Add default values to optional fields in SampleUpdate

backend/app/routers/dewar.py

@@ -313,6 +313,40 @@ async def download_dewar_label(dewar_id: int, db: Session = Depends(get_db)):
     )
 
 
+@router.put("/samples/{sample_id}", response_model=Sample)
+async def update_sample(
+    sample_id: int,
+    sample_update: SampleUpdate,
+    db: Session = Depends(get_db),
+):
+    # Log the payload received from the frontend
+    logging.info(
+        f"Payload received for sample ID {sample_id}: "
+        f"{sample_update.dict(exclude_unset=True)}"
+    )
+
+    # Query the sample from the database
+    sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
+
+    if not sample:
+        logging.error(f"Sample with ID {sample_id} not found")
+        raise HTTPException(status_code=404, detail="Sample not found")
+
+    # Apply updates
+    for key, value in sample_update.dict(exclude_unset=True).items():
+        if hasattr(sample, key):
+            setattr(sample, key, value)
+
+    # Commit changes to the database
+    db.commit()
+    db.refresh(sample)  # Reload the updated sample object
+
+    # Log the updated sample before returning it
+    logging.info(f"Updated sample with ID {sample_id}: {Sample.from_orm(sample)}")
+
+    return Sample.from_orm(sample)
+
+
 @router.get("/dewars/{dewar_id}/samples", response_model=Dewar)
 async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
     # Fetch the Dewar with nested relationships
@@ -374,27 +408,6 @@ async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
     return Dewar(**dewar_data)
 
 
-@router.put("/samples/{sample_id}", response_model=Sample)
-async def update_sample(
-    sample_id: int,
-    sample_update: SampleUpdate,
-    db: Session = Depends(get_db),
-):
-    sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
-    if not sample:
-        raise HTTPException(status_code=404, detail="Sample not found")
-
-    # Apply updates
-    for key, value in sample_update.dict(exclude_unset=True).items():
-        if hasattr(sample, key):
-            setattr(sample, key, value)
-
-    # Save changes
-    db.commit()
-    db.refresh(sample)
-    return Sample.from_orm(sample)
-
-
 @router.get("/", response_model=List[DewarSchema])
 async def get_dewars(db: Session = Depends(get_db)):
     try:

backend/app/schemas.py

@@ -619,12 +619,12 @@ class SlotSchema(BaseModel):
 
 
 class SampleUpdate(BaseModel):
-    sample_name: Optional[str]
+    sample_name: Optional[str] = None
-    proteinname: Optional[str]
+    proteinname: Optional[str] = None
-    priority: Optional[int]
+    priority: Optional[int] = None
-    position: Optional[int]
+    position: Optional[int] = None
-    comments: Optional[str]
+    comments: Optional[str] = None
-    data_collection_parameters: Optional[DataCollectionParameters]
+    data_collection_parameters: Optional[DataCollectionParameters] = None
 
     class Config:
         from_attributes = True

frontend/src/components/SampleSpreadsheetGrid.tsx

@@ -1,5 +1,5 @@
 import React, { useEffect, useState } from "react";
-import { DataGrid, GridColDef, GridCellEditStopParams } from "@mui/x-data-grid";
+import { DataGrid, GridColDef, GridCellEditStopParams, GridRowModel } from "@mui/x-data-grid";
 import { DewarsService } from "../../openapi";
 
 interface SampleSpreadsheetProps {
@@ -34,6 +34,24 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
                             totalrange,
                             transmission,
                             dose,
+                            targetresolution,
+                            aperture,
+                            datacollectiontype,
+                            processingpipeline,
+                            spacegroupnumber,
+                            cellparameters,
+                            rescutkey,
+                            rescutvalue,
+                            userresolution,
+                            pdbid,
+                            autoprocfull,
+                            procfull,
+                            adpenabled,
+                            noano,
+                            ffcscampaig,
+                            trustedhigh,
+                            autoprocextraparams,
+                            chiphiangles
                         } = sample.data_collection_parameters || {};
 
