Add support for data collection parameters across layers

Introduced serialization for `data_collection_parameters` in backend models and processing. Added logic to parse and attach data collection parameters in the frontend. This ensures consistent handling and storage of these parameters throughout the application.

backend/app/routers/dewar.py

@@ -8,7 +8,7 @@ from sqlalchemy.orm import Session, joinedload
 from typing import List
 import logging
 from sqlalchemy.exc import SQLAlchemyError
-from pydantic import ValidationError
+from pydantic import ValidationError, BaseModel
 from app.schemas import (
     Dewar as DewarSchema,
     DewarCreate,
@@ -88,6 +88,26 @@ async def create_dewar(
             db.refresh(puck)
 
             for sample_data in puck_data.samples:
+                logging.debug(
+                    f"data_collection_parameters: "
+                    f"{sample_data.data_collection_parameters}"
+                )
+                if sample_data.data_collection_parameters is None:
+                    serialized_params = {}
+                elif hasattr(sample_data.data_collection_parameters, "to_dict"):
+                    serialized_params = sample_data.data_collection_parameters.to_dict()
+                elif isinstance(sample_data.data_collection_parameters, BaseModel):
+                    serialized_params = sample_data.data_collection_parameters.dict(
+                        exclude_unset=True
+                    )
+                elif isinstance(sample_data.data_collection_parameters, dict):
+                    serialized_params = sample_data.data_collection_parameters
+                else:
+                    raise ValueError(
+                        "data_collection_parameters must be a dictionary,"
+                        "have a to_dict method, or be None"
+                    )
+
                 sample = SampleModel(
                     puck_id=puck.id,
                     sample_name=sample_data.sample_name,
@@ -95,7 +115,7 @@ async def create_dewar(
                     position=sample_data.position,
                     priority=sample_data.priority,
                     comments=sample_data.comments,
-                    data_collection_parameters=sample_data.data_collection_parameters,
+                    data_collection_parameters=serialized_params,
                 )
                 db.add(sample)
                 db.commit()

backend/app/schemas.py

@@ -91,6 +91,12 @@ class DataCollectionParameters(BaseModel):
     chiphiangles: Optional[float] = None  # Optional float field between 0 and 30
     dose: Optional[float] = None  # Optional float field
 
+    def to_dict(self):
+        """Convert the model instance to a dictionary."""
+        return self.dict(
+            exclude_unset=True
+        )  # Use this built-in method for serialization
+
     class Config:
         from_attributes = True
 
@@ -416,6 +422,7 @@ class Sample(BaseModel):
     positioninpuck: Optional[int] = Field(None)
     priority: Optional[int] = None
     comments: Optional[str] = None
+    data_collection_parameters: Optional[DataCollectionParameters]
     events: List[SampleEventCreate] = []
 
 
@@ -423,7 +430,7 @@ class SampleCreate(BaseModel):
     sample_name: str = Field(..., alias="crystalname")
     proteinname: Optional[str] = None
     position: int = Field(..., alias="positioninpuck")
-    data_collection_parameters: Optional[DataCollectionParameters] = None
+    data_collection_parameters: Optional[DataCollectionParameters] = Field(default=None)
     priority: Optional[int] = None
     comments: Optional[str] = None
     results: Optional[Results] = None

frontend/src/components/SpreadsheetTable.tsx

@@ -247,6 +247,7 @@ const SpreadsheetTable = ({
                 continue;
             }
 
+            // Extract values from the appropriate columns
             const dewarName = typeof row.data[dewarNameIdx] === 'string' ? row.data[dewarNameIdx].trim() : null;
             const puckName = row.data[puckNameIdx] !== undefined && row.data[puckNameIdx] !== null ? String(row.data[puckNameIdx]).trim() : null;
             const puckType = typeof row.data[puckTypeIdx] === 'string' ? row.data[puckTypeIdx] : 'Unipuck';
@@ -256,6 +257,34 @@ const SpreadsheetTable = ({
             const priority = row?.data?.[priorityIdx] ? Number(row.data[priorityIdx]) : null;
             const comments = typeof row.data[commentsIdx] === 'string' ? row.data[commentsIdx].trim() : null;
 
+            // Create data_collection_parameters object
+            const dataCollectionParameters = {
+                directory: row.data[fieldToCol['directory']],
+                oscillation: row.data[fieldToCol['oscillation']] ? parseFloat(row.data[fieldToCol['oscillation']]) : undefined,
+                aperture: row.data[fieldToCol['aperture']] ? row.data[fieldToCol['aperture']].trim() : undefined,
+                exposure: row.data[fieldToCol['exposure']] ? parseFloat(row.data[fieldToCol['exposure']]) : undefined,
+                totalrange: row.data[fieldToCol['totalrange']] ? parseInt(row.data[fieldToCol['totalrange']], 10) : undefined,
+                transmission: row.data[fieldToCol['transmission']] ? parseInt(row.data[fieldToCol['transmission']], 10) : undefined,
+                dose: row.data[fieldToCol['dose']] ? parseFloat(row.data[fieldToCol['dose']]) : undefined,
+                targetresolution: row.data[fieldToCol['targetresolution']] ? parseFloat(row.data[fieldToCol['targetresolution']]) : undefined,
+                datacollectiontype: row.data[fieldToCol['datacollectiontype']],
+                processingpipeline: row.data[fieldToCol['processingpipeline']],
+                spacegroupnumber: row.data[fieldToCol['spacegroupnumber']] ? parseInt(row.data[fieldToCol['spacegroupnumber']], 10) : undefined,
+                cellparameters: row.data[fieldToCol['cellparameters']],
+                rescutkey: row.data[fieldToCol['rescutkey']],
+                rescutvalue: row.data[fieldToCol['rescutvalue']] ? parseFloat(row.data[fieldToCol['rescutvalue']]) : undefined,
+                userresolution: row.data[fieldToCol['userresolution']] ? parseFloat(row.data[fieldToCol['userresolution']]) : undefined,
+                pdbid: row.data[fieldToCol['pdbid']],
+                autoprocfull: row.data[fieldToCol['autoprocfull']] === true,
+                procfull: row.data[fieldToCol['procfull']] === true,
+                adpenabled: row.data[fieldToCol['adpenabled']] === true,
+                noano: row.data[fieldToCol['noano']] === true,
+                ffcscampaign: row.data[fieldToCol['ffcscampaign']] === true,
+                trustedhigh: row.data[fieldToCol['trustedhigh']] ? parseFloat(row.data[fieldToCol['trustedhigh']]) : undefined,
+                autoprocextraparams: row.data[fieldToCol['autoprocextraparams']],
+                chiphiangles: row.data[fieldToCol['chiphiangles']] ? parseFloat(row.data[fieldToCol['chiphiangles']]) : undefined,
+            };
+
             if (dewarName && puckName) {
                 let dewar;
                 if (!dewars.has(dewarName)) {
@@ -301,7 +330,7 @@ const SpreadsheetTable = ({
                     position: samplePosition,
                     priority: priority,
                     comments: comments,
-                    data_collection_parameters: null,
+                    data_collection_parameters: dataCollectionParameters, // Attach the parameters
                     results: null // Placeholder for results field
                 };