Feat 363 analysis step

src/aind_data_schema/datamanipulation.py

@@ -0,0 +1,78 @@
+""" schema for processing """
+
+from __future__ import annotations
+
+from datetime import datetime
+from enum import Enum
+from typing import Any, Dict, List, Optional
+
+from pydantic import Field
+
+from aind_data_schema.base import AindCoreModel, AindModel
+from aind_data_schema.imaging.tile import Tile
+from aind_data_schema.processing import ProcessName
+
+
+class TouchType(Enum):
+    ANALYSIS = "Analysis"
+    PROCESSING = "Processing"
+
+    ## These could be subtypes of analysis/processing
+
+class ProcessType(Enum):
+    CURATION = "Curation"
+    SORTING = "Sorting"
+
+class AnalysisType(Enum):
+    uhhh = "some analysis"
+
+
+
+
+class DataTouchInfo:
+    touch_type: TouchType = Field(..., title="Manipulation type")
+    start_date_time: datetime = Field(..., title="Start date time")
+    end_date_time: datetime = Field(..., title="End date time")
+    input_location: str = Field(..., description="Path to data inputs", title="Input location")
+    output_location: str = Field(..., description="Path to data outputs", title="Output location")
+    notes: Optional[str] = None
+
+
+class CodeManipulation:
+    code_url: str = Field(..., description="Path to code respository", title="Code URL")
+    code_version: Optional[str] = Field(None, description="Version of the code", title="Code version")
+    input_parameters: Dict[str, Any] = Field(..., title="Input parameters")
+    output_parameters: Optional[Dict[str, Any]] = Field(..., title="Output parameters")
+    outputs: Optional[Dict[str, Any]] = Field(None, description="Output parameters", title="Outputs")
+
+
+class AnalysisStep(AindModel):
+    """Description of a single processing step"""
+
+    analysis_name: str = Field(..., description="Name of the analysis method used", title="Analysis name")
+    analysis_type: AnalysisType = Field(..., description="Type of analysis performed on dataset", title="Analysis type")
+    touch_info: DataTouchInfo = Field(..., description="General information regarding the data manipulation performed")
+    analysis_code: CodeManipulation = Field(..., description="Info regarding code used to manipulate data")
+
+
+class DataProcess(AindModel):
+    """Description of a single processing step"""
+
+    process_name: ProcessName = Field(..., title="Process name")
+    processing_type: ProcessType = Field(..., description="Type of processing performed on dataset", title="Processing type")
+    touch_info: DataTouchInfo = Field(..., description="General information regarding the data manipulation performed")
+    analysis_code: CodeManipulation = Field(..., description="Info regarding code used to manipulate data")
+
+
+class Processing(AindCoreModel):
+    """Description of all processes run on data"""
+
+    schema_version: str = Field(
+        "0.2.1",
+        description="Schema version",
+        title="Schema version",
+        const=True,
+    )
+    pipeline_version: Optional[str] = Field(None, description="Version of the pipeline", title="Pipeline version")
+    pipeline_url: Optional[str] = Field(None, description="URL to the pipeline code", title="Pipeline URL")
+    data_processes: List[AnalysisStep] = Field(..., title="Data processing", unique_items=True)

src/aind_data_schema/processing.py

@@ -10,6 +10,7 @@
 
 from aind_data_schema.base import AindCoreModel, AindModel
 from aind_data_schema.imaging.tile import Tile
+from aind_data_schema.datamanipulation import DataTouchInfo
 
 
 class ProcessName(Enum):
@@ -37,16 +38,12 @@ class DataProcess(AindModel):
     """Description of a single processing step"""
 
     name: ProcessName = Field(..., title="Name")
+    touch_info: DataTouchInfo = Field(..., description="General information regarding the data manipulation performed")
     version: str = Field(..., description="Version of the software used", title="Version")
-    start_date_time: datetime = Field(..., title="Start date time")
-    end_date_time: datetime = Field(..., title="End date time")
-    input_location: str = Field(..., description="Path to data inputs", title="Input location")
-    output_location: str = Field(..., description="Path to data outputs", title="Output location")
     code_url: str = Field(..., description="Path to code respository", title="Code URL")
     code_version: Optional[str] = Field(None, description="Version of the code", title="Code version")
     parameters: Dict[str, Any] = Field(..., title="Parameters")
     outputs: Optional[Dict[str, Any]] = Field(None, description="Output parameters", title="Outputs")
-    notes: Optional[str] = None
 
 
 class Processing(AindCoreModel):