add data concept

icu_pipeline/concept/__init__.py

@@ -0,0 +1,39 @@
+from abc import ABC
+
+from icu_pipeline.mapper.source import AbstractSourceMapper, DataSource
+from icu_pipeline.mapper.schema.fhir import AbstractFHIRSinkSchema
+from icu_pipeline.mapper.schema.ohdsi import AbstractOHDSISinkSchema
+from icu_pipeline.mapper.sink import AbstractSinkMapper, MappingFormat
+from icu_pipeline.mapper.source import SourceMapperConfiguration, DataSource
+
+
+class AbstractSnomedConcept(ABC):
+    SNOMED_ID: str
+    FHIR_SCHEMA: AbstractFHIRSinkSchema
+    OHDSI_SCHEMA: AbstractOHDSISinkSchema
+    MAPPER: dict[DataSource, AbstractSourceMapper]
+
+    def __init__(
+        self,
+        sink_mapper: AbstractSinkMapper,
+        mapping_format: MappingFormat,
+        source_mapper_configs: dict[DataSource, SourceMapperConfiguration],
+    ) -> None:
+        super().__init__()
+
+        self._sink_mapper = sink_mapper
+        self._mapping_format = mapping_format
+        self._source_mapper_configs = source_mapper_configs
+
+    def map(self):
+        for source, source_mapper in self.MAPPER.items():
+            mapper = source_mapper(
+                self.SNOMED_ID,
+                self.FHIR_SCHEMA,
+                self.OHDSI_SCHEMA,
+                self._source_mapper_configs[source],
+                self._sink_mapper,
+                self._mapping_format,
+            )
+
+            mapper.map()

icu_pipeline/concept/snomed.py

@@ -0,0 +1,12 @@
+from icu_pipeline.concept import AbstractSnomedConcept
+from icu_pipeline.mapper.schema.fhir import FHIRObservation
+from icu_pipeline.mapper.schema.ohdsi import AbstractOHDSISinkSchema
+from icu_pipeline.mapper.source import DataSource
+from icu_pipeline.mapper.source.mimic.labevents import MimicSerumCreatinineMapper
+
+
+class SerumCreatinine(AbstractSnomedConcept):
+    SNOMED_ID = "113075003"
+    FHIR_SCHEMA = FHIRObservation
+    OHDSI_SCHEMA = AbstractOHDSISinkSchema
+    MAPPER = {DataSource.MIMIC: MimicSerumCreatinineMapper}