                         allRows.push({
@@ -53,7 +71,24 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
                             totalRange: totalrange || null,
                             transmission: transmission || null,
                             dose: dose || null,
-                            dataCollectionParameters: sample.data_collection_parameters || {}, // Ensure this is never undefined
+                            targetresolution: targetresolution || null,
+                            aperture: aperture || null,
+                            datacollectiontype: datacollectiontype || null,
+                            processingpipeline: processingpipeline || null,
+                            spacegroupnumber: spacegroupnumber || null,
+                            cellparameters: cellparameters || {},
+                            rescutkey: rescutkey || null,
+                            rescutvalue: rescutvalue || null,
+                            userresolution: userresolution || null,
+                            pdbid: pdbid || null,
+                            autoprocfull: autoprocfull || null,
+                            procfull: procfull || null,
+                            adpenabled: adpenabled || null,
+                            noano: noano || null,
+                            ffcscampaig: ffcscampaig || null,
+                            trustedhigh: trustedhigh || null,
+                            autoprocextraparams: autoprocextraparams || {},
+                            chiphiangles: chiphiangles || null,
                         });
                     });
                 });
@@ -62,30 +97,38 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
 
                 // Define columns for the grid
                 setColumns([
-                    { field: "dewarName", headerName: "Dewar Name", width: 150, editable: false },
+                    { field: "dewarName", headerName: "Dewar Name", width: 150, editable: false }, // not editable for now
-                    { field: "puckName", headerName: "Puck Name", width: 150 },
+                    { field: "puckName", headerName: "Puck Name", width: 150, editable: false  }, // not editable for now
-                    { field: "puckType", headerName: "Puck Type", width: 150 },
+                    { field: "puckType", headerName: "Puck Type", width: 150, editable: false  }, // not editable for now
-                    { field: "crystalName", headerName: "Crystal Name", width: 200, editable: true },
+                    { field: "crystalName", headerName: "Crystal Name", width: 200, editable: false }, // not editable for now
-                    { field: "proteinName", headerName: "Protein Name", width: 200, editable: true },
+                    { field: "proteinName", headerName: "Protein Name", width: 200, editable: false }, // not editable for now
                     { field: "position", headerName: "Position", width: 100, editable: true, type: "number" },
                     { field: "priority", headerName: "Priority", width: 100, editable: true, type: "number" },
                     { field: "comments", headerName: "Comments", width: 300, editable: true },
-                    { field: "directory", headerName: "Directory", width: 200 },
+                    { field: "directory", headerName: "Directory", width: 200, editable: true },
                     { field: "oscillation", headerName: "Oscillation", width: 150, editable: true, type: "number" },
                     { field: "exposure", headerName: "Exposure", width: 150, editable: true, type: "number" },
                     { field: "totalRange", headerName: "Total Range", width: 150, editable: true, type: "number" },
                     { field: "transmission", headerName: "Transmission", width: 150, editable: true, type: "number" },
                     { field: "dose", headerName: "Dose", width: 150, editable: true, type: "number" },
-                    {
+                    { field: "targetresolution", headerName: "Target Resolution", width: 150, editable: true, type: "number" },
-                        field: "dataCollectionParameters",
+                    { field: "aperture", headerName: "Aperture", width: 150, editable: true },
-                        headerName: "Data Collection Parameters (Raw)",
+                    { field: "datacollectiontype", headerName: "Data Collection Type", width: 200, editable: true  },
-                        width: 300,
+                    { field: "processingpipeline", headerName: "Processing Pipeline", width: 200, editable: true },
-                        valueGetter: (params) =>
+                    { field: "spacegroupnumber", headerName: "Space Group Number", width: 200, editable: true },
-                            params.row?.dataCollectionParameters
+                    { field: "cellparameters", headerName: "Cell Parameters", width: 300, editable: true  },
-                                ? JSON.stringify(params.row.dataCollectionParameters)
+                    { field: "rescutkey", headerName: "ResCut Key", width: 150, editable: true  },
-                                : "N/A", // Fallback if undefined
+                    { field: "rescutvalue", headerName: "ResCut Value", width: 150, editable: true, editable: true  },
-                        editable: false,
+                    { field: "userresolution", headerName: "User Resolution", width: 150, editable: true, editable: true  },
-                    },
+                    { field: "pdbid", headerName: "PDB ID", width: 150, editable: true  },
+                    { field: "autoprocfull", headerName: "AutoProc Full", width: 200, editable: true  },
+                    { field: "procfull", headerName: "Proc Full", width: 200, editable: true  },
+                    { field: "adpenabled", headerName: "ADP Enabled", width: 150, editable: true  },
+                    { field: "noano", headerName: "No Anomalous", width: 150, editable: true  },
+                    { field: "ffcscampaig", headerName: "FFCS Campaign", width: 150, editable: true  },
+                    { field: "trustedhigh", headerName: "Trusted High", width: 150, editable: true  },
+                    { field: "autoprocextraparams", headerName: "AutoProc Extra Params", width: 300, editable: true },
+                    { field: "chiphiangles", headerName: "Chi Phi Angles", width: 150, editable: true  },
                 ]);
             } catch (error) {
                 console.error("Error fetching dewar samples:", error);
@@ -98,19 +141,112 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
     // Handle cell editing to persist changes to the backend
     const handleCellEditStop = async (params: GridCellEditStopParams) => {
         const { id, field, value } = params;
+
+        // Validation to ensure we have valid data from the cell edit
         if (!id || !field || value === undefined) {
-            console.error("Invalid edit inputs");
+            console.error("Invalid edit inputs:", { id, field, value });
             return;
         }
 
