reader-workbench 1.0.0__py3-none-any.whl

reader_workbench/protocols/compilers/plate_reader_pipeline.py

@@ -0,0 +1,197 @@
+from __future__ import annotations
+
+from typing import Any
+
+from reader_workbench.workbench.decl.model import PluginStepDecl, RecordInputDecl, RecordOutputDecl, ResourceInputDecl
+
+from .common import _deep_merge, _step
+
+SYNERGY_H1_INGEST_RECIPE_ID = "plate_reader/synergy_h1"
+DUAL_REPORTER_BASE_RECIPE_ID = "plate_reader/dual_reporter_screen_base"
+SINGLE_REPORTER_BASE_RECIPE_ID = "plate_reader/single_reporter_screen_base"
+GROWTH_BASE_RECIPE_ID = "plate_reader/growth_screen_base"
+
+
+def compose_dual_reporter_pipeline(
+    *,
+    ingest_channels: list[str],
+    blank_config: dict[str, Any],
+    overflow_config: dict[str, Any],
+) -> tuple[PluginStepDecl, ...]:
+    return (
+        _step(
+            id="ingest",
+            plugin="ingest/synergy_h1",
+            with_={"channels": ingest_channels},
+            source_recipe=SYNERGY_H1_INGEST_RECIPE_ID,
+        ),
+        *_sample_map_and_preprocessing_steps(
+            blank_config=blank_config,
+            overflow_config=overflow_config,
+            source_recipe=DUAL_REPORTER_BASE_RECIPE_ID,
+        ),
+        _step(
+            id="ratio_yfp_cfp",
+            plugin="transform/ratio",
+            reads={"df": RecordInputDecl(record_id="overflow/df")},
+            with_={"name": "YFP/CFP", "numerator": "YFP", "denominator": "CFP"},
+            source_recipe=DUAL_REPORTER_BASE_RECIPE_ID,
+        ),
+        _step(
+            id="ratio_cfp_od600",
+            plugin="transform/ratio",
+            reads={"df": RecordInputDecl(record_id="ratio_yfp_cfp/df")},
+            with_={"name": "CFP/OD600", "numerator": "CFP", "denominator": "OD600"},
+            source_recipe=DUAL_REPORTER_BASE_RECIPE_ID,
+        ),
+        _step(
+            id="ratio_yfp_od600",
+            plugin="transform/ratio",
+            reads={"df": RecordInputDecl(record_id="ratio_cfp_od600/df")},
+            with_={"name": "YFP/OD600", "numerator": "YFP", "denominator": "OD600"},
+            source_recipe=DUAL_REPORTER_BASE_RECIPE_ID,
+        ),
+    )
+
+
+def compose_single_reporter_pipeline(
+    *,
+    ingest_channels: list[str],
+    reporter_channel: str,
+    normalizer_channel: str,
+    blank_config: dict[str, Any],
+    overflow_config: dict[str, Any],
+) -> tuple[PluginStepDecl, ...]:
+    ratio_name = f"{reporter_channel}/{normalizer_channel}"
+    recipe_arguments = {
+        "reporter_channel": reporter_channel,
+        "normalizer_channel": normalizer_channel,
+    }
+    return (
+        _step(
+            id="ingest",
+            plugin="ingest/synergy_h1",
+            with_={"channels": ingest_channels},
+            source_recipe=SYNERGY_H1_INGEST_RECIPE_ID,
+        ),
+        *_sample_map_and_preprocessing_steps(
+            blank_config=blank_config,
+            overflow_config=overflow_config,
+            source_recipe=SINGLE_REPORTER_BASE_RECIPE_ID,
+            recipe_arguments=recipe_arguments,
+        ),
+        _step(
+            id="ratio_reporter_normalizer",
+            plugin="transform/ratio",
+            reads={"df": RecordInputDecl(record_id="overflow/df")},
+            with_={
+                "name": ratio_name,
+                "numerator": reporter_channel,
+                "denominator": normalizer_channel,
+            },
+            source_recipe=SINGLE_REPORTER_BASE_RECIPE_ID,
+            source_recipe_with=recipe_arguments,
+        ),
+        _step(
+            id="sample_measurements",
+            plugin="validator/to_tidy_plus_map",
+            reads={"df": RecordInputDecl(record_id="ratio_reporter_normalizer/df")},
+            with_={
+                "include_types": ["SAMPLE"],
+                "require_columns": ["treatment", "design_id"],
+                "require_non_null": True,
+                "trim_and_require_non_blank": ["treatment", "design_id"],
+                "require_finite": ["time", "value"],
+            },
+            writes={"df": RecordOutputDecl(record_id="sample_measurements/df")},
+            source_recipe=SINGLE_REPORTER_BASE_RECIPE_ID,
+            source_recipe_with=recipe_arguments,
+        ),
+    )
+
+
+def compose_growth_pipeline(
+    *,
+    ingest_channels: list[str],
+    growth_channel: str,
+    blank_config: dict[str, Any],
+    overflow_config: dict[str, Any],
+) -> tuple[PluginStepDecl, ...]:
+    """Compose a plate-reader pipeline that preserves one growth channel."""
