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added app and ruff
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@aalbino2
aalbino2 committed Sep 30, 2024
1 parent 238d8d3 commit 6714f66
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Showing 7 changed files with 185 additions and 227 deletions.
2 changes: 1 addition & 1 deletion src/pdi_nomad_plugin/characterization/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@
MeasurementResult,
)
from nomad.metainfo import Datetime, Quantity, SchemaPackage, Section, SubSection

from nomad_material_processing.general import (
TimeSeries,
)

from pdi_nomad_plugin.general.schema import (
PDICategory,
)
Expand Down
140 changes: 75 additions & 65 deletions src/pdi_nomad_plugin/general/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,14 @@
BoundLogger,
)

import yaml
import json
import numpy as np
from nomad.config import config
from nomad.datamodel.data import EntryData, EntryDataCategory, ArchiveSection
from nomad.datamodel.data import ArchiveSection, EntryData, EntryDataCategory
from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
from nomad.datamodel.metainfo.basesections import (
EntityReference,
CompositeSystem,
CompositeSystemReference,
EntityReference,
Process,
)
from nomad.metainfo import (
Expand All @@ -40,17 +38,17 @@

from pdi_nomad_plugin.utils import create_archive, set_sample_status

configuration = config.get_plugin_entry_point("pdi_nomad_plugin.general:schema")
configuration = config.get_plugin_entry_point('pdi_nomad_plugin.general:schema')

m_package = SchemaPackage()


class PDICategory(EntryDataCategory):
m_def = Category(label="PDI", categories=[EntryDataCategory])
m_def = Category(label='PDI', categories=[EntryDataCategory])


class PDIMBECategory(EntryDataCategory):
m_def = Category(label="PDI MBE", categories=[EntryDataCategory, PDICategory])
m_def = Category(label='PDI MBE', categories=[EntryDataCategory, PDICategory])


class SystemPDI(CompositeSystem):
Expand All @@ -61,30 +59,30 @@ class SystemPDI(CompositeSystem):

as_delivered = Quantity(
type=bool,
description="Sample is in the same condition as it was delivered",
description='Sample is in the same condition as it was delivered',
a_eln=ELNAnnotation(
component="BoolEditQuantity",
component='BoolEditQuantity',
),
)
fresh = Quantity(
type=bool,
description="Sample is fresh and has not been used",
description='Sample is fresh and has not been used',
a_eln=ELNAnnotation(
component="BoolEditQuantity",
component='BoolEditQuantity',
),
)
processed = Quantity(
type=bool,
description="Sample underwent some processing such as etching, annealing, etc.",
description='Sample underwent some processing such as etching, annealing, etc.',
a_eln=ELNAnnotation(
component="BoolEditQuantity",
component='BoolEditQuantity',
),
)
grown = Quantity(
type=bool,
description="Sample underwent vapor deposition",
description='Sample underwent vapor deposition',
a_eln=ELNAnnotation(
component="BoolEditQuantity",
component='BoolEditQuantity',
),
)

Expand All @@ -96,10 +94,10 @@ class SystemPDIReference(EntityReference):

reference = Quantity(
type=SystemPDI,
description="A reference to a NOMAD `SystemPDI` entry.",
description='A reference to a NOMAD `SystemPDI` entry.',
a_eln=ELNAnnotation(
component="ReferenceEditQuantity",
label="SystemPDI reference",
component='ReferenceEditQuantity',
label='SystemPDI reference',
),
)

Expand Down Expand Up @@ -139,12 +137,12 @@ class EtchingPDI(ProcessPDI, Etching):
"""

m_def = Section(
label="Etching",
links=["http://purl.obolibrary.org/obo/CHMO_0001558"],
label='Etching',
links=['http://purl.obolibrary.org/obo/CHMO_0001558'],
categories=[PDICategory],
)

def normalize(self, archive, logger: "BoundLogger") -> None:
def normalize(self, archive, logger: 'BoundLogger') -> None:
"""
The normalizer sets the sample status if a reference to a sample is given.
"""
Expand All @@ -170,8 +168,8 @@ class EtchingRecipePDI(EtchingRecipe):
"""

m_def = Section(
label="EtchingRecipe",
links=["http://purl.obolibrary.org/obo/CHMO_0001558"],
label='EtchingRecipe',
links=['http://purl.obolibrary.org/obo/CHMO_0001558'],
categories=[PDICategory],
)

