_template
+        # )
+        entry = UIBKSputterDeposition()
+        entry.data_file = filename
+        archive_name = f'{"".join(filename.split(".")[:-1])}.archive.json'
         archive.data = RawFileSputterData(
             measurement=get_reference(
                 archive.metadata.upload_id,
-                get_entry_id_from_file_name(file_name, archive),
+                get_entry_id_from_file_name(archive_name, archive),
             )
         )
-        create_archive(entry, archive, file_name)
+        create_archive(entry, archive, archive_name)

src/nomad_uibk_plugin/schema_packages/XRFschema.py

@@ -20,6 +20,8 @@
     TYPE_CHECKING,
 )
 
+from nomad_uibk_plugin.filereader import XRFreader
+
 if TYPE_CHECKING:
     from nomad.datamodel.datamodel import (
         EntryArchive,
@@ -59,7 +61,7 @@
 from nomad.metainfo import Datetime, Quantity, SchemaPackage, Section, SubSection
 from nomad_measurements.utils import merge_sections
 
-from nomad_uibk_plugin.schema_packages import UIBKCategory, XRFreader
+from nomad_uibk_plugin.schema_packages import UIBKCategory
 
 if TYPE_CHECKING:
     from structlog.stdlib import BoundLogger

src/nomad_uibk_plugin/schema_packages/sputtering.py

@@ -1,3 +1,5 @@
+from typing import TYPE_CHECKING
+
 from nomad.datamodel.data import ArchiveSection, EntryData
 from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
 from nomad.datamodel.metainfo.basesections import (
@@ -27,6 +29,12 @@
 from nomad_uibk_plugin.schema_packages import UIBKCategory
 from nomad_uibk_plugin.schema_packages.sample import UIBKSample
 
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import EntryArchive
+    from structlog.stdlib import BoundLogger
+
+from nomad_measurements.utils import merge_sections  # create_archive
+
 m_package = SchemaPackage()
 
 
@@ -68,6 +76,7 @@ class Target(PVDSource, EntryData):
     """
 
     m_def = Section()
+
     internal_id = Quantity(
         type=int,
         description='The lab ID of the target.',
@@ -225,11 +234,13 @@ class Substrate(EntryData):
     -
     """
 
+    m_def = Section()
+
     type = Quantity(
         type=MEnum(['c-Si die', 'glass', 'polyimide']),
         description='Type of substrate material',
         default='',
-        a_eln={'component': 'AutocompleteEditQuasntity'},
+        a_eln={'component': 'AutocompleteEditQuantity'},
     )
     subtype = Quantity(
         type=str,
@@ -251,25 +262,25 @@ class Substrate(EntryData):
         default='',
         a_eln={'component': 'RadioEnumEditQuantity'},
     )
-    m_def = Section()
+
     size_x = Quantity(
         type=float,
         description='Radius or x-dimension of the sample.',
         a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'mm'},
-        unit='mmm',
+        unit='meter',
     )
     size_y = Quantity(
         type=float,
         description='Y-dimension of the sample.',
         a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'mm'},
-        unit='mmm',
+        unit='meter',
     )
 
     size_z = Quantity(
         type=float,
         description='Height of the sample.',
         a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'mm'},
-        unit='mmm',
+        unit='meter',
     )
 
 
@@ -279,13 +290,12 @@ class SubstrateReference(SectionReference):
 
 class Operator(EntryData):
     author = Quantity(
-        # type = ?
+        type=str,  ## < ?
         description='Authors/Operators',
         a_eln=ELNAnnotation(
-            component=ELNComponentEnum.AuthorEditQuantity,
+            component=ELNComponentEnum.StringEditQuantity,  # AuthorEditQuantity?
         ),
     )
-    # or `UserEditQuantity`:?
 
 
 class OperatorReference(SectionReference):
@@ -316,6 +326,8 @@ class PSU(EntryData):
         - pulse reverse time
     """
 
+    m_def = Section()
+
     internal_id = Quantity(
         type=int,
         description='NOMAD ID of the PSU',
@@ -385,7 +397,7 @@ class PSU(EntryData):
             component=ELNComponentEnum.BoolEditQuantity,
         ),
     )
-    m_def = Section()
+
     operating_hours = Quantity(
         type=int,
         description='NOMAD ID of the PSU',
@@ -403,7 +415,7 @@ class PSU(EntryData):
         type=MEnum(['W', 'V', 'A']),
         description='',
         default='W',
-        a_eln={'component': 'RadioEnumEditQuantityty'},
+        a_eln={'component': 'RadioEnumEditQuantity'},
     )
     setpoint_value = Quantity(
         type=float,
@@ -551,7 +563,7 @@ class SputterParameters(ArchiveSection):
     - sample rotation speed
     """
 
-    pass
+    test = Quantity(type=str)
 
 
 class UIBKSputterDeposition(SputterDeposition, EntryData):
@@ -560,11 +572,32 @@ class UIBKSputterDeposition(SputterDeposition, EntryData):
         label='Sputter Deposition',
     )
 
+    data_file = Quantity(
+        type=str,
+        description='Path to the data file',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.FileEditQuantity,
+        ),
+    )
+
     samples = SubSection(section_def=UIBKSample, repeats=True)
 
     target = SubSection(section_def=TargetReference, repeats=True)
 
-    # parameter = SubSection()
+    parameters = SubSection(section_def=SputterParameters)
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        """Update the data from the data file if it is not already set"""
+
+        from nomad_uibk_plugin.filereader.sputterreader import read_sputter_csv
+
+        # if self.data is None and self.data_file is not None:
+        if self.data_file is not None:
+            with archive.m_context.raw_file(self.data_file) as file:
+                sputter_entry = read_sputter_csv(file, logger)
+                merge_sections(self, sputter_entry, logger)
+
+        super().normalize(archive, logger)
 
 
 m_package.__init_metainfo__()