+
+    recipe_arguments = {"growth_channel": growth_channel}
+    return (
+        _step(
+            id="ingest",
+            plugin="ingest/synergy_h1",
+            with_={"channels": ingest_channels},
+            source_recipe=SYNERGY_H1_INGEST_RECIPE_ID,
+        ),
+        *_sample_map_and_preprocessing_steps(
+            blank_config=blank_config,
+            overflow_config=overflow_config,
+            source_recipe=GROWTH_BASE_RECIPE_ID,
+            recipe_arguments=recipe_arguments,
+        ),
+        _step(
+            id="sample_measurements",
+            plugin="validator/to_tidy_plus_map",
+            reads={"df": RecordInputDecl(record_id="overflow/df")},
+            with_={
+                "include_types": ["SAMPLE"],
+                "require_columns": ["treatment", "design_id"],
+                "require_non_null": True,
+                "trim_and_require_non_blank": ["treatment", "design_id"],
+                "require_finite": ["time", "value"],
+                "allow_instrument_overflow": ["value"],
+            },
+            writes={"df": RecordOutputDecl(record_id="sample_measurements/df")},
+            source_recipe=GROWTH_BASE_RECIPE_ID,
+            source_recipe_with=recipe_arguments,
+        ),
+    )
+
+
+def _sample_map_and_preprocessing_steps(
+    *,
+    blank_config: dict[str, Any],
+    overflow_config: dict[str, Any],
+    source_recipe: str,
+    recipe_arguments: dict[str, Any] | None = None,
+) -> tuple[PluginStepDecl, ...]:
+    source_recipe_with = dict(recipe_arguments or {})
+    return (
+        _step(
+            id="merge_map",
+            plugin="transform/sample_map",
+            reads={
+                "df": RecordInputDecl(record_id="ingest/df"),
+                "sample_map": ResourceInputDecl(resource_id="sample_map"),
+            },
+            source_recipe=source_recipe,
+            source_recipe_with=source_recipe_with,
+        ),
+        _step(
+            id="labels",
+            plugin="transform/assay_labels",
+            reads={"df": RecordInputDecl(record_id="merge_map/df")},
+            source_recipe=source_recipe,
+            source_recipe_with=source_recipe_with,
+        ),
+        _step(
+            id="blank",
+            plugin="transform/blank_correction",
+            reads={"df": RecordInputDecl(record_id="labels/df")},
+            with_=_deep_merge(blank_config),
+            source_recipe=source_recipe,
+            source_recipe_with=source_recipe_with,
+        ),
+        _step(
+            id="overflow",
+            plugin="transform/overflow_handling",
+            reads={"df": RecordInputDecl(record_id="blank/df")},
+            with_=_deep_merge(overflow_config),
+            source_recipe=source_recipe,
+            source_recipe_with=source_recipe_with,
+        ),
+    )