+        // Fetch the current row data (old state) based on its ID
+        const updatedRow = rows.find((row) => row.id === id);
+
+        if (!updatedRow) {
+            console.error("Row not found for ID:", id);
+            return;
+        }
+
+        // Create the updated sample, force-overwriting the changed cell value
+        const updatedSample = {
+            ...updatedRow, // Include other fields from the existing row
+            [field]: value, // Explicitly overwrite the updated field with new value
+        };
+
+        console.log("Payload sent to the backend:", updatedSample); // Log fixed payload
+
         try {
-            // Call the update_sample API endpoint
+            // Optimistically update UI for better experience
-            await DewarsService.updateSampleSampleIdPut(id as number, {
+            setRows((prevRows) =>
-                [field]: value,
+                prevRows.map((row) =>
-            });
+                    row.id === id ? { ...row, [field]: value } : row
-            console.log("Sample updated successfully");
+                )
+            );
+
+            // API call to persist changes
+            await DewarsService.updateSampleDewarsSamplesSampleIdPut(Number(id), updatedSample);
+
+            console.log(`Sample with ID ${id} successfully updated.`);
         } catch (error) {
-            console.error(`Error updating sample (id: ${id}):`, error);
+            console.error(`Failed to update sample with ID ${id}:`, error);
+
+            // Revert optimistic update on error
+            setRows((prevRows) =>
+                prevRows.map((row) => (row.id === id ? updatedRow : row))
+            );
+        }
+    };
+
+    const processRowUpdate = async (newRow: GridRowModel, oldRow: GridRowModel) => {
+        try {
+            console.log("Old row:", oldRow); // Log the original row
+            console.log("Updated row:", newRow); // Log the updated data from the grid
+
+            // Reconstruct 'data_collection_parameters' from the flat table structure
+            const updatedDataCollectionParameters = {
+                ...(oldRow.data_collection_parameters || {}), // Preserve old values
+                directory: newRow.directory ?? oldRow.data_collection_parameters?.directory,
+                oscillation: newRow.oscillation ?? oldRow.data_collection_parameters?.oscillation,
+                exposure: newRow.exposure ?? oldRow.data_collection_parameters?.exposure,
+                totalrange: newRow.totalRange ?? oldRow.data_collection_parameters?.totalrange,
+                transmission: newRow.transmission ?? oldRow.data_collection_parameters?.transmission,
+                dose: newRow.dose ?? oldRow.data_collection_parameters?.dose,
+                targetresolution: newRow.targetresolution ?? oldRow.data_collection_parameters?.targetresolution,
+                aperture: newRow.aperture ?? oldRow.data_collection_parameters?.aperture,
+                datacollectiontype: newRow.datacollectiontype ?? oldRow.data_collection_parameters?.datacollectiontype,
+                processingpipeline: newRow.processingpipeline ?? oldRow.data_collection_parameters?.processingpipeline,
+                spacegroupnumber: newRow.spacegroupnumber ?? oldRow.data_collection_parameters?.spacegroupnumber,
+                //cellparameters: newRow.cellparameters ?? oldRow.data_collection_parameters?.cellparameters,
+                rescutkey: newRow.rescutkey ?? oldRow.data_collection_parameters?.rescutkey,
+                rescutvalue: newRow.rescutvalue ?? oldRow.data_collection_parameters?.rescutvalue,
+                userresolution: newRow.userresolution ?? oldRow.data_collection_parameters?.userresolution,
+                pdbid: newRow.pdbid ?? oldRow.data_collection_parameters?.pdbid,
+                autoprocfull: newRow.autoprocfull ?? oldRow.data_collection_parameters?.autoprocfull,
+                procfull: newRow.procfull ?? oldRow.data_collection_parameters?.procfull,
+                adpenabled: newRow.adpenabled ?? oldRow.data_collection_parameters?.adpenabled,
+                noano: newRow.noano ?? oldRow.data_collection_parameters?.noano,
+                ffcscampaig: newRow.ffcscampaig ?? oldRow.data_collection_parameters?.ffcscampaig,
+                trustedhigh: newRow.trustedhigh ?? oldRow.data_collection_parameters?.trustedhigh,
+                //autoprocextraparams: newRow.autoprocextraparams ?? oldRow.data_collection_parameters?.autoprocextraparams,
+                chiphiangles: newRow.chiphiangles ?? oldRow.data_collection_parameters?.chiphiangles,
+            };
+
+            // Assemble the final payload
+            const payload = {
+                ...oldRow, // Include all original fields
+                ...newRow, // Overwrite or add updated fields
+                data_collection_parameters: updatedDataCollectionParameters, // Include the merged/validated structure
+            };
+
+            console.log("Final payload sent to backend:", payload);
+
+            // Optimistically update the UI
+            setRows((prevRows) =>
+                prevRows.map((row) =>
+                    row.id === newRow.id ? { ...row, ...payload } : row
+                )
+            );
+
+            // Send the payload to the backend
+            await DewarsService.updateSampleDewarsSamplesSampleIdPut(Number(newRow.id), payload);
+
+            console.log(`Successfully updated sample with ID ${newRow.id}.`);
+            return payload; // Return the updated row
+
+        } catch (error) {
+            console.error(`Failed to update sample with ID ${newRow.id}:`, error);
+
+            // On failure, revert to the old row
+            return oldRow;
         }
     };
 