Expand All @@ -182,8 +180,8 @@ class AnnealingRecipePDI(AnnealingRecipe):
"""

m_def = Section(
label="AnnealingRecipe",
links=["http://purl.obolibrary.org/obo/CHMO_0001465"],
label='AnnealingRecipe',
links=['http://purl.obolibrary.org/obo/CHMO_0001465'],
categories=[PDICategory],
)

Expand All @@ -194,7 +192,7 @@ class CleaningRecipePDI(CleaningRecipe):
"""

m_def = Section(
label="CleaningRecipe",
label='CleaningRecipe',
categories=[PDICategory],
)

Expand All @@ -205,12 +203,12 @@ class AnnealingPDI(ProcessPDI, Annealing):
"""

m_def = Section(
label="Annealing",
links=["http://purl.obolibrary.org/obo/CHMO_0001465"],
label='Annealing',
links=['http://purl.obolibrary.org/obo/CHMO_0001465'],
categories=[PDICategory],
)

def normalize(self, archive, logger: "BoundLogger") -> None:
def normalize(self, archive, logger: 'BoundLogger') -> None:
"""
The normalizer sets the sample status if a reference to a sample is given.
"""
Expand All @@ -235,11 +233,11 @@ class CleaningPDI(ProcessPDI, Cleaning):
"""

m_def = Section(
label="Cleaning",
label='Cleaning',
categories=[PDICategory],
)

def normalize(self, archive, logger: "BoundLogger") -> None:
def normalize(self, archive, logger: 'BoundLogger') -> None:
"""
The normalizer sets the sample status if a reference to a sample is given.
"""
Expand All @@ -264,12 +262,12 @@ class BackSideCoatingPDI(ProcessPDI, Process, EntryData):
"""

m_def = Section(
label="BackSideCoating",
a_eln={"hide": ["steps"]},
label='BackSideCoating',
a_eln={'hide': ['steps']},
categories=[PDICategory],
)
recipe = Quantity(
type=Reference(SectionProxy("BackSideCoatingRecipePDI")),
type=Reference(SectionProxy('BackSideCoatingRecipePDI')),
description=""" The recipe used for the process. If a recipe is found,
all the data is copied from the Recipe within the Process.
""",
Expand All @@ -279,23 +277,23 @@ class BackSideCoatingPDI(ProcessPDI, Process, EntryData):
)
temperature = Quantity(
type=np.float64,
description="The temperature of the annealing process.",
a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "celsius"},
unit="celsius",
description='The temperature of the annealing process.',
a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'celsius'},
unit='celsius',
)
duration = Quantity(
type=np.float64,
description="The elapsed time since the annealing process started.",
description='The elapsed time since the annealing process started.',
a_eln=ELNAnnotation(
component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit="minute"
component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
),
unit="second",
unit='second',
)
coating_reagents = SubSection(
section_def=CompositeSystemReference,
)

def normalize(self, archive, logger: "BoundLogger") -> None:
def normalize(self, archive, logger: 'BoundLogger') -> None:
"""
The normalizer sets the sample status if a reference to a sample is given.
"""
Expand All @@ -321,13 +319,13 @@ class BackSideCoatingRecipePDI(BackSideCoatingPDI, Recipe, EntryData):

m_def = Section(
a_eln={
"hide": [
"datetime",
"samples",
"starting_time",
"ending_time",
"location",
"recipe",
'hide': [
'datetime',
'samples',
'starting_time',
'ending_time',
'location',
'recipe',
]
},
)
Expand All @@ -338,7 +336,7 @@ class BackSideCoatingRecipePDI(BackSideCoatingPDI, Recipe, EntryData):
""",
a_eln=ELNAnnotation(
component=ELNComponentEnum.StringEditQuantity,
label="Recipe ID",
label='Recipe ID',
),
)

