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Merged
turbomam merged 2 commits into from
Apr 21, 2025
Merged

sample_annotator/sample_annotator.py with default factories #153

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sample_annotator/sample_annotator.py with default factories
turbomam Apr 21, 2025
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import optimizastion
turbomam Apr 21, 2025
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13 changes: 7 additions & 6 deletions sample_annotator/sample_annotator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,18 @@
import logging
import re
import sys
from dataclasses import dataclass
from dataclasses import dataclass, field
from typing import List

import bioregistry
import click
from linkml_runtime.linkml_model.meta import ClassDefinition
from nmdc_schema.nmdc import slots as nmdc_slots

from .geolocation.geotools import GeoEngine
from sample_annotator.geolocation.geotools import GeoEngine
from sample_annotator.metadata.sample_schema import SampleSchema
from .measurements.measurements import MeasurementEngine
from .metadata.sample_schema import SampleSchema, underscore
from .metadata.sample_schema import underscore
from .report_model import AnnotationReport, PackageCombo, AnnotationMultiSampleReport, Category, SAMPLE, STUDY

KEY_ENV_PACKAGE = nmdc_slots.env_package.name
Expand All @@ -28,10 +29,10 @@ class SampleAnnotator():
"""

target_class: ClassDefinition = None
geoengine: GeoEngine = GeoEngine()
measurement_engine: MeasurementEngine = MeasurementEngine()
geoengine: GeoEngine = field(default_factory=GeoEngine)
measurement_engine: MeasurementEngine = field(default_factory=MeasurementEngine)

schema: SampleSchema = SampleSchema()
schema: SampleSchema = field(default_factory=SampleSchema)

def annotate_all(self, samples: List[SAMPLE], study: STUDY = None) -> AnnotationMultiSampleReport:
"""
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