add pipeline

icu_pipeline/pipeline.py

@@ -0,0 +1,27 @@
+from icu_pipeline.concept import AbstractSnomedConcept
+from icu_pipeline.mapper.sink import AbstractSinkMapper, MappingFormat
+from icu_pipeline.mapper.source import SourceMapperConfiguration, DataSource
+
+
+class Pipeline:
+    def __init__(
+        self,
+        concepts: list[AbstractSnomedConcept],
+        sink_mapper: AbstractSinkMapper,
+        mapping_format: MappingFormat,
+        source_mapper_configs: dict[DataSource, SourceMapperConfiguration],
+    ) -> None:
+        self._concepts = concepts
+        self._sink_mapper = sink_mapper
+        self._mapping_format = mapping_format
+        self._source_mapper_configs = source_mapper_configs
+
+    def transfrom(self):
+        for concept in self._concepts:
+            _concept = concept(
+                self._sink_mapper,
+                self._mapping_format,
+                self._source_mapper_configs,
+            )
+
+            _concept.map()

icu_pipeline/test.py

@@ -0,0 +1,23 @@
+from icu_pipeline.pipeline import (
+    Pipeline,
+    DataSource,
+    MappingFormat,
+    SourceMapperConfiguration,
+)
+from icu_pipeline.mapper.sink.file import CSVFileSinkMapper
+from icu_pipeline.concept.snomed import SerumCreatinine
+
+configs = {
+    DataSource.MIMIC: SourceMapperConfiguration(
+        "postgresql+psycopg://paul@localhost/mimiciv"
+    ),
+}
+
+pipeline = Pipeline(
+    [SerumCreatinine],
+    CSVFileSinkMapper(),
+    MappingFormat.FHIR,
+    configs,
+)
+
+pipeline.transfrom()