@@ -120,7 +256,7 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
                 rows={rows}
                 columns={columns}
                 pageSize={10}
-                onCellEditStop={handleCellEditStop}
+                processRowUpdate={processRowUpdate} // Exclusively handle updates
             />
         </div>
     );

testfunctions.ipynb

@@ -3506,8 +3506,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-09T19:33:01.143326Z",
+     "end_time": "2025-01-09T19:41:14.264895Z",
-     "start_time": "2025-01-09T19:33:01.128023Z"
+     "start_time": "2025-01-09T19:41:14.245643Z"
     }
    },
    "cell_type": "code",
@@ -3518,9 +3518,9 @@
     "    api_instance = aareDBclient.SamplesApi(api_client)\n",
     "\n",
     "    # Define the sample ID and event payload using the expected model\n",
-    "    sample_id = 260\n",
+    "    sample_id = 261\n",
     "    event_payload = SampleEventCreate(\n",
-    "        event_type=\"Unmounted\"  # Replace with actual event type if different\n",
+    "        event_type=\"Failed\"  # Replace with actual event type if different\n",
     "    )\n",
     "\n",
     "    try:\n",
@@ -3543,7 +3543,7 @@
      "text": [
       "The response of post_sample_event:\n",
       "\n",
-      "SampleEventResponse(id=417, sample_id=260, event_type='Unmounted', timestamp=datetime.datetime(2025, 1, 9, 20, 33, 1))\n"
+      "SampleEventResponse(id=418, sample_id=261, event_type='Failed', timestamp=datetime.datetime(2025, 1, 9, 20, 41, 14))\n"
      ]
     },
     {
@@ -3555,13 +3555,13 @@
      ]
     }
    ],
-   "execution_count": 67
+   "execution_count": 70
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-09T19:33:04.470152Z",
+     "end_time": "2025-01-09T19:41:23.052434Z",
-     "start_time": "2025-01-09T19:33:04.454152Z"
+     "start_time": "2025-01-09T19:41:23.036108Z"
     }
    },
    "cell_type": "code",
@@ -3573,7 +3573,7 @@
     "\n",
     "    try:\n",
     "        # Get the last sample event\n",
-    "        last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(260)\n",
+    "        last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(261)\n",
     "        print(\"The response of get_last_sample_event:\\n\")\n",
     "        pprint(last_event_response)\n",
     "\n",
@@ -3588,7 +3588,7 @@
      "text": [
       "The response of get_last_sample_event:\n",
       "\n",
-      "SampleEventResponse(id=417, sample_id=260, event_type='Unmounted', timestamp=datetime.datetime(2025, 1, 9, 20, 33, 1))\n"
+      "SampleEventResponse(id=418, sample_id=261, event_type='Failed', timestamp=datetime.datetime(2025, 1, 9, 20, 41, 14))\n"
      ]
     },
     {
@@ -3600,7 +3600,7 @@
      ]
     }
    ],
-   "execution_count": 68
+   "execution_count": 71
   }
  ],
  "metadata": {