Expand All @@ -349,26 +347,26 @@ class SampleCutPDI(ProcessPDI, Process, EntryData):
"""

m_def = Section(
a_eln={"hide": ["steps", "samples", "instruments"]},
label="Sample Cut",
a_eln={'hide': ['steps', 'samples', 'instruments']},
label='Sample Cut',
categories=[PDICategory],
)
number_of_samples = Quantity(
type=int,
description='The number of samples generated from this "Sample Cut" Task.',
a_eln=dict(component="NumberEditQuantity"),
a_eln=dict(component='NumberEditQuantity'),
)
image = Quantity(
type=str,
description="A photograph or image of the substrate.",
a_browser={"adaptor": "RawFileAdaptor"},
description='A photograph or image of the substrate.',
a_browser={'adaptor': 'RawFileAdaptor'},
a_eln=ELNAnnotation(
component=ELNComponentEnum.FileEditQuantity,
),
)
children_geometry = SubSection(
section_def=Geometry,
description="Section containing the geometry of the substrate.",
description='Section containing the geometry of the substrate.',
)
parent_sample = SubSection(
description="""
Expand All @@ -384,15 +382,15 @@ class SampleCutPDI(ProcessPDI, Process, EntryData):
repeats=True,
)

def normalize(self, archive, logger: "BoundLogger") -> None:
def normalize(self, archive, logger: 'BoundLogger') -> None:
"""
The normalizer sets the sample status if a reference to a sample is given.
"""
from nomad.datamodel import EntryArchive, EntryMetadata

super().normalize(archive, logger)

filetype = "yaml"
filetype = 'yaml'
if not self.number_of_samples:
logger.error(
"Error in SampleCut: 'number_of_samples' expected, but None found."
Expand All @@ -403,9 +401,9 @@ def normalize(self, archive, logger: "BoundLogger") -> None:
)
if self.children_samples:
logger.error(
f"Error in SampleCut: No children samples expected,"
f" but {len(self.children_samples)} children samples given."
f" Remove the children samples and save again to generate children."
f'Error in SampleCut: No children samples expected,'
f' but {len(self.children_samples)} children samples given.'
f' Remove the children samples and save again to generate children.'
)
generated_samples = []
if self.parent_sample and self.number_of_samples:
Expand All @@ -416,7 +414,7 @@ def normalize(self, archive, logger: "BoundLogger") -> None:
self.parent_sample.reference.geometry.height
)
else:
logger.warning("No children geometry found. Using parent geometry.")
logger.warning('No children geometry found. Using parent geometry.')

for sample_index in range(1, self.number_of_samples + 1):
child_name = (
Expand All @@ -425,10 +423,10 @@ def normalize(self, archive, logger: "BoundLogger") -> None:
else self.parent_sample.reference.name
)
children_filename = (
f"{child_name}_{sample_index}.CompositeSystem.archive.{filetype}"
f'{child_name}_{sample_index}.CompositeSystem.archive.{filetype}'
)
children_object.name = f"{child_name}_{sample_index}"
children_object.lab_id = f"{child_name}_{sample_index}"
children_object.name = f'{child_name}_{sample_index}'
children_object.lab_id = f'{child_name}_{sample_index}'
children_archive = EntryArchive(
data=children_object,
m_context=archive.m_context,
Expand All @@ -444,7 +442,7 @@ def normalize(self, archive, logger: "BoundLogger") -> None:
generated_samples.append(
CompositeSystemReference(
name=children_object.name,
reference=f"../uploads/{archive.m_context.upload_id}/archive/{hash(archive.m_context.upload_id, children_filename)}#data",
reference=f'../uploads/{archive.m_context.upload_id}/archive/{hash(archive.m_context.upload_id, children_filename)}#data',
),
)
self.children_samples = generated_samples
Expand All @@ -459,5 +457,17 @@ def normalize(self, archive, logger: "BoundLogger") -> None:
grown=sample.reference.grown if sample.reference.grown else False,
)

set_sample_status(
self.parent_sample.reference,
archive.m_context,
logger,
as_delivered=False,
fresh=False,
processed=True,
grown=self.parent_sample.reference.grown
if self.parent_sample.reference.grown
else False,
)


m_package.__init_metainfo__()
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